Academic Appointments

Research & Scholarship

Current Research and Scholarly Interests

The Parham laboratory investigates the biology, genetics, and evolution of Major Histocompatibility Complex (MHC) class I molecules, natural killer (NK) cell receptors, and other immune system molecules. Classical MHC class I molecules are peptide-binding glycoproteins expressed on the surface of most vertebrate cells where they interact with the receptors of cytolytic CD8+ T lymphocytes and NK cells of the immune system. Both these types of killer lymphocytes are important for defence against viruses - generalised NK cell response at the beginning of infection, and specific T cell response further on if the pathogen is not eliminated by innate immunity. The rapid evolution of viruses selects for diversity of MHC class I molecules within populations of humans and other vertebrates. One consequence of this diversity is that MHC class I difference is a major immunological barrier to tissue transplants between unrelated donors and patients. A second consequence is that MHC class I molecules of different taxonomic species are very different, for example, there is no true orthologue between the classical class I genes of humans and mice. Whereas once considered homogeneous, NK cells are now shown to have both clonal diversity arising from differential expression of NK cell receptors within an individual, and population diversity in haplotype content and gene polymorphism. Clinical consequences analogous to those for MHC class I are expected due to NK cell receptor diversity. In humans, NK cell receptors consist of both immunoglobulin-like molecules and lectin-like molecules, however, only the lectin-like receptors are functional homologues in mice. As with their MHC class I ligands, NK cell receptors have also undergone rapid evolution.

One goal of our research is to understand how the continual battle between vertebrates and viruses has driven the diversification and divergence of MHC class I molecules and NK cell receptors. In human, we examine the polymorphism of NK receptor genes in different populations which are shaped by different histories of pathogen encounters. We also examine the coevolution of MHC class I and NK receptor genes in two close cousins of human, the chimpanzee and the orangutan.

A second goal is to understand the molecular and biochemical interactions between NK cell receptors and their MHC class I ligands. We perform mutagenesis studies to fine map interactions between NK cell receptors and MHC class I molecules. We also examine essential residues that determine the expression or retention of NK cell receptor alleles.

A third goal is to understand how MHC class I and NK cell receptor differences influence the outcomes of clinical transplantation. We follow the recovery of NK cell populations in leukemia and lymphoma patients after bone-marrow transplants and correlate the reconstitution of NK cell with the donor's and patient's genotypes, therapies and clinical consequences.


2014-15 Courses


All Publications

  • The IPD and IMGT/HLA database: allele variant databases NUCLEIC ACIDS RESEARCH Robinson, J., Halliwell, J. A., Hayhurst, J. D., Flicek, P., Parham, P., Marsh, S. G. 2015; 43 (D1): D423-D431
  • A KIR B centromeric region present in Africans but not Europeans protects pregnant women from pre-eclampsia. Proceedings of the National Academy of Sciences of the United States of America Nakimuli, A., Chazara, O., Hiby, S. E., Farrell, L., Tukwasibwe, S., Jayaraman, J., Traherne, J. A., Trowsdale, J., Colucci, F., Lougee, E., Vaughan, R. W., Elliott, A. M., Byamugisha, J., Kaleebu, P., Mirembe, F., Nemat-Gorgani, N., Parham, P., Norman, P. J., Moffett, A. 2015; 112 (3): 845-850


    In sub-Saharan Africans, maternal mortality is unacceptably high, with >400 deaths per 100,000 births compared with <10 deaths per 100,000 births in Europeans. One-third of the deaths are caused by pre-eclampsia, a syndrome arising from defective placentation. Controlling placentation are maternal natural killer (NK) cells that use killer-cell immunoglobulin-like receptor (KIR) to recognize the fetal HLA-C molecules on invading trophoblast. We analyzed genetic polymorphisms of maternal KIR and fetal HLA-C in 484 normal and 254 pre-eclamptic pregnancies at Mulago Hospital, Kampala, Uganda. The combination of maternal KIR AA genotypes and fetal HLA-C alleles encoding the C2 epitope associates with pre-eclampsia [P = 0.0318, odds ratio (OR) = 1.49]. The KIR genes associated with protection are located in centromeric KIR B regions that are unique to sub-Saharan African populations and contain the KIR2DS5 and KIR2DL1 genes (P = 0.0095, OR = 0.59). By contrast, telomeric KIR B genes protect Europeans against pre-eclampsia. Thus, different KIR B regions protect sub-Saharan Africans and Europeans from pre-eclampsia, whereas in both populations, the KIR AA genotype is a risk factor for the syndrome. These results emphasize the importance of undertaking genetic studies of pregnancy disorders in African populations with the potential to provide biological insights not available from studies restricted to European populations.

    View details for DOI 10.1073/pnas.1413453112

    View details for PubMedID 25561558

  • Definition of the Cattle Killer Cell Ig-like Receptor Gene Family: Comparison with Aurochs and Human Counterparts JOURNAL OF IMMUNOLOGY Sanderson, N. D., Norman, P. J., Guethlein, L. A., Ellis, S. A., Williams, C., Breen, M., Park, S. D., Magee, D. A., Babrzadeh, F., Warry, A., Watson, M., Bradley, D. G., MacHugh, D. E., Parham, P., Hammond, J. A. 2014; 193 (12): 6016-6030


    Under selection pressure from pathogens, variable NK cell receptors that recognize polymorphic MHC class I evolved convergently in different species of placental mammal. Unexpectedly, diversified killer cell Ig-like receptors (KIRs) are shared by simian primates, including humans, and cattle, but not by other species. Whereas much is known of human KIR genetics and genomics, knowledge of cattle KIR is limited to nine cDNA sequences. To facilitate comparison of the cattle and human KIR gene families, we determined the genomic location, structure, and sequence of two cattle KIR haplotypes and defined KIR sequences of aurochs, the extinct wild ancestor of domestic cattle. Larger than its human counterpart, the cattle KIR locus evolved through successive duplications of a block containing ancestral KIR3DL and KIR3DX genes that existed before placental mammals. Comparison of two cattle KIR haplotypes and aurochs KIR show the KIR are polymorphic and the gene organization and content appear conserved. Of 18 genes, 8 are functional and 10 were inactivated by point mutation. Selective inactivation of KIR3DL and activating receptor genes leaves a functional cohort of one inhibitory KIR3DL, one activating KIR3DX, and six inhibitory KIR3DX. Functional KIR diversity evolved from KIR3DX in cattle and from KIR3DL in simian primates. Although independently evolved, cattle and human KIR gene families share important function-related properties, indicating that cattle KIR are NK cell receptors for cattle MHC class I. Combinations of KIR and MHC class I are the major genetic factors associated with human disease and merit investigation in cattle.

    View details for DOI 10.4049/jimmunol.1401980

    View details for Web of Science ID 000346082400029

    View details for PubMedID 25398326

  • Coordinated Regulation of NK Receptor Expression in the Maturing Human Immune System JOURNAL OF IMMUNOLOGY Strauss-Albee, D. M., Horowitz, A., Parham, P., Blish, C. A. 2014; 193 (10): 4871-4879
  • KIR diversity in MAori and Polynesians: populations in which HLA-B is not a significant KIR ligand IMMUNOGENETICS Nemat-Gorgani, N., Edinur, H. A., Hollenbach, J. A., Traherne, J. A., Dunn, P. P., Chambers, G. K., Parham, P., Norman, P. J. 2014; 66 (11): 597-611
  • High diversity of MIC genes in non-human primates IMMUNOGENETICS Meyer, A., Carapito, R., Ott, L., Radosavljevic, M., Georgel, P., Adams, E. J., Parham, P., Bontrop, R. E., Blancher, A., Bahram, S. 2014; 66 (9-10): 581-587


    The human MHC class I (MHC-I) chain-related genes A and B (MICA and MICB) encode stress-induced glycoproteins, ligands for the activating receptor NKG2D. They display an unusually high degree of polymorphism, next only to that of classical MHC-I. The functional relevance and selective pressure behind this peculiar polymorphism, which is quite distinct from that of classical MHC-I, remain largely unknown. This study increases the repertoire of allelic sequences determined for the MIC genes of non-human primates. Sequencing (mainly exons 2, 3, 4, 5) MIC genes of 72 Macaca fascicularis (Mafa), 63 Pan troglodytes (Patr), and 18 Gorilla gorilla (Gogo) individuals led to the identification of 35, 14, and 3 new alleles, respectively. Additionally, we confirm the existence of three independent MIC genes in M. fascicularis, i.e., Mafa-MICA, Mafa-MICB, and Mafa-MICB/A, the latter being a hybrid of Mafa-MICB and Mafa-MICA. By multiple sequence alignment and phylogenetic analysis, we further demonstrate that the present day MIC genes most likely derive from a single human MICB-like ancestral gene.

    View details for DOI 10.1007/s00251-014-0791-4

    View details for Web of Science ID 000341835800007

    View details for PubMedID 25073428

  • Donor Killer Cell Ig-like Receptor B Haplotypes, Recipient HLA-C1, and HLA-C Mismatch Enhance the Clinical Benefit of Unrelated Transplantation for Acute Myelogenous Leukemia JOURNAL OF IMMUNOLOGY Cooley, S., Weisdorf, D. J., Guethlein, L. A., Klein, J. P., Wang, T., Marsh, S. G., Spellman, S., Haagenson, M. D., Saeturn, K., Ladner, M., Trachtenberg, E., Parham, P., Miller, J. S. 2014; 192 (10): 4592-4600


    Killer cell Ig-like receptors (KIRs) interact with HLA class I ligands to regulate NK cell development and function. These interactions affect the outcome of unrelated donor hematopoietic cell transplantation (HCT). We have shown previously that donors with KIR B versus KIR A haplotypes improve the clinical outcome for patients with acute myelogenous leukemia by reducing the incidence of leukemic relapse and improving leukemia-free survival (LFS). Both centromeric and telomeric KIR B genes contribute to the effect, but the centromeric genes are dominant. They include the genes encoding inhibitory KIRs that are specific for the C1 and C2 epitopes of HLA-C. We used an expanded cohort of 1532 T cell-replete transplants to examine the interaction between donor KIR B genes and recipient class I HLA KIR ligands. The relapse protection associated with donor KIR B is enhanced in recipients who have one or two C1-bearing HLA-C allotypes, compared with C2 homozygous recipients, with no effect due to donor HLA. The protective interaction between donors with two or more, versus none or one, KIR B motifs and recipient C1 was specific to transplants with class I mismatch at HLA-C (RR of leukemia-free survival, 0.57 [0.40-0.79]; p = 0.001) irrespective of the KIR ligand mismatch status of the transplant. The survival advantage and relapse protection in C1/x recipients compared with C2/C2 recipients was similar irrespective of the particular donor KIR B genes. Understanding the interactions between donor KIR and recipient HLA class I can be used to inform donor selection to improve outcome of unrelated donor hematopoietic cell transplantation for acute myelogenous leukemia.

    View details for DOI 10.4049/jimmunol.1302517

    View details for Web of Science ID 000335973600016

    View details for PubMedID 24748496

  • Exome capture from saliva produces high quality genomic and metagenomic data BMC GENOMICS Kidd, J. M., Sharpton, T. J., Bobo, D., Norman, P. J., Martin, A. R., Carpenter, M. L., Sikora, M., Gignoux, C. R., Nemat-Gorgani, N., Adams, A., Guadalupe, M., Guo, X., Feng, Q., Li, Y., Liu, X., Parham, P., Hoal, E. G., Feldman, M. W., Pollard, K. S., Wall, J. D., Bustamante, C. D., Henn, B. M. 2014; 15
  • Reconstructing the Population Genetic History of the Caribbean PLOS GENETICS Moreno-Estrada, A., Gravel, S., Zakharia, F., McCauley, J. L., Byrnes, J. K., Gignoux, C. R., Ortiz-Tello, P. A., Martinez, R. J., Hedges, D. J., Morris, R. W., Eng, C., Sandoval, K., Acevedo-Acevedo, S., Norman, P. J., Layrisse, Z., Parham, P., Martinez-Cruzado, J. C., Burchard, E. G., Cuccaro, M. L., Martin, E. R., Bustamante, C. D. 2013; 9 (11)
  • Genetic and Environmental Determinants of Human NK Cell Diversity Revealed by Mass Cytometry SCIENCE TRANSLATIONAL MEDICINE Horowitz, A., Strauss-Albee, D. M., Leipold, M., Kubo, J., Nemat-Gorgani, N., Dogan, O. C., Dekker, C. L., Mackey, S., Maecker, H., Swan, G. E., Davis, M. M., Norman, P. J., Guethlein, L. A., Desai, M., Parham, P., Blish, C. A. 2013; 5 (208)
  • Co-evolution of Human Leukocyte Antigen (HLA) Class I Ligands with Killer-Cell Immunoglobulin-Like Receptors (KIR) in a Genetically Diverse Population of Sub-Saharan Africans PLOS GENETICS Norman, P. J., Hollenbach, J. A., Nemat-Gorgani, N., Guethlein, L. A., Hilton, H. G., Pando, M. J., Koram, K. A., Riley, E. M., Abi-Rached, L., Parham, P. 2013; 9 (10)


    Interactions between HLA class I molecules and killer-cell immunoglobulin-like receptors (KIR) control natural killer cell (NK) functions in immunity and reproduction. Encoded by genes on different chromosomes, these polymorphic ligands and receptors correlate highly with disease resistance and susceptibility. Although studied at low-resolution in many populations, high-resolution analysis of combinatorial diversity of HLA class I and KIR is limited to Asian and Amerindian populations with low genetic diversity. At the other end of the spectrum is the West African population investigated here: we studied 235 individuals, including 104 mother-child pairs, from the Ga-Adangbe of Ghana. This population has a rich diversity of 175 KIR variants forming 208 KIR haplotypes, and 81 HLA-A, -B and -C variants forming 190 HLA class I haplotypes. Each individual we studied has a unique compound genotype of HLA class I and KIR, forming 1-14 functional ligand-receptor interactions. Maintaining this exceptionally high polymorphism is balancing selection. The centromeric region of the KIR locus, encoding HLA-C receptors, is highly diverse whereas the telomeric region encoding Bw4-specific KIR3DL1, lacks diversity in Africans. Present in the Ga-Adangbe are high frequencies of Bw4-bearing HLA-B*53:01 and Bw4-lacking HLA-B*35:01, which otherwise are identical. Balancing selection at key residues maintains numerous HLA-B allotypes having and lacking Bw4, and also those of stronger and weaker interaction with LILRB1, a KIR-related receptor. Correspondingly, there is a balance at key residues of KIR3DL1 that modulate its level of cell-surface expression. Thus, capacity to interact with NK cells synergizes with peptide binding diversity to drive HLA-B allele frequency distribution. These features of KIR and HLA are consistent with ongoing co-evolution and selection imposed by a pathogen endemic to West Africa. Because of the prevalence of malaria in the Ga-Adangbe and previous associations of cerebral malaria with HLA-B*53:01 and KIR, Plasmodium falciparum is a candidate pathogen.

    View details for DOI 10.1371/journal.pgen.1003938

    View details for Web of Science ID 000330367200087

    View details for PubMedID 24204327

  • Computational Analyses of an Evolutionary Arms Race between Mammalian Immunity Mediated by Immunoglobulin A and Its Subversion by Bacterial Pathogens PLOS ONE Pinheiro, A., Woof, J. M., Abi-Rached, L., Parham, P., Esteves, P. J. 2013; 8 (9)


    IgA is the predominant immunoglobulin isotype in mucosal tissues and external secretions, playing important roles both in defense against pathogens and in maintenance of commensal microbiota. Considering the complexity of its interactions with the surrounding environment, IgA is a likely target for diversifying or positive selection. To investigate this possibility, the action of natural selection on IgA was examined in depth with six different methods: CODEML from the PAML package and the SLAC, FEL, REL, MEME and FUBAR methods implemented in the Datamonkey webserver. In considering just primate IgA, these analyses show that diversifying selection targeted five positions of the Cα1 and Cα2 domains of IgA. Extending the analysis to include other mammals identified 18 positively selected sites: ten in Cα1, five in Cα2 and three in Cα3. All but one of these positions display variation in polarity and charge. Their structural locations suggest they indirectly influence the conformation of sites on IgA that are critical for interaction with host IgA receptors and also with proteins produced by mucosal pathogens that prevent their elimination by IgA-mediated effector mechanisms. Demonstrating the plasticity of IgA in the evolution of different groups of mammals, only two of the eighteen selected positions in all mammals are included in the five selected positions in primates. That IgA residues subject to positive selection impact sites targeted both by host receptors and subversive pathogen ligands highlights the evolutionary arms race playing out between mammals and pathogens, and further emphasizes the importance of IgA in protection against mucosal pathogens.

    View details for DOI 10.1371/journal.pone.0073934

    View details for Web of Science ID 000324338200084

    View details for PubMedID 24019941

  • Direct binding to antigen-coated beads refines the specificity and cross-reactivity of four monoclonal antibodies that recognize polymorphic epitopes of HLA class I molecules TISSUE ANTIGENS HILTON, H. G., Parham, P. 2013; 81 (4): 212-220


    Monoclonal antibodies with specificity for human leukocyte antigen (HLA) class I determinants of HLA were originally characterized using serological assays in which the targets were cells expressing three to six HLA class I variants. Because of this complexity, the specificities of the antibodies were defined indirectly by correlation. Here we use a direct binding assay, in which the targets are synthetic beads coated with 1 of 111 HLA class I variants, representing the full range of HLA-A, -B and -C variation. We studied one monoclonal antibody with monomorphic specificity (W6/32) and four with polymorphic specificity (MA2.1, PA2.1, BB7.2 and BB7.1) and compared the results with those obtained previously. W6/32 reacted with all HLA class I variants. MA2.1 not only exhibits high specificity for HLA-A*02, -B*57 and -B*58, but also exhibited cross-reactivity with HLA-A*11 and -B*15:16. At low concentration (1 µg/ml), PA2.1 and BB7.2 were both specific for HLA-A*02 and -A*69, and at high concentration (50 µg/ml) exhibited significant cross-reactions with HLA-A*68, -A*23 and -A*24. BB7.1 exhibits specificity for HLA-B*07 and -B*42, as previously described, but reacts equally well with HLA-B*81, a rare allotype defined some 16 years after the description of BB7.1. The results obtained with cell-based and bead-based assays are consistent and, in combination with amino acid sequence comparison, increase understanding of the polymorphic epitopes recognized by the MA2.1, PA2.1, BB7.2 and BB7.1 antibodies. Comparison of two overlapping but distinctive bead sets from two sources gave similar results, but the overall levels of binding were significantly different. Several weaker reactions were observed with only one of the bead sets.

    View details for DOI 10.1111/tan.12095

    View details for Web of Science ID 000316628100004

    View details for PubMedID 23510417

  • Variable NK cell receptors and their MHC class I ligands in immunity, reproduction and human evolution NATURE REVIEWS IMMUNOLOGY Parham, P., Moffett, A. 2013; 13 (2): 133-144


    Natural killer (NK) cells have roles in immunity and reproduction that are controlled by variable receptors that recognize MHC class I molecules. The variable NK cell receptors found in humans are specific to simian primates, in which they have progressively co-evolved with MHC class I molecules. The emergence of the MHC-C gene in hominids drove the evolution of a system of NK cell receptors for MHC-C molecules that is most elaborate in chimpanzees. By contrast, the human system of MHC-C receptors seems to have been subject to different selection pressures that have acted in competition on the immunological and reproductive functions of MHC class I molecules. We suggest that this compromise facilitated the development of the bigger brains that enabled archaic and modern humans to migrate out of Africa and populate other continents.

    View details for DOI 10.1038/nri3370

    View details for Web of Science ID 000314906600015

    View details for PubMedID 23334245

  • 16(th) IHIW: Review of HLA typing by NGS INTERNATIONAL JOURNAL OF IMMUNOGENETICS De Santis, D., Dinauer, D., Duke, J., Erlich, H. A., HOLCOMB, C. L., Lind, C., Mackiewicz, K., Monos, D., Moudgil, A., Norman, P., Parham, P., Sasson, A., Allcock, R. J. 2013; 40 (1): 72-76


    Human leucocyte antigen (HLA) genes play an important role in the success of organ transplantation and are associated with autoimmune and infectious diseases. Current DNA-based genotyping methods, including Sanger sequence-based typing (SSBT), have identified a high degree of polymorphism. This level of polymorphism makes high-resolution HLA genotyping challenging, resulting in ambiguous typing results due to an inability to resolve phase and/or defining polymorphisms lying outside the region amplified. Next-generation sequencing (NGS) may resolve the issue through the combination of clonal amplification, which provides phase information, and the ability to sequence larger regions of genes, including introns, without the additional effort or cost associated with current methods. The NGS HLA sequencing project of the 16IHIW aimed to discuss the different approaches to (i) template preparation including short- and long-range PCR amplicons, exome capture and whole genome; (ii) sequencing platforms, including GS 454 FLX, Ion Torrent PGM, Illumina MiSeq/HiSeq and Pacific Biosciences SMRT; (iii) data analysis, specifically allele-calling software. The pilot studies presented at the workshop demonstrated that although individual sequencers have very different performance characteristics, all produced sequence data suitable for the resolution of HLA genotyping ambiguities. The developments presented at this workshop clearly highlight the potential benefits of NGS in the HLA laboratory.

    View details for DOI 10.1111/iji.12024

    View details for Web of Science ID 000313488000012

    View details for PubMedID 23302098

  • The IMGT/HLA database. Nucleic acids research Robinson, J., Halliwell, J. A., McWilliam, H., Lopez, R., Parham, P., Marsh, S. G. 2013; 41 (Database issue): D1222-7


    It is 14 years since the IMGT/HLA database was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region of human chromosome 6 and contains more than 220 genes of diverse function. Of these, 21 genes encode proteins of the immune system that are highly polymorphic. The naming of these HLA genes and alleles and their quality control is the responsibility of the World Health Organization Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to these data through the website Regular updates to the website ensure that new and confirmatory sequences are dispersed to the HLA community and the wider research and clinical communities. This article describes the latest updates and additional tools added to the IMGT/HLA project.

    View details for DOI 10.1093/nar/gks949

    View details for PubMedID 23080122

  • The IMGT/HLA database NUCLEIC ACIDS RESEARCH Robinson, J., Halliwell, J. A., McWilliam, H., Lopez, R., Parham, P., Marsh, S. G. 2013; 41 (D1): D1222-D1227

    View details for DOI 10.1093/nar/gks949

    View details for Web of Science ID 000312893300173

  • Natural selection on marine carnivores elaborated a diverse family of classical MHC class I genes exhibiting haplotypic gene content variation and allelic polymorphism IMMUNOGENETICS Hammond, J. A., Guethlein, L. A., Norman, P. J., Parham, P. 2012; 64 (12): 915-933


    Pinnipeds, marine carnivores, diverged from terrestrial carnivores ~45 million years ago, before their adaptation to marine environments. This lifestyle change exposed pinnipeds to different microbiota and pathogens, with probable impact on their MHC class I genes. Investigating this question, genomic sequences were determined for 71 MHC class I variants: 27 from harbor seal and 44 from gray seal. These variants form three MHC class I gene lineages, one comprising a pseudogene. The second, a candidate nonclassical MHC class I gene, comprises a nonpolymorphic transcribed gene related to dog DLA-79 and giant panda Aime-1906. The third is the diversity lineage, which includes 62 of the 71 seal MHC class I variants. All are transcribed, and they minimally represent six harbor and 12 gray seal MHC class I genes. Besides species-specific differences in gene number, seal MHC class I haplotypes exhibit gene content variation and allelic polymorphism. Patterns of sequence variation, and of positions for positively selected sites, indicate the diversity lineage genes are the seals' classical MHC class I genes. Evidence that expansion of diversity lineage genes began before gray and harbor seals diverged is the presence in both species of two distinctive sublineages of diversity lineage genes. Pointing to further expansion following the divergence are the presence of species-specific genes and greater MHC class I diversity in gray seals than harbor seals. The elaboration of a complex variable family of classical MHC class I genes in pinnipeds contrasts with the single, highly polymorphic classical MHC class I gene of dog and giant panda, terrestrial carnivores.

    View details for DOI 10.1007/s00251-012-0651-z

    View details for Web of Science ID 000311025500007

    View details for PubMedID 23001684

  • Mutation at positively selected positions in the binding site for HLA-C shows that KIR2DL1 is a more refined but less adaptable NK cell receptor than KIR2DL3. Journal of immunology Hilton, H. G., Vago, L., Older Aguilar, A. M., Moesta, A. K., Graef, T., Abi-Rached, L., Norman, P. J., Guethlein, L. A., Fleischhauer, K., Parham, P. 2012; 189 (3): 1418-1430


    Through recognition of HLA class I, killer cell Ig-like receptors (KIR) modulate NK cell functions in human immunity and reproduction. Although a minority of HLA-A and -B allotypes are KIR ligands, HLA-C allotypes dominate this regulation, because they all carry either the C1 epitope recognized by KIR2DL2/3 or the C2 epitope recognized by KIR2DL1. The C1 epitope and C1-specific KIR evolved first, followed several million years later by the C2 epitope and C2-specific KIR. Strong, varying selection pressure on NK cell functions drove the diversification and divergence of hominid KIR, with six positions in the HLA class I binding site of KIR being targets for positive diversifying selection. Introducing each naturally occurring residue at these positions into KIR2DL1 and KIR2DL3 produced 38 point mutants that were tested for binding to 95 HLA- A, -B, and -C allotypes. Modulating specificity for HLA-C is position 44, whereas positions 71 and 131 control cross-reactivity with HLA-A*11:02. Dominating avidity modulation is position 70, with lesser contributions from positions 68 and 182. KIR2DL3 has lower avidity and broader specificity than KIR2DL1. Mutation could increase the avidity and change the specificity of KIR2DL3, whereas KIR2DL1 specificity was resistant to mutation, and its avidity could only be lowered. The contrasting inflexibility of KIR2DL1 and adaptability of KIR2DL3 fit with C2-specific KIR having evolved from C1-specific KIR, and not vice versa. Substitutions restricted to activating KIR all reduced the avidity of KIR2DL1 and KIR2DL3, further evidence that activating KIR function often becomes subject to selective attenuation.

    View details for DOI 10.4049/jimmunol.1100431

    View details for PubMedID 22772445

  • Human-specific evolution of killer cell immunoglobulin-like receptor recognition of major histocompatibility complex class I molecules PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Parham, P., Norman, P. J., Abi-Rached, L., Guethlein, L. A. 2012; 367 (1590): 800-811


    In placental mammals, natural killer (NK) cells are a population of lymphocytes that make unique contributions to immune defence and reproduction, functions essential for survival of individuals, populations and species. Modulating these functions are conserved and variable NK-cell receptors that recognize epitopes of major histocompatibility complex (MHC) class I molecules. In humans, for example, recognition of human leucocyte antigen (HLA)-E by the CD94:NKG2A receptor is conserved, whereas recognition of HLA-A, B and C by the killer cell immunoglobulin-like receptors (KIRs) is diversified. Competing demands of the immune and reproductive systems, and of T-cell and NK-cell immunity-combined with the segregation on different chromosomes of variable NK-cell receptors and their MHC class I ligands-drive an unusually rapid evolution that has resulted in unprecedented levels of species specificity, as first appreciated from comparison of mice and humans. Counterparts to human KIR are present only in simian primates. Observed in these species is the coevolution of KIR and the four MHC class I epitopes to which human KIR recognition is restricted. Unique to hominids is the emergence of the MHC-C locus as a supplier of specialized and superior ligands for KIR. This evolutionary trend is most highly elaborated in the chimpanzee. Unique to the human KIR locus are two groups of KIR haplotypes that are present in all human populations and subject to balancing selection. Group A KIR haplotypes resemble chimpanzee KIR haplotypes and are enriched for genes encoding KIR that bind HLA class I, whereas group B KIR haplotypes are enriched for genes encoding receptors with diminished capacity to bind HLA class I. Correlating with their balance in human populations, B haplotypes favour reproductive success, whereas A haplotypes favour successful immune defence. Evolution of the B KIR haplotypes is thus unique to the human species.

    View details for DOI 10.1098/rstb.2011.0266

    View details for Web of Science ID 000300390100005

    View details for PubMedID 22312047

  • Review: Immunogenetics of human placentation PLACENTA Parham, P., Norman, P. J., Abi-Rached, L., HILTON, H. G., Guethlein, L. A. 2012; 33: S71-S80


    Natural killer (NK) cells are a population of lymphocytes that function in both immune defense and reproduction. Diversifying NK cell phenotype and function are interactions between NK cell receptors and major histocompatibility complex (MHC) class I ligands. As a consequence of strong and variable selection these ligand-receptor systems are polymorphic, rapidly evolving, and considerably species-specific. Counterparts to the human system of HLA class I ligands and killer cell immunoglobulin-like receptors (KIR) are present only in apes and Old World monkeys. HLA-C, the dominant ligand for human KIR and the only polymorphic HLA class I expressed by trophoblast, is further restricted to humans and great apes. Even then, the human system appears qualitatively different from that of chimpanzees, in that it has evolved a genetic balance between particular groups of receptors and ligands that favor reproductive success and other groups of receptors and ligands that have been correlated with disordered placentation. Human populations that have survived successive episodes of epidemic disease and population bottlenecks maintain a breadth of diversity for KIR and HLA class I, implying that loss of such diversity disfavors long-term survival of a human population.

    View details for DOI 10.1016/j.placenta.2011.11.020

    View details for Web of Science ID 000301868000014

    View details for PubMedID 22177321

  • NK Cells-From Bench to Clinic BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION Murphy, W. J., Parham, P., Miller, J. S. 2012; 18 (1): S2-S7


    After decades of mouse and human research, we now know that natural killer (NK) cells have unique properties including memory. Although initially described as major histocompatibility complex (MHC) unrestricted killers, NK cells have several families of receptors that directly recognize MHC including Ly49 receptors in the mouse and killer immunoglobulin-like receptors (KIR) in humans. The strength of this signal is determined by polymorphisms in NK cell inhibitory receptor genes and their MHC ligands inherited on different chromosomes. Inhibitory receptors protect "self"-expressing normal tissue from being killed by NK cells and protecting against autoimmunity. Therefore, for NK cells to kill and produce cytokines, they must encounter activating receptor ligands in the context of "missing self" that occurs with some viral infections and malignant transformation. The second property of inhibitory receptors is to educate or license NK cells to acquire function. This is best demonstrated in the mouse and in humans by enhanced function on self-inhibitory receptor-expressing NK cells when in a host expressing cognate ligate. In contrast, NK cells without inhibitory receptors or with nonself-inhibitory receptors are relatively hyporesponsive. The basic biology of NK cells in response to cytokines, education, and viruses will translate into strategies to manipulate NK cells for therapeutic purposes.

    View details for DOI 10.1016/j.bbmt.2011.10.033

    View details for Web of Science ID 000299239500002

    View details for PubMedID 22226108

  • The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans SCIENCE Abi-Rached, L., Jobin, M. J., Kulkarni, S., McWhinnie, A., Dalva, K., Gragert, L., Babrzadeh, F., Gharizadeh, B., Luo, M., Plummer, F. A., Kimani, J., Carrington, M., Middleton, D., Rajalingam, R., Beksac, M., Marsh, S. G., Maiers, M., Guethlein, L. A., Tavoularis, S., Little, A., Green, R. E., Norman, P. J., Parham, P. 2011; 334 (6052): 89-94


    Whole genome comparisons identified introgression from archaic to modern humans. Our analysis of highly polymorphic human leukocyte antigen (HLA) class I, vital immune system components subject to strong balancing selection, shows how modern humans acquired the HLA-B*73 allele in west Asia through admixture with archaic humans called Denisovans, a likely sister group to the Neandertals. Virtual genotyping of Denisovan and Neandertal genomes identified archaic HLA haplotypes carrying functionally distinctive alleles that have introgressed into modern Eurasian and Oceanian populations. These alleles, of which several encode unique or strong ligands for natural killer cell receptors, now represent more than half the HLA alleles of modern Eurasians and also appear to have been later introduced into Africans. Thus, adaptive introgression of archaic alleles has significantly shaped modern human immune systems.

    View details for DOI 10.1126/science.1209202

    View details for Web of Science ID 000295580300046

    View details for PubMedID 21868630

  • Rhesus macaque KIR bind human MHC class I with broad specificity and recognize HLA-C more effectively than HLA-A and HLA-B IMMUNOGENETICS Aguilar, A. M., Guethlein, L. A., Hermes, M., Walter, L., Parham, P. 2011; 63 (9): 577-585


    Human killer cell immunoglobulin-like receptors (KIR) recognize A3/11, Bw4, C1, and C2 epitopes carried by mutually exclusive subsets of human leukocyte antigen (HLA)-A, -B, and -C allotypes. Chimpanzee and orangutan have counterparts to HLA-A, -B, and -C, and KIR that recognize the A3/11, Bw4, C1, and C2 epitopes, either individually or in combination. Because rhesus macaque has counterparts of HLA-A and -B, but not HLA-C, we expected that rhesus KIR would better recognize HLA-A and -B, than HLA-C. Comparison of the interactions of nine rhesus KIR3D with 95 HLA isoforms, showed the KIR have broad specificity for HLA-A, -B, and -C, but vary in avidity. Considering both the strength and breadth of reaction, HLA-C was the major target for rhesus KIR, followed by HLA-B, then HLA-A. Strong reactions with HLA-A were restricted to the minority of allotypes carrying the Bw4 epitope, whereas strong reactions with HLA-B partitioned between allotypes having and lacking Bw4. Contrasting to HLA-A and -B, every HLA-C allotype bound to the nine rhesus KIR. Sequence comparison of high- and low-binding HLA allotypes revealed the importance of polymorphism in the helix of the ?(1) domain and the peptide-binding pockets. At peptide position 9, nonpolar residues favor binding to rhesus KIR, whereas charged residues do not. Contrary to expectation, rhesus KIR bind more effectively to HLA-C, than to HLA-A and -B. This property is consistent with major histocompatibility complex (MHC)-C having evolved in hominids to be a generally superior ligand for KIR than MHC-A and MHC-B.

    View details for DOI 10.1007/s00251-011-0535-7

    View details for Web of Science ID 000293855600003

    View details for PubMedID 21614583

  • Natural variation at position 45 in the D1 domain of lineage III killer cell immunoglobulin-like receptors (KIR) has major effects on the avidity and specificity for MHC class I. Immunogenetics Older Aguilar, A. M., Guethlein, L. A., Abi-Rached, L., Parham, P. 2011; 63 (8): 543-547


    Alternative lysine and methionine residues at position 44 in the D1 domain determine the specificities of human lineage III killer cell immunoglobulin-like receptors (KIR) for the C1 and C2 epitopes of HLA-C. KIR having glutamate 44 are also present in orangutans (Popy2DLB) and chimpanzees (Pt-2DL9) but notably absent from humans. Popy2DLB exhibits broad specificity for both the C1 and C2 epitopes, whereas Pt-2DL9 has narrow specificity for C2. Mutation of phenylalanine 45 in Popy2DLB to the cysteine residue present in Pt-2DL9 was sufficient to narrow the Popy2DLB specificity to be like that of Pt-2DL9. In contrast, replacement of cysteine 45 in Pt-2DL9 by phenylalanine had no effect on its C2 specificity, but reduced the avidity. In a similar manner, replacement of phenylalanine 45 with cysteine in Popy2DLA, which has lysine 44 and recognizes C1, maintained this specificity while reducing avidity. Position 45 is exceptionally variable, exhibiting twelve residues that distinguish KIR of different lineages and species. Our study demonstrates the potential for variation at position 45 to modulate KIR avidity and specificity for HLA-C. The various effects of position 45 mutation are consistent with a model in which a Popy2DLB-like receptor, having glutamate 44 and broad specificity for C1 and C2, facilitated the evolution of the C2 epitope from the C1 epitope and C2-specific KIR from C1-specific KIR. With the acquisition of C2 and C2-specific receptors, the selection against this broadly specific receptor led to its loss from the human line and narrowing of its specificity on the chimpanzee line.

    View details for DOI 10.1007/s00251-011-0527-7

    View details for PubMedID 21541786

  • Variable NK Cell Receptors Exemplified by Human KIR3DL1/S1 JOURNAL OF IMMUNOLOGY Parham, P., Norman, P. J., Abi-Rached, L., Guethlein, L. A. 2011; 187 (1): 11-19


    Variegated expression of variable NK cell receptors for polymorphic MHC class I broadens the range of an individual's NK cell response and the capacity for populations and species to survive disease epidemics and population bottlenecks. On evolutionary time scales, this component of immunity is exceptionally dynamic, unstable, and short-lived, being dependent on coevolution of ligands and receptors subject to varying, competing selection pressures. Consequently these systems of variable NK cell receptors are largely species specific and have recruited different classes of glycoprotein, even within the primate order of mammals. Such disparity helps to explain substantial differences in NK cell biology between humans and animal models, for which the population genetics is largely ignored. KIR3DL1/S1, which recognizes the Bw4 epitope of HLA-A and -B and is the most extensively studied of the variable NK cell receptors, exemplifies how variation in all possible parameters of function is recruited to diversify the human NK cell response.

    View details for DOI 10.4049/jimmunol.0902332

    View details for Web of Science ID 000291799300005

    View details for PubMedID 21690332

  • Characterization of killer immunoglobulin-like receptor genetics and comprehensive genotyping by pyrosequencing in rhesus macaques BMC GENOMICS Moreland, A. J., Guethlein, L. A., Reeves, R. K., Broman, K. W., Johnson, R. P., Parham, P., O'Connor, D. H., Bimber, B. N. 2011; 12


    Human killer immunoglobulin-like receptors (KIRs) play a critical role in governing the immune response to neoplastic and infectious disease. Rhesus macaques serve as important animal models for many human diseases in which KIRs are implicated; however, the study of KIR activity in this model is hindered by incomplete characterization of KIR genetics.Here we present a characterization of KIR genetics in rhesus macaques (Macaca mulatta). We conducted a survey of KIRs in this species, identifying 47 novel full-length KIR sequences. Using this expanded sequence library to build upon previous work, we present evidence supporting the existence of 22 Mamu-KIR genes, providing a framework within which to describe macaque KIRs. We also developed a novel pyrosequencing-based technique for KIR genotyping. This method provides both comprehensive KIR genotype and frequency estimates of transcript level, with implications for the study of KIRs in all species.The results of this study significantly improve our understanding of macaque KIR genetic organization and diversity, with implications for the study of many human diseases that use macaques as a model. The ability to obtain comprehensive KIR genotypes is of basic importance for the study of KIRs, and can easily be adapted to other species. Together these findings both advance the field of macaque KIRs and facilitate future research into the role of KIRs in human disease.

    View details for DOI 10.1186/1471-2164-12-295

    View details for Web of Science ID 000292144300001

    View details for PubMedID 21645414

  • Hunter-gatherer genomic diversity suggests a southern African origin for modern humans PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Henn, B. M., Gignoux, C. R., Jobin, M., Granka, J. M., Macpherson, J. M., Kidd, J. M., Rodriguez-Botigue, L., Ramachandran, S., Hon, L., Brisbin, A., Lin, A. A., Underhill, P. A., Comas, D., Kidd, K. K., Norman, P. J., Parham, P., Bustamante, C. D., Mountain, J. L., Feldman, M. W. 2011; 108 (13): 5154-5162


    Africa is inferred to be the continent of origin for all modern human populations, but the details of human prehistory and evolution in Africa remain largely obscure owing to the complex histories of hundreds of distinct populations. We present data for more than 580,000 SNPs for several hunter-gatherer populations: the Hadza and Sandawe of Tanzania, and the ?Khomani Bushmen of South Africa, including speakers of the nearly extinct N|u language. We find that African hunter-gatherer populations today remain highly differentiated, encompassing major components of variation that are not found in other African populations. Hunter-gatherer populations also tend to have the lowest levels of genome-wide linkage disequilibrium among 27 African populations. We analyzed geographic patterns of linkage disequilibrium and population differentiation, as measured by F(ST), in Africa. The observed patterns are consistent with an origin of modern humans in southern Africa rather than eastern Africa, as is generally assumed. Additionally, genetic variation in African hunter-gatherer populations has been significantly affected by interaction with farmers and herders over the past 5,000 y, through both severe population bottlenecks and sex-biased migration. However, African hunter-gatherer populations continue to maintain the highest levels of genetic diversity in the world.

    View details for DOI 10.1073/pnas.1017511108

    View details for Web of Science ID 000288894800009

    View details for PubMedID 21383195

  • Although Divergent in Residues of the Peptide Binding Site, Conserved Chimpanzee Patr-AL and Polymorphic Human HLA-A*02 Have Overlapping Peptide-Binding Repertoires JOURNAL OF IMMUNOLOGY Gleimer, M., Wahl, A. R., Hickman, H. D., Abi-Rached, L., Norman, P. J., Guethlein, L. A., Hammond, J. A., Draghi, M., Adams, E. J., Juo, S., Jalili, R., Gharizadeh, B., Ronaghi, M., Garcia, K. C., Hildebrand, W. H., Parham, P. 2011; 186 (3): 1575-1588


    Patr-AL is an expressed, non-polymorphic MHC class I gene carried by ?50% of chimpanzee MHC haplotypes. Comparing Patr-AL(+) and Patr-AL(-) haplotypes showed Patr-AL defines a unique 125-kb genomic block flanked by blocks containing classical Patr-A and pseudogene Patr-H. Orthologous to Patr-AL are polymorphic orangutan Popy-A and the 5' part of human pseudogene HLA-Y, carried by ?10% of HLA haplotypes. Thus, the AL gene alternatively evolved in these closely related species to become classical, nonclassical, and nonfunctional. Although differing by 30 aa substitutions in the peptide-binding ?(1) and ?(2) domains, Patr-AL and HLA-A*0201 bind overlapping repertoires of peptides; the overlap being comparable with that between the A*0201 and A*0207 subtypes differing by one substitution. Patr-AL thus has the A02 supertypic peptide-binding specificity. Patr-AL and HLA-A*0201 have similar three-dimensional structures, binding peptides in similar conformation. Although comparable in size and shape, the B and F specificity pockets of Patr-AL and HLA-A*0201 differ in both their constituent residues and contacts with peptide anchors. Uniquely shared by Patr-AL, HLA-A*0201, and other members of the A02 supertype are the absence of serine at position 9 in the B pocket and the presence of tyrosine at position 116 in the F pocket. Distinguishing Patr-AL from HLA-A*02 is an unusually electropositive upper face on the ?(2) helix. Stimulating PBMCs from Patr-AL(-) chimpanzees with B cells expressing Patr-AL produced potent alloreactive CD8 T cells with specificity for Patr-AL and no cross-reactivity toward other MHC class I molecules, including HLA-A*02. In contrast, PBMCs from Patr-AL(+) chimpanzees are tolerant of Patr-AL.

    View details for DOI 10.4049/jimmunol.1002990

    View details for Web of Science ID 000286381200037

    View details for PubMedID 21209280

  • The IMGT/HLA database NUCLEIC ACIDS RESEARCH Robinson, J., Mistry, K., McWilliam, H., Lopez, R., Parham, P., Marsh, S. G. 2011; 39: D1171-D1176


    It is 12 years since the IMGT/HLA database was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and are highly polymorphic. The naming of these HLA genes and alleles and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data through the web site Regular updates to the web site ensure that new and confirmatory sequences are dispersed to the HLA community, and the wider research and clinical communities.

    View details for DOI 10.1093/nar/gkq998

    View details for Web of Science ID 000285831700184

    View details for PubMedID 21071412

  • Interactions of NK Cell Receptor KIR3DL1*004 with Chaperones and Conformation-Specific Antibody Reveal a Functional Folded State As Well As Predominant Intracellular Retention JOURNAL OF IMMUNOLOGY Taner, S. B., Pando, M. J., Roberts, A., Schellekens, J., Marsh, S. G., Malmberg, K., Parham, P., Brodsky, F. M. 2011; 186 (1): 62-72


    Variable interaction between the Bw4 epitope of HLA-B and the polymorphic KIR3DL1/S1 system of inhibitory and activating NK cell receptors diversifies the development, repertoire formation, and response of human NK cells. KIR3DL1*004, a common KIR3DL1 allotype, in combination with Bw4(+) HLA-B, slows progression of HIV infection to AIDS. Analysis in this study of KIR3DL1*004 membrane traffic in NK cells shows this allotype is largely misfolded but stably retained in the endoplasmic reticulum, where it binds to the chaperone calreticulin and does not induce the unfolded protein response. A small fraction of KIR3DL1*004 folds correctly and leaves the endoplasmic reticulum to be expressed on the surface of primary NK and transfected NKL cells, in a form that can be triggered to inhibit NK cell activation and secretion of IFN-?. Consistent with this small proportion of correctly folded molecules, trace amounts of MHC class I coimmunoprecipitated with KIR3DL1*004. There was no indication of any extensive intracellular interaction between unfolded KIR3DL1*004 and cognate Bw4(+) HLA-B. A similarly limited interaction of Bw4 with KIR3DL1*002, when both were expressed by the same cell, was observed despite the efficient folding of KIR3DL1*002 and its abundance on the NK cell surface. Several positions of polymorphism modulate KIR3DL1 abundance at the cell surface, differences that do not necessarily correlate with the potency of allotype function. In this context, our results suggest the possibility that the effect of Bw4(+) HLA-B and KIR3DL1*004 in slowing progression to AIDS is mediated by interaction of Bw4(+) HLA-B with the small fraction of cell surface KIR3DL1*004.

    View details for DOI 10.4049/jimmunol.0903657

    View details for Web of Science ID 000285688700013

    View details for PubMedID 21115737

  • Different Patterns of Evolution in the Centromeric and Telomeric Regions of Group A and B Haplotypes of the Human Killer Cell Ig-Like Receptor Locus PLOS ONE Pyo, C., Guethlein, L. A., Vu, Q., Wang, R., Abi-Rached, L., Norman, P. J., Marsh, S. G., Miller, J. S., Parham, P., Geraghty, D. E. 2010; 5 (12)


    The fast evolving human KIR gene family encodes variable lymphocyte receptors specific for polymorphic HLA class I determinants. Nucleotide sequences for 24 representative human KIR haplotypes were determined. With three previously defined haplotypes, this gave a set of 12 group A and 15 group B haplotypes for assessment of KIR variation. The seven gene-content haplotypes are all combinations of four centromeric and two telomeric motifs. 2DL5, 2DS5 and 2DS3 can be present in centromeric and telomeric locations. With one exception, haplotypes having identical gene content differed in their combinations of KIR alleles. Sequence diversity varied between haplotype groups and between centromeric and telomeric halves of the KIR locus. The most variable A haplotype genes are in the telomeric half, whereas the most variable genes characterizing B haplotypes are in the centromeric half. Of the highly polymorphic genes, only the 3DL3 framework gene exhibits a similar diversity when carried by A and B haplotypes. Phylogenetic analysis and divergence time estimates, point to the centromeric gene-content motifs that distinguish A and B haplotypes having emerged ~6 million years ago, contemporaneously with the separation of human and chimpanzee ancestors. In contrast, the telomeric motifs that distinguish A and B haplotypes emerged more recently, ~1.7 million years ago, before the emergence of Homo sapiens. Thus the centromeric and telomeric motifs that typify A and B haplotypes have likely been present throughout human evolution. The results suggest the common ancestor of A and B haplotypes combined a B-like centromeric region with an A-like telomeric region.

    View details for DOI 10.1371/journal.pone.0015115

    View details for Web of Science ID 000285793200015

    View details for PubMedID 21206914

  • Human-Specific Evolution and Adaptation Led to Major Qualitative Differences in the Variable Receptors of Human and Chimpanzee Natural Killer Cells PLOS GENETICS Abi-Rached, L., Moesta, A. K., Rajalingam, R., Guethlein, L. A., Parham, P. 2010; 6 (11)


    Natural killer (NK) cells serve essential functions in immunity and reproduction. Diversifying these functions within individuals and populations are rapidly-evolving interactions between highly polymorphic major histocompatibility complex (MHC) class I ligands and variable NK cell receptors. Specific to simian primates is the family of Killer cell Immunoglobulin-like Receptors (KIR), which recognize MHC class I and associate with a range of human diseases. Because KIR have considerable species-specificity and are lacking from common animal models, we performed extensive comparison of the systems of KIR and MHC class I interaction in humans and chimpanzees. Although of similar complexity, they differ in genomic organization, gene content, and diversification mechanisms, mainly because of human-specific specialization in the KIR that recognizes the C1 and C2 epitopes of MHC-B and -C. Humans uniquely focused KIR recognition on MHC-C, while losing C1-bearing MHC-B. Reversing this trend, C1-bearing HLA-B46 was recently driven to unprecedented high frequency in Southeast Asia. Chimpanzees have a variety of ancient, avid, and predominantly inhibitory receptors, whereas human receptors are fewer, recently evolved, and combine avid inhibitory receptors with attenuated activating receptors. These differences accompany human-specific evolution of the A and B haplotypes that are under balancing selection and differentially function in defense and reproduction. Our study shows how the qualitative differences that distinguish the human and chimpanzee systems of KIR and MHC class I predominantly derive from adaptations on the human line in response to selective pressures placed on human NK cells by the competing needs of defense and reproduction.

    View details for DOI 10.1371/journal.pgen.1001192

    View details for Web of Science ID 000284587100007

    View details for PubMedID 21079681

  • Pregnancy immunogenetics: NK cell education in the womb? JOURNAL OF CLINICAL INVESTIGATION Parham, P., Guethlein, L. A. 2010; 120 (11): 3801-3804


    During embryo implantation and initiation of pregnancy, uterine NK (uNK) cells engage invasive fetal trophoblasts to remodel vessels that conduct blood to the placenta. This partnership, involving uNK cell receptors that recognize HLA-C ligands on trophoblasts, varies the course of human pregnancy because the genes for both receptors and ligands are extraordinarily diverse. Several pregnancy disorders are attributed to insufficient trophoblast invasion and the limitation it imposes on human reproduction. Previously, a particular combination of fetal HLA-C and maternal inhibitory uNK cell receptor was associated with predisposition for preeclampsia. In this issue of the JCI, Hiby and colleagues extend this correlation to recurrent miscarriage and fetal growth restriction, revealing the common mechanism underlying these common pregnancy syndromes. Equally important, they show that mothers with an activating receptor of similar specificity to the inhibitory receptor are less likely to suffer disordered pregnancy.

    View details for DOI 10.1172/JCI44559

    View details for Web of Science ID 000283621800010

    View details for PubMedID 20972330

  • Humans Differ from Other Hominids in Lacking an Activating NK Cell Receptor That Recognizes the C1 Epitope of MHC Class I JOURNAL OF IMMUNOLOGY Moesta, A. K., Graef, T., Abi-Rached, L., Aguilar, A. M., Guethlein, L. A., Parham, P. 2010; 185 (7): 4233-4237


    Modulation of human NK cell function by killer cell Ig-like receptors (KIR) and MHC class I is dominated by the bipartite interactions of inhibitory lineage III KIR with the C1 and C2 epitopes of HLA-C. In comparison, the ligand specificities and functional contributions of the activating lineage III KIR remain poorly understood. Using a robust, sensitive assay of KIR binding and a representative panel of 95 HLA class I targets, we show that KIR2DS1 binds C2 with ~50% the avidity of KIR2DL1, whereas KIR2DS2, KIR2DS3, and KIR2DS5 have no detectable avidity for C1, C2, or any other HLA class I epitope. In contrast, the chimpanzee has activating C1- and C2-specific lineage III KIR with strong avidity, comparable to those of their paired inhibitory receptors. One variant of chimpanzee Pt-KIR3DS2, the activating C2-specific receptor, has the same avidity for C2 as does inhibitory Pt-KIR3DL4, and a second variant has ~73% the avidity. Chimpanzee Pt-KIR3DS6, the activating C1-specific receptor, has avidity for C1 that is ~70% that of inhibitory Pt-KIR2DL6. In both humans and chimpanzees we observe an evolutionary trend toward reducing the avidity of the activating C1- and C2-specific receptors through selective acquisition of attenuating substitutions. However, the extent of attenuation has been extreme in humans, as exemplified by KIR2DS2, an activating C1-specific receptor that has lost all detectable avidity for HLA class I. Supporting such elimination of activating C1-specific receptors as a uniquely human phenomenon is the presence of a high-avidity activating C1-specific receptor (Gg-KIR2DSa) in gorilla.

    View details for DOI 10.4049/jimmunol.1001951

    View details for Web of Science ID 000282059500050

    View details for PubMedID 20802150

  • Coevolution of Killer Cell Ig-Like Receptors with HLA-C To Become the Major Variable Regulators of Human NK Cells JOURNAL OF IMMUNOLOGY Aguilar, A. M., Guethlein, L. A., Adams, E. J., Abi-Rached, L., Moesta, A. K., Parham, P. 2010; 185 (7): 4238-4251


    Interactions between HLA class I and killer cell Ig-like receptors (KIRs) diversify human NK cell responses. Dominant KIR ligands are the C1 and C2 epitopes of MHC-C, a young locus restricted to humans and great apes. C1- and C1-specific KIRs evolved first, being present in orangutan and functionally like their human counterparts. Orangutans lack C2 and C2-specific KIRs, but have a unique C1+C2-specific KIR that binds equally to C1 and C2. A receptor with this specificity likely provided the mechanism by which C2-KIR interaction evolved from C1-KIR while avoiding a nonfunctional intermediate, that is, either orphan receptor or ligand. Orangutan inhibitory MHC-C-reactive KIRs pair with activating receptors of identical avidity and specificity, contrasting with the selective attenuation of human activating KIRs. The orangutan C1-specific KIR reacts or cross-reacts with all four polymorphic epitopes (C1, C2, Bw4, and A3/11) recognized by human KIRs, revealing their structural commonality. Saturation mutagenesis at specificity-determining position 44 demonstrates that KIRs are inherently restricted to binding just these four epitopes, either individually or in combination. This restriction frees most HLA-A and HLA-B variants to be dedicated TCR ligands, not subject to conflicting pressures from the NK cell and T cell arms of the immune response.

    View details for DOI 10.4049/jimmunol.1001494

    View details for Web of Science ID 000282059500051

    View details for PubMedID 20805421

  • Primate-specific regulation of natural killer cells Parham, P., Abi-Rached, L., Matevosyan, L., Moesta, A. K., Norman, P. J., Aguilar, A. M., Guethlein, L. A. WILEY-BLACKWELL PUBLISHING, INC. 2010: 194-212


    Natural killer (NK) cells are circulating lymphocytes that function in innate immunity and placental reproduction. Regulating both development and function of NK cells is an array of variable and conserved receptors that interact with major histocompatibility complex (MHC) class I molecules. Families of lectin-like and immunoglobulin-like receptors are determined by genes in the natural killer complex (NKC) and leukocyte receptor complex (LRC), respectively. As a consequence of the strong, varying pressures on the immune and reproductive systems, NK cell receptors and their MHC class I ligands evolve rapidly, are highly diverse and exhibit dramatic species-specific differences. The variable, polymorphic family of killer cell immunoglobulin-like receptors (KIR) that regulate human NK cell development and function arose recently, from a single-copy gene during the evolution of simian primates. Our studies of KIR and MHC class I genes in representative species show how these two unlinked but functionally intertwined genetic complexes have co-evolved. In humans, combinations of KIR and HLA class I factors are associated with infectious diseases, including HIV/AIDS, autoimmunity, reproductive success and the outcome of therapeutic transplantation. The extraordinary, and unanticipated, divergence of human NK cell receptors and MHC class I ligands from their mouse counterparts can in part explain the difficulties experienced in finding informative mouse models for human diseases. Non-human primate models have far greater potential, but to realize their promise will first require more complete definition of the genetics and function of KIR and MHC variation in non-human primate species, at a level comparable to that achieved for the human species.

    View details for DOI 10.1111/j.1600-0684.2010.00432.x

    View details for Web of Science ID 000279448900003

    View details for PubMedID 20618586

  • A Small, Variable, and Irregular Killer Cell Ig-Like Receptor Locus Accompanies the Absence of MHC-C and MHC-G in Gibbons JOURNAL OF IMMUNOLOGY Abi-Rached, L., Kuhl, H., Roos, C., ten Hallers, B., Zhu, B., Carbone, L., de Jong, P. J., Mootnick, A. R., Knaust, F., Reinhardt, R., Parham, P., Walter, L. 2010; 184 (3): 1379-1391


    The killer cell Ig-like receptors (KIRs) of NK cells recognize MHC class I ligands and function in placental reproduction and immune defense against pathogens. During the evolution of monkeys, great apes, and humans, an ancestral KIR3DL gene expanded to become a diverse and rapidly evolving gene family of four KIR lineages. Characterizing the KIR locus are three framework regions, defining two intervals of variable gene content. By analysis of four KIR haplotypes from two species of gibbon, we find that the smaller apes do not conform to these rules. Although diverse and irregular in structure, the gibbon haplotypes are unusually small, containing only two to five functional genes. Comparison with the predicted ancestral hominoid KIR haplotype indicates that modern gibbon KIR haplotypes were formed by a series of deletion events, which created new hybrid genes as well as eliminating ancestral genes. Of the three framework regions, only KIR3DL3 (lineage V), defining the 5' end of the KIR locus, is present and intact on all gibbon KIR haplotypes. KIR2DL4 (lineage I) defining the central framework region has been a major target for elimination or inactivation, correlating with the absence of its putative ligand, MHC-G, in gibbons. Similarly, the MHC-C-driven expansion of lineage III KIR genes in great apes has not occurred in gibbons because they lack MHC-C. Our results indicate that the selective forces shaping the size and organization of the gibbon KIR locus differed from those acting upon the KIR of other hominoid species.

    View details for DOI 10.4049/jimmunol.0903016

    View details for Web of Science ID 000273956400030

    View details for PubMedID 20026738

  • Co-evolution of KIR2DL3 with HLA-C in a human population retaining minimal essential diversity of KIR and HLA class I ligands PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Gendzekhadze, K., Norman, P. J., Abi-Rached, L., Graef, T., Moesta, A. K., Layrisse, Z., Parham, P. 2009; 106 (44): 18692-18697


    Natural killer (NK) cells contribute to immunity and reproduction. Guiding these functions, and NK cell education, are killer cell Ig-like receptors (KIR), NK cell receptors that recognize HLA class I. In most human populations, these highly polymorphic receptors and ligands combine with extraordinary diversity. To assess how much of this diversity is necessary, we studied KIR and HLA class I at high resolution in the Yucpa, a small South Amerindian population that survived an approximate 15,000-year history of population bottleneck and epidemic infection, including recent viral hepatitis. The Yucpa retain the three major HLA epitopes recognized by KIR. Through balancing selection on a few divergent haplotypes the Yucpa maintain much of the KIR variation found worldwide. HLA-C*07, the strongest educator of C1-specific NK cells, has reached unusually high frequency in the Yucpa. Concomitantly, weaker variants of the C1 receptor, KIR2DL3, were selected and have largely replaced the form of KIR2DL3 brought by the original migrants from Asia. HLA-C1 and KIR2DL3 homozygosity has previously been correlated with resistance to viral hepatitis. Selection of weaker forms of KIR2DL3 in the Yucpa can be seen as compensation for the high frequency of the potent HLA-C*07 ligand. This study provides an estimate of the minimal KIR-HLA system essential for long-term survival of a human population. That it contains all functional elements of KIR diversity worldwide, attests to the competitive advantage it provides, not only for surviving epidemic infections, but also for rebuilding populations once infection has passed.

    View details for DOI 10.1073/pnas.0906051106

    View details for Web of Science ID 000271429800051

    View details for PubMedID 19837691

  • KIR2DS4 is a product of gene conversion with KIR3DL2 that introduced specificity for HLA-A*11 while diminishing avidity for HLA-C JOURNAL OF EXPERIMENTAL MEDICINE Graef, T., Moesta, A. K., Norman, P. J., Abi-Rached, L., Vago, L., Aguilar, A. M., Gleimer, M., Hammond, J. A., Guethlein, L. A., Bushnell, D. A., Robinson, P. J., Parham, P. 2009; 206 (11): 2557-2572


    Human killer cell immunoglobulin-like receptors (KIRs) are distinguished by expansion of activating KIR2DS, whose ligands and functions remain poorly understood. The oldest, most prevalent KIR2DS is KIR2DS4, which is represented by a variable balance between "full-length" and "deleted" forms. We find that full-length 2DS4 is a human histocompatibility leukocyte antigen (HLA) class I receptor that binds specifically to subsets of C1+ and C2+ HLA-C and to HLA-A*11, whereas deleted 2DS4 is nonfunctional. Activation of 2DS4+ NKL cells was achieved with A*1102 as ligand, which differs from A*1101 by unique substitution of lysine 19 for glutamate, but not with A*1101 or HLA-C. Distinguishing KIR2DS4 from other KIR2DS is the proline-valine motif at positions 71-72, which is shared with KIR3DL2 and was introduced by gene conversion before separation of the human and chimpanzee lineages. Site-directed swap mutagenesis shows that these two residues are largely responsible for the unique HLA class I specificity of KIR2DS4. Determination of the crystallographic structure of KIR2DS4 shows two major differences from KIR2DL: displacement of contact loop L2 and altered bonding potential because of the substitutions at positions 71 and 72. Correlation between the worldwide distributions of functional KIR2DS4 and HLA-A*11 points to the physiological importance of their mutual interaction.

    View details for DOI 10.1084/jem.20091010

    View details for Web of Science ID 000271164000022

    View details for PubMedID 19858347

  • Dimorphic Motifs in D0 and D1+D2 Domains of Killer Cell Ig-Like Receptor 3DL1 Combine to Form Receptors with High, Moderate, and No Avidity for the Complex of a Peptide Derived from HIV and HLA-A*2402 JOURNAL OF IMMUNOLOGY Sharma, D., Bastard, K., Guethlein, L. A., Norman, P. J., Yawata, N., Yawata, M., Pando, M., Thananchai, H., Dong, T., Rowland-Jones, S., Brodsky, F. M., Parham, P. 2009; 183 (7): 4569-4582


    Comparison of mutant killer cell Ig-like receptor (KIR) 3DL1*015 substituted at natural positions of variation showed that tryptophan/leucine dimorphism at position 283 uniquely changes receptor conformation and can strongly influence binding of the A24nef tetramer. Dimorphic motifs at positions 2, 47, and 54 in D0 and 182 and 283 in D1+D2 distinguish the two 3DL1 lineages, typified by 3DL1*005 and 3DL1*015. The interlineage recombinant, KIR3DL1*001, combines D0 of 3DL1*005 with D1+D2 of 3DL1*015 and binds A24nef more strongly than either parent. In contrast, the reciprocal recombinant with D0 from 3DL1*015 and D1+D2 from 3DL1*005 cannot bind A24nef. Thus, D0 polymorphism directly affects the avidity of the KIR3DL1 ligand binding site. From these observations, multiple sequence alignment, and homology modeling, we constructed structural models for KIR3DL1 and its complex with A24nef. In these models, D0, D1, and D2 come together to form a binding surface for A24nef, which is contacted by all three Ig-like domains. A central pocket binds arginine 83, the only Bw4 motif residue essential for KIR3DL1 interaction, similar to the binding of lysine 80 in HLA-C by KIR2DL1. Central to this interaction is a salt bridge between arginine 83 of Bw4 and glutamate 282 of 3DL1, which juxtaposes the functionally influential dimorphism at position 283. Further 3DL1 mutants were tested and shown to have A24nef-binding properties consistent with the models. A24nef was not bound by KIR3DS1, the activating counterpart of KIR3DL1. Moreover, introducing any one of three residues specific to KIR3DS1, serine 163, arginine 166, or leucine 199, into 3DL1*015, abrogated A24nef binding.

    View details for DOI 10.4049/jimmunol.0901734

    View details for Web of Science ID 000270522500052

    View details for PubMedID 19752231

  • Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes GENOME RESEARCH Norman, P. J., Abi-Rached, L., Gendzekhadze, K., Hammond, J. A., Moesta, A. K., Sharma, D., Graef, T., McQueen, K. L., Guethlein, L. A., Carrington, C. V., Chandanayingyong, D., Chang, Y., Crespi, C., Saruhan-Direskeneli, G., Hameed, K., Kamkamidze, G., Koram, K. A., Layrisse, Z., Matamoros, N., Mila, J., Park, M. H., Pitchappan, R. M., Ramdath, D. D., Shiau, M., Stephens, H. A., Struik, S., Tyan, D., Verity, D. H., Vaughan, R. W., Davis, R. W., Fraser, P. A., Riley, E. M., Ronaghi, M., Parham, P. 2009; 19 (5): 757-769


    Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC) Class I molecules expressed by other cells. For primate NK cells, the killer-cell immunoglobulin-like receptors (KIR) are a variable and rapidly evolving family of MHC Class I receptors. Studied here is KIR3DL1/S1, which encodes receptors for highly polymorphic human HLA-A and -B and comprises three ancient allelic lineages that have been preserved by balancing selection throughout human evolution. While the 3DS1 lineage of activating receptors has been conserved, the two 3DL1 lineages of inhibitory receptors were diversified through inter-lineage recombination with each other and with 3DS1. Prominent targets for recombination were D0-domain polymorphisms, which modulate enhancer function, and dimorphism at position 283 in the D2 domain, which influences inhibitory function. In African populations, unequal crossing over between the 3DL1 and 3DL2 genes produced a deleted KIR haplotype in which the telomeric "half" was reduced to a single fusion gene with functional properties distinct from its 3DL1 and 3DL2 parents. Conversely, in Eurasian populations, duplication of the KIR3DL1/S1 locus by unequal crossing over has enabled individuals to carry and express alleles of all three KIR3DL1/S1 lineages. These results demonstrate how meiotic recombination combines with an ancient, preserved diversity to create new KIR phenotypes upon which natural selection acts. A consequence of such recombination is to blur the distinction between alleles and loci in the rapidly evolving human KIR gene family.

    View details for DOI 10.1101/gr.085738.108

    View details for Web of Science ID 000265668800009

    View details for PubMedID 19411600

  • Chimpanzees Use More Varied Receptors and Ligands Than Humans for Inhibitory Killer Cell Ig-Like Receptor Recognition of the MHC-C1 and MHC-C2 Epitopes JOURNAL OF IMMUNOLOGY Moesta, A. K., Abi-Rached, L., Norman, P. J., Parham, P. 2009; 182 (6): 3628-3637


    Humans and chimpanzees have orthologous MHC class I, but few orthologous killer cell Ig-like receptors (KIR). Most divergent are lineage III KIR, which in humans include the inhibitory KIR2DL1 and 2DL2/3 specific for HLA-C. Six lineage III chimpanzee KIR were identified as candidate inhibitory MHC-C receptors and studied using cytolytic assays, to assess the capacity of a defined KIR to function with a defined MHC class I allotype, and direct binding assays with KIR-Fc fusion proteins. Pt-KIR2DL6 and 2DL8 were demonstrated to be inhibitory C1 receptors with a specificity and specificity-determining residue (lysine 44) like KIR2DL3. Analogously, Pt-KIR2DL7 is like KIR2DL1, an inhibitory C2 receptor having methionine 44. Pt-KIR3DL4 and 3DL5 are unusual lineage III KIR with D0 domains, which are also inhibitory C2 receptors with methionine 44. Removal of D0 from KIR3DL, or its addition to KIR2DL, had no effect on KIR function. Pt-KIR2DL9, a fourth inhibitory C2 receptor, has glutamate 44, a previously uncharacterized specificity-determining residue that is absent from human KIR. Reconstruction of the ancestral hominoid KIR sequence shows it encoded lysine 44, indicating that KIR having methionine 44 and glutamate 44 subsequently evolved by independent point substitutions. Thus, MHC-C2-specific KIR have evolved independently on at least two occasions. None of the six chimpanzee KIR studied resembles KIR2DL2, which interacts strongly with C1 and cross-reacts with C2. Whereas human HLA-B allotypes that have functional C1 epitopes are either rare (HLA-B*73) or geographically localized (HLA-B*46), some 25% of Patr-B allotypes have the C1 epitope and are functional KIR ligands.

    View details for DOI 10.4049/jimmunol.0803401

    View details for Web of Science ID 000264084100033

    View details for PubMedID 19265141

  • Evolution and Survival of Marine Carnivores Did Not Require a Diversity of Killer Cell Ig-Like Receptors or Ly49 NK Cell Receptors JOURNAL OF IMMUNOLOGY Hammond, J. A., Guethlein, L. A., Abi-Rached, L., Moesta, A. K., Parham, P. 2009; 182 (6): 3618-3627


    Ly49 lectin-like receptors and killer cell Ig-like receptors (KIR) are structurally unrelated cell surface glycoproteins that evolved independently to function as diverse NK cell receptors for MHC class I molecules. Comparison of primates and various domesticated animals has shown that species have either a diverse Ly49 or KIR gene family, but not both. In four pinniped species of wild marine carnivore, three seals and one sea lion, we find that Ly49 and KIR are each represented by single, orthologous genes that exhibit little polymorphism and are transcribed to express cell surface protein. Pinnipeds are therefore species in which neither Ly49 nor KIR are polygenic, but retain the ancestral single-copy state. Whereas pinniped Ly49 has been subject to purifying selection, we find evidence for positive selection on KIR3DL during pinniped evolution. This selection, which focused on the D0 domain and the stem, points to the functionality of the KIR and most likely led to the sea lion's loss of D0. In contrast to the dynamic and rapid evolution of the KIR and Ly49 genes in other species, the pinniped KIR and Ly49 have been remarkably stable during the >33 million years since the last common ancestor of seals and sea lions. These results demonstrate that long-term survival of placental mammal species need not require a diverse system of either Ly49 or KIR NK cell receptors.

    View details for DOI 10.4049/jimmunol.0803026

    View details for Web of Science ID 000264084100032

    View details for PubMedID 19265140

  • Donors with group B KIR haplotypes improve relapse-free survival after unrelated hematopoietic cell transplantation for acute myelogenous leukemia BLOOD Cooley, S., Trachtenberg, E., Bergemann, T. L., Saeteurn, K., Klein, J., Le, C. T., Marsh, S. G., Guethlein, L. A., Parham, P., Miller, J. S., Weisdorf, D. J. 2009; 113 (3): 726-732


    Survival for patients with acute myeloid leukemia (AML) is limited by treatment-related mortality (TRM) and relapse after unrelated donor (URD) hematopoietic cell transplantation (HCT). Natural killer (NK)-cell alloreactivity, determined by donor killer-cell immunoglobulin-like receptors (KIRs) and recipient HLA, correlates with successful HCT for AML. Hypothesizing that donor KIR genotype (A/A: 2 A KIR haplotypes; B/x: at least 1 B haplotype) would affect outcomes, we genotyped donors and recipients from 209 HLA-matched and 239 mismatched T-replete URD transplantations for AML. Three-year overall survival was significantly higher after transplantation from a KIR B/x donor (31% [95% CI: 26-36] vs 20% [95% CI: 13-27]; P = .007). Multivariate analysis demonstrated a 30% improvement in the relative risk of relapse-free survival with B/x donors compared with A/A donors (RR: 0.70 [95% CI: 0.55-0.88]; P = .002). B/x donors were associated with a higher incidence of chronic graft-versus-host disease (GVHD; RR: 1.51 [95% CI: 1.01-2.18]; P = .03), but not of acute GVHD, relapse, or TRM. This analysis demonstrates that unrelated donors with KIR B haplotypes confer significant survival benefit to patients undergoing T-replete HCT for AML. KIR genotyping of prospective donors, in addition to HLA typing, should be performed to identify HLA-matched donors with B KIR haplotypes.

    View details for DOI 10.1182/blood-2008-07-171926

    View details for Web of Science ID 000262491900034

    View details for PubMedID 18945962

  • The IMGT/HLA database NUCLEIC ACIDS RESEARCH Robinson, J., Waller, M. J., Fail, S. C., McWilliam, H., Lopez, R., Parham, P., Marsh, S. G. 2009; 37: D1013-D1017


    It is 10 years since the IMGT/HLA database was released, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and are highly polymorphic. The naming of these HLA genes and alleles, and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data through the website The first release contained 964 sequences, the most recent release 3300 sequences, with around 450 new sequences been added each year. The tools provided on the website have been updated to allow more complex alignments, which include genomic sequence data, as well as the development of tools for probe and primer design and the inclusion of data from the HLA Dictionary. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the HLA community, and the wider research and clinical communities.

    View details for DOI 10.1093/nar/gkn662

    View details for Web of Science ID 000261906200179

    View details for PubMedID 18838392

  • The genetic and evolutionary balances in human NK cell receptor diversity SEMINARS IN IMMUNOLOGY Parham, P. 2008; 20 (6): 311-316


    In primates and cattle two ancient killer-cell immunoglobulin-like receptor (KIR) lineages independently evolved to become diverse NK cell receptors. In mice, KIR genes were sidelined to the X chromosome, a possible consequence of pathogen-mediated selection on the receptor for IgA-Fc. In humans, KIR uniquely form two omnipresent haplotype groups (A and B), postulated here to play complementary and necessary roles in immune defense and reproduction. The basis of KIR3DL1/S1 polymorphism is three ancient lineages maintained by long-term balancing selection and present in all human populations. Conserved and variable NK cell receptors produce structurally diverse NK cell receptor repertoires within a defined range of missing-self-response.

    View details for DOI 10.1016/j.smim.2008.10.002

    View details for Web of Science ID 000261702300002

    View details for PubMedID 19036608

  • The evolution of NK cell diversity SEMINARS IN IMMUNOLOGY Makrigiannis, A. P., Parham, P. 2008; 20 (6): 309-310

    View details for DOI 10.1016/j.smim.2008.09.004

    View details for Web of Science ID 000261702300001

    View details for PubMedID 18938087

  • Polymorphic Sites Away from the Bw4 Epitope That Affect Interaction of Bw4(+) HLA-B with KIR3DL1 JOURNAL OF IMMUNOLOGY Sanjanwala, B., Draghi, M., Norman, P. J., Guethlein, L. A., Parham, P. 2008; 181 (9): 6293-6300


    KIR3DL1 is a polymorphic, inhibitory NK cell receptor specific for the Bw4 epitope carried by subsets of HLA-A and HLA-B allotypes. The Bw4 epitope of HLA-B*5101 and HLA-B*1513 is determined by the NIALR sequence motif at positions 77, 80, 81, 82, and 83 in the alpha(1) helix. Mutation of these positions to the residues present in the alternative and nonfunctional Bw6 motif showed that the functional activity of the Bw4 epitopes of B*5101 and B*1513 is retained after substitution at positions 77, 80, and 81, but lost after substitution of position 83. Mutation of leucine to arginine at position 82 led to loss of function for B*5101 but not for B*1513. Further mutagenesis, in which B*1513 residues were replaced by their B*5101 counterparts, showed that polymorphisms in all three extracellular domains contribute to this functional difference. Prominent were positions 67 in the alpha(1) domain, 116 in the alpha(2) domain, and 194 in the alpha(3) domain. Lesser contributions were made by additional positions in the alpha(2) domain. These positions are not part of the Bw4 epitope and include residues shaping the B and F pockets that determine the sequence and conformation of the peptides bound by HLA class I molecules. This analysis shows how polymorphism at sites throughout the HLA class I molecule can influence the interaction of the Bw4 epitope with KIR3DL1. This influence is likely mediated by changes in the peptides bound, which alter the conformation of the Bw4 epitope.

    View details for Web of Science ID 000260659000055

    View details for PubMedID 18941220

  • MHC class I-specific inhibitory receptors and their ligands structure diverse human NK-cell repertoires toward a balance of missing self-response BLOOD Yawata, M., Yawata, N., Draghi, M., Partheniou, F., Little, A., Parham, P. 2008; 112 (6): 2369-2380


    Variegated expression of 6 inhibitory HLA class I-specific receptors on primary NK cells was studied using high-dimension flow cytometry in 58 humans to understand the structure and function of NK-cell repertoires. Sixty-four subsets expressing all possible receptor com-binations were present in each repertoire, and the frequency of receptor-null cells varied among the donors. Enhancement in missing-self response between NK subsets varied substantially where subset responses were defined by donor KIR/HLA allotypes, reflecting the differences in interaction between inhibitory receptors and their ligands. This contrasted to the enhancement conferred by NKG2A, which was constant and of intermediate strength. We infer a mechanism that modulates frequencies of the NK subsets displaying diverse levels of missing-self response, a system that reduces the presence of KIR-expressing subsets that display either too strong or too weak a response and effectively replaces them with NKG2A-expressing cells in the repertoire. Through this high-resolution analysis of inhibitory receptor expression, 5 types of NK-cell repertoire were defined by their content of NKG2A(+)/NKG2A(-) cells, frequency of receptor-null cells, and degree of KIR receptor coexpression. The analyses provide new perspective on how personalized human NK-cell repertoires are structured.

    View details for DOI 10.1182/blood-2008-03-143727

    View details for Web of Science ID 000259088000032

    View details for PubMedID 18583565

  • Novel KIR3DL1 alleles and their expression levels on NK cells: Convergent evolution of KIR3DL1 phenotype variation? JOURNAL OF IMMUNOLOGY Thomas, R., Yamada, E., Alter, G., Martin, M. P., Bashirova, A. A., Norman, P. J., Altfeld, M., Parham, P., Anderson, S. K., McVicar, D. W., Carrington, M. 2008; 180 (10): 6743-6750


    KIR3DL1 shows extensive polymorphism, and its variation has functional significance in terms of cell-surface expression levels and inhibitory capacity. We characterized nine KIR3DL1 alleles (*022, *028, *029, *033, *035, *051, *052, *053, and *054), four of which were identified for the first time in this study, and compared them to known alleles in phylogenetic analysis. Blood was available from eight individuals with these alleles, and cell-surface expression on NK cells could be determined for six of them using the KIR3DL1-specific Ab DX9. Four of the alleles were expressed at clearly detectable levels, and two others showed exceptionally low levels of expression. Site-directed mutagenesis demonstrated that single amino acid changes can result in either diminished or enhanced DX9 staining compared with the respective related KIR3DL1 allotypes. These results raise the possibility that KIR3DL1 evolution maintains variation in KIR3DL1 cell-surface expression levels, potentially due to the effect of such variation on functional capacity.

    View details for Web of Science ID 000257507100039

    View details for PubMedID 18453594

  • Analytic approximation of spatial epidemic models of foot and mouth disease THEORETICAL POPULATION BIOLOGY Parham, P. E., Singh, B. K., Ferguson, N. M. 2008; 73 (3): 349-368


    The effect of spatial heterogeneity in epidemic models has improved with computational advances, yet far less progress has been made in developing analytical tools for understanding such systems. Here, we develop two classes of second-order moment closure methods for approximating the dynamics of a stochastic spatial model of the spread of foot and mouth disease. We consider the performance of such 'pseudo-spatial' models as a function of R(0), the locality in disease transmission, farm distribution and geographically-targeted control when an arbitrary number of spatial kernels are incorporated. One advantage of mapping complex spatial models onto simpler deterministic approximations lies in the ability to potentially obtain a better analytical understanding of disease dynamics and the effects of control. We exploit this tractability by deriving analytical results in the invasion stages of an FMD outbreak, highlighting key principles underlying epidemic spread on contact networks and the effect of spatial correlations.

    View details for DOI 10.1016/j.tpb.2007.12.010

    View details for Web of Science ID 000255852500004

    View details for PubMedID 18313709

  • Synergistic polymorphism at two positions distal to the ligand-binding site makes KIR2DL2 a stronger receptor for HLA-C than KIR2DL3 JOURNAL OF IMMUNOLOGY Moesta, A. K., Norman, P. J., Yawata, M., Yawata, N., Gleimer, M., Parham, P. 2008; 180 (6): 3969-3979


    Interactions between HLA-C ligands and inhibitory killer cell Ig-like receptors (KIR) control the development and response of human NK cells. This regulatory mechanism is usually described by mutually exclusive interactions of KIR2DL1 with C2 having lysine 80, and KIR2DL2/3 with C1 having asparagine 80. Consistent with this simple rule, we found from functional analysis and binding assays to 93 HLA-A, HLA-B, and HLA-C isoforms that KIR2DL1*003 bound all C2, and only C2, allotypes. The allotypically related KIR2DL2*001 and KIR2DL3*001 interacted with all C1, but they violated the simple rule through interactions with several C2 allotypes, notably Cw*0501 and Cw*0202, and two HLA-B allotypes (B*4601 and B*7301) that share polymorphisms with HLA-C. Although the specificities of the "cross-reactions" were similar for KIR2DL2*001 and KIR2DL3*001, they were stronger for KIR2DL2*001, as were the reactions with C1. Mutagenesis explored the avidity difference between KIR2DL2*001 and KIR2DL3*001. Recombinant mutants mapped the difference to the Ig-like domains, where site-directed mutagenesis showed that the combination, but not the individual substitutions, of arginine for proline 16 in D1 and cysteine for arginine 148 in D2 made KIR2DL2*001 a stronger receptor than KIR2DL3*001. Neither residue 16 or 148 is part of, or near to, the ligand-binding site. Instead, their juxtaposition near the flexible hinge between D1 and D2 suggests that their polymorphisms affect the ligand-binding site by changing the hinge angle and the relative orientation of the two domains. This study demonstrates how allelic polymorphism at sites distal to the ligand-binding site of KIR2DL2/3 has diversified this receptor's interactions with HLA-C.

    View details for Web of Science ID 000257506600044

    View details for PubMedID 18322206

  • Unusual selection on the KIR3DL1/S1 natural killer cell receptor in Africans NATURE GENETICS Norman, P. J., Abi-Rached, L., Gendzekhadze, K., Korbel, D., Gleimer, M., Rowley, D., Bruno, D., Carrington, C. V., Chandanayingyong, D., Chang, Y., Crespi, C., Saruhan-Direskeneli, G., Fraser, P. A., Hameed, K., Kamkamidze, G., Koram, K. A., Layrisse, Z., Matamoros, N., Mila, J., Park, M. H., Pitchappan, R. M., Ramdath, D. D., Shiau, M., Stephens, H. A., Struik, S., Verity, D. H., Vaughan, R. W., Tyan, D., Davis, R. W., Riley, E. M., Ronaghi, M., Parham, P. 2007; 39 (9): 1092-1099


    Interactions of killer cell immunoglobulin-like receptors (KIRs) with major histocompatibility complex (MHC) class I ligands diversify natural killer cell responses to infection. By analyzing sequence variation in diverse human populations, we show that the KIR3DL1/S1 locus encodes two lineages of polymorphic inhibitory KIR3DL1 allotypes that recognize Bw4 epitopes of protein">HLA-A and HLA-B and one lineage of conserved activating KIR3DS1 allotypes, also implicated in Bw4 recognition. Balancing selection has maintained these three lineages for over 3 million years. Variation was selected at D1 and D2 domain residues that contact HLA class I and at two sites on D0, the domain that enhances the binding of KIR3D to HLA class I. HLA-B variants that gained Bw4 through interallelic microconversion are also products of selection. A worldwide comparison uncovers unusual KIR3DL1/S1 evolution in modern sub-Saharan Africans. Balancing selection is weak and confined to D0, KIR3DS1 is rare and KIR3DL1 allotypes with similar binding sites predominate. Natural killer cells express the dominant KIR3DL1 at a high frequency and with high surface density, providing strong responses to cells perturbed in Bw4 expression.

    View details for DOI 10.1038/ng2111

    View details for Web of Science ID 000249122400018

    View details for PubMedID 17694054

  • A subpopulation of human peripheral blood NK cells that lacks inhibitory receptors for self-MHC is developmentally immature BLOOD Cooley, S., Xiao, F., Pitt, M., Gleason, M., McCullar, V., Bergemann, T. L., McQueen, K. L., Guethlein, L. A., Parham, P., Miller, J. S. 2007; 110 (2): 578-586


    How receptor acquisition correlates with the functional maturation of natural killer (NK) cells is poorly understood. We used quantitative real-time polymerase chain reaction (PCR) assays to compare NKG2 and killer immunoglobulin-like receptor (KIR) gene expression in NK cells from allogeneic transplant recipients and their donors. Marked differences were observed in the NK subsets of recipients who had 8-fold more CD56(bright) cells, diminished KIR expression (except 2DL4), and increased NKG2A. In normal blood not all CD56(dim) cells express KIR, and a novel subpopulation of cells committed to the NK-cell lineage was defined. These cells, which comprise 19.4% +/- 2.8% of the CD56(dim) NK population in healthy donors, express the activating NKG2D and NKG2E receptors but no KIR or NKG2A. Although the CD56(dim) NKG2A(-) KIR(-) NK cells lack "at least one" inhibitory receptor for autologous MHC class I, they are not fully responsive, but rather functionally immature cells with poor cytotoxicity and IFN-gamma production. Upon culture with IL-15 and a stromal cell line, CD56(dim) and CD56(bright) KIR(-) NK cells proliferate, express KIR, and develop cytotoxicity and cytokine-producing potential. These findings have implications for the function of NK cells reconstituting after transplantation and support a model for in vivo development in which CD56(bright) cells precede CD56(dim) cells.

    View details for DOI 10.1182/blood-2006-07-036228

    View details for Web of Science ID 000248112400020

    View details for PubMedID 17392508

  • High-throughput killer cell immunoglobulin-like receptor genotyping by MALDI-TOF mass spectrometry with discovery of novel alleles IMMUNOGENETICS Houtchens, K. A., Nichols, R. J., Ladner, M. B., Boal, H. E., Sollars, C., Geraghty, D. E., Davis, L. M., Parham, P., Trachtenberg, E. A. 2007; 59 (7): 525-537


    The killer cell immunoglobulin-like receptors (KIR) interact with major histocompatibility complex (MHC) class I ligands to regulate the functions of natural killer cells and T cells. Like human leukocyte antigens class I, human KIR are highly variable and correlated with infection, autoimmunity, pregnancy syndromes, and transplantation outcome. Limiting the scope of KIR analysis is the low resolution, sensitivity, and speed of the established methods of KIR typing. In this study, we describe a first-generation single nucleotide polymorphism (SNP)-based method for typing the 17 human KIR genes and pseudogenes that uses analysis by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. It is a high-throughput method that requires minute amounts of genomic DNA for discrimination of KIR genes with some allelic resolution. A study of 233 individuals shows that the results obtained by the SNP-based KIR/MALDI-TOF method are consistent with those obtained with the established sequence-specific oligonucleotide probe or sequence-specific polymerase chain reaction methods. The added sensitivity of the KIR/MALDI-TOF method allowed putative novel alleles of the KIR2DL1, KIR3DL1, KIR2DS5, and KIR2DL5 genes to be identified. Sequencing the KIR2DL5 variant proved it was a newly discovered allele, one that appears associated with Hispanic and Native American populations. This KIR/MALDI-TOF method of KIR typing should facilitate population and disease-association studies that improve knowledge of the immunological functions of KIR-MHC class I interactions.

    View details for DOI 10.1007/s00251-007-0222-x

    View details for Web of Science ID 000247386300001

    View details for PubMedID 17464504

  • Evolution of killer cell Ig-like receptor (KIR) genes: Definition of an orangutan KIR haplotype reveals expansion of lineage IIIKIR associated with the emergence of MHC-C JOURNAL OF IMMUNOLOGY Guethlein, L. A., Aguilar, A. M., Abi-Rached, L., Parham, P. 2007; 179 (1): 491-504


    Orangutan (Pongo pygmaeus) MHC-C appears less evolved than human HLA-C: Popy-C is not fixed and its alleles encode only one (C1) of the two motifs for killer cell Ig-like receptor (KIR) ligands. To assess the structure and complexity of the orangutan KIR locus, the complete nucleotide sequence of an orangutan KIR haplotype was determined. The PopyKIR locus is flanked by LILR and FCAR and consists of seven genes and pseudogenes, two novel and five corresponding to known cDNA. Distinguishing all KIRs in this rapidly evolving KIR locus from the KIR3DX1 gene is an LTR33A/MLT1D element in intron 3. These two forms of KIR represent lineages that originated by duplication of a common ancestor. The conserved, framework regions of primate KIR loci comprise the 5' part of a lineage V KIR, the 3' part of a pseudogene, the complete 2DL4 gene, and the 3' part of a lineage II KIR. Although previously defined PopyKIR2DL4 alleles contain premature termination codons, the sequenced haplotype's PopyKIR2DL4 allele encodes a full-length protein. A model for KIR evolution is proposed. Distinguishing the orangutan KIR haplotype from the proposed common ancestor of primate KIR haplotypes is an increased number to give three lineage III KIR genes in the centromeric part of the locus, the site for most human lineage III genes encoding HLA-C specific KIR. Thus, expansion of lineage III KIR is associated with emergence of MHC-C.

    View details for Web of Science ID 000247497600059

    View details for PubMedID 17579070

  • Episodes of natural selection shaped the interactions of IgA-Fc with Fc alpha RI and bacterial decoy proteins JOURNAL OF IMMUNOLOGY Abi-Rached, L., Dorighi, K., Norman, P. J., Yawata, M., Parham, P. 2007; 178 (12): 7943-7954


    FcalphaRI, a receptor for IgA-Fc, recruits myeloid cells to attack IgA-coated pathogens. By competing with FcalphaRI for IgA, bacterial decoys, like SSL7 of Staphylococcus aureus, subvert this defense. We examined how pathogen selection has driven the diversification and coevolution of IgA and FcalphaRI. In higher primates, the IgA binding site of FcalphaRI diversified under positive selection, a strong episode occurring in hominoid ancestors about the time of the IgA gene duplication. The differential binding of SSL7 to IgA-Fc of different species correlates with substitution at seven positions in IgA-Fc, two of which were positively selected in higher primates. Two others, which reduce SSL7 binding, emerged during episodes of positive selection in the rabbit and rodent lineages. The FcalphaRI-IgA interaction evolves episodically under two types of positive selection: pressure from pathogen decoys selects for IgA escape variants which, in turn, selects for FcalphaRI variants to keep up with the novel IgA. When FcalphaRI cannot keep up, its function is lost and the gene becomes susceptible to elimination, as occurred in the mouse genome, either by chance or selection on one of the many linked, variable immune system genes. A cluster of positively selected residues presents a putative binding site for unknown IgA-binding factors.

    View details for Web of Science ID 000247189500053

    View details for PubMedID 17548632

  • Innate partnership of HLA-B and KIR3DL1 subtypes against HIV-1 NATURE GENETICS Martin, M. P., Qi, Y., Gao, X., Yamada, E., Martin, J. N., Pereyra, F., Colombo, S., Brown, E. E., Shupert, W. L., Phair, J., Goedert, J. J., Buchbinder, S., Kirk, G. D., Telenti, A., Connors, M., O'Brien, S. J., Walker, B. D., Parham, P., Deeks, S. G., McVicar, D. W., Carrington, M. 2007; 39 (6): 733-740


    Allotypes of the natural killer (NK) cell receptor KIR3DL1 vary in both NK cell expression patterns and inhibitory capacity upon binding to their ligands, HLA-B Bw4 molecules, present on target cells. Using a sample size of over 1,500 human immunodeficiency virus (HIV)+ individuals, we show that various distinct allelic combinations of the KIR3DL1 and HLA-B loci significantly and strongly influence both AIDS progression and plasma HIV RNA abundance in a consistent manner. These genetic data correlate very well with previously defined functional differences that distinguish KIR3DL1 allotypes. The various epistatic effects observed here for common, distinct KIR3DL1 and HLA-B Bw4 combinations are unprecedented with regard to any pair of genetic loci in human disease, and indicate that NK cells may have a critical role in the natural history of HIV infection.

    View details for DOI 10.1038/ng2035

    View details for Web of Science ID 000246859100017

    View details for PubMedID 17496894

  • Missing KIR ligands are associated with less relapse and increased graft-versus-host disease (GVHD) following unrelated donor allogeneic HCT BLOOD Miller, J. S., Cooley, S., Parham, P., Farag, S. S., Verneris, M. R., McQueen, K. L., Guethlein, L. A., Trachtenberg, E. A., Haagenson, M., Horowitz, M. M., Klein, J. P., Weisdorf, D. J. 2007; 109 (11): 5058-5061


    Natural killer (NK) cells can alter the outcome of hematopoietic cell transplantation (HCT) if donor alloreactivity targets the recipient. Since most NK cells express inhibitory killer-immunoglobulin receptors (KIRs), we hypothesized that the susceptibility of recipient cells to donor NK cell-mediated lysis is genetically predetermined by the absence of known KIR ligands. We analyzed data from 2062 patients undergoing unrelated donor HCT for acute myeloid leukemia (AML; n = 556), chronic myeloid leukemia (CML; n = 1224), and myelodysplastic syndrome (MDS; n = 282). Missing 1 or more KIR ligands versus the presence of all ligands protected against relapse in patients with early myeloid leukemia (relative risk [RR] = 0.54; n = 536, 95% confidence interval [CI] 0.30-0.95, P = .03). In the subset of CML patients that received a transplant beyond 1 year from diagnosis (n = 479), missing a KIR ligand independently predicted a greater risk of developing grade 3-4 acute graft-versus-host disease (GVHD; RR = 1.58, 95% CI 1.13-2.22; P = .008). These data support a genetically determined role for NK cells following unrelated HCT in myeloid leukemia.

    View details for DOI 10.1182/blood-2007-01-065383

    View details for Web of Science ID 000246946100069

    View details for PubMedID 17317850

  • The expanded cattle KIR genes are orthologous to the conserved single-copy KIR3DX1 gene of primates IMMUNOGENETICS Guethlein, L. A., Abi-Rached, L., Hammond, J. A., Parham, P. 2007; 59 (6): 517-522


    Cattle are the only non-primate species for which expansion of the killer cell immunoglobulin-like receptor (KIR) genes has been reported. We analyzed cattle KIR sequences to determine their relationship to the two divergent lineages of primate KIR: one comprising the KIR3DX1 gene of unknown function, the second comprising all other primate KIR genes, which encode variable major histocompatibility complex class I receptors. Phylogenetics and analysis of repetitive elements shows that cattle KIR subdivide into the same two lineages as primate KIR. Unlike the primates, the lineage of variable and likely functional cattle KIR corresponds to the KIR3DX1 lineage of primate KIR, whereas the variable lineage of primate KIR is represented in cattle by one KIR gene and a related gene fragment.

    View details for DOI 10.1007/s00251-007-0214-x

    View details for Web of Science ID 000246175000010

    View details for PubMedID 17450355

  • Donor-recipient combinations of group A and BKIR haplotypes and HLA class I ligand affect the outcome of HLA-matched, sibling donor hematopoietic cell transplantation HUMAN IMMUNOLOGY McQueen, K. L., Dorighi, K. M., Guethlein, L. A., Wong, R., Sanianwala, B., Parham, P. 2007; 68 (5): 309-323


    The influence of donor and recipient killer immunoglobulin-like receptor (KIR) genotype on the outcome of hematopoietic cell transplantation between human leukocyte antigen (HLA)-matched siblings was investigated. Transplants were divided into four groups according to the combination of group A and B KIR haplotypes in the transplant donor and recipient. Overall survival of myeloid patients varied with KIR genotype combination. Best survival was associated with the donor lacking and the recipient having group B KIR haplotypes; poorest survival was associated with the donor having and the recipient lacking group B KIR haplotypes. The latter combination was also associated with increased relapse and acute graft-versus-host disease (GVHD). However, its detrimental effects were seen only for transplants where the recipient and donor were homozygous for the C1 KIR ligand and therefore lacked the C2 ligand. Presence of the Bw4 ligand was also associated with increased acute GVHD. In contrast presence of both KIR3DL1 and its cognate Bw4 ligand was associated with decreased nonrelapse mortality. Analysis of the KIR genes individually revealed KIR2DS3 as a protective factor for chronic GVHD. The results suggest how simple assessments of KIR genotype might inform the selection of donors for hematopoietic cell transplantation.

    View details for DOI 10.1016/j.humimm.2007.01.019

    View details for Web of Science ID 000246227800001

    View details for PubMedID 17462498

  • NKp46 and NKG2D recognition of infected dendritic cells is necessary for NK cell activation in the human response to influenza infection JOURNAL OF IMMUNOLOGY Draghi, M., Pashine, A., Sanjanwala, B., Gendzekhadze, K., Cantoni, C., Cosman, D., Moretta, A., Valiante, N. M., Parham, P. 2007; 178 (5): 2688-2698


    At an early phase of viral infection, contact and cooperation between dendritic cells (DCs) and NK cells activates innate immunity, and also influences recruitment, when needed, of adaptive immunity. Influenza, an adaptable fast-evolving virus, annually causes acute, widespread infections that challenge the innate and adaptive immunity of humanity. In this study, we dissect and define the molecular mechanisms by which influenza-infected, human DCs activate resting, autologous NK cells. Three events in NK cell activation showed different requirements for soluble mediators made by infected DCs and for signals arising from contact with infected DCs. IFN-alpha was mainly responsible for enhanced NK cytolysis and also important for CD69 up-regulation, whereas IL-12 was necessary for enhancing IFN-gamma production. Increased CD69 expression and IFN-gamma production, but not increased cytolysis, required recognition of influenza-infected DCs by two NK cell receptors: NKG2D and NKp46. Abs specific for these receptors or their known ligands (UL16-binding proteins 1-3 class I-like molecules for NKG2D and influenza hemagglutinin for NKp46) inhibited CD69 expression and IFN-gamma production. Activation of NK cells by influenza-infected DCs and polyinosinic:polycytidylic acid (poly(I:C))-treated DCs was distinguished. Poly(I:C)-treated DCs did not express the UL16-binding protein 3 ligand for NKG2D, and in the absence of the influenza hemagglutinin there was no involvement of NKp46.

    View details for Web of Science ID 000244734500019

    View details for PubMedID 17312110

  • Cutting edge: Allele-specific and peptide-dependent interactions between KIR3DL1 and HLA-A and HLA-B JOURNAL OF IMMUNOLOGY Thananchai, H., Gillespie, G., Martin, M. P., Bashirova, A., Yawata, N., Yawata, M., Easterbrook, P., McVicar, D. W., Maenaka, K., Parham, P., Carrington, M., Dong, T., Rowland-Jones, S. 2007; 178 (1): 33-37


    Although it is clear that KIR3DL1 recognizes Bw4(+) HLA-B, the role of Bw4(+) HLA-A allotypes as KIR3DL1 ligands is controversial. We therefore examined the binding of tetrameric HLA-A and -B complexes, including HLA*2402, a common Bw4(+) HLA-A allotype, to KIR3DL1*001, *005, *007, and *1502 allotypes. Only Bw4(+) tetramers bound KIR3DL1. Three of four HLA-A*2402 tetramers bound one or more KIR3DL1 allotypes and all four KIR3DL1 allotypes bound to one or more HLA-A*2402 tetramers, but with different binding specificities. Only KIR3DL1*005 bound both HLA-A*2402 and HLA-B*5703 tetramers. HLA-A*2402-expressing target cells were resistant to lysis by NK cells expressing KIR3DL1*001 or *005. This study shows that HLA-A*2402 is a ligand for KIR3DL1 and demonstrates how the binding of KIR3DL1 to Bw4(+) ligands depends upon the bound peptide as well as HLA and KIR3DL1 polymorphism.

    View details for Web of Science ID 000243120900004

    View details for PubMedID 17182537

  • Functional polymorphism of the KIR3DL1/S1 receptor on human NK cells JOURNAL OF IMMUNOLOGY O'Connor, G. M., Guinan, K. J., Cunningham, R. T., Middleton, D., Parham, P., Gardiner, C. M. 2007; 178 (1): 235-241


    NK cells express both inhibitory and activatory receptors that allow them to recognize target cells through HLA class I Ag expression. KIR3DL1 is a receptor that recognizes the HLA-Bw4 public epitope of HLA-B alleles. We demonstrate that polymorphism within the KIR3DL1 receptor has functional consequences in terms of NK cell recognition of target. Inhibitory alleles of KIR3DL1 differ in their ability to recognize HLA-Bw4 ligand, and a consistent hierarchy of ligand reactivity can be defined. KIR3DS1, which segregates as an allele of KIR3DL1, has a short cytoplasmic tail characteristic of activatory receptors. Because it is very similar to KIR3DL1 in the extracellular domains, it has been assumed that KIR3DS1 will recognize a HLA-Bw4 ligand. In this study, we demonstrate that KIR3DS1 is expressed as a protein at the cell surface of NK cells, where it is recognized by the Z27 Ab. Using this Ab, we found that KIR3DS1 is expressed on a higher percentage of NK cells in KIR3DS1 homozygous compared with heterozygous donors. In contrast to the inhibitory KIR3DL1 allotypes, KIR3DS1 did not recognize HLA-Bw4 on EBV-transformed cell lines.

    View details for Web of Science ID 000243120900027

    View details for PubMedID 17182560

  • Do NK-cell receptors and alloreactivity affect solid organ transplantation? TRANSPLANT IMMUNOLOGY Vilches, C., Parham, P. 2006; 17 (1): 27-30


    Although natural killer cells lyse targets without pre-sensitization, and in an MHC-unrestricted manner, they can also respond to healthy allogeneic cells of different MHC type. Such alloreactivity is a consequence of NK cells using clonally distributed, inhibitory MHC class I receptors to achieve tolerance to healthy autologous cells. Absence of an appropriate MHC class I ligand on an allogeneic cell erroneously informs the NK cell that the allogeneic cell has lost MHC class I expression and should be killed. Potential NK-cell allo-reactivities are common in non-HLA-identical hematopoietic cell transplants and can have both beneficial and detrimental effects. Less is known of NK-cell allo-reactivities in solid organ transplantation. In animal models NK cells are neither necessary nor sufficient for acute transplant rejection, but they can make a contribution by helping activate T cells. Genes encoding NK-cell receptors for polymorphic MHC class I molecules are also highly polymorphic, contributing to variability of the NK-cell repertoire and response in the human population. These receptors could represent intrinsic patient factors that influence the success of their transplanted solid organs.

    View details for DOI 10.1016/j.trim.2006.09.022

    View details for Web of Science ID 000243270400008

    View details for PubMedID 17157210

  • Taking license with natural killer cell maturation and repertoire development IMMUNOLOGICAL REVIEWS Parham, P. 2006; 214: 155-160


    Combining population analysis with in-depth analysis of selected individuals, the tolerance of human natural killer (NK) cells to autologous major histocompatibility complex (MHC) class I and potential reactivity to allogeneic MHC class I have been studied. Analysis of NK cell clones in long-term culture and peripheral blood NK cells after short-term culture (20-24 h) shows that NK cell tolerance is determined by interactions of autologous MHC class I with CD94:NKG2A and inhibitory killer cell immunoglobulin-like receptors (KIRs). Alloreactivity is predicted whenever the donor of the allogeneic target lacks a cognate MHC class I-KIR, ligand-receptor pair that is present in the NK cell donor. In the human population, there is a wide variation in the NK cell repertoire of KIRs and CD94:NKG2A expression. Variation is principally due to KIR gene variation and polymorphism, with a smaller effect due to MHC class I. The presence of MHC class I increases the frequency of NK cells expressing the cognate KIR, an effect that is diminished by the presence of other cognate-ligand pairs. The minor influence of MHC class I on the KIR repertoire indicates that NK cell development is an efficient process in which the expression of inhibitory MHC class I receptors at the final stages ensures that functionally active human NK cells are self-tolerant.

    View details for Web of Science ID 000241892800013

    View details for PubMedID 17100883

  • High KIR diversity in Amerindians is maintained using few gene-content haplotypes IMMUNOGENETICS Gendzekhadze, K., Norman, P. J., Abi-Rached, L., Layrisse, Z., Parham, P. 2006; 58 (5-6): 474-480


    Interaction between killer cell immunoglobulin-like receptors (KIR) and cognate HLA class I ligands influences the innate and adaptive immune response to infection. The KIR family varies in gene content and allelic polymorphism, thereby, distinguishing individuals and populations. KIR gene content was determined for 230 individuals from three Amerindian tribes from Venezuela: the Yucpa, Bari and Warao. Gene-content haplotypes could be assigned to 212 individuals (92%) because only five different haplotypes were present-group A and four group B. Six different haplotype combinations accounted for >80% of individuals. Each tribe has distinctive genotype frequencies. Despite few haplotypes, all 14 KIR genes are at high frequency in the three tribes, with the exception of 2DS3. Each population has an even frequency of group A and B haplotypes. Allele-level analysis of 3DL1/S1 distinguished five group A haplotypes and six group B haplotypes. The high frequency and divergence of the KIR haplotypes in the Amerindian tribes provide greater KIR diversity than is present in many larger populations. An extreme case being the Yucpa, for whom two gene-content haplotypes account for >90% of the population. These comprise the group A haplotype and a group B haplotype containing all the KIR genes, except 2DS3, that typify the group B haplotypes. Here is clear evidence for balancing selection on the KIR system and the biological importance of both A and B haplotypes for the survival of human populations.

    View details for DOI 10.1007/s00251-006-0108-3

    View details for Web of Science ID 000238014900017

    View details for PubMedID 16738943

  • Immunology - Adaptable innate killers NATURE Parham, P. 2006; 441 (7092): 415-416

    View details for DOI 10.1038/441415a

    View details for Web of Science ID 000237778900025

    View details for PubMedID 16724046

  • Roles for HLA and KIR polymorphisms in natural killer cell repertoire selection and modulation of effector function JOURNAL OF EXPERIMENTAL MEDICINE Yawata, M., Yawata, N., Draghi, M., Little, A. M., Partheniou, F., Parham, P. 2006; 203 (3): 633-645


    Interactions between killer cell immunoglobulin-like receptors (KIRs) and human leukocyte antigen (HLA) class I ligands regulate the development and response of human natural killer (NK) cells. Natural selection drove an allele-level group A KIR haplotype and the HLA-C1 ligand to unusually high frequency in the Japanese, who provide a particularly informative population for investigating the mechanisms by which KIR and HLA polymorphism influence NK cell repertoire and function. HLA class I ligands increase the frequencies of NK cells expressing cognate KIR, an effect modified by gene dose, KIR polymorphism, and the presence of other cognate ligand-receptor pairs. The five common Japanese KIR3DLI allotypes have distinguishable inhibitory capacity, frequency of cellular expression, and level of cell surface expression as measured by antibody binding. Although KIR haplotypes encoding 3DL1*001 or 3DL1*005, the strongest inhibitors, have no activating KIR, the dominant haplotype encodes a moderate inhibitor, 3DL1*01502, plus functional forms of the activating receptors 2DL4 and 2DS4. In the population, certain combinations of KIR and HLA class I ligand are overrepresented or underrepresented in women, but not men, and thus influence female fitness and survival. These findings show how KIR-HLA interactions shape the genetic and phenotypic KIR repertoires for both individual humans and the population.

    View details for DOI 10.1084/jem.20051884

    View details for Web of Science ID 000236520800018

    View details for PubMedID 16533882

  • The inhibitory receptor NKG2A determines lysis of vaccinia virus-infected autologous targets by NK cells JOURNAL OF IMMUNOLOGY Brooks, C. R., Elliott, T., Parham, P., Khakoo, S. I. 2006; 176 (2): 1141-1147


    Signals transduced by inhibitory receptors that recognize self-MHC class I molecules prevent NK cells from being activated by autologous healthy target cells. In order for NK cells to be activated upon contact with an infected cell, the balance between the activating and inhibitory signals that regulate NK cell function must be altered in favor of activation. By studying liver-derived NK cells, we show that only a subpopulation of NK cells expressing high levels of the inhibitory receptor NKG2A are able to lyse autologous vaccinia-infected targets, and that this is due to selective down-regulation of HLA-E. These data demonstrate that release from an inhibitory receptor:ligand interaction is one mechanism that permits NK cell recognition of a virally infected target, and that the variegated expression of inhibitory receptors in humans generates a repertoire of NK cells with different antiviral potentials.

    View details for Web of Science ID 000234553800057

    View details for PubMedID 16434388

  • KIR3DL1 polymorphisms that affect NK cell inhibition by HLA-Bw4 ligand JOURNAL OF IMMUNOLOGY Carr, W. H., Pando, M. J., Parham, P. 2005; 175 (8): 5222-5229


    The killer cell Ig-like receptor (KIR) gene family encodes MHC class I receptors expressed by NK cells and several T cell subpopulations. Factors contributing to human KIR haplotype diversity are differences in gene number, gene content, and allelic polymorphism. Whereas functional and clinical consequences of the first two factors are established, knowledge of the effects of KIR gene polymorphism is limited to special cases in which signaling function is reversed or cell surface expression lost. In this study we use retrovirally transduced human cell lines to show that 3DL1*002 is a stronger inhibitory receptor for HLA-Bw4 ligands than 3DL1*007. Analysis of mutant 3DL1*002 and 3DL1*007 molecules demonstrates that residue 238 in the D2 domain and 320 in the transmembrane region contribute to the difference in receptor strength. Neither position 238 nor 320 is predicted to interact directly with HLA-Bw4 ligand. This study also revealed that KIR3DL1 and LILRB1 both contribute to developing an inhibitory response to HLA-Bw4 ligands.

    View details for Web of Science ID 000232443500046

    View details for PubMedID 16210627

  • Clathrin heavy and light chain isoforms originated by independent mechanisms of gene duplication during chordate evolution PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wakeham, D. E., Abi-Rached, L., Towler, M. C., Wilbur, J. D., Parham, P., Brodsky, F. M. 2005; 102 (20): 7209-7214


    In humans, there are two isoforms each of clathrin heavy chain (CHC17 and CHC22) and light chain (LCa and LCb) subunits, all encoded by separate genes. CHC17 forms the ubiquitous clathrin-coated vesicles that mediate membrane traffic. CHC22 is implicated in specialized membrane organization in skeletal muscle. CHC17 is bound and regulated by LCa and LCb, whereas CHC22 does not functionally interact with either light chain. The imbalanced interactions between clathrin subunit isoforms suggest a distinct evolutionary history for each isoform pair. Phylogenetic and sequence analysis placed both heavy and light chain gene duplications during chordate evolution, 510-600 million years ago. Genes encoding CHC22 orthologues were found in several vertebrate species, with only a pseudogene present in mice. Multiple paralogons surrounding the CHC genes (CLTC and CLTD) were identified, evidence that genomic or large-scale gene duplication produced the two CHC isoforms. In contrast, clathrin light chain genes (CLTA and CLTB) apparently arose by localized duplication, within 1-11 million years of CHC gene duplication. Analysis of sequence divergence patterns suggested that structural features of the CHCs were maintained after gene duplication, but new interactions with regulatory proteins evolved for the CHC22 isoform. Thus, independent mechanisms of gene duplication expanded clathrin functions, concomitant with development of neuromuscular sophistication in chordates.

    View details for DOI 10.1073/pnas.0502058102

    View details for Web of Science ID 000229292200029

    View details for PubMedID 15883369

  • Natural selection drives recurrent formation of activating killer cell immunoglobulin-like receptor and Ly49 from inhibitory homologues JOURNAL OF EXPERIMENTAL MEDICINE Abi-Rached, L., Parham, P. 2005; 201 (8): 1319-1332


    Expression of killer cell Ig-like receptors (KIRs) diversifies human natural killer cell populations and T cell subpopulations. Whereas the major histocompatibility complex class I binding functions of inhibitory KIR are known, specificities for the activating receptors have resisted analysis. To understand better activating KIR and their relationship to inhibitory KIR, we took the approach of reconstructing their natural history and that of Ly49, the analogous system in rodents. A general principle is that inhibitory receptors are ancestral, the activating receptors having evolved from them by mutation. This evolutionary process of functional switch occurs independently in different species to yield activating KIR and Ly49 genes with similar signaling domains. Selecting such convergent evolution were the signaling adaptors, which are older and more conserved than any KIR or Ly49. After functional shift, further activating receptors form through recombination and gene duplication. Activating receptors are short lived and evolved recurrently, showing they are subject to conflicting selections, consistent with activating KIR's association with resistance to infection, reproductive success, and susceptibility to autoimmunity. Our analysis suggests a two-stage model in which activating KIR or Ly49 are initially subject to positive selection that rapidly increases their frequency, followed by negative selection that decreases their frequency and leads eventually to loss.

    View details for DOI 10.1084/jem.20042558

    View details for Web of Science ID 000228521900013

    View details for PubMedID 15837816

  • Nomenclature for factors of the HLA system, 2004 TISSUE ANTIGENS Marsh, S. G., Albert, E. D., Bodmer, W. F., Bontrop, R. E., DuPont, B., Erlich, H. A., Geraghty, D. E., Hansen, J. A., Hurley, C. K., Mach, B., Mayr, W. R., Parham, P., Petersdorf, E. W., Sasazuki, T., Schreuder, G. M., STROMINGER, J. L., Svejgaard, A., Terasaki, P. I., Trowsdale, J. 2005; 65 (4): 301-369
  • Complex interactions: The immunogenetics of human leukocyte antigen and killer cell immunoglobulin-like receptors SEMINARS IN HEMATOLOGY Norman, P. J., Parham, P. 2005; 42 (2): 65-75


    The killer cell immunoglobulin-like receptors (KIR) for human leukocyte antigen (HLA) modulate innate and adaptive immunity by controlling effector cells. HLA and KIR are encoded in genomic regions that have complex organization and exhibit exceptional diversity within and among human population groups. This diversity is likely to have arisen to combat a constantly evolving pathogen challenge. Numerous variations influence the expression level or function of KIR molecules and can affect their interaction with HLA, with important implications for the immune response. The functional variety of natural immune responses that are controlled by HLA and KIR interactions is genetically determined and maintained by natural selection.

    View details for DOI 10.1053/j.seminhematol.2005.01.007

    View details for Web of Science ID 000228661400002

    View details for PubMedID 15846572

  • Single-cell analysis of the human NK cell response to missing self and its inhibition by HLA class I BLOOD Draghi, M., Yawata, N., Gleimer, M., Yawata, M., Valiante, N. M., Parham, P. 2005; 105 (5): 2028-2035


    Natural killer (NK) cells activate quickly in response to pathogens, tumors, and allogeneic hematopoietic cell transplants. Modulating the NK cell response are clonally distributed NK cell receptors that survey cells for change in the expression of major histocompatibility complex (MHC) class I and structurally related ligands. Here the enzyme-linked immunospot (ELISPOT) assay, intracellular cytokine staining (ICS), and short-term culture were used to quantify the response of bulk NK cell populations from human donors to HLA class I-deficient 221 cells and to 221 cells transfected with single HLA class I allotypes. NK cells in cultures containing interleukin-2 (IL-2) or IL-12 exhibited specificities of HLA class I-mediated inhibition that correlated well with those previously defined using NK cell clones in long-term culture and with the frequencies of cells expressing particular inhibitory HLA class I receptors. Culture with IL-12, but not IL-2, gave an increased frequency of cells expressing CD94: NKG2A but no change in killer immunoglobulin-like receptor (KIR) expression. For some heterozygote combinations of KIR3DL1 alleles, ICS can be used to compare the functional properties of the 2 allotypes. Thus, both the low-expressing KIR3DL1*005 and the high-expressing KIR3DL1*002 gave similar inhibitory response on challenge with an HLA-B*5801 ligand. The single-cell assays developed here should facilitate future population study and clinical analysis of human NK cell regulation by MHC class I.

    View details for DOI 10.1182/blood-2004-08-3174

    View details for Web of Science ID 000227308400036

    View details for PubMedID 15528315

  • MHC class I molecules and KIRs in human history, health and survival NATURE REVIEWS IMMUNOLOGY Parham, P. 2005; 5 (3): 201-214


    MHC class I molecules are ligands for the killer-cell immunoglobulin-like receptors (KIRs), which are expressed by natural killer cells and T cells. The interactions between these molecules contribute to both innate and adaptive immunity. KIRs and MHC class I molecules are encoded by unlinked polymorphic gene families that distinguish all but the most related individuals. Combinations of MHC class I and KIR variants influence resistance to infections, susceptibility to autoimmune diseases and complications of pregnancy, as well as outcome after haematopoietic stem-cell transplantation. Such correlations raise the possibility that interplay between KIR and MHC class I polymorphisms has facilitated human survival in the presence of epidemic infections and has influenced both reproduction and population growth.

    View details for DOI 10.1038/nri1570

    View details for Web of Science ID 000227302400011

    View details for PubMedID 15719024

  • Immunogenetics of killer cell immunoglobulin-like receptors MOLECULAR IMMUNOLOGY Parham, P. 2005; 42 (4): 459-462


    The killer cell immunoglobulin receptor locus (KIR) on human chromosome 19 encodes activating and inhibitory receptors that are expressed principally by NK cells but also by subpopulations of T cells. For some of the KIR the ligands are known to be MHC class I molecules, for others ligands are elusive. In humans the KIR locus is highly diverse. KIR haplotypes differ in gene content and the individual genes exhibit allelic polymorphism; these two components work together to diversify haplotypes, which in pairwise combination diversify human KIR genotypes. The divergence of KIR between different human populations, as well as between closely related hominoid species, seem likely to be the products of balancing and directional selection upon the functions of KIR-expressing lymphocytes. Consistent with this model are the results of several studies associating KIR differences with disease susceptibility, immune responsiveness and events following allogeneic transplantation.

    View details for DOI 10.1016/j.molimm.2004.07.027

    View details for Web of Science ID 000227142200012

    View details for PubMedID 15607799

  • Putting a face to MHC restriction JOURNAL OF IMMUNOLOGY Parham, P. 2005; 174 (1): 3-5

    View details for Web of Science ID 000225852900001

    View details for PubMedID 15611221

  • Influence of KIR diversity on human immunity MECHANISMS OF LYMPHOCYTE ACTIVATION AND IMMUNE REGULATION X: INNATE IMMUNITY Parham, P. 2005; 560: 47-50

    View details for Web of Science ID 000232367600006

    View details for PubMedID 15932019

  • Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primates GENOME RESEARCH Sambrook, J. G., Bashirova, A., Palmer, S., Sims, S., Trowsdale, J., Abi-Rached, L., Parham, P., Carrington, M., Beck, S. 2005; 15 (1): 25-35


    The human killer immunoglobulin-like receptors (KIR) are encoded within the Leukocyte Receptor Complex (LRC) on chromosome 19q13.4. Here we report the comparative genomic analysis of single KIR haplotypes in two other primates. In the common chimpanzee (Pan troglodytes), seven KIR genes (ptKIRnewI, ptKIRnewII, ptKIR2DL5, ptKIRnewIII, ptKIR3DP1, ptKIR2DL4, ptKIR3DL1/2) have been identified, and five KIR genes (mmKIRnewI, mmKIR1D, mmKIR2DL4, mmKIR3DL10, mmKIR3DL1) are present in the haplotype sequenced for the rhesus macaque (Macaca mulatta). Additional cDNA analysis confirms the genes predicted from the genomic sequence and reveals the presence of a fifth novel KIR gene (mmKIRnewII) in the second haplotype of the rhesus macaque. While all known human haplotypes contain both activating and inhibitory KIR genes, only inhibitory KIR genes (characterized by long cytoplasmic tails) were found by in silico and cDNA analyses in the two primate haplotypes studied here. Comparison of the two human and the two non-human primate haplotypes demonstrates rapid diversification of the KIR gene family members, many of which have diverged in a species-specific manner. An analysis of the intronic regions of the two non-human primates reveals the presence of ancient repeat elements, which are indicative of the duplication events that have taken place since the last common ancestor.

    View details for DOI 10.1101/gr.2381205

    View details for Web of Science ID 000226170900003

    View details for PubMedID 15632087

  • T cell-dependent production of IFN-gamma by NK cells in response to influenza A virus JOURNAL OF CLINICAL INVESTIGATION He, X. S., Draghi, M., Mahmood, K., Holmes, T. H., Kemble, G. W., Dekker, C. L., Arvin, A. M., Parham, P., Greenberg, H. B. 2004; 114 (12): 1812-1819


    The role of human NK cells in viral infections is poorly understood. We used a cytokine flow-cytometry assay to simultaneously investigate the IFN-gamma response of NK and T lymphocytes to influenza A virus (fluA). When PBMCs from fluA-immune adult donors were incubated with fluA, IFN-gamma was produced by both CD56(dim) and CD56(bright) subsets of NK cells, as well as by fluA-specific T cells. Purified NK cells did not produce IFN-gamma in response to fluA, while depletion of T lymphocytes reduced to background levels the fluA-induced IFN-gamma production by NK cells, which indicates that T cells are required for the IFN-gamma response of NK cells. The fluA-induced IFN-gamma production of NK cells was suppressed by anti-IL-2 Ab, while recombinant IL-2 replaced the helper function of T cells for IFN-gamma production by NK cells. This indicates that IL-2 produced by fluA-specific T cells is involved in the T cell-dependent IFN-gamma response of NK cells to fluA. Taken together, these results suggest that at an early stage of recurrent viral infection, NK-mediated innate immunity to the virus is enhanced by preexisting virus-specific T cells.

    View details for DOI 10.1172/JCI200422797

    View details for Web of Science ID 000225695800016

    View details for PubMedID 15599406

  • NK cells and trophoblasts: Partners in pregnancy JOURNAL OF EXPERIMENTAL MEDICINE Parham, P. 2004; 200 (8): 951-955


    In placental mammals, viviparity--the production of living young within the mother's body--evolved under the auspices of the immune system. Elements of immunity were incorporated, giving pregnancy a mildly inflammatory character. Formation of the placenta, the organ that feeds the fetus, involves a cooperation between maternal natural killer (NK) cells and fetal trophoblast cells that remodels the blood supply. Recent research reveals that this process and human reproductive success are influenced by polymorphic HLA-C ligands and their killer cell immunoglobulin-like receptors (KIR).

    View details for DOI 10.1084/jem.20041783

    View details for Web of Science ID 000224677900001

    View details for PubMedID 15492121

  • Immunology. NK cells lose their inhibition. Science Parham, P. 2004; 305 (5685): 786-787

    View details for PubMedID 15297654

  • Killer cell immunoglobulin-like receptor diversity: balancing signals in the natural killer cell response IMMUNOLOGY LETTERS Parham, P. 2004; 92 (1-2): 11-13


    Killer cell immunoglobulin-like receptors (KIR) are a family of inhibitory and activating receptors that are expressed by most natural killer (NK) cells and by small subpopulations of T cells. In humans the KIR genes form part of the leukocyte receptor complex (LRC) on chromosome 19. Within an individual NK cell clones are distinguished by the combinations of KIR genes they express, patterns which are established during NK cell development and remain stable. Within the human population KIR haplotypes and genotypes differ in their gene content, in the balance between genes encoding activating and inhibitory receptors, and by allelic polymorphism at the individual KIR genes. Investigation of the KIR gene family in non-human primate species shows that species-specific genes outnumber the conserved genes. The KIR gene family is seen to be both highly diverse and rapidly evolving. Such characteristics suggest that novel KIR variants provide competitive advantages in primate survival or reproduction, which are of short duration on the evolutionary time-scale.

    View details for DOI 10.1016/j.imlet.2003.11.016

    View details for Web of Science ID 000221166400003

    View details for PubMedID 15081521

  • The beta(2)-microglobulin locus of rainbow trout (Oncorhynchus mykiss) contains three polymorphic genes JOURNAL OF IMMUNOLOGY Magor, K. E., Shum, B. P., Parham, P. 2004; 172 (6): 3635-3643


    Beta2-microglobulin (beta2m) associates with MHC and related class I H chains to form cell surface glycoproteins that mediate a variety of functions in defense. In humans, monomorphism of a single beta2m gene contrasts with the diversity and polymorphism of the class I H chain genes, and a similar picture was seen in almost all other species examined. In this regard, rainbow trout (Oncorhynchus mykiss) appeared unusual: trout beta2m genes gave a complicated and polymorphic pattern in Southern blots, and a minimum of 10 different mRNA encoding two distinct types of beta2m were expressed by a single fish. Characterization of genomic clones from the same fish now shows that the rainbow trout beta2m locus consists of two expressed genes and one partial gene that are closely linked. Four copies of the locus were identified and allelic variants of each gene defined, largely through comparison of the noncoding regions. A dramatic variation in the lengths of introns is caused by variable repetitive elements and accounts for the complex pattern seen in Southern blots. By comparison to noncoding sequences, the coding regions are conserved but the three loci differ within a cluster of codons that encode residues of beta2m that do not interact with class I H chains. Additional diversity in the trout beta2m genes appears to be due to somatic mutation that might be facilitated by the abundance of repetitive DNA elements within the 12 beta2m genes of an individual rainbow trout.

    View details for Web of Science ID 000220096000036

    View details for PubMedID 15004166

  • Defense strategies and immunity-related genes EUROPEAN JOURNAL OF IMMUNOLOGY Trowsdale, J., Parham, P. 2004; 34 (1): 7-17


    The immune system is of crucial importance in defense against infection. It has to cope with a large number of different pathogens that relentlessly develop new ways to avoid recognition or elimination. Yet most infections are cleared. Immune-system genes must evolve to keep pace with increasingly sophisticated evasion by pathogens. In this article we examine features of human defense genes that reflect the demands imposed by such intense selection. Key examples are MHC and KIR genes, where features such as polygeny and polymorphism facilitate the comprehensive logistics needed to counteract infection.

    View details for DOI 10.1002/eji.200324693

    View details for Web of Science ID 000188412400001

  • Domain shuffling has been the main mechanism forming new hominoid killer cell Ig-like receptors JOURNAL OF IMMUNOLOGY Rajalingam, R., Parham, P., Abi-Rached, L. 2004; 172 (1): 356-369


    The killer cell Ig-like receptor (KIR) gene family encodes MHC class I-specific receptors, which regulate NK cell responses and are also expressed on subpopulations of T cells. KIR haplotypes vary in gene content, which, in combination with allelic polymorphism, extensively diversifies the KIR genotype both within and between human populations. Species comparison indicates that formation of new KIR genes and loss of old ones are frequent events, so that few genes are conserved even between closely related species. In this regard, the hominoids define a time frame that is particularly informative for understanding the processes of KIR evolution and its potential impact on killer cell biology. KIR cDNA were characterized from PBMC of three gorillas, and genomic DNA were characterized for six additional individuals. Eleven gorilla KIR genes were defined. With attainment of these data, a set of 75 KIR sequences representing five hominoid species was assembled, which also included rhesus monkey, cattle, and rodent KIR. Searching this data set for recombination events, and phylogenetic analysis using Bayesian methods, demonstrated that new KIR were usually the result of recombination between loci in which complete protein domains were shuffled. Further phylogenetic analysis of the KIR sequences after removal of confounding recombined segments showed that only two KIR genes, KIR2DL4 and KIR2DL5, have been preserved throughout hominoid evolution, and one of them, KIR2DL4, is also common to rhesus monkey and hominoids. Other KIR genes represent recombinant forms present in a minority of species, often only one, as exemplified by 8 of the 11 gorilla KIR genes.

    View details for Web of Science ID 000187427700046

    View details for PubMedID 14688344

  • The protein made from a common allele of KIR3DL1 (3DL1*004) is poorly expressed at cell surfaces due to substitution at positions 86 in Ig domain 0 and 182 in Ig domain 1 JOURNAL OF IMMUNOLOGY Pando, M. J., Gardiner, C. M., Gleimer, M., McQueen, K. L., Parham, P. 2003; 171 (12): 6640-6649


    KIR3DL1 is an inhibitory HLA-B receptor of human NK and T cells that exhibits genetic and phenotypic polymorphism. KIR3DL1*004, a common allotype, cannot be detected on the surface of PBLs using the KIR3DL1-specific Ab DX9. The nature of this phenotype was investigated through comparison of 3DL1*004 with 3DL1*002, an allele giving high DX9 binding to cell surfaces. Analysis of Jurkat T cell transfectants with 3DL1*004 cDNA showed that 3DL1*004 is poorly expressed at the cell surface, but detectable intracellularly. Analysis of recombinant mutants made between 3DL1*004 and 3DL1*002 showed that polymorphism in Ig domains 0 and 1 (D0 and D1) causes the intracellular retention of 3DL1*004. Reciprocal point mutations were introduced into 3DL1*004 and 3DL1*002 at positions 44 and 86 of the D0 domain, where 3DL1*004 has unique residues, and at position 182 of the D1 domain, where 3DL1*004 resembles 3DL1*005, an allotype giving low DX9-binding phenotype. Leucine 86 in 3DL1*004 is the principal cause of its intracellular retention, with a secondary and additive contribution from serine 182. By contrast, glycine 44, which is naturally present in 3DL1*004, slightly increased cell surface expression when introduced into 3DL1*002. In 3DL1*004, the presence of leucine at position 86 corrupts the WSXPS motif implicated in proper folding of the KIR D0 Ig-like domain. This study demonstrates how a difference between KIR3DL1 allotypes in the D0 domain profoundly affects cell surface expression and function.

    View details for Web of Science ID 000187227700045

    View details for PubMedID 14662867

  • Activation of a subset of human NK cells upon contact with Plasmodium falciparum-infected erythrocytes JOURNAL OF IMMUNOLOGY Artavanis-Tsakonas, K., Eleme, K., McQueen, K. L., Cheng, N. W., Parham, P., Davis, D. M., Riley, E. M. 2003; 171 (10): 5396-5405


    Human NK cells are the earliest source of the protective cytokine IFN-gamma when PBMC from nonimmune donors are exposed to Plasmodium falciparum-infected RBC (iRBC) in vitro. In this study, we show that human NK cells form stable conjugates with iRBC but not with uninfected RBC and that induction of IFN-gamma synthesis is dependent on direct contact between the NK cell and the iRBC. NK cells respond to iRBC only in the presence of a source of IL-12/IL-18 and the subset of NK cells that preferentially respond to iRBC express high levels of the lectin-like receptor CD94/NKG2A. There is heterogeneity between donors in their ability to respond to iRBC. DNA analysis has revealed considerable heterogeneity of killer Ig-like receptor (KIR) genotype among the donor population and has identified 21 new KIR allelic variants in the donors of African and Asian descent. Importantly, we find evidence for significant associations between KIR genotype and NK responsiveness to iRBC. This emphasizes the need for large-scale population-based studies to address associations between KIR genotype and susceptibility to malaria.

    View details for Web of Science ID 000186643300057

    View details for PubMedID 14607943

  • Stress management: MHC class I and class I-like molecules as reporters of cellular stress IMMUNITY Gleimer, M., Parham, P. 2003; 19 (4): 469-477


    The evolutionarily ancient intracellular stress response protects cells from the effects of external and internal forces which perturb cellular metabolism. Members of the major histocompatibility complex (MHC) class I-like superfamily act as cell surface indicators of the intracellular stress response. Cellular immunity employs these indicators as a cue for elimination of damaged, infected, and malignant cells, promoting the health of the individual and the evolutionary success of the species.

    View details for Web of Science ID 000186051900004

    View details for PubMedID 14563312

  • Immunogenetics of killer-cell immunoglobulin-like receptors TISSUE ANTIGENS Parham, P. 2003; 62 (3): 194-200


    The immunogenetics of cell-surface antigens began with the study of red cells and then moved onto the white cells. HLA class I antigens were analyzed on leukocytes and HLA class II antigens on B cells. In the last decade the natural killer (NK) cell has become a target for immunogeneticists, in particular the family of genes encoding the killer-cell immunoglobulin-like receptors (KIRs).

    View details for Web of Science ID 000185198600003

    View details for PubMedID 12956873

  • Killer-cell immunoglobulin-like receptor (KIR) nomenclature report, 2002 TISSUE ANTIGENS Marsh, S. G., Parham, P., DuPont, B., Geraghty, D. E., Trowsdale, J., Middleton, D., Vilches, C., Carrington, M., Witt, C., Guethlein, L. A., Shilling, H., Garcia, C. A., Hsu, K. C., Wain, H. 2003; 62 (1): 79-86

    View details for Web of Science ID 000184107800008

    View details for PubMedID 12859599

  • Killer-cell immunoglobulin-like receptor (KIR) nomenclature report, 2002 IMMUNOGENETICS Marsh, S. G., Parham, P., DuPont, B., Geraghty, D. E., Trowsdale, J., Middleton, D., Vilches, C., Carrington, M., Witt, C., Guethlein, L. A., Shilling, H., Garcia, C. A., Hsu, K. C., Wain, H. 2003; 55 (4): 220-226

    View details for DOI 10.1007/s00251-003-0571-z

    View details for Web of Science ID 000184345400004

    View details for PubMedID 12838378

  • Human KIR sequences 2003 IMMUNOGENETICS Garcia, C. A., Robinson, J., Guethlein, L. A., Parham, P., Madrigal, J. A., Marsh, S. G. 2003; 55 (4): 227-239


    We have compiled the nucleotide sequences and their amino acid translations from a total of 89 Killer Immunoglobulin-like Receptor (KIR) alleles, derived from 17 different KIR genes. The alignments use the KIR3DL2*001 allele as a reference sequence. Each of the KIR sequences included in these alignments has been checked and where discrepancies have arisen between reported sequences, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation.

    View details for DOI 10.1007/s00251-003-0572-y

    View details for Web of Science ID 000184345400005

    View details for PubMedID 12838379

  • Reconstitution of NK cell receptor repertoire following HLA-matched hematopoietic cell transplantation BLOOD Shilling, H. G., McQueen, K. L., Cheng, N. W., Shizuru, J. A., Negrin, R. S., Parham, P. 2003; 101 (9): 3730-3740


    Interactions between killer immunoglobulin-like receptors (KIRs) and human leukocyte antigen (HLA) class I ligands influence development of natural killer (NK) cell repertoire and response to infection, cancer, and allogeneic tissue. As KIRs and HLA class I molecules are highly polymorphic, clinical allogeneic hematopoietic cell transplantation is predicted to frequently involve KIR mismatch, and thus to provide a unique system for study of human NK cell receptor repertoire development. Eighteen leukemia patients undergoing HLA-matched transplantation and their donors were analyzed for KIR genotype. Ten of 13 HLA-identical donor-patient pairs were KIR mismatched and 3 were matched; all HLA-matched unrelated pairs were KIR mismatched. Reconstitution of recipient NK cell repertoire following transplantation was examined using flow cytometry and monoclonal antibodies specific for KIR and CD94:NKG2A. These data form 3 groups. Six to 9 months after transplantation, 8 patients (group 1) reconstituted an NK cell repertoire resembling that of their donor, and for KIR-mismatched transplants, distinct from the recipient before transplantation. In the first year after transplantation, 5 patients (group 2) exhibited a generally depressed frequency of KIR-expressing NK cells and concomitant high frequency of CD94:NKG2A expression. By 3 years after transplantation, the frequency of KIR-expressing NK cells had increased to donor values, in the 3 patients from group 2 analyzed for this period. The remaining 5 patients experienced severe clinical complications following transplantation and displayed unique features in their NK cell receptor reconstitution. These results demonstrate that a majority of HLA-matched hematopoietic cell transplantations involve KIR mismatch and reveal differences in NK cell repertoire having potential impact for immune responsiveness and transplantation outcome.

    View details for Web of Science ID 000182625600068

    View details for PubMedID 12511415

  • Innate immunity: The unsung heroes. Nature Parham, P. 2003; 423 (6935): 20-?

    View details for PubMedID 12721604

  • Alloreactive killer cells: Hindrance and help for haematopoietic transplants NATURE REVIEWS IMMUNOLOGY Parham, P., McQueen, K. L. 2003; 3 (2): 108-122


    Haematopoietic-cell transplantation is a treatment for leukaemia and lymphoma. To reduce the incidence of graft-versus-host disease (GVHD) caused by transplanted T cells, donors and recipients are HLA matched. For patients for whom a matched donor is not available, one option is transplantation from an HLA-mismatched relative who shares one HLA haplotype. This procedure is distinguished by the use of a stronger conditioning regimen for the patient and of a T-cell-depleted graft containing numerous stem cells. After transplantation, natural killer cells are prevalent, and they can include alloreactive cells that kill tumour cells and prevent GVHD. The alloreactions seem to be determined by the mismatched HLA class I ligands and their killer-cell immunoglobulin-like receptors.

    View details for DOI 10.1038/nri999

    View details for Web of Science ID 000181944800012

    View details for PubMedID 12563295

  • IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex NUCLEIC ACIDS RESEARCH Robinson, J., Waller, M. J., Parham, P., De Groot, N., Bontrop, R., Kennedy, L. J., Stoehr, P., Marsh, S. G. 2003; 31 (1): 311-314


    The IMGT/HLA database ( has provided a centralized repository for the sequences of the alleles named by the WHO Nomenclature Committee for Factors of the HLA System for the past four years. Since its initial release the database has grown and is the primary source of information for the study of sequences of the human major histocompatibilty complex. The initial release of the database contained a limited number of tools. As a result of feedback from our users and developments in HLA we have been able to provide new tools and facilities. The HLA sequences have also been extended to include intron sequences and the 3' and 5' untranslated regions in the alignments and also the inclusion of new genes such as MICA. The IMGT/MHC database ( was released in March 2002 to provide a similar resource for other species. The first release of IMGT/MHC contains the sequences of non-human primates (apes, new and old world monkeys), canines and feline sequences. Further species will be added shortly and the database aims to become the primary source of MHC data for non-human sequences.

    View details for DOI 10.1093/nar/GKG070

    View details for Web of Science ID 000181079700074

    View details for PubMedID 12520010

  • Cloning and sequencing full-length HLA-B and -C genes TISSUE ANTIGENS Cox, S. T., McWhinnie, A. J., Robinson, J., Marsh, S. G., Parham, P., Madrigal, J. A., Little, A. M. 2003; 61 (1): 20-48


    Currently most available HLA-A, -B and -C DNA sequences cover exons 2 and 3 with a limited number extending to include other exons and introns. We have developed a method for the accurate determination of full-length genomic DNA sequences for HLA-A, -B and -C alleles. The method involves cloning of PCR amplified full-length HLA genes to separate alleles at heterozygous loci. The approach avoids any ambiguities from sequencing heterozygous PCR products directly and also avoids ambiguities from sequencing overlapping PCR products to achieve full-length sequence. To date we have sequenced full-length genomic sequences from representatives of all the major HLA-B and -C allele groups.

    View details for Web of Science ID 000181373900003

    View details for PubMedID 12622774

  • Nomenclature for factors of the HLA system, 2002. Tissue antigens Marsh, S. G., Albert, E. D., Bodmer, W. F., Bontrop, R. E., DuPont, B., Erlich, H. A., Geraghty, D. E., Hansen, J. A., Mach, B., Mayr, W. R., Parham, P., Petersdorf, E. W., Sasazuki, T., SCHREUDER, G. M., STROMINGER, J. L., Svejgaard, A., Terasaki, P. I. 2002; 60 (5): 407-464

    View details for PubMedID 12492818

  • NK cell-mediated lysis of autologous HCMV-infected skin fibroblasts is highly variable among NK cell clones and polyclonal NK cell lines CLINICAL IMMUNOLOGY Carr, W. H., Little, A. M., Mocarski, E., Parham, P. 2002; 105 (2): 126-140


    Lysis of human cytomegalovirus (HCMV)-infected fibroblasts by autologous natural killer (NK) cells was examined in vitro. For NK cell clones, receptor expression was determined at the level of mRNA and cell-surface protein and compared to the lysis of HCMV AD169 strain-infected fibroblasts in which HLA class I was >70% downregulated. The clones ranged broadly in their ability to lyse AD169-infected fibroblasts, correlating neither with the expression of inhibitory KIR, leukocyte inhibitory receptor-1, or CD94:NKG2A receptors nor with the number of different inhibitory KIR expressed per clone. Some lines of polyclonal NK cells preferentially lysed AD169-infected cells and similarly lysed fibroblasts infected with mutant virus RV798, which lacks the genes for downregulating HLA class I. These results demonstrate that NK cell lysis of HCMV-infected autologous fibroblasts is more complex than a simple missing-self mechanism involving downregulation of HLA class I and failure to engage inhibitory self-specific KIR.

    View details for DOI 10.1006/clim.2002.5273

    View details for Web of Science ID 000179807400003

    View details for PubMedID 12482387

  • Predominance of group A KIR haplotypes in Japanese associated with diverse NK cell repertoires of KIR expression IMMUNOGENETICS Yawata, M., Yawata, N., McQueen, K. L., Cheng, N. W., Guethlein, L. A., Rajalingam, R., Shilling, H. G., Parham, P. 2002; 54 (8): 543-550


    Genomic DNA from a panel of 41 healthy unrelated Japanese individuals was typed for the presence or absence of 16 KIR genes and pseudogenes. Only eight different KIR genotypes were found. Group A haplotypes outnumbered group B haplotypes in frequency by approximately 3:1, with individuals having two group A haplotypes accounting for 56% of the panel. The frequency of A haplotypes in the Japanese is higher than that observed in other populations. Flow cytometric comparison of KIR expression in 19 panel members showed considerable diversity in NK cell repertoire, which was also seen within the group of individuals having two A haplotypes. This diversity is likely due to allelic polymorphism in expressed genes of the A haplotype. In comparison to other populations, the Japanese appear less heterogeneous in KIR genotype as assessed by gene content.

    View details for DOI 10.1007/s00251-002-0497-x

    View details for Web of Science ID 000179744800002

    View details for PubMedID 12439616

  • The DO domain of KIR3D acts as a major histocompatibility complex class I binding enhancer JOURNAL OF EXPERIMENTAL MEDICINE Khakoo, S. I., Geller, R., Shin, S., Jenkins, J. A., Parham, P. 2002; 196 (7): 911-921


    In contrast to the KIR2D:HLA-C interaction, little is known of KIR3DL1's interaction with HLA-B or the role of D0, the domain not present in KIR2D. Differences in the strength and specificity for major histocompatibility complex class I of KIR3DL1 and its common chimpanzee homologue Pt-KIR3DL1/2 were exploited to address these questions. Domain-swap, deletion, and site-directed mutants of KIR3DL1 were analyzed for HLA-B binding using a novel, positively signaling cell-cell binding assay. Natural 'deletion' of residues 50 and 51 from its D0 domain causes Pt-KIR3DL1/2 to bind Bw4(+) HLA-B allotypes more avidly than does KIR3DL1. Deletion of these residues from KIR3DL1, or their substitution for alanine, enhanced binding of Bw4(+) HLA-B. None of 15 different point mutations in D0 abrogated KIR3DL1 binding to Bw4(+) HLA-B. In contrast point mutations in the D1 and D2 domains of KIR3DL1, made from knowledge of KIR2D:HLA-C interactions, disrupted binding to Bw4(+) HLA-B. The results are consistent with a model in which D1 and D2 make the principal contacts between KIR3DL1 and HLA-B while D0 acts through a different mechanism to enhance the interaction. This modulatory role for D0 is compatible with natural loss of expression of the D0 domain, a repeated event in the evolution of functional KIR genes.

    View details for DOI 10.1084/jem.20020304

    View details for Web of Science ID 000178518100005

    View details for PubMedID 12370253

  • Variable receptors controlling activation and inhibition of NK cells CURRENT OPINION IN IMMUNOLOGY McQueen, K. L., Parham, P. 2002; 14 (5): 615-621


    NK cells are important effector lymphocytes of innate immunity; they kill infected cells and produce cytokines that stimulate other immune effects. Once considered relatively homogeneous, NK cells are now seen to be highly diverse. Within an individual, expression of different combinations of inhibitory and stimulatory receptors creates a diverse NK cell repertoire, which exhibits specificity in the immune response. Rapid evolution of NK cell receptor gene families distinguishes members of a species and causes substantial species-specific differences in NK cell receptor systems. All known ligands for these diverse receptors are MHC class I molecules, or molecules of host or pathogen origin that are homologous to MHC class I.

    View details for Web of Science ID 000177716100012

    View details for PubMedID 12183162

  • Some human KIR haplotypes contain two KIR2DL5 genes: KIR2DL5A and KIR2DL5B IMMUNOGENETICS Gomez-Lozano, N., Gardiner, C. M., Parham, P., Vilches, C. 2002; 54 (5): 314-319


    Killer-cell immunoglobulin-like receptors (KIR) comprise a family of structurally diverse proteins encoded by a compact cluster of genes located in human Chromosome 19q13.4. The most recently described member of the KIR family, KIR2DL5, is represented in human populations by at least four gene variants, whose exons differ by two to eight nucleotides. We show here that these structurally similar variants are encoded by alleles of two different loci, KIR2DL5A and KIR2DL5B, which map to different regions of the KIR-gene cluster. Regarding KIR2DL5, four groups of KIR haplotypes can be distinguished: those having both KIR2DL5A and KIR2DL5B, those having either KIR2DL5A or KIR2DL5B, and those lacking KIR2DL5. Positive association between KIR2DL5A and KIR2DL5B was detected but did not reach statistical significance. These results are consistent with a model in which KIR2DL5A and KIR2DL5B are products of a gene duplication, which through the action of subsequent recombination have became separated on some haplotypes.

    View details for DOI 10.1007/s00251-002-0476-2

    View details for Web of Science ID 000177862300004

    View details for PubMedID 12185535

  • Genetic control of human NK cell repertoire JOURNAL OF IMMUNOLOGY Shilling, H. G., Young, N., Guethlein, L. A., Cheng, N. W., Gardiner, C. M., Tyan, D., Parham, P. 2002; 169 (1): 239-247


    Through differential killer cell Ig-like receptor (KIR) and CD94:NKG2 gene expression, human NK cells generate diverse repertoires, each cell having an inhibitory receptor for autologous HLA class I. Using a new method for measuring repertoire difference that integrates multiple flow cytometry parameters, we found individual repertoire stability, but population variability. Correlating repertoire differences with KIR and HLA genotype for 85 sibling pairs reveals the dominant influence of KIR genotype; HLA genotype having a subtle, modulating effect on relative KIR expression frequencies. HLA and/or KIR genotype also influences CD94:NKG2A expression. After HLA-matched stem cell transplantation, KIR repertoires either recapitulated that of the donor or were generally depressed for KIR expression. Human NK cell repertoires are defined by combinations of variable KIR and HLA class I genes and conserved CD94:NKG2 genes.

    View details for Web of Science ID 000176360400031

    View details for PubMedID 12077250

  • NK cell receptors of the Orangutan (Pongo pygmaeus): A pivotal species for tracking the colevolution of killer cell Ig-like receptors with MHC-C JOURNAL OF IMMUNOLOGY Guethlein, L. A., Flodin, L. R., Adams, E. J., Parham, P. 2002; 169 (1): 220-229


    CD94, NKG2, Ly49, and killer cell Ig-like receptor (KIR) expressed by orangutan peripheral blood cells were examined by cloning and sequencing cDNA from a panel of individuals. Orthologs of human CD94, NKG2A, D, and F were defined. NKG2C and E are represented by one gene, Popy-NKG2CE, that is equidistant from the two human genes. Several Popy-CD94, NKG2A, and NKG2CE alleles were defined. Popy-Ly49L is expressed in cultured NK cells and has a sequence consistent with it encoding a functional receptor. Orangutan KIR corresponding to the three KIR lineages expressed in humans and chimpanzees were defined. Popy-KIR2DL4 of lineage I is the only ortholog of a human or chimpanzee KIR, but in all individuals examined, the transcripts of this gene produced premature termination, either in the D2 domain or at the beginning of the cytoplasmic domain. Ten Popy-KIR3DL and one Popy-KIR3DS of lineage II are all closely related, but represent the products of at least two genes. The two Popy-KIR2DL and four Popy-KIR2DS of lineage III also represent two genes, both being more related to KIR2DS4 than to other human and chimpanzee KIR of lineage III. The Popy-KIR2D include ones predicted to be specific for the C1 epitope of MHC-C, but none specific for C2. This correlates with the observation that all orangutan MHC-C allotypes examined have the C1 motif.

    View details for Web of Science ID 000176360400029

    View details for PubMedID 12077248

  • Definition of gene content for nine common group B haplotypes of the Caucasoid population: KIR haplotypes contain between seven and eleven KIR genes IMMUNOGENETICS Uhrberg, M., Parham, P., Wernet, P. 2002; 54 (4): 221-229


    The segregation of killer cell immunoglobulin-like receptor ( KIR) genes was determined for a panel of 21 Caucasoid families: 23 different KIR gene patterns were found and could be assigned to combinations of 16 different haplotypes. Four loci were held in common by all haplotypes: KIR2DL4, KIR3DL2, the putative pseudogene KIR3DL3 and KIR2DL2/KIR2DL3, the latter likely being alleles of one gene. Group A haplotypes, which have a unique combination of seven KIR genes, were found at 80% frequency in the family panel, the polygenic group B haplotypes at 65% frequency. KIR gene segregation was fully determined for the nine group B haplotypes, which occurred at highest frequencies in both the family panel and a panel of unrelated individuals. The group B haplotypes carried between seven and 11 KIR genes and encoded inhibitory KIR for one, two, or all three major HLA class I epitopes. Analysis of human leucocyte antigen (HLA) class I genotypes revealed that most, but not all, individuals possess an inhibitory KIR for a self HLA class I epitope. The number of stimulatory KIR genes in group B haplotypes varied considerably between one and five. The data show that group B haplotypes possess a broad spectrum of KIR gene patterns, which is largely complementary to the KIR gene set of group A haplotypes. The results suggest that rapid diversification of group B haplotypes is the result of pathogen-mediated selection for KIR genotypes that have more than the set of KIR genes provided by the group A haplotype.

    View details for DOI 10.1007/s00251-002-0463-7

    View details for Web of Science ID 000177465200001

    View details for PubMedID 12136333

  • Structures of two major histocompatibility complex class I genes of the rainbow trout (Oncorhynchus mykiss) IMMUNOGENETICS Shum, B. P., Mason, P. M., Magor, K. E., Flodin, L. R., Stet, R. J., Parham, P. 2002; 54 (3): 193-199


    Here we describe two rainbow trout major histocompatibility complex (MHC) class I genes characterized from lambda phage genomic clones prepared from a single fish. Clone GC71 contains all exons except a leader peptide-encoding exon. An open reading frame is maintained, and thus the gene MhcOnmy-U71 could be expressed in this individual. The class I gene found on clone GC41 lacks exons encoding the leader peptide and cytoplasmic domain. This gene, MhcOnmy-U41p, is a pseudogene due to a deletion in the alpha(2) domain-encoding exon causing premature termination. Both the Onmy-U71 and Onmy-U41p genes are distinguished by long introns between the exons encoding the alpha(1) and alpha(2) domains. Clone GC41 also contains the 3' exons of the LMP7/ PSMB8 gene encoding the gamma-interferon-induced proteosome subunit of rainbow trout.

    View details for DOI 10.1007/s00251-002-0450-z

    View details for Web of Science ID 000176803100006

    View details for PubMedID 12073148

  • Linkage of Patr-AL to Patr-A and-B in the major histocompatibility complex of the common chimpanzee (Pan troglodytes) IMMUNOGENETICS Geller, R., Adams, E. J., Guethlein, L. A., Little, A. M., Madrigal, J. A., Parham, P. 2002; 54 (3): 212-215


    Patr-AL is a recently described gene found only in the common chimpanzee, but closely related in structure to the highly polymorphic Patr-A and HLA-A genes of the chimpanzee and human MHCs, respectively. Unlike Patr-A and HLA-A, the Patr-AL gene has little polymorphism and is not fixed in the chimpanzee genome. To determine whether Patr-AL is located in the MHC or elsewhere, we compared segregation of the Patr-AL gene with segregation of Patr-A and - B alleles in chimpanzee families. The results demonstrate that Patr-AL is an MHC class I gene present on different MHC haplotypes as defined by their combination of Patr-A and B alleles.

    View details for DOI 10.1007/s00251-002-0452-x

    View details for Web of Science ID 000176803100009

    View details for PubMedID 12073151

  • A human genome diversity cell line panel SCIENCE Cann, H. M., de Toma, C., Cazes, L., Legrand, M. F., Morel, V., Piouffre, L., Bodmer, J., Bodmer, W. F., Bonne-Tamir, B., Cambon-Thomsen, A., Chen, Z., Chu, J. Y., Carcassi, C., Contu, L., Du, R. F., Excoffier, L., Ferrara, G. B., Friedlaender, J. S., Groot, H., Gurwitz, D., Jenkins, T., Herrera, R. J., Huang, X. Y., Kidd, J., Kidd, K. K., Langaney, A., Lin, A. A., Mehdi, S. Q., Parham, P., Piazza, A., Pistillo, M. P., Qian, Y. P., Shu, Q. F., Xu, J. J., Zhu, S., Weber, J. L., Greely, H. T., Feldman, M. W., Thomas, G., Dausset, J., Cavalli-Sforza, L. L. 2002; 296 (5566): 261-262

    View details for Web of Science ID 000175000300018

    View details for PubMedID 11954565

  • Allelic polymorphism synergizes with variable gene content to individualize human KIR genotype JOURNAL OF IMMUNOLOGY Shilling, H. G., Guethlein, L. A., Cheng, N. W., Gardiner, C. M., Rodriguez, R., Tyan, D., Parham, P. 2002; 168 (5): 2307-2315


    Killer Ig-like receptor (KIR) genes are a multigene family on human chromosome 19. KIR genes occur in various combinations on different haplotypes. Additionally, KIR genes are polymorphic. To examine how allelic polymorphism diversifies KIR haplotypes with similar or identical combinations of KIR genes, we devised methods for discriminating alleles of KIR2DL1, -2DL3, -3DL1, and -3DL2. These methods were applied to 143 individuals from 34 families to define 98 independent KIR haplotypes at the allele level. Three novel 3DL2 alleles and a chimeric 3DL1/3DL2 sequence were also identified. Among the A group haplotypes were 22 different combinations of 2DL1, 2DL3, 3DL1, and 3DL2 alleles. Among the B group haplotypes that were unambiguously determined were 15 distinct haplotypes involving 9 different combinations of KIR genes. A and B haplotypes both exhibit strong linkage disequilibrium (LD) between 2DL1 and 2DL3 alleles, and between 3DL1 and 3DL2 alleles. In contrast, there was little LD between the 2DL1/2DL3 and 3DL1/3DL2 pairs that define the two halves of the KIR gene complex. The synergistic combination of allelic polymorphism and variable gene content individualize KIR genotype to an extent where unrelated individuals almost always have different KIR types. This level of diversity likely reflects strong pressure from pathogens on the human NK cell response.

    View details for Web of Science ID 000173990200030

    View details for PubMedID 11859120

  • Distinctive KIR and HLA diversity in a panel of north Indian Hindus IMMUNOGENETICS Rajalingam, R., Krausa, P., Shilling, H. G., Stein, J. B., Balamurugan, A., McGinnis, M. D., Cheng, N. W., Mehra, N. K., Parham, P. 2002; 53 (12): 1009-1019


    HLA and KIR are diverse and rapidly evolving gene complexes that work together in human immunity mediated by cytolytic lymphocytes. Understanding their complex immunogenetic interaction requires study of both HLA and KIR diversity in the same human population. Here a panel of 72 unrelated north Indian Hindus was analyzed. HLA- A, B, C, DRB1, DQA1, and DQB1 alleles and their frequencies were determined by sequencing or high-resolution typing of genomic DNA; KIR genotypes were determined by gene-specific typing and by allele-level DNA typing for KIR2DL1, 2DL3, 2DL5, 3DL1, and 3DL2. From HLA analysis, the north Indian population is seen to have several characteristics shared either with Caucasian or East Asian populations, consistent with the demographic history of north India, as well as specific features, including several alleles at high frequency that are rare or absent in other populations. A majority of the north Indian KIR gene profiles have not been seen in Caucasian and Asian populations. Most striking is a higher frequency of the B group of KIR haplotypes, resulting in equal frequencies for A and B group haplotypes in north Indians. All 72 members of the north Indian panel have different HLA genotype and different KIR genotype.

    View details for DOI 10.1007/s00251-001-0425-5

    View details for Web of Science ID 000174860100003

    View details for PubMedID 11904677

  • Variation within the human killer cell immunoglobulin-like receptor (KIR) gene family CRITICAL REVIEWS IN IMMUNOLOGY Yawata, M., Yawata, N., Abi-Rached, L., Parham, P. 2002; 22 (5-6): 463-482


    The killer cell immunoglobulin-like receptors (KIR) form a family of highly homologous immune receptors that regulate the response of natural killer (NK) cells and some T cells. The genetics of the human KIR family is reviewed in this article. In human populations, diversity in KIR genotype arises from variations in gene content and allelic polymorphism. Comparisons of 81 human KIR sequences reveal past events ofgene duplication and recombination, and indicate that individual KIR genes have diversified from the influence of natural selection. Comparison and compilation of population studies reveal extensive KIR genotype variability within human populations and among them. Genomic analysis shows the KIR genes to be close to each other and separated by homologous sequences that promote haplotype diversification through assymetric recombination. In contrast, homologous recombination appears favored at a unique sequence in the center of the KIR locus, and much haplotypic diversity can be explained by recombination between a limited number of gene-content motifs in the centromeric and telomeric halves of the locus. The importance of NK cells for early defenses against infection suggests that human KIR genotype diversity is the accumulated consequence of a history of numerous and successive selective episodes by different pathogens on human NK-cell responses.

    View details for Web of Science ID 000182776300007

    View details for PubMedID 12803322

  • KIR: Diverse, rapidly evolving receptors of innate and adaptive immunity ANNUAL REVIEW OF IMMUNOLOGY Vilches, C., Parham, P. 2002; 20: 217-251


    KIR genes have evolved in primates to generate a diverse family of receptors with unique structures that enable them to recognize MHC-class I molecules with locus and allele-specificity. Their combinatorial expression creates a repertoire of NK cells that surveys the expression of almost every MHC molecule independently, thus antagonizing the spread of pathogens and tumors that subvert innate and adaptive defense by selectively downregulating certain MHC class I molecules. The genes encoding KIR that recognize classical MHC molecules have diversified rapidly in human and primates; this contrasts with conservation of immunoglobulin- and lectin-like receptors for nonclassical MHC molecules. As a result of the variable KIR-gene content in the genome and the polymorphism of the HLA system, dissimilar numbers and qualities of KIR:HLA pairs function in different humans. This diversity likely contributes variability to the function of NK cells and T-lymphocytes by modulating innate and adaptive immune responses to specific challenges.

    View details for Web of Science ID 000175012600010

    View details for PubMedID 11861603

  • Conservation and variation in human and common chimpanzee CD94 and NKG2 genes JOURNAL OF IMMUNOLOGY Shum, B. P., Flodin, L. R., Muir, D. G., Rajalingam, R., Khakoo, S. I., Cleland, S., Guethlein, L. A., Uhrberg, M., Parham, P. 2002; 168 (1): 240-252


    To assess polymorphism and variation in human and chimpanzee NK complex genes, we determined the coding-region sequences for CD94 and NKG2A, C, D, E, and F from several human (Homo sapiens) donors and common chimpanzees (Pan troglodytes). CD94 is highly conserved, while the NKG2 genes exhibit some polymorphism. For all the genes, alternative mRNA splicing variants were frequent among the clones obtained by RT-PCR. Alternative splicing acts similarly in human and chimpanzee to produce the CD94B variant from the CD94 gene and the NKG2B variant from the NKG2A gene. Whereas single chimpanzee orthologs for CD94, NKG2A, NKG2E, and NKG2F were identified, two chimpanzee paralogs of the human NKG2C gene were defined. The chimpanzee Pt-NKG2CI gene encodes a protein similar to human NKG2C, whereas in the chimpanzee Pt-NKG2CII gene the translation frame changes near the beginning of the carbohydrate recognition domain, causing premature termination. Analysis of a panel of chimpanzee NK cell clones showed that Pt-NKG2CI and Pt-NKG2CII are independently and clonally expressed. Pt-NKG2CI and Pt-NKG2CII are equally diverged from human NKG2C, indicating that they arose by gene duplication subsequent to the divergence of chimpanzee and human ancestors. Genomic DNA from 80 individuals representing six primate species were typed for the presence of CD94 and NKG2. Each species gave distinctive typing patterns, with NKG2A and CD94 being most conserved. Seven different NK complex genotypes within the panel of 48 common chimpanzees were due to differences in Pt-NKG2C and Pt-NKG2D genes.

    View details for Web of Science ID 000172934000031

    View details for PubMedID 11751968

  • Exon 5 encoding the transmembrane region of HLA-A contains a transitional region for the induction of nonsense-mediated mRNA decay JOURNAL OF IMMUNOLOGY Watanabe, Y., Magor, K. E., Parham, P. 2001; 167 (12): 6901-6911


    HLA class I alleles containing premature termination codons (PTCs) are increasingly being found. To understand their effects on MHC class I expression, HLA-A*2402 mutants containing PTCs were transfected into class I-deficient cells, and expression of HLA-A mRNA and protein was determined. In exons 2, 3, and 4, and in the 5' part of exon 5, PTCs reduced mRNA levels by up to 90%, whereas in the 3' part of exon 5 and in exons 6 and 7 they had little effect. Transition in the extent of nonsense-mediated mRNA decay occurred within a 48-nt segment of exon 5, placed 58 nt upstream from the exon 5/exon 6 junction. This transition did not conform to the positional rule obeyed by other genes, which predicted it to be approximately 50-55 nt upstream of the exon 7/exon 8 junction and thus placing it in exon 6. Mutants containing extra gene segments showed the difference is caused by the small size of exons 5 and 6, which renders them invisible to the surveillance machinery. For the protein, a transition from secretion to membrane association occurs within a 26-nt segment of exon 5, 17 nt upstream of the exon 5/exon 6 junction. Premature termination in exon 5 can produce secreted and membrane-associated HLA-A variants expressed at high levels.

    View details for Web of Science ID 000172613400027

    View details for PubMedID 11739508

  • Comparison of chimpanzee and human leukocyte Ig-like receptor genes reveals framework and rapidly evolving genes JOURNAL OF IMMUNOLOGY CANAVEZ, F., Young, N. T., Guethlein, L. A., Rajalingam, R., Khakoo, S. I., Shum, B. P., Parham, P. 2001; 167 (10): 5786-5794


    The leukocyte receptor complex (LRC) on human chromosome 19 contains related Ig superfamily killer cell Ig-like receptor (KIR) and leukocyte Ig-like receptor (LIR) genes. Previously, we discovered much difference in the KIR genes between humans and chimpanzees, primate species estimated to have approximately 98.8% genomic sequence similarity. Here, the common chimpanzee LIR genes are identified, characterized, and compared with their human counterparts. From screening a chimpanzee splenocyte cDNA library, clones corresponding to nine different chimpanzee LIRs were isolated and sequenced. Analysis of genomic DNA from 48 unrelated chimpanzees showed 42 to have all nine LIR genes, and six animals to lack just one of the genes. In structural diversity and functional type, the chimpanzee LIRs cover the range of human LIRs. Although both species have the same number of inhibitory LIRs, humans have more activating receptors, a trend also seen for KIRs. Four chimpanzee LIRs are clearly orthologs of human LIRs. Five other chimpanzee LIRs have paralogous relationships with clusters of human LIRs and have undergone much recombination. Like the human genes, chimpanzee LIR genes appear to be organized into two duplicated blocks, each block containing two orthologous genes. This organization provides a conserved framework within which there are clusters of faster evolving genes. Human and chimpanzee KIR genes have an analogous arrangement. Whereas both KIR and LIR genes can exhibit greater interspecies differences than the genome average, within each species the LIR gene family is more conserved than the KIR gene family.

    View details for Web of Science ID 000172106400035

    View details for PubMedID 11698452

  • A novel, nonclassical MHC class I molecule specific to the common chimpanzee JOURNAL OF IMMUNOLOGY Adams, E. J., Cooper, S., Parham, P. 2001; 167 (7): 3858-3869


    All expressed human MHC class I genes (HLA-A, -B, -C, -E, -F, and -G) have functional orthologues in the MHC of the common chimpanzee (Pan troglodytes). In contrast, a nonclassical MHC class I gene discovered in the chimpanzee is not present in humans or the other African ape species. In exons and more so in introns, this Patr-AL gene is similar to the expressed A locus in the orangutan, Popy-A, suggesting they are orthologous. Patr-AL/Popy-A last shared a common ancestor with the classical MHC-A locus >20 million years ago. Population analysis revealed little Patr-AL polymorphism: just three allotypes differing only at residues 52 and 91. Patr-AL is expressed in PBMC and B cell lines, but at low level compared with classical MHC class I. The Patr-AL polypeptide is unusually basic, but its glycosylation, association with beta(2)-microglobulin, and antigenicity at the cell surface are like other MHC class I. No Patr-AL-mediated inhibition of polyclonal chimpanzee NK cells was detected. The Patr-AL gene is present in 50% of chimpanzee MHC haplotypes, correlating with presence of a 9.8-kb band in Southern blots. The flanking regions of Patr-AL contain repetitive/retroviral elements not flanking other class I genes. In sequenced HLA class I haplotypes, a similar element is present in the A*2901 haplotype but not the A*0201 or A*0301 haplotypes. This element, 6 kb downstream of A*2901, appears to be the relic of a human gene related to Patr-AL. Patr-AL has characteristics of a class I molecule of innate immunity with potential to provide common chimpanzees with responses unavailable to humans.

    View details for Web of Science ID 000172392100041

    View details for PubMedID 11564803

  • Species-specific evolution of MHC class I genes in the higher primates IMMUNOLOGICAL REVIEWS Adams, E. J., Parham, P. 2001; 183: 41-64


    Humans express three highly polymorphic 'classical' (HLA-A,B and C) and three conserved 'non-classical' (HLA-E, F and G) MHC class I genes. Their comparison with the MHC class I genes of apes and monkeys reveals the differential extent to which MHC class I genes have been preserved during primate evolution. African apes have orthologues of all six human genes, and although allelic lineages of the A and C loci are shared, these species share none of the human alleles. In Asian apes, several MHC class I genes show significant differences from the human genes, a trend which continues with the Old World monkeys, and even more so in the New World monkeys, where E and F are the only human gene orthologues. The C locus is confined to humans and apes. Multiple A-related and B-related loci have been identified in apes and Old World monkeys showing that duplication of these loci has been a common event during primate evolution. Certain of the daughter loci exhibit low polymorphism, suggesting they have adopted a non-classical function. The differing rates at which MHC class I genes have evolved during primate evolution likely reflects their differing functions in the immune response.

    View details for Web of Science ID 000172961600004

    View details for PubMedID 11782246

  • New nomenclature for MHC receptors NATURE IMMUNOLOGY Andre, P., Biassoni, R., Colonna, M., Cosman, D., Lanier, L. L., Long, E. O., Lopez-Botet, M., Moretta, A., Moretta, L., Parham, P., Trowsdale, J., Vivier, E., Wagtmann, N., Wilson, M. J. 2001; 2 (8): 661-661

    View details for Web of Science ID 000170230100002

    View details for PubMedID 11477395

  • Conserved organization of the ILT/LIR gene family within the polymorphic human leukocyte receptor complex IMMUNOGENETICS Young, N. T., CANAVEZ, F., Uhrberg, M., Shum, B. P., Parham, P. 2001; 53 (4): 270-278


    The human leukocyte receptor complex (LRC) at Chromosome 19q13.4 encodes Ig superfamily proteins which regulate the function of various hematopoietic cell types. We investigated characteristics of the Ig-like transcript (ILT)/leukocyte Ig-like receptor (LIR) group of LRC genes in comparison with the other major LRC loci encoding the killer cell Ig-like receptors (KIRs). In direct contrast to KIR genes, the ILT/LIR loci of ethnically diverse individuals did not display haplotypic variations in gene number. Investigation of gene expression identified novel cDNA sequences related to the ILT2/LIR1, ILT4/LIR2, ILT3/LIR5, and ILT7 loci, while phylogenetic analysis revealed two distinct lineages of ILT/LIR genes. These two lineages differ in both the nature and extent of their sequence polymorphism. The presence of certain transcription factor-related motifs in the 5' untranslated region of ILT/LIR cDNAs correlates with the specific cell types in which particular ILT/LIR genes are expressed. Although extensive gene duplications and conversion events have apparently forged the LRC, our results indicate striking conservation in the organization of the ILT/LIR genes when compared with the related and closely linked KIR genes. This suggests the evolutionary maintenance of a significant function consistent with the cellular distribution of the ILT/LIR proteins.

    View details for Web of Science ID 000170123000003

    View details for PubMedID 11491530

  • Genomic analysis of common chimpanzee major histocompatibility complex class I genes IMMUNOGENETICS Adams, E. J., Parham, P. 2001; 53 (3): 200-208


    To investigate how MHC class I genes have changed in the approximately 5 million years since chimpanzees and humans diverged, we characterized six genomic fragments ranging in size from 5.1 to 6.1 kb, each containing the complete coding region, introns, and flanking regions of one of the following chimpanzee class I genes: Patr-A, Patr-E, Patr-F, Patr-G, Patr-H, and Patr-J. In humans, these genes are closely linked within the class I region and are representatives of three distinct functional categories of class I genes: the highly polymorphic Ia genes (HLA-A), the conserved Ib genes (HLA-E, HLA-F, and HLA-G), and the class I pseudogenes (HLA-H and HLA-J). Southern blot analysis of chimpanzee and human class I genes produced nearly identical patterns, suggesting that the organization and linkage of these genes differs little in the two species. Comparison of the chimpanzee fragment sequences with their human orthologues revealed structural conservation of these genes yet differences in their degree of functional constraint. This is apparent in the location and nature of the amino acid changes between species and the substantial differences in levels of divergence at functional and nonfunctional sites. Additionally, there is no correlation between patterns of divergence at these sites and intraspecific variation, an observation explained by either appreciable gene conversion or high levels of recombination, the latter unlikely given the observed strong linkage disequilibrium of these loci.

    View details for Web of Science ID 000168845700003

    View details for PubMedID 11398964

  • The repertoire of killer cell Ig-like receptor and CD94 : NKG2A receptors in T cells: clones sharing identical alpha beta TCR rearrangement express highly diverse killer cell Ig-like receptor patterns JOURNAL OF IMMUNOLOGY Uhrberg, M., Valiante, N. M., Young, N. T., Lanier, L. L., Phillips, J. H., Parham, P. 2001; 166 (6): 3923-3932


    Killer cell Ig-like receptor (KIR) and CD94:NKG2A molecules were first defined as human NK cell receptors (NKR), but now are known to be expressed and to function on subpopulations of T cells. Here the repertoires of KIR and CD94:NKG2A expression by T cells from two donors were examined and compared with their previously defined NK cell repertoires. T cell clones generated from peripheral blood of both donors expressed multiple NKR in different combinations and used the range of receptors expressed by NK cells. In both donors alpha beta T cells less frequently expressed the inhibitory receptors CD94:NKG2A and KIR2DL1 than either gamma delta T cells or NK cells. In contrast to NK cells, not all NKR(+) T cells expressed an inhibitory receptor for autologous HLA class I. This lack of specific inhibitory NKR was especially apparent on alpha beta T cells of one donor. Overall, alpha beta T cells exhibited a distinct pattern of NKR expression different from that of gamma delta T and NK cells, which expressed highly similar NKR repertoires. In one donor, analysis of TCR rearrangement revealed a dominant subset of NKR(+) T cells sharing identical TCR alpha- and beta-chains. Remarkably, among 55 T cell clones sharing the same TCR alpha beta rearrangement 18 different KIR phenotypes were seen, suggesting that KIR expression was initiated subsequently to TCR rearrangement.

    View details for Web of Science ID 000167437700040

    View details for PubMedID 11238637

  • Differential expression of leukocyte receptor complex-encoded Ig-like receptors correlates with the transition from effector to memory CTL JOURNAL OF IMMUNOLOGY Young, N. T., Uhrberg, M., Phillips, J. H., Lanier, L. L., Parham, P. 2001; 166 (6): 3933-3941


    The human leukocyte receptor complex (LRC) on chromosome 19q13.4 encodes Ig superfamily receptors expressed on hemopoietic cells. Killer Ig-like receptors (KIR) are expressed in cytotoxic lymphocytes but other LRC molecules (Ig-like transcript(ILT)/leukocyte Ig-like receptor (LIR)) are more ubiquitous. We investigated expression of the ILT2/LIR1 inhibitory receptor compared with the related KIR. Both ILT2/LIR1 and KIR were expressed by peripheral CD8(+) T cells with a memory/effector phenotype. ILT2/LIR1(+) T cells demonstrated diverse TCRBV repertoires in contrast to KIR(+) T cells, while numbers of peripheral ILT2/LIR1(+) T cells were greater than KIR(+) T cells and the majority of ILT2/LIR1(+) T cells did not coexpress KIR. Analysis of CD8(+) T cells with specific HLA class I tetramers confirmed this pattern of expression, indicating differential regulation of LRC gene expression in T lymphocytes. Only a minor proportion of ILT2/LIR1(+) KIR(-) clones survived in vitro cloning, were more susceptible to anti-CD3 or cognate peptide induced cell death than KIR(+) T cells and exhibited lower levels of the Bcl-2 survival molecule. Our results indicate a sequential program of LRC-encoded receptor expression with initial ILT2/LIR1 expression in effector T cells and KIR gene transcription in the minor proportion of expanded clones which survives activation-induced cell death to become long term memory T cells.

    View details for Web of Science ID 000167437700041

    View details for PubMedID 11238638

  • Different NK cell surface phenotypes defined by the DX9 antibody are due to KIR3DL1 gene polymorphism JOURNAL OF IMMUNOLOGY Gardiner, C. M., Guethlein, L. A., Shilling, H. G., Pando, M., Carr, W. H., Rajalingam, R., Vilches, C., Parham, P. 2001; 166 (5): 2992-3001


    KIR3DL1 and KIR3DL2 are NK cell receptors for polymorphic HLA-B and -A determinants. The proportion of NK cells that bind anti-KIR3DL1-specific Ab DX9 and their level of binding vary between individuals. To determine whether these differences are due to KIR polymorphism, we assessed KIR3D gene diversity in unrelated individuals and families. Both KIR3DL1 and KIR3DL2 are highly polymorphic genes, with KIR3DS1 segregating like an allele of KIR3DL1. A KIR haplotype lacking KIR3DL1 and KIR3DS1 was defined. The two KIR3DL1 alleles of a heterozygous donor were expressed by different, but overlapping, subsets of NK cell clones. Sequence variation in KIR3DL1 and KIR3DL2 appear distinct; recombination is more evident in KIR3DL1, and point mutation is more evident in KIR3DL2. The KIR3DL1 genotype correlates well with levels of DX9 binding by NK cells, but not with the frequency of DX9-binding cells. Different KIR3DL1 alleles determine high, low, and no binding of DX9 Ab. Consequently, heterozygotes for high and low binding KIR3DL1 alleles have distinct subpopulations of NK cells that bind DX9 at high and low levels, giving characteristic bimodal distributions in flow cytometry. The Z27 Ab gave binding patterns similar to those of DX9. Four KIR3DL1 alleles producing high DX9 binding phenotypes were distinguished from four alleles producing low or no binding phenotypes by substitution at one or more of four positions in the encoded protein: 182 and 283 in the extracellular Ig-like domains, 320 in the transmembrane region, and 373 in the cytoplasmic tail.

    View details for Web of Science ID 000167115300012

    View details for PubMedID 11207248

  • Nomenclature for factors of the HLA system, 2000. Marsh, S. G., Bodmer, J. G., Albert, E. D., Bodmer, W. F., Bontrop, R. E., DuPont, B., Erlich, H. A., Hansen, J. A., Mach, B., Mayr, W. R., Parham, P., Petersdorf, E. W., Sasazuki, T., Schreuder, G. M., STROMINGER, J. L., Svejgaard, A., Terasaki, P. I. 2001: 236-283

    View details for PubMedID 11285132

  • Modes of salmonid MHC class I and II evolution differ from the primate paradigm JOURNAL OF IMMUNOLOGY Shum, B. P., Guethlein, L., Flodin, L. R., Adkison, M. A., Hedrick, R. P., Nehring, R. B., Stet, R. J., Secombes, C., Parham, P. 2001; 166 (5): 3297-3308


    Rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta) represent two salmonid genera separated for 15--20 million years. cDNA sequences were determined for the classical MHC class I heavy chain gene UBA and the MHC class II beta-chain gene DAB from 15 rainbow and 10 brown trout. Both genes are highly polymorphic in both species and diploid in expression. The MHC class I alleles comprise several highly divergent lineages that are represented in both species and predate genera separation. The class II alleles are less divergent, highly species specific, and probably arose after genera separation. The striking difference in salmonid MHC class I and class II evolution contrasts with the situation in primates, where lineages of class II alleles have been sustained over longer periods of time relative to class I lineages. The difference may arise because salmonid MHC class I and II genes are not linked, whereas in mammals they are closely linked. A prevalent mechanism for evolving new MHC class I alleles in salmonids is recombination in intron II that shuffles alpha 1 and alpha 2 domains into different combinations.

    View details for Web of Science ID 000167115300049

    View details for PubMedID 11207285

  • Short KIR haplotypes in pygmy chimpanzee (Bonobo) resemble the conserved framework of diverse human KIR haplotypes JOURNAL OF EXPERIMENTAL MEDICINE Rajalingam, R., Hong, M., Adams, E. J., Shum, B. P., Guethlein, L. A., Parham, P. 2001; 193 (1): 135-146


    Some pygmy chimpanzees (also called Bonobos) give much simpler patterns of hybridization on Southern blotting with killer cell immunoglobulin-like receptor (KIR) cDNA probes than do either humans or common chimpanzees. Characterization of KIRs from pygmy chimpanzees having simple and complex banding patterns identified nine different KIRs, representing seven genes. Five of these genes have orthologs in the common chimpanzee, and three of them (KIRCI, KIR2DL4, and KIR2DL5) also have human orthologs. The remaining two genes are KIR3D paralogous to the human and common chimpanzee major histocompatibility complex A- and/or -B-specific KIRs. Within a pygmy chimpanzee family, KIR haplotypes were defined. Simple patterns on Southern blot were due to inheritance of "short" KIR haplotypes containing only three KIR genes, KIRCI, KIR2DL4, and KIR3D, each of which represents one of the three major KIR lineages. These three genes in pygmy chimpanzees or their corresponding genes in humans and common chimpanzees form the conserved "framework" common to all KIR haplotypes in these species and upon which haplotypic diversity is built. The fecundity and health of individual pygmy chimpanzees who are homozygotes for short KIR haplotypes attest to the viability of short KIR haplotypes, indicating that they can provide minimal, essential KIRs for the natural killer and T cells of the hominoid immune system.

    View details for Web of Science ID 000166356500012

    View details for PubMedID 11136827

  • IMGT/HLA Database - a sequence database for the human major histocompatibility complex NUCLEIC ACIDS RESEARCH Robinson, J., Waller, M. J., Parham, P., Bodmer, J. G., Marsh, S. G. 2001; 29 (1): 210-213


    The IMGT/HLA Database ( specialises in sequences of polymorphic genes of the HLA system, the human major histocompatibility complex (MHC). The HLA complex is located within the 6p21.3 region on the short arm of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and these include the 21 highly polymorphic HLA genes, which influence the outcome of clinical transplantation and confer susceptibility to a wide range of non-infectious diseases. The database contains sequences for all HLA alleles officially recognised by the WHO Nomenclature Committee for Factors of the HLA System and provides users with online tools and facilities for their retrieval and analysis. These include allele reports, alignment tools and detailed descriptions of the source cells. The online IMGT/HLA submission tool allows both new and confirmatory sequences to be submitted directly to the WHO Nomenclature Committee. The latest version (release 1.7.0 July 2000) contains 1220 HLA alleles derived from over 2700 component sequences from the EMBL/GenBank/DDBJ databases. The HLA database provides a model which will be extended to provide specialist databases for polymorphic MHC genes of other species.

    View details for Web of Science ID 000166360300058

    View details for PubMedID 11125094

  • Identification of seventeen novel KIR variants: fourteen of them from two non-Caucasian donors TISSUE ANTIGENS Rajalingam, R., Gardiner, C. M., CANAVEZ, F., Vilches, C., Parham, P. 2001; 57 (1): 22-31


    The killer-cell immunoglobulin-like receptors (KIR) expressed by human natural killer (NK) cells are encoded by a family of genes on chromosome 19. The number of KIR genes varies with haplotype and the individual genes exhibit polymorphism. To investigate KIR diversity we studied KIR cDNA and genes of four human donors: two Caucasians, one Black American and one Asian Indian. From analysis of these donors seventeen novel KIR variants were identified and characterized. Fifteen of the new variants appear to have a simple allelic relationship with a known KIR, whereas two of them combine the sequences of two different KIR genes. Fourteen of the seventeen KIR variants were isolated from the two non-Caucasoid blood donors. These data show that much human KIR diversity remains to be characterized, particularly in non-Caucasoid populations.

    View details for Web of Science ID 000166985400004

    View details for PubMedID 11169255

  • MHC I-dependent antigen presentation is inhibited by poliovirus protein 3A PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Deitz, S. B., Dodd, D. A., Cooper, S., Parham, P., Kirkegaard, K. 2000; 97 (25): 13790-13795


    The effects of poliovirus 3A protein expression and poliovirus infection on the presentation of hepatitis C virus antigens in cultured chimpanzee cells were examined. Expression of poliovirus 3A protein inhibits protein secretion when expressed in isolation and was sufficient to protect chimpanzee cells from lysis by hepatitis C virus-specific cytotoxic T cells in standard (51)Cr-release assays. Poliovirus infection also inhibited antigen presentation, as determined by decreased cytotoxic T cell activation. A mutation in 3A that abrogates the inhibition of protein secretion also abolished the effects of poliovirus on antigen presentation. These results demonstrate that the inhibition of secretion observed in poliovirus-infected cells substantially reduces the presentation of new antigens on the cell surface. These observations may reflect a general mechanism by which nonenveloped viruses such as poliovirus and other viruses that do not require a functional protein secretory apparatus can evade detection by the cellular immune response.

    View details for Web of Science ID 000165728800061

    View details for PubMedID 11095746

  • Gene structure and promoter variation of expressed and nonexpressed variants of the KIR2DL5 gene JOURNAL OF IMMUNOLOGY Vilches, C., Gardiner, C. M., Parham, P. 2000; 165 (11): 6416-6421


    Two variants of the novel KIR2DL5 gene (KIR2DL5.1 and.2) were identified in genomic DNA of a single donor. However, only the KIR2DL5.1 variant was transcribed in PBMC. In this study, analysis of seven additional donors reveals two new variants of the KIR2DL5 gene and indicates that transcription, or its lack, are consistently associated with particular variants of this gene. Comparison of the complete nucleotide sequences of the exons and introns of KIR2DL5.1 and KIR2DL5.2 reveals no structural abnormalities, but similar open reading frames for both variants. In contrast, the promoter region of KIR2DL5 shows a high degree of sequence polymorphism that is likely relevant for expression. Substitution within a putative binding site for the transcription factor acute myeloid leukemia gene 1 could determine the lack of expression for some KIR2DL5 variants.

    View details for Web of Science ID 000165467100050

    View details for PubMedID 11086080

  • Discovery of two novel variants of KIR2DS5 reveals this gene to be a common component of human KIR 'B' haplotypes TISSUE ANTIGENS Vilches, C., Pando, M. J., Rajalingam, R., Gardiner, C. M., Parham, P. 2000; 56 (5): 453-456


    The gene encoding the non-inhibitory receptor KIR2DS5 has so far been represented by a single cDNA sequence, NKAT9. A previous study by polymerase chain reaction using sequence-specific primers (PCR-SSP) failed to detect NKAT9 in genomic DNA of 52 donors, which suggested that KIR2DS5 could be a rare gene. Here, we have characterized two novel variants of KIR2DS5 that differ from NKAT9 by 8 and 10 nucleotide substitutions. The frequency of KIR2DS5 was then re-assessed by PCR-SSP using primers specific for conserved sequences of all three known KIR2DS5 variants. We found KIR2DS5 is not a rare gene, but one present in 26% of 34 donors representing the major ethnic groups. Like other non-inhibitory KIR, the distribution of KIR2DS5 is restricted to the 'B' subset of KIR-gene haplotypes. Transcription of the KIR2DS5 gene was studied by reverse transcriptase (RT)-PCR in natural killer (NK) cells from one donor and shown to follow the clonal distribution seen for most other KIR genes.

    View details for Web of Science ID 000165656400010

    View details for PubMedID 11144295

  • Genes encoding human killer-cell Ig-like receptors with D1 and D2 extracellular domains all contain untranslated pseudoexons encoding a third Ig-like domain IMMUNOGENETICS Vilches, C., Pando, M. J., Parham, P. 2000; 51 (8-9): 639-646


    Human killer-cell immunoglobulin-like receptors (KIR) show three types of organization of their extracellular domains: D0-D1-D2 in KIR3D, D1-D2 in the majority of KIR2D, and D0-D2 in KIR2DL4 and the novel KIR2DL5. The gene for a KIR2DL3 variant, which has a D1-D2 structure, has been shown previously to have a nonexpressed region (pseudoexon 3) that is paralogous to the exon encoding the D0 domain of other KIR. This pseudoexon is not expressed because it is skipped during splicing of pre-mRNA. In this study, we demonstrate that all eight genes encoding human KIR with D1-D2 configuration (KIR2DL1-KIR2DL3, KIR2DS1-KIR2DS5) have similarly untranslated pseudoexons. Whereas the pseudoexons of four of these KIR genes bear nonsense mutations and/or altered splicing sites, the pseudoexons in the other four KIR genes have no major structural abnormalities, indicating that other mechanisms are responsible for inactivation of their exons 3. A comparison of the sequences on pseudoexons 3 with the paralogous expressed exons suggests that an exonic splicing enhancer may be necessary for the expression of exon 3 in KIR genes.

    View details for Web of Science ID 000088507400004

    View details for PubMedID 10941835

  • KIR2DL5, a novel killer-cell receptor with a D0-D2 configuration of Ig-like domains JOURNAL OF IMMUNOLOGY Vilches, C., Rajalingam, R., Uhrberg, M., Gardiner, C. M., Young, N. T., Parham, P. 2000; 164 (11): 5797-5804


    Four novel killer-cell Ig-like receptor (KIR) genes were discovered by analysis of genomic DNA from a human donor. One gene, KIR2DL5, is expressed by subpopulations of NK cells and T cells, whereas expression of the other three genes could not be detected. KIR2DL5 has two extracellular Ig-like domains of the D0 and D2 type, a structural configuration that was previously unique to KIR2DL4. Although having a similar structure overall, the KIR2DL4 and KIR2DL5 receptors have distinctive amino acid sequences in the ligand-binding extracellular domains and differ in the transmembrane and cytoplasmic motifs that determine signal transduction. Whereas the KIR2DL4 gene is present on all KIR haplotypes and is expressed by all human NK cells, the KIR2DL5 gene is restricted to the "B" subset of KIR haplotypes and is clonally expressed by NK cells within an individual. Chimpanzee genes for KIR2DL4 and KIR2DL5 have been defined and are very similar in sequence to their human orthologs. The donor in whom KIR2DL5 was first detected bears two variants of it that differ by five nucleotide substitutions in the coding region. Although the substitutions are not predicted to affect gene expression, transcription of only one of the two KIR2DL5 variants could be detected.

    View details for Web of Science ID 000087154800032

    View details for PubMedID 10820258

  • Rapid evolution of NK cell receptor systems demonstrated by comparison of chimpanzees and humans IMMUNITY Khakoo, S. I., Rajalingam, R., Shum, B. P., Weidenbach, K., Flodin, L., Muir, D. G., CANAVEZ, F., COOPER, S. L., Valiante, N. M., Lanier, L. L., Parham, P. 2000; 12 (6): 687-698


    That NK cell receptors engage fast-evolving MHC class I ligands suggests that they, too, evolve rapidly. To test this hypothesis, the structure and class I specificity of chimpanzee KIR and CD94:NKG2 receptors were determined and compared to their human counterparts. The KIR families are divergent, with only three KIR conserved between chimpanzees and humans. By contrast, CD94:NKG2 receptors are conserved. Whereas receptors for polymorphic class I are divergent, those for nonpolymorphic class I are conserved. Although chimpanzee and human NK cells exhibit identical receptor specificities for MHC-C, they are mediated by nonorthologous KIR. These results demonstrate the rapid evolution of NK cell receptor systems and imply that "catching up" with class I is not the only force driving this evolution.

    View details for Web of Science ID 000087937300010

    View details for PubMedID 10894168

  • Common chimpanzees have greater diversity than humans at two of the three highly polymorphic MHC class I genes IMMUNOGENETICS Adams, E. J., Cooper, S., Thomson, G., Parham, P. 2000; 51 (6): 410-424


    MHC class I polymorphism improves the defense of vertebrate species against viruses and other intracellular pathogens. To see how polymorphism at the same class I genes can evolve in different species we compared the MHC-A, MHC-B, and MHC-C loci of common chimpanzees and humans. Diversity in 23 Patr-A, 32 Patr-B, and 18 Patr-C alleles obtained from study of 48 chimpanzees was compared to diversity in 66 HLA-A, 149 HLA-B, and 41 HLA-C alleles obtained from a study of over 1 million humans. At each locus, alleles group hierarchically into families and then lineages. No alleles or families are shared by the two species, commonality being seen only at the lineage level. The overall nucleotide sequence diversity of MHC class I is estimated to be greater for modern chimpanzees than humans. Considering the numbers of lineages, families, and alleles, Patr-B and Patr-C have greater diversity than the HLA-B and HLA-C, respectively. In contrast, Patr-A has less polymorphism than HLA-A, due to the absence of A2 lineage alleles. The results are consistent with ancestral humans having passed through a narrower population bottleneck than chimpanzees, and with pathogen-mediated selection having favored either preservation of A2 lineage alleles on the human line and/or their extinction on the chimpanzee line.

    View details for Web of Science ID 000087393200003

    View details for PubMedID 10866107

  • NK cell receptors: Of missing sugar and missing self CURRENT BIOLOGY Parham, P. 2000; 10 (5): R195-R197


    Natural killer cells in mice detect cells in distress using lectin-like receptors that bind to self-MHC class I molecules. A new co-crystal structure suggests how NK cell maturation and attack may be mediated by receptor interaction at two distinct sites on the MHC class I molecule, both involving glycosylation.

    View details for Web of Science ID 000088977800009

    View details for PubMedID 10712900

  • IMGT/HLA Database - a sequence database for the human major histocompatibility complex TISSUE ANTIGENS Robinson, J., Malik, A., Parham, P., Bodmer, J. G., Marsh, S. G. 2000; 55 (3): 280-287


    The IMGT/HLA Database is a specialist database for sequences of the human major histocompatibility (MHC) system. It includes all the HLA sequences officially recognised and named by the WHO Nomenclature Committee for Factors of the HLA System. The database provides users with online tools and facilities for the retrieval and analysis of these sequences. These include allele reports, alignment tools and a detailed database of all source cells. The online IMGT/HLA submission tool allows the submission of both new and confirmatory allele sequences directly to the WHO Nomenclature Committee for Factors of the HLA System. The latest version (release 1.4.1, November 1999) contains 1,015 HLA alleles from over 2,270 component sequences derived from the EMBL/GenBank/DDBJ databases. From its release in December 1998 until December 1999 the IMGT/HLA website received approximately 100,000 hits. The database currently focuses on the human major histocompatibility complex but will be used as a model system to provide specialist databases for the MHC sequences of other species.

    View details for Web of Science ID 000086099100014

    View details for PubMedID 10777106

  • Distinguishing recombination and intragenic gene conversion by linkage disequilibrium patterns GENETICS RESEARCH Wiehe, T., Mountain, J., Parham, P., Slatkin, M. 2000; 75 (1): 61-73


    Deterministic theory suggests that reciprocal recombination and intragenic, interallelic conversion have different effects on the linkage disequilibrium between a pair of genetic markers. Under a model of reciprocal recombination, the decay rate of linkage disequilibrium depends on the distance between the two markers, while under conversion the decay rate is independent of this distance, provided that conversion tracts are short. A population genetic three-locus model provides a function Q of two-locus linkage disequilibria. Viewed as a random variable, Q is the basis for a test of the relative impact of conversion and recombination. This test requires haplotype frequency data of a sufficiently variable three-locus system. One of the few examples currently available is data from the Human Leukocyte Antigen (HLA) class I genes of three Amerindian populations. We find that conversion may have played a dominant role in shaping haplotype patterns over short stretches of DNA, whereas reciprocal recombination may have played a greater role over longer stretches of DNA. However, in order to draw firm conclusions more independent data are necessary.

    View details for Web of Science ID 000086118600007

    View details for PubMedID 10740922

  • Population frequencies and putative haplotypes of the killer cell immunoglobulin-like receptor sequences and evidence for recombination TRANSPLANTATION Witt, C. S., Dewing, C., Sayer, D. C., Uhrberg, M., Parham, P., Christiansen, F. T. 1999; 68 (11): 1784-1789


    The killer cell immunoglobulin-like receptors (KIR) are a family of receptors expressed on natural killer (NK) cells and some T cells. Class I HLA molecules on target cells are the ligands for the KIR receptors. The number of KIR genes has been reported to vary between individuals, resulting in different KIR haplotypes. There is little published data on the frequency of each KIR gene and the linkage disequilibrium between the genes. Because there is evidence that NK cells may be involved in bone marrow transplant rejection, we have determined the KIR gene frequencies and possible haplotypic arrangements by linkage disequilibrium analysis in an Australian population.Controls, patients with leukemia, and unrelated bone marrow donor-recipient pairs were typed for the presence of 11 KIR genes by polymerase chain reaction-sequence specific priming.Ninety percent of the population was found to have a sufficient number and variety of KIR genes to detect any mismatch of HLA-A, -B, and -C alleles on NK target cells. The 11 KIR genes could be divided into two groups based on linkage disequilibrium between pairs of genes. Evidence for a recombination within the KIR gene complex is presented.Typing for the presence of particular KIR genes may be indicated for bone marrow donor-recipient pairs for whom a class I HLA mismatch is unavoidable.

    View details for Web of Science ID 000084305800024

    View details for PubMedID 10609957

  • Immunogenetics - Soaring costs in defence NATURE Parham, P. 1999; 401 (6756): 870-871

    View details for Web of Science ID 000083464700040

    View details for PubMedID 10553900

  • Evidence for an HLA-C-like locus in the orangutan Pongo pygmaeus IMMUNOGENETICS Adams, E. J., Thomson, G., Parham, P. 1999; 49 (10): 865-871


    HLA-B and C are related class I genes which are believed to have arisen by duplication of a common ancestor. Previous study showed the presence of orthologues for both HLA-B and C in African apes but only for HLA-B in Asian apes. These observations suggested that the primate C locus evolved subsequent to the divergence of the Pongidae and Hominidae. From an analysis of orangutan Tengku two HLA-C-like alleles (Popy C*0101 and Popy C*0201) were defined as well as three HLA-B-like (Popy-B) alleles. By contrast, no Popy-C alleles were obtained from orangutan Hati, although three Popy-B alleles were defined. Thus an HLA-C-like locus exists in the orangutan (as well as a duplicated B locus), implying that the primate C locus evolved prior to the divergence of the Pongidae and Hominidae and is at least 12-13 million years old. Uncertain is whether all orangutan MHC haplotypes contain a C locus, as the failure to find C alleles in some individuals could be due to a mispairing of HLA-C-specific primers with certain Popy-C alleles. These results raise the possibilities that other primate species have a C locus and that the regulation of natural killer cells by C allotypes evolved earlier in primate evolution than has been thought.

    View details for Web of Science ID 000082144000006

    View details for PubMedID 10436180

  • A divergent non-classical class I gene conserved in salmonids IMMUNOGENETICS Shum, B. P., Rajalingam, R., Magor, K. E., Azumi, K., Carr, W. H., Dixon, B., Stet, R. J., Adkison, M. A., Hedrick, R. P., Parham, P. 1999; 49 (6): 479-490


    Complementary DNA for two class I genes of the rainbow trout, Oncorhynchus mykiss, were characterized. MhcOnmy-UBA*01 is similar to Onmy-UAC32 and the classical major histocompatibility complex class I genes of other fish species, whereas Onmy-UAA*01 is divergent from all class I genes so far characterized. Onmy-UAA*01 is expressed at lower levels than Onmy-UBA*01. Although Onmy-UAA*01 exhibits restriction fragment length polymorphism on Southern blotting, the encoded protein is highly conserved. Two allotypes, which differ only by substitution at amino acid position 223 of the alpha 3 domain, have been defined. Onmy-UAA*01 has an exon-intron organization like other class I genes and contains a Tc1-like transposon element in intron III. Orthologues of Onmy-UAA*01 have been characterized in four other species of salmonid. Between four species of Oncorhynchus, UAA*01 proteins differ by only 2-6 amino acids, whereas comparison of Oncorhynchus with Salmo trutta (brown trout) reveals 14-16 amino acid differences. The Onmy-UAA*01 gene has properties indicative of a particularly divergent non-classical class I gene.

    View details for Web of Science ID 000080331100002

    View details for PubMedID 10380691

  • Molecular phylogeny of New World primates (Platyrrhini) based on beta(2)-microglobulin DNA sequences MOLECULAR PHYLOGENETICS AND EVOLUTION Canavez, F. C., Moreira, M. A., Ladasky, J. J., Pissinatti, A., Parham, P., Seuanez, H. N. 1999; 12 (1): 74-82


    Neotropical primates, traditionally grouped in the infraorder Platyrrhini, comprise 16 extant genera. Cladistic analyses based on morphological characteristics and molecular data resulted in topologic arrangements depicting disparate phylogenetic relationships, indicating that the evolution of gross morphological characteristics and molecular traits is not necessarily congruent. Here we present a phylogenetic arrangement for all neotropical primate genera obtained from DNA sequence analyses of the beta2-microglobulin gene. Parsimony, distance, and maximum likelihood analyses favored two families, Atelidae and Cebidae, each containing 8 genera. Atelids were resolved into atelines and pitheciines. The well-supported ateline clade branched into alouattine (Alouatta) and ateline (Ateles, Lagothrix, Brachyteles) clades. In turn, within the Ateline clade, Lagothrix and Brachyteles were well-supported sister groups. The pitheciines branched into well-supported callicebine (Callicebus) and pitheciine (Pithecia, Cacajao, Chiropotes) clades. In turn, within the pitheciine clade, Cacajao and Chiropotes were well-supported sister groups. The cebids branched into callitrichine (Saguinus, Leontopithecus, Callimico, Callithrix-Cebuella), cebine (Cebus, Saimiri), and aotine (Aotus) clades. While the callitrichine clade and the groupings of species and genera within this clade were all well supported, the cebine clade received only modest support, and the position of Aotus could not be clearly established. Cladistic analyses favored the proposition of 15 rather than 16 extant genera by including Cebuella pygmaea in the genus Callithrix as the sister group of the Callithrix argentata species group. These analyses also favored the sister grouping of Callimico with Callithrix and then of Leontopithecus with the Callithrix-Callimico clade.

    View details for Web of Science ID 000080208000007

    View details for PubMedID 10222163

  • Nomenclature for factors of the HLA system, 1998 TISSUE ANTIGENS Bodmer, J. G., Marsh, S. G., Albert, E. D., Bodmer, W. F., Bontrop, R. E., DuPont, B., Erlich, H. A., Hansen, J. A., Mach, B., Mayr, W. R., Parham, P., Petersdorf, E. W., Sasazuki, T., Schreuder, G. M., STROMINGER, J. L., Svejgaard, A., Terasaki, P. I. 1999; 53 (4): 407-446

    View details for Web of Science ID 000079880500001

    View details for PubMedID 10321590

  • Residue 3 of beta(2)-microglobulin affects binding of class I MHC molecules by the W6/32 antibody IMMUNOGENETICS Ladasky, J. J., Shum, B. P., CANAVEZ, F., Seuanez, H. N., Parham, P. 1999; 49 (4): 312-320


    Previous studies of class I MHC molecules have shown that the owl monkey (Aotus) possesses at least two variants of the beta2-microglobulin (beta2m) protein. These two variants have different isoelectric points, and exhibit differential reactivity with the monoclonal antibody W6/32. We report cDNA sequences of the B2m gene, from W6/32-positive and W6/32-negative Aotus cell lines. The two beta2m variants we identified exhibit a single amino acid difference at position three. An arginine residue at position 3 was correlated with W6/32 reactivity, whereas histidine was associated with non-reactivity. W6/32 reactivity was conferred to a W6/32-negative Aotus cell line when it was transfected with the B2m from the W6/32-positive cell line. Residue 3 of beta2m is located at the surface of the class I molecule. It is also close to position 121 of the MHC class I heavy chain, which has previously been shown to influence W6/32 antibody binding. We conclude that W6/32 binds a compact epitope on the class I molecule that includes both residue 3 of beta2m and residue 121 of the heavy chain. We examined the distribution of the two beta2m motifs in a sample Aotus population using an allele-specific polymerase chain reaction assay. The pattern of beta2m segregation we observed matches that which was defined previously by serology. Additionally, we identified laboratory-born hybrid animals who possess both variants of beta2m.

    View details for Web of Science ID 000079153300009

    View details for PubMedID 10079295

  • Analysis of a successful immune response against hepatitis C virus IMMUNITY Cooper, S., Erickson, A. L., Adams, E. J., Kansopon, J., Weiner, A. J., Chien, D. Y., Houghton, M., Parham, P., Walker, C. M. 1999; 10 (4): 439-449


    To investigate the type of immunity responsible for resolution of hepatitis C virus (HCV) infection, we monitored antibody and intrahepatic cytotoxic T lymphocyte (CTL) responses during acute (<20 weeks) infection in chimpanzees. Two animals who terminated infection made strong CTL but poor antibody responses. In both resolvers, CTL targeted at least six viral regions. In contrast, animals developing chronic hepatitis generated weaker acute CTL responses. Extensive analysis of the fine specificity of the CTL in one resolver revealed nine peptide epitopes and restriction by all six MHC class I allotypes. Every specificity shown during acute hepatitis persisted in normal liver tissue more than 1 yr after resolution. These results suggest that CD8+CTL are better correlated with protection against HCV infection than antibodies.

    View details for Web of Science ID 000079989600005

    View details for PubMedID 10229187

  • Virtual reality in the MHC IMMUNOLOGICAL REVIEWS Parham, P. 1999; 167: 5-15

    View details for Web of Science ID 000079851100001

    View details for PubMedID 10319247

  • Hepatitis C virus envelope glycoprotein E1 originates in the endoplasmic reticulum and requires cytoplasmic processing for presentation by class I MHC molecules JOURNAL OF IMMUNOLOGY Selby, M., Erickson, A., Dong, C., Cooper, S., Parham, P., Houghton, M., Walker, C. M. 1999; 162 (2): 669-676


    We investigated whether hepatitis C virus envelope glycoprotein E1 is transported from the endoplasmic reticulum (ER) to the cytoplasm of infected cells for class I MHC processing. Target cells expressing E1 were killed by CTL lines from a hepatitis C virus-infected chimpanzee, and synthetic peptides were used to define an epitope (amino acids 233-GNASRCWVA-241) presented by the Patr-B*1601 class I MHC molecule. An unusually high concentration (>100 nM) of this nonameric peptide was required for target cell lysis, but this could be reduced at least 1000-fold by replacing the asparagine at amino acid position 234 (Asn234) with aspartic acid (Asp), the anticipated anchor residue for NH2-terminal peptide binding to Patr-B*1601. Conspicuously, position 234 is part of an N-glycosylation motif (Asn-Xaa-Ser/Thr), suggesting that the Asn234 to Asp substitution might occur naturally within the cell due to deglycosylation/deamidation of this amino acid by the cytosolic enzyme peptide N-glycanase. In support of this model, we demonstrate that presentation of the epitope depended on 1) cotranslational synthesis of E1 in the ER, 2) glycosylation of the E1 molecule, and 3) a functional TAP transporter to shuttle peptide from the cytosolic to ER compartment. These results indicate for the first time that during infection of the host, viral envelope glycoproteins originating in the ER are processed in the cytoplasm for class I MHC presentation. That a posttranslational change in amino acid sequence from Asn to Asp alters the repertoire of peptides presented to CD8+ CTL has implications for the design of antiviral vaccines.

    View details for Web of Science ID 000077951400006

    View details for PubMedID 9916684

  • Evolutionary disruptions of human syntenic groups 3, 12, 14, and 15 in Ateles paniscus chamek (Platyrrhini, Primates) CYTOGENETICS AND CELL GENETICS Canavez, F. C., Moreira, M. A., Bonvicino, C. R., Parham, P., Seuanez, H. N. 1999; 87 (3-4): 182-188


    Comparative gene assignments of 18 markers, based on analyses of somatic cell hybrids and previous data in the literature, indicated that human (HSA) syntenic groups 3, 12, 14, and 15 are dissociated in the spider monkey species Ateles paniscus chamek (APC). Markers present in HSA 3p were allocated to APC 3 and APC 9. The HSA 12 cluster was split into two syntenic groups, one mainly including HSA 12p markers in APC 16 and the other, including HSA 12q markers, in APC 2p. The HSA 14q cluster split into three syntenic groups, corresponding to APC 2q, APC 6, and APC 12. Finally, the HSA 15 cluster split into two syntenic groups, APC 2q and APC 3. Comparisons with previous gene assignments and human SROs led to the tentative postulation of rearrangements having occurred during the evolutionary divergence of man and A. paniscus chamek. Chromosome painting data in the congeneric species A. geoffroyi, other New World and Old World primates, and several representative non-primate animals were compared in an attempt to delineate the ancestral and derived conditions underlying the evolutionary rearrangement of syntenic groups in mammals.

    View details for Web of Science ID 000085572800005

    View details for PubMedID 10702662

  • Phylogenetic relationships of the callitrichinae (Platyrrhini, primates) based on beta(2)-microglobulin DNA sequences AMERICAN JOURNAL OF PRIMATOLOGY Canavez, F. C., Moreira, M. A., Simon, F., Parham, P., Seuanez, H. N. 1999; 48 (3): 225-236


    The phylogenetic relationships of callitrichine primates have been determined by DNA sequence analyses of exons 1, 2, and 3 of the beta2-microglobulin gene. Parsimony, distance, and maximum likelihood analyses of ca. 900 base pairs of 21 taxa, representing all callitrichine genera, indicated that Saguinus was the most basal offshoot. Within Saguinus, S. fuscicollis appeared as the first divergent lineage followed by an unresolved trichotomy formed by S. mystax/S. imperator, S. midas/S. bicolor, and S. oedipus. A second callitrichine lineage was formed by Leontopithecus; each of the three species studied showed identical nucleotide sequences. Callimico appeared as the sister taxon of Callithrix/Cebuella. Genetic distances within this latter group were very small, although a stronger association between Cebuella and species of the Callithrix argentata group was observed. The inclusion of Cebuella in the genus Callithrix is suggested. These studies indicated that tamarins are more plesiomorphic than marmosets in agreement with the phyletic dwarfism hypothesis.

    View details for Web of Science ID 000080622600004

    View details for PubMedID 10380996

  • Polymorphism and evolution of HLA class I and II genes and molecules. Reviews in immunogenetics Little, A. M., Parham, P. 1999; 1 (1): 105-123


    Genes in the HLA complex, the human major histocompatibility complex (MHC), encode polymorphic HLA class I and II molecules that help T lymphocytes recognise and respond to foreign antigens. Certain HLA class I allotypes also regulate the response of natural killer cells. HLA class I and II molecules with little or no polymorphism contribute a variety of functions to the immune response, as do class I molecules coded by genes outside of the HLA region. Knowledge of the organisation of HLA class I and II genes, of the nucleotide sequences of their alleles, and the three-dimensional structures of their protein products, has facilitated analysis of the evolution and polymorphism of HLA class I and II genes and molecules. In turn, these analyses have provided insight into the mechanisms and selective forces driving change in the HLA complex.

    View details for PubMedID 11256568

  • CK-1, a putative chemokine of rainbow trout (Oncorhynchus mykiss) IMMUNOLOGICAL REVIEWS Dixon, B., Shum, B., Adams, E. J., Magor, K. E., Hedrick, R. P., Muir, D. G., Parham, P. 1998; 166: 341-348


    Chemokines are small inducible proteins that direct the migration of leukocytes. While chemokines are well characterised in mammals, they have yet to be identified in fish. We have isolated a cDNA clone from rainbow trout (Oncorhynchus mykiss) which encodes a protein (CK-1) having structural features typical of chemokines. Amino-acid residues that define the beta-chemokines of mammals are conserved in CK-1, including the paired cysteine motif, CC. Further similarities are shared with the C6 subfamily of beta-chemokines. In contrast, the organisation of the CK-1 gene is closer to that of mammalian alpha-chemokine genes than beta-chemokine genes. The CK-1 gene is present in all four salmonid species examined and the nucleotide sequences of the exons are highly conserved. CK-1 has characteristics in common with mammalian alpha and beta-chemokine genes, suggesting that this salmonid chemokine gene preserves traits once present in the ancestral chemokine gene from which modern mammalian chemokine genes evolved.

    View details for Web of Science ID 000077835300027

    View details for PubMedID 9914924

  • Evidence for recombination as a mechanism for KIR diversification IMMUNOGENETICS Shilling, H. G., Lienert-Weidenbach, K., Valiante, N. M., Uhrberg, M., Parham, P. 1998; 48 (6): 413-416

    View details for Web of Science ID 000076754500007

    View details for PubMedID 9799338

  • Direct binding and functional transfer of NK cell inhibitory receptors reveal novel patterns of HLA-C allotype recognition JOURNAL OF IMMUNOLOGY WINTER, C. C., Gumperz, J. E., Parham, P., Long, E. O., Wagtmann, N. 1998; 161 (2): 571-577


    Cytotoxicity of human NK cells is under negative control of killer cell Ig-like receptors (KIR) specific for HLA class I. To determine the specificity of five KIR containing two Ig domains (KIR2D), direct binding of soluble recombinant KIR2D to a panel of HLA class I transfectants was assayed. One soluble KIR2D, derived from an inhibitory receptor with a long cytoplasmic tail (KIR2DL1), bound to HLA-C allotypes containing asparagine 77 and lysine 80 in the heavy chain, as expected, since these allotypes inhibit lysis by NK cells expressing KIR2DL1. Surprisingly, another KIR2D (KIR2DL2), which inhibits NK lysis of cells expressing HLA-C molecules with serine 77 and asparagine 80, bound to HLA-C allotypes carrying either amino acid motif. Expression of the KIR2DL receptors in NK cells using recombinant vaccinia viruses confirmed these patterns of recognition, and identified KIR2DL3 as another KIR reacting with both groups of HLA-C allotypes. Mutagenesis of amino acid 44 in KIR2DL1 and KIR2DL2 suggested this residue controls the affinity of KIR for the 77/80 motif of HLA-C molecules. Two other soluble KIR2D, derived from noninhibitory receptors with short cytoplasmic tails (KIR2DS), did not bind to any of the HLA class I allotypes tested. One of these receptors (KIR2DS2) is closely related in sequence to KIR2DL2. Substitution of tyrosine 45 with the phenylalanine conserved in other KIR was sufficient to permit specific binding of KIR2DS2 to HLA-C. These results show that KIR2DL receptors are specific for HLA-C, but that recognition of HLA-C allotypes appears more permissive than indicated by previous functional experiments.

    View details for Web of Science ID 000074728400006

    View details for PubMedID 9670929

  • The influence of exogenous peptide on beta(2)-microglobulin exchange in the HLA complex: analysis in real-time IMMUNOGENETICS Morgan, C. L., Ruprai, A. K., Solache, A., Lowdell, M., Price, C. P., Cohen, S. B., Parham, P., Madrigal, J. A., Newman, D. J. 1998; 48 (2): 98-107


    We used an optical biosensor to determine the relative binding affinity of peptides to purified HLA class I molecules. In this assay we monitor beta2-microglobulin (beta2m) exchange within the HLA-A2 molecule, whereby native beta2m in the complex is replaced by beta2m immobilized at the surface of the biosensor. Quantitative kinetic measurements permit us to obtain association rate (kass), dissociation rate (kdiss) and affinity constants (KA) for the beta2m exchange reaction, alone, (control) and in the presence of exogenous peptide. We tested a panel of six peptides which had been designed and synthesized with an HLA-A2 binding motif, and had also been tested by the T2-cell binding assay, along with control peptides. The biosensor results demonstrate that exogenous peptide influences the dynamics of beta2m exchange in a sequence-specific manner. Five of six peptides increased the association rate, decreased the dissociation rate, and significantly increased the affinity (KA=1. 55-1.88x10(9) M-1) of HLA-A2 for immobilized beta2m compared with the control (KA =1.14+/-0.04x10(9)M-1), demonstrating stabilization of the complex. One peptide was unable to stabilize the complex, as also shown in the T2 binding assay. However, analysis of peptide sequences demonstrated that the HLA-A2 secondary motif as well as primary motif residues are required for HLA-A2 stabilization. Further experiments demonstrated that beta2m exchange alone cannot stabilize the HLA class I complex at the cell surface until a peptide of sufficient binding affinity is bound. Hence kinetics equal to or below the control values in our biosensor assay probably represent an unstable complex in vivo. Unlike other methods described for the analysis of peptide stabilization, this approach is significantly faster, provides full kinetic analysis, and is simpler, since it requires no labeling of peptides. Furthermore, this may have important implications in the assessment of peptide vaccines.

    View details for Web of Science ID 000074747100002

    View details for PubMedID 9634473

  • beta(2)-microglobulin in neotropical primates (Platyrrhini) IMMUNOGENETICS Canavez, F. C., Ladasky, J. J., Muniz, J. A., Seuanez, H. N., Parham, P. 1998; 48 (2): 133-140


    Nucleotide sequences for the three exons of the beta2-microglobulin (beta2m) gene (B2m) were determined for 135 animals representing 37 species and all 16 genera of neotropical primates (Platyrrhini). Twenty-eight different nucleotide sequences, encoding for 26 different proteins, were obtained. In comparison with those of other primate species, the beta2-microglobulins of the Platyrrhini form a distinct clade. Individual genera of neotropical primates have distinctive B2m sequences, but within a genera species can have either the same or different B2m sequences. B2m polymorphism was found within three of the species sampled: Callicebus personatus, Saguinus midas, and Aotus azarae. Of these only the polymorphism in A. azarae has an effect upon the mature, functional beta2m protein: residue 4 being either alanine or threonine. The A. azarae B2m allele encoding alanine at position 4 is shared with another species of Aotus (A. infulatus). In pairwise comparison the mature beta2m proteins of neotropical primates differ by 1-9 amino acid substitutions which can occur at 18 positions within the sequence. The substitutions are distributed throughout the primary structure but are more commonly found in loops rather than beta strands of the tertiary structure. Of 17 residues of beta2m which hydrogen-bond with the class I heavy chain in human MHC class I molecules, 13 are conserved in the neotropical primates. The overall pattern of sequence variation in the B2m genes of the Platyrrhini is consistent with an evolution by successive selectively neutral events.

    View details for Web of Science ID 000074747100006

    View details for PubMedID 9634477

  • The Bw4/Bw6 difference between HLA-B*0802 and HLA-B*0801 changes the peptides endogenously bound and the stimulation of alloreactive T cells IMMUNOGENETICS Arnett, K. L., Huang, W., Valiante, N. M., Barber, L. D., Parham, P. 1998; 48 (1): 56-61


    HLA-B*0801 is unique among HLA-B allotypes in having dominant amino acid anchors at positions 3 and 5 of the peptide-binding motif. HLA-B*0802 is a variant of HLA-B*0801 in which the Bw6 sequence motif is replaced by a Bw4 sequence motif. This change, involving substitutions at positions 77, 80, 81, 82, and 83 of the B*08 heavy chain, is probably the result of a single evolutionary event of interallelic conversion. Moreover, the difference between B*0802 and B*0801 is sufficient to stimulate a cytotoxic T-cell response. To assess further the functional impact of the Bw4 motif on a B8 background, we compared the peptide-binding specificity of the B*0801 and B*0802 allotypes by sequencing the mixture of peptides endogenously bound to B*0802 and 12 individual peptides purified from that mixture. The HLA-B*0802 allotype, while able to bind some peptides bound by B*0801, has a broader repertoire of endogenously bound peptides than B*0801: the peptides bound by B*0802 are more variable in length and exhibit greater diversity in the carboxyl-terminal amino acid which interacts with the F pocket.

    View details for Web of Science ID 000074434700008

    View details for PubMedID 9601944

  • Comparative gene assignment in Ateles paniscus chamek (Platyrrhini, Primates) and man: association of three separate human syntenic groups and evolutionary considerations CHROMOSOMA CANAVEZ, F., Moreira, M. A., Bonvicino, C. R., Parham, P., Seuanez, H. N. 1998; 107 (2): 73-79


    Regional assignment of eight markers to chromosome 2 of Ateles paniscus chamek (APC) confirmed a syntenic association similar to human (HSA) 12q + 14q + 15q. Three HSA 12q markers (RAP1B, PAH and ALDH2) were allocated to a shortest region of overlap (SRO) in APC 2p and found to be syntenic to other HSA 12q markers (PEPB and TCF1). Five HSA 14q markers (CTLA, PAX9, NSP, FOS and CHGA) were allocated to APC 2q and found to be syntenic to other HSA 14q markers (NP, TGM1, and CALM1) and to four HSA 15q markers (THBS1, B2M, HEXA and MPI) but dissociated from markers close to HSA 14qter (CKB) and HSA 15qter (FES-IDH2). Karyotypic comparisons showed an evident homoeology between APC 2p and HSA 12q while APC 2q was similar to an HSA 14qter::HSA 15qter fusion product. Comparative gene mapping data show that the HSA 14q + HSA 15q syntenic association is an ancestral mammalian gene cluster that has been maintained in several primate taxa. Conversely, in Ateles, it has been further associated with HSA 12q while, in Hominoids and Cebus, it has been independently dissociated into two separate syntenic groups, similar to HSA 14q and HSA 15q.

    View details for Web of Science ID 000074093800002

    View details for PubMedID 9601975

  • HLA class I region sequences, 1998 TISSUE ANTIGENS Mason, P. M., Parham, P. 1998; 51 (4): 417-466

    View details for Web of Science ID 000073017700002

    View details for PubMedID 9583801

  • Clathrin self-assembly is regulated by three light-chain residues controlling the formation of critical salt bridges EMBO JOURNAL Ybe, J. A., Greene, B., Liu, S. H., Pley, U., Parham, P., Brodsky, F. M. 1998; 17 (5): 1297-1303


    Clathrin self-assembly into a polyhedral lattice mediates membrane protein sorting during endocytosis and organelle biogenesis. Lattice formation occurs spontaneously in vitro at low pH and, intracellularly, is triggered by adaptors at physiological pH. To begin to understand the cellular regulation of clathrin polymerization, we analyzed molecular interactions during the spontaneous assembly of recombinant hub fragments of the clathrin heavy chain, which bind clathrin light-chain subunits and mimic the self-assembly of intact clathrin. Reconstitution of hubs using deletion and substitution mutants of the light-chain subunits revealed that the pH dependence of clathrin self-assembly is controlled by only three acidic residues in the clathrin light-chain subunits. Salt inhibition of hub assembly identified two classes of salt bridges which are involved and deletion analysis mapped the clathrin heavy-chain regions participating in their formation. These combined observations indicated that the negatively charged regulatory residues, identified in the light-chain subunits, inhibit the formation of high-affinity salt bridges which would otherwise induce clathrin heavy chains to assemble at physiological pH. In the presence of light chains, clathrin self-assembly depends on salt bridges that form only at low pH, but is exquisitely sensitive to regulation. We propose that cellular clathrin assembly is controlled via the simple biochemical mechanism of reversing the inhibitory effect of the light-chain regulatory sequence, thereby promoting high-affinity salt bridge formation.

    View details for Web of Science ID 000072572100013

    View details for PubMedID 9482727

  • A major histocompatibility complex class I allele shared by two species of chimpanzee IMMUNOGENETICS Cooper, S., Adams, E. J., WELLS, R. S., Walker, C. M., Parham, P. 1998; 47 (3): 212-217


    Little is known regarding the rates at which natural selection can modify or retain antigen presenting alleles at the major histocompatibility complex (MHC). Discovery of identical [1101 base pairs (bp)] coding regions at the MHC class I C locus in Pan troglodytes and Pan paniscus, chimpanzee species that diverged approximately 2.3 million years ago, now indicates that a class I allotype can survive for at least this period. Remarkable conservation was also reflected in the (1799 bp) introns where a maximum of only six substitutions distinguished five alleles (three from P. troglodytes and two from P. paniscus) that encoded the identical heavy chain allotype. Analysis of a more distantly related human allele, HLA-Cw*0702, corroborated that intron variation was non-uniform along the gene. Thus we provide a clear reference frame for the lifetime of an MHC class I allotype, a direct estimate of allelic substitution rates, and evidence for an unusual evolution of MHC class I introns.

    View details for Web of Science ID 000071797500004

    View details for PubMedID 9435339

  • Characterization of chimpanzee TCRV gene polymorphism: how old are human TCRV alleles? IMMUNOGENETICS Jaeger, E. E., Bontrop, R. E., Parham, P., Wickings, E. J., Kadwell, M., Lanchbury, J. S. 1998; 47 (2): 115-123


    The functional relevance of the majority of human T-cell receptor A and B variable region gene polymorphisms is controversial. Studies of human and nonhuman primate major histocompatibility complex (MHC) class I and II polymorphisms show that allelic lineages predate human speciation and indicate that selection favors the long-term maintenance of these advantageous mutations. We investigated at the DNA level whether 15 human TCRA and B polymorphisms exist in contemporary chimpanzee populations. Polymorphisms consisted of variable region replacements, a recombination signal sequence base change, and silent mutations. With one exception, none of these human TCR polymorphisms were observed in contemporary chimpanzees. Investigation of the same polymorphisms in a range of other nonhuman primates showed little evidence of the existence of human polymorphism prespeciation. Chimpanzee TCRAV and BV regions were however polymorphic for variation so far not observed in human groups. Levels of mitochondrial and nuclear DNA sequence variation in contemporary chimpanzees suggest that population bottlenecks have not been a feature of chimpanzee evolution and it is therefore probable that most human TCR polymorphisms have evolved in the estimated five million years since the speciation of human and chimpanzees. Thus, over the evolutionary time period studied, ancient TCRA and B polymorphisms have not been maintained by selection to the same degree as postulated for MHC polymorphisms.

    View details for Web of Science ID 000071336100002

    View details for PubMedID 9396857

  • Functionally and structurally distinct NK cell receptor repertoires in the peripheral blood of two human donors IMMUNITY Valiante, N. M., Uhrberg, M., Shilling, H. G., Lienert-Weidenbach, K., Arnett, K. L., D'Andrea, A., Phillips, J. H., Lanier, L. L., Parham, P. 1997; 7 (6): 739-751


    The expression of KIR and CD94:NKG2 receptors was determined for more than 100 natural killer (NK) cell clones obtained from two blood donors who differ in their HLA class I and KIR genes. More than 98% of the clones were inhibited by individual autologous class I allotypes, and every clone was inhibited by the combination of autologous allotypes. The patterns of inhibition correlate with expression of inhibitory receptors of defined specificity. One donor possesses three class I ligands for KIR, and a majority of NK cells use KIR as their inhibitory receptor; the second donor possesses only a single ligand for KIR, and a majority of NK cells use the more broadly reactive CD94:NKG2a as their inhibitory receptor. Because of these differences, the first donor has subpopulations of NK cells that kill cells of the second donor, whereas the NK cells of the second donor are universally tolerant of cells from the first donor.

    View details for Web of Science ID 000071351300002

    View details for PubMedID 9430220

  • Human diversity in killer cell inhibitory receptor genes IMMUNITY Uhrberg, M., Valiante, N. M., Shum, B. P., Shilling, H. G., Lienert-Weidenbach, K., Corliss, B., Tyan, D., Lanier, L. L., Parham, P. 1997; 7 (6): 753-763


    The presence and expression of killer inhibitory receptor (KIR) and CD94:NKG2 genes from 68 donors were analyzed using molecular typing techniques. The genes encoding CD94:NKG2 receptors were present in each person, but KIR gene possession varied. Most individuals expressed inhibitory KIR for the three well-defined HLA-B and -C ligands, but noninhibitory KIR genes were more variable. Twenty different KIR phenotypes were defined. Two groups of KIR haplotypes were distinguished and occurred at relatively even frequency. Group A KIR haplotypes consist of six genes: the main inhibitory KIR, one noninhibitory KIR, and a structurally divergent KIR. Allelic polymorphism within five KIR genes was detected. Group B comprises more noninhibitory KIR genes and contains at least one additional gene not represented in group A. The KIR locus therefore appears to be polygenic and polymorphic within the human population.

    View details for Web of Science ID 000071351300003

    View details for PubMedID 9430221

  • Mismatches for two major and one minor histocompatibility antigen correlate with a patient's rejection of a bone marrow graft from a serologically HLA-identical sibling. Biology of blood and marrow transplantation Lienert-Weidenbach, K., Valiante, N. M., Brown, C., White, C., Johnston-Dow, L., McGinnis, M., Krausa, P., Lakes, D. M., Wolf, J. L., Blume, K. G., Parham, P. 1997; 3 (5): 255-260


    We describe the case of a patient with chronic myeloid leukemia who rejected a bone marrow (BM) graft from a sibling donor believed to be HLA identical. Sequencing of the HLA genes showed the mother to be heterozygous for two closely related HLA haplotypes that could not be resolved by serological typing. The donor and the recipient had each inherited a different maternal haplotype resulting in allelic mismatches for the HLA-B35 and the HLA-DR11 genes. T cell cytotoxicity directed towards the donor's B35 allele was detected in the patient, in addition to CTL specificity for an HLA-B7-restricted minor histocompatibility antigen carried by the donor, resulting in three histocompatibility mismatches between the BM donor and the recipient.

    View details for PubMedID 9450920

  • Natural killer cells, HLA class I molecules, and marrow transplantation. Biology of blood and marrow transplantation Valiante, N. M., Parham, P. 1997; 3 (5): 229-235

    View details for PubMedID 9450917

  • Filling in the blanks TISSUE ANTIGENS Parham, P. 1997; 50 (4): 318-321

    View details for Web of Science ID A1997XY34500002

    View details for PubMedID 9349612

  • Episodic evolution and turnover of HLA-B in the indigenous human populations of the Americas TISSUE ANTIGENS Parham, P., Arnett, K. L., Adams, E. J., Little, A. M., Tees, K., Barber, L. D., Marsh, S. G., Ohta, T., Markow, T., PETZLERLER, M. L. 1997; 50 (3): 219-232


    Nucleotide sequences were determined for the HLA-A, B and C alleles of three populations of Amerindians: the Havasupai tribe from North America, and the Guarani and Kaingang tribes from South America. All 15 Havasupai alleles are found in Eastern Hemisphere populations, whereas the Guarani and Kaingang each have six alleles that appear to be present only in the Western Hemisphere. Nine of the "new" alleles come from HLA-B, one comes from HLA-A and one from HLA-C: ten appear to be the result of recombination and one the result of point substitution. Of the 14 Guarani alleles and 16 Kaingang alleles, only four are held in common. Despite their differences, the three tribes possess comparable numbers of HLA class I alleles, revealing a trend for "allele turnover", in which new alleles tends to supplant older alleles rather than supplement them. Although many new HLA-B alleles have been produced in Latin America, their net effect has been to differentiate populations, not to increase allele diversity within a population. From sequence comparisons, the Amerindian subset of HLA class I allotypes appears to cover the overall ranges of peptide binding specificity, natural killer-cell interactions, and CD8 interactions, that are found in all HLA class I. The recombinations that produced the new alleles of the Kaingang and Guarani class I are predicted to have modulated these functional properties rather than radically change them. Exchange of Bw4 and Bw6 motifs by recombination are noticeably absent in the events forming new alleles in America, whereas they have been the most common of recombinations elsewhere.

    View details for Web of Science ID A1997XX09000002

    View details for PubMedID 9331945

  • Interactions of HLA-B*4801 with peptide and CD8 TISSUE ANTIGENS MARTINEZNAVES, E., Barber, L. D., Madrigal, J. A., Vullo, C. M., CLAYBERGER, C., Lyu, S. C., Williams, R. C., Gorodezky, C., Markow, T., PETZLERLER, M. L., Parham, P. 1997; 50 (3): 258-264


    Functional properties of the B*4801 allotype were investigated using HLA class I-deficient 221 cells transfected with B*4801 cDNA. From pool sequence analysis of endogenously bound peptides, B*4801 was shown to select for nonamer peptides having glutamine or lysine at position 2 and leucine at the carboxyl-terminus. In an in vitro cell-cell binding assay, B*4801 binds CD8 alpha homodimers weakly due to the presence of a threonine residue at position 245 in the alpha 3 domain. A mutant B*4801 molecule in which alanine replaces threonine 245, binds CD8 alpha homodimers at levels comparable to those of other HLA class I allotypes. Despite the low affinity of B*4801 for CD8 alpha, alloreactive T-cells that recognize B*4801 molecules expressed by the 221 transfectant are inhibited by anti-CD8 monoclonal antibodies. Analysis of 25 B*48-expressing individuals from various populations showed threonine 245 was encoded by every B*48 allele.

    View details for Web of Science ID A1997XX09000005

    View details for PubMedID 9331948

  • A new HLA-B44 variant (B44BO [B*4408]) identified by serology TISSUE ANTIGENS Darke, C., Street, J., FUSSELL, H., Thomas, M., Guttridge, M., Goldberg, T. E., Arnett, K. L., Parham, P. 1997; 50 (1): 32-37


    Using HLA serology, we detected a new variant of HLA-B44- B44BO- in two families. This antigen reacts with B44 antisera and is negative with over one-third of B12 (B44, B45) sera but reacts with 50% antisera with a B62 component, especially if they contain anti-B57. The variant, B*4408, differs from the common B*4402 by 4 nucleotide substitutions in exon 2: 193, 206 and 209, which produce changes in the the alpha 1 domain at positions 41, 45 and 46 (TKE in B*4402 and AMA in B44BO); and nucleotide 213, a silent substitution. At each of these positions, B*4408 is identical to B*46 B*57 and may B*15 alleles. As anticipated from its predicted iso-electric point (5.71), one-dimensional isoelectric focusing studies showed that B44BO focuses at the same position as B*4402. The sequence and serological reactivity of this rare antigen allowed the identification of two likely epitopes shared by two different groups of HLA-B antigens.

    View details for Web of Science ID A1997XJ71000005

    View details for PubMedID 9243752

  • Natural inactivation of a common HLA allele (A*2402) has occurred on at least three separate occasions JOURNAL OF IMMUNOLOGY Magor, K. E., Taylor, E. J., Shen, S. Y., MARTINEZNAVES, E., Valiante, N. M., WELLS, R. S., Gumperz, J. E., Adams, E. J., Little, A. M., Williams, F., Middleton, D., Gao, X. J., McCluskey, J., Parham, P., LienertWeidenbach, K. 1997; 158 (11): 5242-5250


    HLA-A*2402 is common and widely distributed in human populations. Several individuals were identified who type genotypically for A*2402, but are serologically null for the HLA-A24 Ag. Sequencing and transfection of genomic DNA fragments containing null and wild-type A*2402 alleles, and the related A*2301 allele, revealed three different null alleles (A*2409N, A*2411N, and A*2402(low)), each of which differs from A*2402 by a single nucleotide change within the 6.7-kb sequence. The A*2301 and A*2402 sequences differ by no substitutions additional to those previously determined for the 1.1-kb cDNA. In exon 4, A*2409N has an in-frame stop codon, while A*2411N has a nucleotide insertion that alters the reading frame, causing premature termination. A*2402(low) has a nucleotide substitution near the splice acceptor site for intron 2 that impairs the production of correctly spliced mRNA. For A*2409N and A*2411N, mRNA is undetectable by Northern analysis, whereas A*2402(low) produces a low level of mRNA and a concomitant amount of normal A*2402 protein at the cell surface. The protein expressed from the A*2402(low) allele is sufficient to stimulate an alloreactive T cell response. On a background of unexpected sequence homogeneity, the single nucleotide changes in the A*2409N, A*2411, and A*2402(low) alleles have dramatic effects upon gene expression and are of likely importance for HLA matching in clinical transplantation. Segregation of at least three independently inactivated A*2402 alleles in human populations raises the possibility that loss of A*2402 may be the result of natural selection.

    View details for Web of Science ID A1997XA06300026

    View details for PubMedID 9164942

  • Conserved and variable residues within the Bw4 motif of HLA-B make separable contributions to recognition by the NKB1 killer cell-inhibitory receptor JOURNAL OF IMMUNOLOGY Gumperz, J. E., Barber, L. D., Valiante, N. M., Percival, L., Phillips, J. H., Lanier, L. L., Parham, P. 1997; 158 (11): 5237-5241


    Allotypes from four divergent HLA-B families (B8, B15, B16, and B27) were compared for their inhibition of cytolysis by NK cells expressing the NKB1 receptor. Allotypes differing solely at the Bw4/Bw6 region were examined as were a more divergent subset of B15 allotypes. The capacity to interact with NKB1 correlated precisely with possession of a Bw4 sequence motif at residues 77-83, whereas no correlation was made with the peptide-binding specificities of two Bw4 and four Bw6 allotypes of the B15 family. HLA-B allotypes having four different Bw4 motifs were examined and all interact with NKB1. In contrast, HLA-A allotypes, which have a Bw4 motif identical with one of those present in HLA-B, do not. Mutation at leucine 82 and arginine 83, the residues common to Bw4 motifs, shows they contribute to NKB1 interaction but are not essential. Three types of polymorphism are implicated in formation of the ligand recognized by NKB1: ones shared by Bw4 motifs; ones distinguishing Bw4 motifs; and ones outside the Bw4/Bw6 region that distinguish HLA-B from HLA-A.

    View details for Web of Science ID A1997XA06300025

    View details for PubMedID 9164941

  • HLA class I genotyping by cDNA sequence of a Vietnamese family expressing a weak B46 antigen TISSUE ANTIGENS Tzeng, C. M., Percival, L., Barber, L. D., Cooper, S., Adams, E. J., Stewart, D., Parham, P. 1997; 49 (5): 519-522


    Serological heterogeneity in HLA-B46 antigens has been described. Previous studies have identified B*4601 as the allele encoding the "strong" B46 antigen found in Chinese populations. Serological characterization of a Vietnamese family revealed a "weak" B46 antigen. Complementary DNA for the HLA-A, B and C alleles of three family members were cloned and the coding regions sequenced. The allele encoding the weak B46 antigen has the same coding sequence as B*4601, demonstrating that the antigenic differences are not due to polymorphism in the amino acid sequence of the HLA-B heavy chain. The recently described HLA-B*1525 and HLA-Cw*0403 alleles were also found to segregate in this Vietnamese family.

    View details for Web of Science ID A1997WZ50800016

    View details for PubMedID 9174148

  • Nomenclature for factors of the HLA system, 1996 TISSUE ANTIGENS Bodmer, J. G., Marsh, S. G., Albert, E. D., Bodmer, W. F., Bontrop, R. E., Charron, D., DuPont, B., Erlich, H. A., FAUCHET, R., Mach, B., Mayr, W. R., Parham, P., Sasazuki, T., Schreuder, G. M., STROMINGER, J. L., Svejgaard, A., Terasaki, P. I. 1997; 49 (3): 297-321

    View details for Web of Science ID A1997WN30500002

    View details for PubMedID 9098945

  • Events in the adaptation of natural killer cell receptors to MHC class I polymorphisms RESEARCH IN IMMUNOLOGY Parham, P. 1997; 148 (3): 190-194

    View details for Web of Science ID A1997XK65500011

    View details for PubMedID 9255873

  • Putting a hold on 'HLA-H' NATURE GENETICS Bodmer, J. G., Parham, P., Albert, E. D., Marsh, S. G. 1997; 15 (3): 234-235

    View details for Web of Science ID A1997WK38600010

    View details for PubMedID 9054933

  • Polymorphism in the alpha(1) helix of the HLA-B heavy chain can have an overriding influence on peptide-binding specificity JOURNAL OF IMMUNOLOGY Barber, L. D., Percival, L., Arnett, K. L., Gumperz, J. E., Chen, L., Parham, P. 1997; 158 (4): 1660-1669


    Previously, we reported overlap in the repertoires of peptides endogenously bound by a group of HLA-B allotypes related to HLA-B7. Extending such analysis to four members of the B17 family and seven members of the B15 family shows that allotypes that share sequence identity in the alpha 1 helix of the class I heavy chain possess markedly similar peptide-binding specificities. Members of the B17 family share a preference for peptides with serine, threonine, or alanine at position 2 and aromatic residues at the carboxyl terminus. Strikingly, the presence of a segment of the B17 alpha 1 helix in B*1516 and B*1517 confers the B17-like peptide-binding motif. The strong influence of natural variation in the alpha 1 helix is exemplified by the differences in peptide-binding specificity of B15 allotypes related by conversion events that replaced segments of the alpha 1 helix. In contrast, evolutionary changes that are confined to the alpha 2 domain confer less dramatic change. They do not perturb the primary anchors of the peptide-binding motif but can modulate the specificity through development and diversification of secondary anchors. Our results, in combination with those obtained previously for other HLA-B allotypes, suggest a general trend whereby polymorphism in the alpha 1 helix is the overriding influence on peptide-binding specificity of HLA-B allotypes, while amino acid substitutions in the alpha 2 domain play a more modulatory role.

    View details for Web of Science ID A1997WG30400020

    View details for PubMedID 9029102

  • Killer cell receptors: Keeping pace with MHC class I evolution IMMUNOLOGICAL REVIEWS Valiante, N. M., LIENERT, K., Shilling, H. G., Smits, B. J., Parham, P. 1997; 155: 155-164


    NK cells express receptors that bind to polymorphic determinants of MHC class I heavy chains. MHC ligands vary greatly between mammalian species, and the use of distinct molecular families of NK cell receptors by humans and mice suggests that the receptors too can be evolving rapidly. The KIR (killer cell inhibitory receptor) family of receptors are found in primates and recognize class I epitopes that are of relatively recent origin in primate evolution. Therefore, KIR molecules have probably evolved class I receptor function more recently than C-type lectins, which are represented in both humans and mice. Individual humans express NK cell receptors for which they have no class I ligand, demonstrating a looseness in the coupling of expression between the receptors and their ligands. However, study of a single donor suggests that every NK cell expresses at least one inhibitory receptor for a self-HLA class I allotype, consistent with the missing self hypothesis. Thus the NK-cell receptor-class I interaction appears to control the NK-cell repertoire during ontogeny of the individual and has the potential to be a selective factor influencing both MHC class I and NK cell receptor diversity in the evolution of populations and species.

    View details for Web of Science ID A1997WH02900014

    View details for PubMedID 9059891

  • Assignment of TCF1, TGM1, CALM1, CKB, THBS1, B2M, and FES in Ateles paniscus chamek (Platyrrhini, Primates) CYTOGENETICS AND CELL GENETICS Moreira, M. A., CANAVEZ, F., Parham, P., Seuanez, H. N. 1997; 79 (1-2): 92-96


    Regional assignment of five markers to chromosome 2 of Ateles paniscus chamek (APC) confirmed a syntenic association similar to human (HSA) 12q + 14q + 15q. TCF1 was allocated to a shortest region of overlap (SRO) in APC 2p and found to be syntenic to PEPB, while TGM1, CALM1, THBS1, and B2M were assigned to APC 2q, being syntenic to NP, HEXA, and MPI. Conversely, markers close to HSA 14qter (CKB) and HSA 15qter (FES-IDH2) were relocated to other Ateles syntenic groups. Karyotypic comparisons showed an evident homoeology between APC 2p and HSA 12q, whereas APC 2q was similar to an HSA 14qter::HSA 15qter fusion product.

    View details for Web of Science ID 000072562300073

    View details for PubMedID 9533020

  • Cw*1701 defines a divergent African HLA-C allelic lineage IMMUNOGENETICS WELLS, R. S., Seielstad, M. T., Bunce, M., Tyan, D. B., Bekele, E., Parham, P. 1997; 46 (3): 173-180


    The complete sequence of a new HLA-C allele, Cw*1701, was determined from a South African Zulu individual. Unique features that distinguish Cw*1701 from other HLA-C alleles include multiple point substitutions and an 18 nucleotide insertion in exon 5, which encodes the transmembrane domain. In a phylogenetic analysis of HLA-C sequences, Cw*1701 forms a third, distinct allelic lineage. A comparison of the transmembrane domain of Cw*1701 with other HLA-B and -C alleles reveals that duplications and deletions have been common in the evolution of these loci. A polymerase chain reaction based typing method was used to determine the distribution of this unusual allele in human populations. In contrast to the other two lineages of HLA-C alleles, the Cw*17 lineage is found at high frequencies only in populations of African descent. In addition, the HLA-B/Cw*17 haplotype diversity is higher in Africa.

    View details for Web of Science ID A1997XL60100001

    View details for PubMedID 9211742

  • Presentation of HLA class I-derived peptides: Potential involvement in allorecognition and HLA-B27-associated arthritis IMMUNOLOGICAL REVIEWS Parham, P. 1996; 154: 137-154


    Some 25 years ago, when purified HLA class I allotypes were first being analyzed, of major concern was that the papain used for solubilization might produce a mess of proteolytic fragments that would prove impossible to separate and sequence. Those fears proved unfounded (Parham et al. 1975), and the homogeneity of the preparations was sufficient to allow crystallization and determination of the three-dimensional structure (Bjorkman et al. 1987). Ironically the least ordered region of the electron density map provoked the most interest because it gave a first view of the diverse peptides bound by an MHC molecule. With this image a second chapter of HLA class I biochemistry began, its charge to determine the structures of bound peptides and their influence on the immune system. The extraordinary polymorphism of HLA class I heavy chains now seems quite manageable compared to the vast complexity of the peptides, and our present ignorance as to which ones are important for health and disease. The comparative weakness of most HLA class I associations with disease has made HLA-B27 an especially favored target for investigation, and more is known of the structure and peptide-presenting function of HLA-B27 than for any other HLA-B allotype (López de Castro 1994). Much of this information relates to the native HLA-B27 molecule and has been collected in the belief that disease is a direct consequence of its antigen-presenting function. If one subscribes to the relevance of the transgenic rodent models, this position has almost become untenable. For rats and mice 'non-functional' forms of HLA-B27 are the agents of disease, raising the possibility that B27-associated arthritis is induced by HLA class II presentation of a B27-derived peptide, a variant of the mechanism advanced for the classical HLA class II-associated diseases: type 1 diabetes, multiple sclerosis and rheumatoid arthritis (Gregersen et al. 1987, Roudier et al. 1989, Cucca & Todd 1996, Hall & Bowness 1996). Such speculation invites the obvious question as to whether other diseases associated with HLA class I and chronic inflammation, HLA-C and psoriasis for example (Tiilikainen et al. 1980, Yanagisawa et al. 1995), result from class II presentation of class I peptides.

    View details for Web of Science ID A1996WE14800006

    View details for PubMedID 9034866

  • Killer cell inhibitory receptor recognition of human leukocyte antigen (HLA) class I blocks formation of a pp36/PLC-gamma signaling complex in human natural killer (NK) cells JOURNAL OF EXPERIMENTAL MEDICINE Valiante, N. M., Phillips, J. H., Lanier, L. L., Parham, P. 1996; 184 (6): 2243-2250


    The killer cell inhibitory receptors (KIR) of human natural killer (NK) cells recognize human leukocyte antigen class I molecules and inhibit NK cell cytotoxicity through their interaction with protein tyrosine phosphatases (PTP). Here, we report that KIR recognition of class I ligands inhibits distal signaling events and ultimately NK cell cytotoxicity by blocking the association of an adaptor protein (pp36) with phospholipase C-gamma in NK cells. In addition, we demonstrate that pp36 can serve as a substrate in vitro for the KIR-associated PTP, PTP-1C (also called SHP-1), and that recognition of class I partially disrupts tyrosine phosphorylation of NK cell proteins, providing evidence for KIR-induced phosphatase activity.

    View details for Web of Science ID A1996VZ41300017

    View details for PubMedID 8976179

  • Pictures of MHC restriction NATURE Parham, P. 1996; 384 (6605): 109-110

    View details for Web of Science ID A1996VT33600031

    View details for PubMedID 8906779

  • A novel recombinant HLA-B*39 allele (B*3910) in a South African Zulu TISSUE ANTIGENS WELLS, R. S., Parham, P. 1996; 48 (5): 595-597


    The sequence of a new B*39 allele has been identified in a South African Zulu individual. This allele designated B*3910, differs at two nucleotide positions (246 and 272) from B*39011. The difference at position 246 is silent, while that at position 272 results in an amino acid change from cysteine (B*39011) to tyrosine (B*3910). As these same differences are found in other HLA-B alleles, they were probably introduced into the B*3910 sequence by a short gene conversion event with another allele. This finding provides further evidence for the diversification of HLA-B allelic sequences via recombination.

    View details for Web of Science ID A1996VY74300013

    View details for PubMedID 8988545

  • Functions for MHC class I carbohydrates inside and outside the cell TRENDS IN BIOCHEMICAL SCIENCES Parham, P. 1996; 21 (11): 427-433


    Major histocompatibility complex (MHC) class I heavy chain glycoproteins have an invariant N-linked glycosylation site at Asn86, which is found between two extremely variable protein domains. For human MHC class I molecules, Asn is the only site of glycosylation and the attached oligosaccharides are remarkably uniform. The carbohydrate initiates interactions with calnexin in the endoplasmic reticulum that facilitate the assembly of MHC class I molecules and their delivery to the cell surface. However, recognition of MHC class I molecules by antibodies and T cells is indifferent to the carbohydrate, although lines of circumstantial evidence implicate lectins and carbohydrates in the recognition of MHC class I glycoproteins by natural killer cells.

    View details for Web of Science ID A1996VV78600006

    View details for PubMedID 8987398

  • Specificity of two anti-class I HLA monoclonal antibodies that block class I recognition by the NKB1 killer cell inhibitory receptor TISSUE ANTIGENS Gumperz, J. E., Paterson, J. C., Litwin, V., VALIANTE, N., Lanier, L. L., Parham, P., Little, A. M. 1996; 48 (4-I): 278-284


    Cytolysis by NK cells that possess the NKB1 killer cell inhibitory receptor is inhibited by target cell expression of Bw4+ HLA-B molecules. The inhibitory effect can be prevented by addition of mAbs which block recognition of class I molecules by NKB1. The epitopes recognized by two anti-class I mAbs, DX15 and DX16, which inhibit the interaction of NKB1 with class I have been characterized. Binding of DX15 and DX16 to class I allotypes was investigated by flow cytometric analysis of transfected cell lines which express just one HLA-A, B, or C allele, and by immunoprecipitation of class I molecules from HLA typed B-lymphoblastoid cell lines, followed by isoelectric focusing. The DX16 mAb recognizes class I allotypes which possess alanine at position 71 of the alpha 1 helix, and therefore has a specificity resembling that of the ME1 mAb but with broader specificity. Class I recognition by DX15 is affected by polymorphisms of the C-terminal part of the alpha 1 helix, and the N-terminal part of the alpha 2 helix. DX15 thus appears to recognize a complex epitope near the end of the peptide binding groove which may be conformationally determined. Both antibodies are as effective as the anti-NKB1 mAb (DX9) in preventing class I recognition by the NKB1 receptor. DX16 also blocked recognition by a B*0702 allospecific CTL clone, whereas DX15 did not.

    View details for Web of Science ID A1996VR92800006

  • Peptides bound endogenously by HLA-Cw*0304 expressed in LCL 721.221 cells include a peptide derived from HLA-E TISSUE ANTIGENS Tzeng, C. M., Adams, E. J., Gumperz, J. E., Percival, L., WELLS, R. S., Parham, P., Barber, L. D. 1996; 48 (4-I): 325-328


    The peptide-binding specificity of HLA-Cw*0304 was determined. Sequence analysis of endogenously-bound peptides isolated from Cw*0304 expressed by LCL 721.221 (221 for short) cells transfected with Cw*0304 cDNA revealed this class I allotype preferentially binds peptides possessing alanine at position 2 and leucine or methionine at the C-terminus. One peptide isolated from Cw*0304 expressed by 221 cells has sequence identity to residues 116-126 of HLA-E. Expression of HLA-E by 221 cells was confirmed by isolation of mRNA transcripts for HLA-E*0101 and detection of beta 2-microglobulin (beta 2-m)-associated HLA-E protein.

    View details for Web of Science ID A1996VR92800012

  • Response: peopling the americas. Science Parham, P. 1996; 273 (5276): 724-725

    View details for PubMedID 17769682

  • The inter-locus recombinant HLA-B*4601 has high selectivity in peptide binding and functions characteristic of HLA-C JOURNAL OF EXPERIMENTAL MEDICINE Barber, L. D., Percival, L., Valiante, N. M., Chen, L., Lee, C., Gumperz, J. E., Phillips, J. H., Lanier, L. L., BIGGE, J. C., Parekh, R. B., Parham, P. 1996; 184 (2): 735-740


    The vast majority of new human HLA class I alleles are formed by conversions between existing alleles of the same locus. A notable exception to this rule is HLA-B*4601 formed by replacement of residues 66-76 of the alpha 1 helix of B*1501 by the homologous segment of Cw*0102. This inter-locus recombination, which brings together characteristic elements of HLA-B and HLA-C structure, is shown here to influence function dramatically. Naturally processed peptides bound by B*4601 are distinct from those of its parental allotypes B*1501 and Cw*0102 and dominated by three high abundance peptides. Such increased peptide selectivity by B*4601 is unique among HLA-A,B,C allotypes. For other aspects of function, presence of the small segment of HLA-C-derived sequence in an otherwise HLA-B framework converts B*4601 to an HLA-C-like molecule. Alloreactive cytotoxic T lymphocytes (CTL), natural killer (NK) cells, and cellular glycosidases all recognize B*4601 as though it were an HLA-C allotype. These unusual properties are those of an allotype which has frequencies as high as 20% in south east Asian populations and is associated with predisposition to autoimmune diseases and nasopharyngeal carcinoma.

    View details for Web of Science ID A1996VC33700045

    View details for PubMedID 8760827

  • CD94 and a novel associated protein (94AP) form a NK cell receptor involved in the recognition of HLA-A, HLA-B, and HLA-C allotypes IMMUNITY Phillips, J. H., Chang, C. W., Mattson, J., Gumperz, J. E., Parham, P., Lanier, L. L. 1996; 5 (2): 163-172


    Whereas the human killer cell inhibitory receptors (KIRs) for HLA class I are immunoglobulin-like monomeric type I glycoproteins, the murine Ly49 receptors for H-2 are type II homodimers of the C-type lectin superfamily. Here, we demonstrate that human NK cells also express C-type lectin receptors that influence recognition of polymorphic HLA-A, HLA-B, and HLA-C molecules. These receptors are heterodimers composed of CD94 chains covalently associated with novel tyrosine-phosphorylated glycoproteins (94AP). Some NK clones recognize a common HLA-C ligand using both KIRs and CD94-94AP receptors. These findings suggest the existence of human inhibitory MHC class I receptors of the immunoglobulin and C-type lectin superfamilies and indicate overlap in ligand specificity.

    View details for Web of Science ID A1996VE58900006

    View details for PubMedID 8769479

  • HLA-C typing of eleven Papua New Guineans: Identification of an HLA-Cw4/Cw2 hybrid allele TISSUE ANTIGENS Little, A. M., Mason, A., Marsh, S. G., Parham, P. 1996; 48 (2): 113-117


    HLA-C polymorphism of 11 individuals from Papua New Guinea was studied by serology and DNA typing (SSP ARMS-PCR). To resolve certain discrepancies HLA-C alleles were cloned and sequenced. Five alleles were identified by sequencing, four of which; Cw*0304, Cw*0401, Cw*12022 and Cw*1502 have been identified previously in other populations. The fifth allele, which was found in four individuals is a novel HLA-C allele. The new allele, called HLA-Cw*0403 is most similar to HLA-Cw*0401, differing by 10 nucleotides, 9 of which are located in the region from nucleotide 98 to 218. This region of Cw*0403 is identical to both HLA-Cw*0201 and Cw*02022. The 9 nucleotide differences between Cw*0401 and Cw*0403 result in 6 amino acid differences in the alpha 1 domain. These amino acids in Cw*0403 may contribute to the serological typing of some, but not all Cw*0403 expressing cells. The Final difference between Cw*0401 and Cw*0403 is a coding substitution at nucleotide 979 in exon 5. The guanine found in Cw*0403 is identical to all HLA-C alleles except HLA-Cw*0401, which has an adenine. The Cw*0403 allele was most likely formed by a gene conversion event between Cw*02 and Cw*04, involving a minimum of 121 to a maximum of 215 nucleotides.

    View details for Web of Science ID A1996VG06500006

    View details for PubMedID 8883300

  • Evolution of MHC class I genes in higher primates IMMUNOLOGY AND CELL BIOLOGY LIENERT, K., Parham, P. 1996; 74 (4): 349-356


    The classical major histocompatibility complex (MHC) class I genes are conserved in higher primates. Motifs common to human, chimpanzee and gorilla alleles indicate that class I alleles diverged from ancestral sequences that existed before separation of these species. Analysis of native human populations such as Australian Aborigines and Amerindians shows that HLA-B is characterized by rapid generation of new alleles. HLA-A and -C appear to be evolving more slowly. Comparison of alleles for orthologous class I genes in humans and other primates confirms that similar mechanisms contribute to the generation of new alleles in these species.

    View details for Web of Science ID A1996VD31300009

    View details for PubMedID 8872186

  • Immunology: Keeping mother at bay CURRENT BIOLOGY Parham, P. 1996; 6 (6): 638-641


    Like its better-known polymorphic relatives, HLA-G, a relatively unpolymorphic class I MHC molecule expressed by fostal trophoblast cells, binds short peptides with a defined sequence motif; HLA-G may play an important role in maternal tolerance to a fostus.

    View details for Web of Science ID A1996UR92800011

    View details for PubMedID 8793281

  • Characterization of the peptide-binding specificity of HLA-B*7301 TISSUE ANTIGENS Barber, L. D., Percival, L., Parham, P. 1996; 47 (6): 472-477


    Previous studies showed the human MHC class I heavy chain HLA-B*7301 has a sequence very divergent from other class I alleles. Despite the unusual sequence, we predicted B*7301 would retain the peptide-binding function typical of other HLA-A, B and C glycoproteins, and sequence similarity to B*2705 in a region of the peptide-binding site known as the B pocket suggested B*7301 would bind peptides with Arg at position 2. To test this hypothesis, the peptide-binding specificity of B*7301 was investigated. Sequence analysis of peptides bound endogenously by B*7301 indeed found selectivity for nonamer peptides possessing Arg at position 2 and a preference for small nonpolar residues such as Pro or Ala at the C terminus was also revealed. B*7301 therefore possesses the potential to function as a conventional antigen presenting class I glycoprotein. Functional similarities between B*7301 and B*2705 are discussed in the context of the association of B*27 subtypes with susceptibility to ankylosing sponylitis and arthritic diseases.

    View details for Web of Science ID A1996UT07300004

    View details for PubMedID 8813735

  • HLA-A*2607: Sequence of a novel A*26 subtype predicted by DNA typing which shares the MA2.1 epitope with A*02, B*57 and B*58 TISSUE ANTIGENS Arnett, K. L., Moses, J. H., Williams, F., Marsh, S. G., Bodmer, J. G., Parham, P., Middleton, D. 1996; 47 (5): 422-425

    View details for Web of Science ID A1996UQ08100009

    View details for PubMedID 8795143

  • The presence of HLA-A*2403 and HLA-B*1512 on the same haplotype in a Thai family TISSUE ANTIGENS Chandanayingyong, D., Adams, E. J., Arnett, K. L., Hildebrand, W. H., Parham, P., Lau, M. 1996; 47 (5): 426-427

    View details for Web of Science ID A1996UQ08100010

    View details for PubMedID 8795144

  • Unusual uniformity of the N-linked oligosaccharides of HLA-A, -B, and -C glycoproteins JOURNAL OF IMMUNOLOGY Barber, L. D., Patel, T. P., Percival, L., Gumperz, J. E., Lanier, L. L., Phillips, J. H., BIGGE, J. C., Wormald, M. R., Parekh, R. B., Parham, P. 1996; 156 (9): 3275-3284


    MHC class I glycoproteins possess an invariant site for N-linked oligosaccharide addition at position 86 of the heavy chain. For human HLA-A, -B, and -C class I glycoproteins, position 86 is the only site of N-linked glycosylation. Comparison of the size and relative abundance of oligosaccharides associated with nine HLA-A, -B, or -C allotypes isolated from EBV-transformed B cell lines and mixtures of HLA-A, -B, and -C allotypes isolated from pooled PBLs revealed a very restricted set of structures. Allotypes encoded by the HLA-A and -B loci have two predominant glycan structures that were almost exclusively di-sialylated. In contrast, HLA-C allotypes have four glycan structures, comprising those associated with HLA-A and -B and two additional glycans. Identical oligosaccharides were present on different allotypes of a class I HLA locus, and in particular, HLA-C allotypes defining two inhibitory specificities for NK cells were shown to possess the same set of oligosaccharides. The uniformity of oligosaccharide structure associated with different HLA-A, -B, and -C products and the relative lack of heterogeneity for any given allotype are unusual features for a mammalian glycoprotein. Particularly striking is that such conserved oligosaccharide structures juxtapose the major regions of amino acid sequence variation within the Ag recognition site, including the polymorphisms of the alpha 1 helix that determine the inhibitory ligands for human NK cells.

    View details for Web of Science ID A1996UF74200024

    View details for PubMedID 8617950

  • On the sequence of A*3101 TISSUE ANTIGENS Arnett, K. L., Adams, E. J., Parham, P. 1996; 47 (5): 428-430

    View details for Web of Science ID A1996UQ08100011

    View details for PubMedID 8795145

  • Population biology of antigen presentation by MHC class I molecules SCIENCE Parham, P., Ohta, T. 1996; 272 (5258): 67-74


    In principle, the function of major histocompatibility complex (MHC) molecules is simple: to bind a peptide and engage a T cell. In practice, placing this function within the context of the immune response begs questions of population biology; How does the immune response emerge from the interactions among populations of peptides, T cells and MHC molecules? Within a population of vertebrates, how does MHC polymorphism stamp individuality on the response? Does polymorphism confer differential advantages in responding to parasites? How are the pressures on the MHC reflected in turnover of alleles? The role of mutation, recombination, selection, and drift in the generation and maintenance of MHC class 1 polymorphism are considered.

    View details for Web of Science ID A1996UD59700038

    View details for PubMedID 8600539

  • Unexpected beta(2)-microglobulin sequence diversity in individual rainbow trout PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Shum, B. P., Azumi, K., Zhang, S. W., Kehrer, S. R., Raison, R. L., Detrich, H. W., Parham, P. 1996; 93 (7): 2779-2784


    For mammals beta2-microglobulin (beta2m), the light chain of major histocompatibility complex (MHC) class I molecules, is invariant (or highly conserved) and is encoded by a single gene unlinked to the MHC. We find that beta2m of a salmonid fish, the rainbow trout (Oncorhynchus mykiss), does not conform to the mammalian paradigm. Ten of 12 randomly selected beta2m cDNA clones from an individual fish have different nucleotide sequences. A complex restriction fragment length polymorphism pattern is observed with rainbow trout, suggesting multiple beta2m genes in the genome, in excess of the two genes expected from the ancestral salmonid tetraploidy. Additional duplication and diversification of the beta2m genes might have occurred subsequently. Variation in the beta2m cDNA sequences is mainly at sites that do not perturb the structure of the mature beta2m protein, showing that the observed diversity of the trout beta2m genes is not primarily a result of pathogen selection.

    View details for Web of Science ID A1996UD37500030

    View details for PubMedID 8610117

  • Patr-A and B, the orthologues of HLA-A and b, present hepatitis C virus epitopes to CD8(+) cytotoxic T cells from two chronically infected chimpanzees JOURNAL OF EXPERIMENTAL MEDICINE Kowalski, H., Erickson, A. L., Cooper, S., DOMENA, J. D., Parham, P., Walker, C. M. 1996; 183 (4): 1761-1775


    Common chimpanzees (Pan troglodytes) infected with hepatitis C virus (HCV) show a disease progression similar to that observed for human patients. Although most infected animals develop a chronic hepatitis, virus persistence is associated with an ongoing immune response, for which the beneficial or detrimental effects are uncertain. Lines of virus-specific cytotoxic CD8+ T lymphocytes (CTL) have been previously established from liver biopsies of two common chimpanzees chronically infected with HCV-1. The viral epitopes recognized by six lines of CTL have been defined using synthetic peptides and shown to consist of 8 to 9-residue peptides derived from various viral proteins. Five of the epitopes derive from sequences that vary among strains of HCV. The majority of the corresponding variant epitopes from different HCV strains were either recognized less efficiently or not at all by the CTL, suggesting their response may have limited potential for controlling replication of HCV variants. Complementary DNAs encoding class I alleles of the two common chimpanzees, Patr-A, -B, and -C were cloned, sequenced, and transfected individually into a class I-deficient human cell line. Analysis of peptide presentation by the class I transfectants to CTL identified the Patr class I allotypes that present the six epitopes defined here and an additional epitope defined previously. The assignment of epitopes to class I allotypes based upon analysis of the transfected cells correlates precisely with the segregation of antigen-presenting function within a panel of common chimpanzee cell lines and the expression of class I heavy chains as defined by isoelectric focusing. Five of the HCV-1 epitopes are presented by Patr-B allotypes, two epitopes are presented by a Patr-A allotype, and none is presented by Patr-C allotypes.

    View details for Web of Science ID A1996UH14400049

    View details for PubMedID 8666933

  • Heterogeneous phenotypes of expression of the NKB1 natural killer cell class I receptor among individuals of different human histocompatibility leukocyte antigens types appear genetically regulated, but not linked to major histocompatibility complex haplotype JOURNAL OF EXPERIMENTAL MEDICINE Gumperz, J. E., Valiante, N. M., Parham, P., Lanier, L. L., Tyan, D. 1996; 183 (4): 1817-1827


    Natural killer (NK) cells that express the NKB1 receptor are inhibited from killing target cells that possess human histocompatibility leukocyte antigen (HLA) B molecules bearing the Bw4 serological epitope. To investigate whether NKB1 expression is affected by HLA type, peripheral blood lymphocytes of 203 HLA-typed donors were examined. Most donors had a single population of NKB1+ cells, but some had two populations expressing different cell surface levels of NKB1, and others had no detectable NKB1+ cells. Among the donors expressing NKB1, both the relative abundance of NKB1+ NK cells and their level of cell surface expression varied substantially. The percentage of NKB1+ NK cells ranged from 0 to >75% (mean 14.7%), and the mean fluorescence of the positive population varied over three orders of magnitude. For each donor, the small percentage of T cells expressing NKB1 (usually <2%), had a pattern of expression mirroring that of the NK cells. NKB1 expression by NK and T cells remained stable over the 2-yr period that five donors were tested. Patterns of NKB1 expression were not associated with Bw4 or Bw6 serotype of the donor or with the presence of any individual HLA-A or -B antigens. Cells expressing NKB1 are often found in donors who do not possess an appropriate class I ligand, and can be absent in those who express Bw4+ HLA-B antigens. Family studies further suggested that the phenotype of NKB1 expression is inherited but not HLA linked. Whereas identical twins show matching patterns of NKB1 expression, HLA-identical siblings can differ in NKB1 expression, and conversely, HLA-disparate siblings can be similar. Thus NKB1 expression phenotypes are tightly regulated and extremely heterogeneous, but not correlated with HLA type.

    View details for Web of Science ID A1996UH14400054

    View details for PubMedID 8666938

  • The presentation of a hepatitis C viral peptide by distinct major histocompatibility complex class I allotypes from two chimpanzee species JOURNAL OF EXPERIMENTAL MEDICINE Cooper, S., Kowalski, H., Erickson, A. L., Arnett, K., Little, A. M., Walker, C. M., Parham, P. 1996; 183 (2): 663-668


    A cytotoxic T lymphocyte (CTL) line, derived from the liver of a common chimpanzee (Pan troglodytes) with hepatitis C, specifically recognized a hepatitis C viral 9-mer peptide (KHP-DATYSR in single-letter amino acid code) bound by the major histocompatibility complex (MHC) class I molecule, Patr-A04. This same CTL line also recognized the identical peptide bound by a structurally different class I molecule, Papa-A06, derived from the separate chimpanzee species, Pan paniscus or pygmy chimpanzee. These class I allotypes differ by six amino acids but, in spite of the structural differences, share the same antigen-presenting function. This is the first observation of antigen presentation to a given T cell receptor by different MHC class I allotypes from separate species.

    View details for Web of Science ID A1996TW10900033

    View details for PubMedID 8627179

  • NK cells and CTL: Opposite sides of the same coin MOLECULAR BASIS OF NK CELL RECOGNITION AND FUNCTION Valiante, N. M., Parham, P. 1996; 64: 146-163

    View details for Web of Science ID A1996BG58U00011

    View details for PubMedID 8942078

  • B27 polymorphism and peptide repertoire Parham, P. SPRINGER. 1996: 72-73


    Over 130 HLA-B alleles have been defined at the level of nucleotide sequence. Nine of these are subtypes of HLA-B27. To understand how HLA-B27 predisposes towards arthritis it is important to determine which B27 subtypes are associated with disease susceptibility and which are not. A characteristic of HLAB27 is the binding of peptides having arginine at position 2. However, HLA-B*7301, a rare and unusual allele of European populations, has an identical "B" subpocket to B*27 and also binds peptides with arginine at position 2. The association of the Bw4 public epitope with inhibition of certain NK cells raises the possibility that NK cell responses may contribute to HLA-B27-associated disease.

    View details for Web of Science ID A1996TV35800016

    View details for PubMedID 8835508

  • THE ENIGMA OF THE NATURAL-KILLER-CELL NATURE Gumperz, J. E., Parham, P. 1995; 378 (6554): 245-248


    Natural killer (NK) cells are controlled by receptors specific for polymorphic determinants of class I molecules of the major histocompatibility complex (MHC). The contrasting properties of NK and cytotoxic T cell (CTL) class I receptors provide complementarity in the cytolytic lymphocyte response to viruses, tumours and transplants. Whereas human NK cell class I receptors consist of immunoglobulin domains, their mouse counterparts resemble C-type lectins. This difference may reflect the receptors' diverse and rapidly evolving class I ligands.

    View details for Web of Science ID A1995TE85800038

    View details for PubMedID 7477341

  • Three new HLA-B alleles found in Mexican-Americans TISSUE ANTIGENS Adams, E. J., Little, A. M., Arnett, K. L., MCAULEY, J. E., Williams, R. C., Parham, P. 1995; 46 (5): 414-416

    View details for Web of Science ID A1995TK99900014

    View details for PubMedID 8838356

  • HOMOGENEITY OF ALLELIC SEQUENCE FOR SEROLOGICAL VARIANTS OF HLA-B53 TISSUE ANTIGENS Adams, E. J., Scott, I., Shah, A., Arnett, K. L., Marsh, S. G., Madrigal, J. A., Parham, P. 1995; 46 (4): 330-332

    View details for Web of Science ID A1995RZ63900009

    View details for PubMedID 8560454

  • EXPRESSION OF AN UNUSUAL BW4 EPITOPE BY A SUBTYPE OF HLA-B8 [B-ASTERISK-0802] TISSUE ANTIGENS Arnett, K. L., Adams, E. J., Gumperz, J. E., Darke, C., Marsh, S. G., Gelsthorpe, K., Parham, P. 1995; 46 (4): 316-321


    The primary structure of a variant HLA-B8 antigen has been determined by cDNA cloning and sequencing. The variant, B*0802 differs, from the common B*0801 subtype at positions 77-83 of the alpha 1 helix that determine the Bw4 and Bw6 public epitopes. Whereas B*0801 has the common Bw6 motif, B*0802 has the Bw4 motif found in B*13 and B*44 allotypes. Serological analysis of B cell lines expressing B*0802 and of a B*0802 transfectant made with the HLA-A,B negative cell line 721.221 shows that B*0802 reacts with Bw4-specific antibodies, but at a level much lower than expected for Bw4 positive HLA-B allotypes.

    View details for Web of Science ID A1995RZ63900006

    View details for PubMedID 8560451

  • HLA class I nucleotide sequences, 1995. Tissue antigens Arnett, K. L., Parham, P. 1995; 46 (3 ): 217-257

    View details for PubMedID 8525484

  • Identification of a novel HLA-B40 allele (B*4008) in a patient with leukemia. Tissue antigens Adams, E. J., Little, A. M., Arnett, K. L., Leushner, J., Parham, P. 1995; 46 (3 ): 204-205

    View details for PubMedID 8525480



    Natural killer (NK) cells have been shown to express a clonally distributed ability to recognize HLA class I alleles. The previously defined NK clones belonging to "group 1" recognize HLA-C*0401 (Cw4) and other HLA-C alleles sharing Asn at position 77 and Lys at position 80. Conversely, the "group 2" NK clones recognize HLA-Cw*0302 (Cw3) and other HLA-C alleles characterized by Ser at position 77 and Asn at position 80. We assessed directly the involvement of these two residues in the capacity of NK cell clones to discriminate between the two groups of HLA-C alleles. To this end, Cw3 and Cw4 alleles were subjected to site-directed mutagenesis. Substitution of the amino acids typical of the Cw3 allele (Ser-77 and Asn-80) with those present in Cw4 (Asn-77 and Lys-80) resulted in a Cw3 mutant that was no longer recognized by group 2 NK cell clones, but that was recognized by group 1 clones. Analysis of Cw3 or Cw4 molecules containing single amino acid substitutions indicates roles for Lys-80 in recognition mediated by group 1 clones and for Ser-77 in recognition mediated by group 2 clones. These results demonstrate that NK-mediated specific recognition of HLA-C allotypes is affected by single natural amino acid substitutions at positions 77 and 80 of the heavy chain.

    View details for Web of Science ID A1995RL09800038

    View details for PubMedID 7629517

  • ON THE NUCLEOTIDE-SEQUENCES OF B-ASTERISK-2702 AND B-ASTERISK-2705 TISSUE ANTIGENS Moses, J. H., Marsh, S. G., Arnett, K. L., Adams, E. J., Bodmer, J. G., Parham, P. 1995; 46 (1): 50-53

    View details for Web of Science ID A1995RE88900006

    View details for PubMedID 7482496


    View details for Web of Science ID A1995RK52700002

    View details for PubMedID 7576126



    A study of the nurse shark has revealed a type of rearranging gene that has yet to be seen in mammals; it encodes a secreted 'new antigen receptor' which, unlike shark immunoglobulin, revels in somatic hypermutation.

    View details for Web of Science ID A1995RL95300001

    View details for PubMedID 7583106



    In comparison with HLA-A and -B, the protein products of the HLA-C locus are poorly characterized, in part because of their low level of expression at the cell surface. Here, we examine how protein-protein interactions during assembly and regulation of the mRNA level affect cell surface expression of HLA-C. We find that intrinsic properties of the HLA-C heavy chain proteins do not correlate with low cell surface expression: HLA-C heavy chains associate and dissociate with beta 2-microglobulin (beta 2m) at rates comparable to those found for HLA-A and -B, and increased competition for beta 2m does not alter the surface expression of HLA-C. From studies of chimeric genes spliced from the HLA-B7 and -Cw3 genes, we find that chimeric proteins containing the B7 peptide-binding groove can have low cell surface expression, suggesting that inefficiency in binding peptides is not the cause of low cell surface expression for HLA-C. The surface levels of HLA-A, -B, or -C in cells transfected with cDNA can be similar, implicating noncoding regions of HLA-C heavy chain genes in the regulation of surface expression. We find that HLA-C mRNA is expressed at lower levels than HLA-B mRNA and that this difference results from faster degradation of the HLA-C message. Experiments examining chimeric B7/Cw3 and B7/Cw6 genes suggest that a region determining low expression of HLA-C is to be found between the 3' end of exon 3 and a site in the 3' untranslated region, approximately 600 bases downstream of the translation stop codon.

    View details for Web of Science ID A1995RA60500017

    View details for PubMedID 7760000



    A rabbit antiserum "ABR2" was raised against a peptide with sequence identity to 10 amino acids of the cytoplasmic tail of HLA class I heavy chains. Western blotting and immunoprecipitation analyses demonstrate that ABR2 reacts with HLA class I heavy chains. The antiserum reacts poorly with beta 2-microglobulin (beta 2-m)-associated heavy chains and reacts strongly with free heavy chains. ABR2 reacts with immature heavy chains from the endoplasmic reticulum that have yet to bind beta 2-m and mature heavy chains that have dissociated from beta 2-m at the plasma membrane. Comparison with HC10, a mAb that recognizes an epitope defined by polymorphism at residue 62 of the alpha 1 helix of free HLA class I heavy chains, shows that ABR2 reacts with overlapping populations of free heavy chains (for those allotypes that react with both Abs), but it also identifies populations that bind to one Ab and not the other. ABR2 induces dissociation of beta 2-m from HLA-B38 molecules expressed by the human B cell line "TEM," a phenomenon not detected with other allotypes or with the same allotype in a different cell line. This study shows that association of beta 2-m with the extracellular domains of HLA class I heavy chains can cause a change in the cytoplasmic tail that prevents binding of Abs present in the ABR2 antiserum. Similar findings have been made for mouse H-2 class I molecules, which suggests that this is a general property of class I MHC molecules.

    View details for Web of Science ID A1995QW90100033

    View details for PubMedID 7537301



    During screening of potential bone marrow donors, a previously undescribed banding position for the serologically defined HLA-B7 antigen was identified in three unrelated families using one dimensional isoelectric focusing and class I specific Western blot analysis. The isoelectric point of the new variant is more acidic than the two HLA-B7 variants that had been defined before. In each family the new B7 variant was found linked to HLA-A2 and -Cw7. Cloning and sequencing of full-length clones of complementary DNA showed that the new allele (B*0704) differs from B*0702, the common allele encoding HLA-B7, by three nucleotide substitutions within the codon for residue 156 of the mature heavy chain. As a result of these differences amino acid 156 is changed from arginine to aspartic acid, a difference consistent with the isoelectric points. The group of three nucleotide substitutions that distinguish B*0704 from B*0702 is present in other HLA-B alleles.

    View details for Web of Science ID A1995QZ01000005

    View details for PubMedID 7652739



    Bacterial superantigens bind with high affinity to major histocompatibility complex (MHC) class II antigens on antigen-presenting cells and with T cell antigen receptor (TCR) beta chains on T lymphocytes, which results in the T cell activation responsible for toxic shock syndrome and food poisoning. Many cytotoxic T lymphocyte (CTL) clones were shown to have receptors for human leukocyte antigen (HLA) class I molecules that inhibited superantigen-induced cytotoxicity against appropriate class I-bearing target cells. One type of inhibitory receptor, NKB1, was present on CD4+ and CD8+TCR alpha beta+ CTL clones and blocked the killing of staphylococcal enterotoxin B (SEB)-coated targets bearing certain polymorphic HLA-B molecules. Expression of HLA-A, -B, and -C molecules on the SEB-coated targets also protected against cytolysis mediated by many NKB1-negative T cell clones, suggesting the presence of additional inhibitory MHC class I receptors. These HLA class I receptors may limit tissue destruction and possibly autoimmunity caused by activated T lymphocytes.

    View details for Web of Science ID A1995QU57200035

    View details for PubMedID 7716542



    NK cells lyse hematopoietic cells that lack expression of MHC class I molecules on the cell surface. Transfection of certain MHC class I negative cell lines with MHC class I genes renders these cells resistant to NK cell-mediated cytotoxicity. Recently, we described an NK cell receptor, NKB1, that inhibits NK cells from killing target cells expressing Bw4-reactive HLA-B molecules (-B*2705, -B*5101, -B*5801). In this study, we have demonstrated that another structurally distinct NK cell membrane glycoprotein, HP-3E4, is involved in the recognition of certain polymorphic HLA-C molecules (-Cw*0401 and -Cw*1503). NK cell clones co-expressing both the NKB1 and HP-3E4 receptors fail to lyse targets expressing HLA-Cw*0401 and -B*5801, but are able to kill the transfectants in the presence of mAbs against both receptors. These studies demonstrate that a single NK cell clone may possess multiple structurally distinct receptors for different polymorphic HLA class I molecules that function independently.

    View details for Web of Science ID A1995QN45900028

    View details for PubMedID 7897214

  • ANTIBODY STRUCTURE - THE DUCKS DILEMMA NATURE Parham, P. 1995; 374 (6517): 16-17

    View details for Web of Science ID A1995QK07900028

    View details for PubMedID 7870165



    Although inhibition of natural killer (NK) cell-mediated lysis by the class I HLA molecules of target cells is an established phenomenon, knowledge of the features of class I molecules which induce this effect remains rudimentary. Using class I alleles HLA-B*1502 and B*1513 which differ only at residues 77-83 which define the Bw4 and Bw6 serological epitopes, we tested the hypothesis that the presence of the Bw4 epitope on class I molecules determines recognition by NKB1+ NK cells. HLA-B*1513 possesses the Bw4 epitope, whereas B*1502 has the Bw6 epitope. Lysis by NKB1+ NK cell clones of transfected target cells expressing B*1513 as the only HLA-A, -B, or -C molecule was inhibited, whereas killing of transfectants expressing B*1502 was not. Addition of an an anti-NKB1 monoclonal antibody reconstituted lysis of the targets expressing B*1513, but did not affect killing of targets bearing B*1502. The inhibitory effect of B*1513 could be similarly prevented by the addition of an anti-class I monoclonal antibody. These results show that the presence of the Bw4 epitope influences recognition of HLA-B molecules by NK cells that express NKB1, and suggest that the NKB1 molecule may act as a receptor for Bw4+ HLA-B alleles. Sequences outside of the Bw4 region must also affect recognition by NKB1+ NK cells, because lysis of transfectants expressing HLA-A*2403 or A*2501, which possess the Bw4 epitope but are in other ways substantially different from HLA-B molecules, was not increased by addition of the anti-NKB1 antibody. Asparagine 86, the single site of N-linked glycosylation on class I molecules, is in close proximity to the Bw4/Bw6 region. The glycosylation site of the Bw4-positive molecule B*5801 was mutated, and the mutant molecules tested for inhibition of NKB1+ NK cells. Inhibition that could be reversed by addition of the anti-NKB1 monoclonal antibody was observed, showing the presence of the carbohydrate moiety is not essential for class I recognition by NKB1+ NK cell clones.

    View details for Web of Science ID A1995QH74700029

    View details for PubMedID 7532677



    The binding of clathrin-coated vesicles, clathrin triskelions, and free clathrin light chains to calmodulin-Sepharose was compared. When isolated from bovine brain, all three components bound to calmodulin-Sepharose in the presence of calcium and could be eluted by its removal. In contrast, coated vesicles and triskelions isolated from bovine adrenal gland did not bind to calmodulin-Sepharose, although the free light chains from adrenal gland bound as effectively as those from brain. As distinct isoforms of the clathrin light chains are expressed by brain and adrenal gland, these results implicate the clathrin light chains as the calmodulin-binding component of coated vesicles and triskelions. Furthermore, the insertion sequences found in the neuron-specific isoforms, although not necessary for the binding of free clathrin light chains to calmodulin, must facilitate the interaction of heavy chain-associated light chains with calmodulin. Recombinant mutants of LCa, with deletions spanning the entire sequence, were tested for binding to calmodulin-Sepharose. Those mutants retaining structural integrity, as assessed by the binding of a panel of monoclonal antibodies, exhibited varying amounts of calmodulin binding activity. However, deletion of the carboxyl-terminal 20 residues abolished calmodulin interaction. Thus, the carboxyl terminus of LCa appears to constitute a calmodulin-binding site. Peptides corresponding to the carboxyl terminus of LCa or LCb inhibited the interaction of the light chains with calmodulin, suggesting that this region forms the calmodulin-binding site of both LCa and LCb. The carboxyl-terminal peptides of LCa and LCb inhibited the interaction of light chains with calmodulin approximately 10-fold less effectively than a calmodulin-binding peptide derived from smooth muscle myosin light chain kinase, but much more effectively than a calmodulin-binding peptide derived from adenylate cyclase. This comparison places the clathrin light chain-calmodulin interaction within the physiological range seen for other calmodulin-binding proteins.

    View details for Web of Science ID A1995QE49300063

    View details for PubMedID 7836475



    Polymorphism among class I molecules of the major histocompatibility complex (MHC) confers allotypic specificity on the peptides that these molecules bind and present to cytotoxic T lymphocytes. Evolution of new human HLA class I alleles usually involves gene recombination events that replace a segment of one allele with the homologous region of another. In this study, the impact of these evolutionary changes has been assessed by comparison of the peptide-binding specificities of six related HLA-B allotypes.Endogenous peptides bound by HLA-B*5401, HLA-B*5501, HLA-B*5502, HLA-B*5601, HLA-B*6701 and HLA-B*0702 were characterized. Despite differing by 1-9 of the amino-acid residues comprising their peptide-binding sites, all these allotypes share a dominant preference for peptides that have proline at position 2. Polymorphism results in differing selection of carboxy-terminal and secondary anchor residues, but the peptide-binding specificities are sufficiently similar that there is overlap in the repertoires of peptides bound by these allotypes. Complete sequence determination of individual peptides revealed four that could be isolated from two or more allotypes. Members of the closely related HLA-B22 family--HLA-B*5401, HLA-B*5501, HLA-B*5502 and HLA-B*5601--show only minor differences in their peptide-binding specificities. This marked similarity is reflected at the functional level, as alloreactive cytotoxic T lymphocytes generated against HLA-B*5401 and HLA-B*5501 exhibited cross-reactive recognition.The isolation of identical endogenously bound peptides from six HLA-B allotypes demonstrates overlap in the repertoires of peptides bound in vivo by different allotypes. We speculate that the shared preference for binding peptides with proline at position 2 reflects a selective pressure to retain this specificity, which may be based upon peptide availability in vivo. Characterization of the overlap between the repertoires of peptides bound by HLA-B allotypes could simplify the development of peptide-based vaccines that are targeted to cytotoxic T cells, as single peptides would be effective for humans of different HLA types.

    View details for Web of Science ID A1995QG89200018

    View details for PubMedID 7743181

  • THE ORIGINS OF HLA-A,B,C POLYMORPHISM IMMUNOLOGICAL REVIEWS Parham, P., Adams, E. J., Arnett, K. L. 1995; 143: 141-180

    View details for Web of Science ID A1995QR14900008

    View details for PubMedID 7558075



    The ST-16 antigenic specificity of the HLA-B locus is defined as a B39 variant of Mexican-Americans. Nucleotide sequencing of cDNA shows the ST-16 allele (B*3905) differs from B*39011 by a single substitution that substitutes tyrosine for aspartic acid at position 74 of the mature class I heavy chain. The complete coding region sequence for the common caucasoid allele encoding the B38 antigen has been determined. This B*3801 allele differs from B*3802 at two nucleotide substitutions within the Bw4 sequence motif. B*3801 and B*3802 may have been derived independently from B*39011 by conversion events with B alleles donating distinctive Bw4 motifs. A novel allele B*39022 derived from a Colombian Indian differs from the B*39021 allele of Japanese origin at two widely separated silent substitutions. Comparison of sequences for the known B16 alleles suggest that B*39021 and B*39022 were independently derived by recombination from B*39013 and B*39011 respectively.

    View details for Web of Science ID A1995QD28800003

    View details for PubMedID 7725307



    Previous studies have shown that immature mouse class I molecules transiently associate with a resident endoplasmic reticulum protein of 88 kD that has been proposed to act as a chaperone for class I assembly. Subsequently, this protein was demonstrated to be identical to calnexin and to associate with immature forms of the T cell receptor complex, immunoglobulin, and human class I HLA heavy chains. In this paper we define further the interaction of human class I HLA heavy chains with chaperone proteins and find key differences with the complexes observed in the mouse system. First, calnexin and immunoglobulin binding protein (BiP) both associate with immature HLA class I heavy chains. The two chaperones are not found within the same molecular complex, suggesting that calnexin and BiP do not interact simultaneously with the same HLA class I heavy chain. Second, only free HLA class I heavy chains, and not beta 2-microglobulin (beta 2m)-associated heavy chains are found associated with the chaperones. Indeed, addition of free beta 2m in vitro induces dissociation of chaperone-class I HLA heavy chain complexes. The kinetics for dissociation of the class I HLA heavy chain-chaperone complexes and for formation of the class I HLA heavy chain-beta 2m complex display a reciprocity that suggests the interactions with chaperone and beta 2m are mutually exclusive. Mouse class I heavy chains expressed in human cells exhibit the mouse pattern of interaction with human chaperones and human beta 2m and not the human pattern, showing the difference in behavior is purely a function of the class I heavy chain sequence.

    View details for Web of Science ID A1995QA04200032

    View details for PubMedID 7807012

  • The rise and fall of great class I genes. Seminars in immunology Parham, P. 1994; 6 (6): 373-382


    Class I major histocompatibility complex molecules are components of the vertebrate immune system. Polymorphic classical class I molecules determine the specificity of cytolytic T cell and natural killer cell responses and are found in all species. During the timeframe of mammalian evolution, the lifetimes of a functional class I locus are short and those of individual alleles even shorter. In this seminar the role of heterozygote advantage frequency-dependent selection, disease-specific selection and drift in driving this rapid evolution is discussed. The other, non-classical genes, perform other functions within the immune system. They are of more recent invention than the classical class I genes and appear to have evolved from classical class I alleles.

    View details for PubMedID 7654994


    View details for Web of Science ID A1994PR81700007

    View details for PubMedID 7878658

  • THE ESSENCE OF EPITOPES JOURNAL OF EXPERIMENTAL MEDICINE Barber, L. D., Parham, P. 1994; 180 (4): 1191-1194

    View details for Web of Science ID A1994PJ70300002

    View details for PubMedID 7523566

  • A SMALL TEST OF A SEQUENCE-BASED TYPING METHOD - DEFINITION OF THE B-ASTERISK-1520 ALLELE TISSUE ANTIGENS DOMENA, J. D., Little, A. M., Arnett, K. L., Adams, E. J., Marsh, S. G., Parham, P. 1994; 44 (4): 217-224


    Santamaria et al. (Human Immunology 1993 37: 39-50) describe a method of sequence-based typing (SBT) for HLA-A, B and C alleles said to give "unambiguous typing of any sample, heterozygous or homozygous, without requiring additional typing information". From SBT analysis, which involves determination of partial sequences of mixed alleles, these investigators reported that cell lines KT17 (HLA-B35,62) and OLGA (HLA-B62) from the reference panel of the 10th International Histocompatibility Workshop express novel variants of HLA-B15 (B1501-MN6) and HLA-B35 (B3501-MN7) respectively. To study further the novel alleles, we cloned and sequenced full-length HLA-B cDNA clones isolated from the KT17 and OLGA cell lines. We find that KT17 expresses B*3501, as assigned by SBT, and B*1501, the common allele encoding the B62 antigen. We were unable to confirm that KT17 expresses the novel B1501-MN6 variant identified by SBT. For OLGA our analysis confirms the partial sequences obtained by SBT. Thus OLGA expresses B*1501 and a novel HLA-B allele. The complete sequence of the latter shows it is a hybrid having exons 1 and 2 in common with B*1501 and other B15 subtypes and exons 3-7 in common with B*3501 and related molecules including B*5301 and B*5801. The novel allele has been designated B*1520 because of its sequence similarity with the B15 group; furthermore, serological analysis shows that the B*1520 product does not express epitopes in common with either B35, B53 or B58. The B*1520 heavy chain has a similar isoelectric point to A*3101; B*1520 was undetected by previous applications of isoelectric focusing because B*1520 and A31 are both expressed by OLGA. In conclusion, HLA-B typing of two cell lines by cDNA cloning and sequencing gives concordant results with SBT for three of the four alleles. The cause of the discrepancy for the fourth allele is unknown, however, this finding indicates that the novel HLA-A, B and C sequences emerging from SBT studies need independent verification.

    View details for Web of Science ID A1994PL83300003

    View details for PubMedID 7871522



    CD4 and CD8 are cell surface glycoproteins that serve as co-receptors for Ag with the TCR. Recent studies have shown that both CD4 and CD8 interact with conserved regions of MHC class II and class I, respectively. To investigate further the roles of CD4 and CD8 in the immune response, we prepared synthetic peptides corresponding to the HLA sequences with which CD4 and CD8 are thought to interact. The peptide corresponding to residues 222 to 235 of the HLA class I heavy chain blocked the differentiation of human CTL precursors into active effect cells but affected neither the ability of PBLs to proliferate in response to mitogen nor the cytotoxic activity of established CTLs. In contrast, the peptide corresponding to residues 134 to 152 of the HLA-DR beta-chain inhibited the differentiation of CTL precursors, the proliferative response of freshly isolated PBL, and the proliferation of an established alloreactive CD4+ T cell clone to Ag. The inhibitory effect of the DR.134-152 peptide on CTL differentiation could be overcome by addition of exogenous IL-2 to the limiting dilution cultures, whereas the effect of the HLA-1.222-235 peptide was unaffected by exogenous IL-2. These results directly demonstrate a functional role for these regions of MHC molecules and underscore the central role of both CD4 and CD8 in the effective initiation of a CTL response.

    View details for Web of Science ID A1994NY34200004

    View details for PubMedID 8027565

  • THE HLA-B7QUI ANTIGEN IS ENCODED BY A NEW SUBTYPE OF HLA-B27 (B-ASTERISK-2708) TISSUE ANTIGENS Hildebrand, W. H., DOMENA, J. D., Shen, S. Y., Marsh, S. G., Bunce, M., Guttridge, M. G., Darke, C., Parham, P. 1994; 44 (1): 47-51

    View details for Web of Science ID A1994NX88800006

    View details for PubMedID 7974468


    View details for Web of Science ID A1994NX88800008

    View details for PubMedID 7974470

  • ASHI Rose Payne Lecture. Of Payne, polymorphism, and populations. Human immunology Parham, P. 1994; 40 (2): 77-92

    View details for PubMedID 7928447



    T cells can be selected positively or negatively by the same peptide under different conditions. The type of selection depends on the avidity of the interaction between the T cell and the antigen-presenting cell.

    View details for Web of Science ID A1994NL99700013

    View details for PubMedID 7922361

  • THE HLA-B73 ANTIGEN HAS A MOST UNUSUAL STRUCTURE THAT DEFINES A 2ND LINEAGE OF HLA-B ALLELES TISSUE ANTIGENS Parham, P., Arnett, K. L., Adams, E. J., Barber, L. D., DOMENA, J. D., Stewart, D., Hildebrand, W. H., Little, A. M. 1994; 43 (5): 302-313


    The nucleotide sequence of cDNA encoding the HLA-B73 antigen was determined; it is unusually divergent, differing from other HLA-B alleles by 44-77 nucleotide substitutions. Features that distinguish the B*7301 heavy chain from other HLA-B heavy chains include multiple substitutions in the alpha 3 domain and a duplication-deletion within the transmembrane region that increases the length of B*7301 compared to other HLA-B heavy chains. The duplication-deletion is shared with subsets of B alleles from the homologous gorilla (Gogo-B) and chimpanzee (Patr-B) loci. Other unusual features of B*7301 are individually shared with certain alleles of the HLA-A, HLA-C, HLA-F, Gogo-B and Patr-B loci. The B*7301 molecules has sequence elements in common with members of the B7 crossreacting group in the alpha 1 domain and is shown to possess the ME1 epitope, which is held in common with the B7, B22, B27, B42 and B67 antigens. B*7301 has a unique cysteine at position 270 of the alpha 3 domain which appears accessible but probably does not form disulphide-bonded B*7301 dimers in cell membranes. B*7301 represents a newly discovered but ancient lineage of HLA-B alleles that appears poorly represented in the modern human population.

    View details for Web of Science ID A1994NT39800005

    View details for PubMedID 7524186

  • HLA-B15 - A WIDESPREAD AND DIVERSE FAMILY OF HLA-B ALLELES TISSUE ANTIGENS Hildebrand, W. H., DOMENA, J. D., Shen, S. Y., Lau, M., Terasaki, P. I., Bunce, M., Marsh, S. G., Guttridge, M. G., BIAS, W. B., Parham, P. 1994; 43 (4): 209-218


    HLA-B15 embraces a multiplicity of antigenic specificities which vary in their distribution amongst human populations. To correlate B15 molecular structure with the serological picture we have sequenced alleles encoding the various subspecificities of the B15 antigen: B62, B63, B75, B76 and B77, and a number of "variants" of these antigens including the 8w66 split of B63. HLA-B63 (B*1517) and 8w66 (B*1516) heavy chains have sequence identity to B17 in the alpha 1 helix correlating with the antigenic crossreactivity of these molecules. HLA-B77(B*1513) and B75 (B*1502) heavy chains differ solely in segments determining the Bw4 and Bw6 public epitopes, consistent with the serological description of the B77 and B75 antigens. One allele encoding the B76 antigen (B*1512) appears to be the product of gene conversion between the HLA-A and -B loci and differs from B*1501 in codons 166 and 167. In contrast, a second allele encoding the B76 antigen (B*1514) differs from B*1501 by an unrelated substitution in codon 167 which confers similarily with B45, an antigen crossreactive with B76. A third allele encoding B76, B*1519, differs from B*1512 by a unique point substitution in exon 4. Three alleles encoding variant B15 and B62 antigens (B*1508, B*1511 and B*1515) differ from B*1501 by localized clusters of substitutions that probably result from interallelic conversion. The B15 sequences described in this paper, in combination with those previously determined, define a family of 22 alleles, including those encoding the B46 and B70 antigens. Within this family the patterns of allelic substitution are analogous to those of other HLA-A and -B families, in that pairwise differences almost always involve functional positions of the antigen recognition site and recombination is the major agent of diversification.

    View details for Web of Science ID A1994NN62600001

    View details for PubMedID 7521976

  • HLA-B67 - A MEMBER OF THE HLA-B16 FAMILY THAT EXPRESSES THE ME1 EPITOPE TISSUE ANTIGENS Little, A. M., DOMENA, J. D., Hildebrand, W. H., Shen, S. Y., Barber, L. D., Marsh, S. G., BIAS, W. B., Parham, P. 1994; 43 (1): 38-43


    HLA-B67 is an uncommon antigen that has been defined by serological crossreactivity with the HLA-B7 and HLA-B16 (B38 and B39) antigens. It is found at highest frequency in certain Oriental populations and has been best defined in the Japanese. Nucleotide sequencing of cDNA encoding B67 reveals the B*6701 allele to be a subtype of B39 which differs from B*39011 by substitution at residues 67-71 of the alpha 1 helix. In the region of difference B*6701 is identical in sequence to B7, B22, B27 and related molecules that express the epitope recognized by the ME1 monoclonal antibody. That the HLA-B67 molecule binds strongly to the ME1 antibody was demonstrated by immunoprecipitation and cell surface binding assays. Identical B*6701 nucleotide sequences were obtained for the B67 alleles isolated from 2 unrelated Japanese and 1 North American caucasoid.

    View details for Web of Science ID A1994MU52800006

    View details for PubMedID 7517584


    View details for Web of Science ID A1994BA72A00008

    View details for PubMedID 7939907

  • STRUCTURAL HETEROGENEITY IN HLA-B70, A HIGH-FREQUENCY ANTIGEN OF BLACK POPULATIONS TISSUE ANTIGENS DOMENA, J. D., Little, A. M., Madrigal, A. J., Hildebrand, W. H., JOHNSTONDOW, L., Dutoit, E., BIAS, W. B., Parham, P. 1993; 42 (5): 509-517


    Although the B70 antigen exhibits allele frequencies of 8-23% in African and American black populations, it remains poorly defined. Cloning and sequencing of cDNA encoding B70 antigens from six cell lines has identified a group of three closely related alleles: B*1503, B*1509 and B*1510, that form a subgroup of the B15 family. The sequences of these alleles and, in particular, B*1503, are close to that of the HLA-B consensus consistent with the difficulty in their serological definition. The products of the three alleles correspond to three electrophoretically detected variants of the B70 antigen and some correlation with the B71 and B72 subspecificities of the B70 antigen can be made. A fourth allele, B*7901, previously described by Choo et al. (J. Immunol. 147: 174-180, 1991) that was not serologically typed as B70, differs by a single nucleotide substitution from B*1510. The sensitivity of alloantibodies to single differences in peptide binding residues suggest a role for bound peptides in the HLA-B70 alloantigenic specificities. The heavy chains encoded by the four alleles differ at four peptide binding residues of the antigen recognition site, the evolutionary modification of which can be explained in terms of interallelic recombination events.

    View details for Web of Science ID A1993MN11500007

    View details for PubMedID 8146861

  • A sixth family of HLA-A alleles defined by HLA-A*8001. Tissue antigens DOMENA, J. D., Hildebrand, W. H., BIAS, W. B., Parham, P. 1993; 42 (3): 156-159

    View details for PubMedID 8284791


    View details for Web of Science ID A1993LG60600005

    View details for PubMedID 8362411

  • Disease resistance: good news from Gambia. Current biology Parham, P. 1993; 3 (4): 223-225

    View details for PubMedID 15335772


    View details for Web of Science ID A1993KR69300010

    View details for PubMedID 8475490


    View details for Web of Science ID A1993KK64100004

    View details for PubMedID 8443151


    View details for Web of Science ID A1993KN62100187

    View details for PubMedID 8438388


    View details for Web of Science ID A1993KN62100055

    View details for PubMedID 8438260



    Clathrin constitutes the coat of vesicles involved in three receptor-mediated intracellular transport pathways; the export of aggregated material from the trans-Golgi network for regulated secretion, the transfer of lysosomal hydrolases from the trans-Golgi network to lysosomes and receptor-mediated endocytosis at the plasma membrane. The clathrin subunits and the other major coat constituents, the adaptor polypeptides, interact in specific ways to build the characteristic polygonal clathrin lattice and to attach the coat to integral membrane receptors. Both clathrin coat assembly and disassembly on the cytoplasmic side of the membrane are multistep processes that are regulated by the coat constituents themselves and by cytosolic proteins and factors. Neurons represent a cell type with distinct morphology and special demands on exocytic and endocytic pathways that requires neuron-specific constituents and modifications of clathrin-coated vesicles.

    View details for Web of Science ID A1993MA73700002

    View details for PubMedID 8269710

  • HLA CLASS-I NUCLEOTIDE-SEQUENCES, 1992 IMMUNOBIOLOGY ZEMMOUR, J., Parham, P. 1993; 187 (1-2): 70-101


    The HLA Class I sequences included in this compilation are taken from publications listed in the papers: Nomenclature for factors of the HLA system, 1991 (1), Nomenclature for factors of the HLA system, 1990 (2) and factors of the HLA system, 1989 (3). Due to the increased number of sequences we have only included sequences for exons 2, 3 and 4 in this compilation. Where discrepancies have arisen between reported sequences, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments, identity between nucleotides is indicated by a hyphen (-). An unavailable sequence is indicated by a period (.). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number. A number of sequences that do not appear in the last Nomenclature report are given in the sequence alignment. The HLA allele and the submitting authors are the following; -BeWo C.1 (S. Ellis); Cl.10, Cl.9 (L. Cianetti), Cw6W (E. Weiss); A*68012, B*5104, Cw*0803 (P. Parham); B*4802, B*52012, B*3903, C*X (D. Watkins); B*39013 (M. Takiguchi). Full information regarding these sequences will be given in the next Nomenclature report. In addition, the B*2705W allele shown in this sequence alignment and reported by the group of E. Weiss was found to differ by 3 silent substitutions from the B*2705 (that appeared in the last published alignment). Differences are the following: B*2705: position 245 (Exon 3) 'T'; position 71 (Exon 4) 'A'; position 161 (Exon 4) 'G'. B*2705W: position 245 (Exon 3) 'G'; position 71 (Exon 4) 'G'; position 161 (Exon 4) 'A'.

    View details for Web of Science ID A1993KP24200006

    View details for PubMedID 8505061



    The HLA class I sequences included in this compilation are taken from publications listed in the papers: Nomenclature for factors of the HLA system, 1991 (Bodmer et al. 1992); Nomenclature for factors of the HLA system, 1990 (Bodmer et al. 1991); and Nomenclature for factors of the HLA system, 1989 (Bodmer et al. 1990). Due to the increased number of sequences we have only included sequences for exons 2, 3, and 4 in this compilation. Where discrepancies have arisen between reported sequences, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments, identity between nucleotides is indicated by a hyphen (-). An unavailable sequence is indicated by a period (.). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number.

    View details for Web of Science ID A1993KD73700001

    View details for PubMedID 8420833


    View details for Web of Science ID A1993MJ36600006

    View details for PubMedID 7506551



    Previous analysis has emphasized the correlation between primary structures of class I HLA molecules and their patterns of serologic cross-reactivity. Here we describe the structures of two serologic groups of HLA-B alleles for which this is not the case. HLA-B45, an allele associated with black populations, is serologically paired with B44 in the B12 group; its structure, however, is divergent from that of B44 but closely related to B50. The BN21 (B*4005) allele is associated with native Americans and is serologically grouped with B50 in the B21 group; its structure, however, is more closely related to alleles of the B40 group. The B44 and B45 serologically cross-reactive molecules differ at seven functional positions of the Ag recognition site; the B50 and BN21 molecules differ at four such residues. These differences are predicted to alter peptide presentation and be capable of eliciting strong alloreactive T cell responses. For these pairs of B12 and B21 Ag, serology appears dominated by epitopes formed by short sequences of the alpha 2 helix which have been shuffled by recombination between alleles. The implications of these results for HLA matching in transplantation are discussed.

    View details for Web of Science ID A1992JY87500019

    View details for PubMedID 1385528


    View details for Web of Science ID A1992JZ97600005

    View details for PubMedID 1481201

  • HLA CLASS-I NUCLEOTIDE-SEQUENCES, 1992 TISSUE ANTIGENS ZEMMOUR, J., Parham, P. 1992; 40 (5): 221-228


    The HLA Class I sequences included in this compilation are taken from publications listed in the papers: Nomenclature for factors of the HLA system, 1991 (1), Nomenclature for factors of the HLA system, 1990 (2), and Nomenclature for factors of the HLA system, 1989 (3). Due to the increased number of sequences, we have only included sequences for exons 2, 3 and 4 in this compilation. Where discrepancies have arisen between reported sequences, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments, identity between nucleotides is indicated by a hyphen (-). An unavailable sequence is indicated by a period (.). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number.

    View details for Web of Science ID A1992JZ97600002

    View details for PubMedID 1362294

  • The B*4002 allele encodes the B61 antigen: B40* is identical to B61. Tissue antigens DOMENA, J. D., Johnston-Dow, L., Parham, P. 1992; 40 (5): 254-256

    View details for PubMedID 1362296



    The HLA-C locus remains an enigma. The serological polymorphism is poorly defined, HLA-C molecules are expressed at the cell surface at about 10% the levels of HLA-A and -B, and their importance for antigen presentation to either CD8-bearing T cells or natural killer cells is unclear. Our understanding of HLA-C polymorphism has also lagged behind that of HLA-A and -B. We have applied the polymerase chain reaction to the characterization of cDNA encoding HLA-C antigens. Combining the recent results with previously characterized HLA-C alleles gives a data base of 26 sequences, which was used to analyze the nature of HLA-C polymorphism and compare it to the variation seen in HLA-A and -B. The sequences form 10 families of alleles that correlate well with the patterns of serological crossreactivity, including the C blanks, and all major HLA-C allelic families appear to have been sampled. The families further divide into two groups of HLA-C alleles defined on the basis of linked substitutions in the 3' exons. In comparison with HLA-A and -B, HLA-C alleles are more closely related to each other, there being less variation in residues of the antigen recognition site and more variation at other positions. In particular, the helix of the alpha 1 domain of HLA-C molecules is unusually conserved. Despite the reduced diversity in the antigen recognition site, it is evident that HLA-C genes have been the target of past selection for polymorphism. Within the antigen recognition site, it is the alpha 1 domain that is most diagnostic of HLA-C, whereas the alpha 2 domain is similar to that of HLA-B, the locus to which HLA-C is most closely related. In particular, conserved motifs in the alpha 1 helix and the conserved glycine at the base of the B pocket (position 45) provide a combination of features that is uniquely found in HLA-C molecules. We hypothesize that these features restrict the peptides bound by HLA-C molecules and in this manner reduce the efficiency of HLA-C assembly and expression at the cell surface. The overall picture HLA-C polymorphism obtained from this sampling of HLA-C alleles is unlikely to change as further alleles are characterized.

    View details for Web of Science ID A1992JP86200003

    View details for PubMedID 1383381


    View details for Web of Science ID A1992JV60900010

    View details for PubMedID 1428015


    View details for Web of Science ID A1992JQ86700010

    View details for PubMedID 1420120



    The HLA class I sequences included in this compilation are taken from articles listed in the literature: "Nomenclature for Factors of the HLA System, 1991" [1], "Nomenclature for Factors of the HLA System, 1990" [2], and "Nomenclature for Factors of the HLA System, 1989" [3]. Because of the increased number of sequences, we have only included sequences for exons 2-4 in this compilation. Where discrepancies have arisen between reported sequences, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list, and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments, identity between nucleotides is indicated by a hyphen (-). An unavailable sequence is indicated by a period (.). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number.

    View details for Web of Science ID A1992KB11400001

    View details for PubMedID 1464551


    View details for Web of Science ID A1992HX43200008

    View details for PubMedID 1612644



    The polymerase chain reaction was used to isolate clones with class I major histocompatibility complex sequences from fish (carp), amphibian (axolotl), and two species of reptile (lizard and snake). The lizard and snake clones were used to isolate class I cDNA clones. All the sequences showed the expected evolutionary relatedness. The carp and axolotl clones and one lizard cDNA clone lacked the first cysteine in the alpha 3 domain which in other class I heavy chains forms an intradomain disulfide bond. A small number of amino acid residues are conserved in the class I heavy chain sequences from all five classes of vertebrates. In the first two domains they are symmetrically clustered and contribute to intra- and interdomain contacts. None of these invariant residues are at peptide-binding, T-cell receptor-interacting, or CD8-binding positions.

    View details for Web of Science ID A1992JA06900004

    View details for PubMedID 1612650

  • UNUSUAL HLA-B ALLELES IN 2 TRIBES OF BRAZILIAN INDIANS NATURE Belich, M. P., Madrigal, J. A., Hildebrand, W. H., ZEMMOUR, J., Williams, R. C., LUZ, R., PETZLERLER, M. L., Parham, P. 1992; 357 (6376): 326-329


    The Kaingang and Guarani are culturally and linguistically distinct tribes of southern Brazil. Like all Amerindian groups they show limited HLA polymorphism, which probably reflects the small founder populations that colonized America by overland migration from Asia 11,000-40,000 years ago. We find the nucleotide sequences of HLA-B alleles from the Kaingang and Guarani to be distinct from those characterized in caucasian, oriental and other populations. By comparison, the HLA-A and C alleles are familiar. These results and those reported in the accompanying paper on the Waorani of Ecuador reveal that a marked evolution of HLA-B has occurred since humans first entered South America. New alleles have been formed through recombination between pre-existing alleles, not by point mutation, giving rise to distinctive diversification of HLA-B in different South American Indian tribes.

    View details for Web of Science ID A1992HW13200047

    View details for PubMedID 1317015

  • THE MOLECULAR-BASIS FOR REACTIVITY OF ANTI-CW1 AND ANTI-CW3 ALLOANTISERA WITH HLA-B46 HAPLOTYPES TISSUE ANTIGENS ZEMMOUR, J., Gumperz, J. E., Hildebrand, W. H., Ward, F. E., Marsh, S. G., Williams, R. C., Parham, P. 1992; 39 (5): 249-257


    HLA haplotypes containing the HLA-B46 allele react with both anti-Cw1 and anti-Cw3 alloantisera, a pattern of reactivity defined as the Cw11 antigen and postulated to involve either a distinctive Cw11 allele or a duplicated HLA-C locus. From serological characterization of CIR cells transfected with B46 cDNA we now demonstrate that the anti-Cw3 reactivity with these haplotypes is solely due to the B46 molecule and not to an HLA-C molecule. Furthermore, isolation and characterization of HLA-C mRNA from cells expressing B46 strongly suggest that anti-Cw1 reactions are directed against the product of a conventional Cw1 allele. The antigenic cross-reactivities of B46 with B62 and Cw3 correlate with its chimaeric primary structure, which is identical to that of B62, except in the alpha 1 helix where it is identical to both Cw3 and Cw1. The structure, distribution and genetic linkage of B46 indicate it is of recent, Asian origin and is the result of a gene conversion, involving Cw1 as the donor gene and B62 as the recipient. These results demonstrate that the Cw11 antigen neither corresponds to a novel HLA-C allele nor a duplicated HLA-C locus, but to a combination of epitopes contributed by linked Cw1 and B46 alleles. The nucleotide sequence we previously and erroneously attributed to a distinct Cw11 allele is now demonstrated to encode Cw8. Isolation of the cDNA clone with this sequence from a library made from a cell homozygous for the B46 haplotype was probably an artefact of contamination.

    View details for Web of Science ID A1992HY72400004

    View details for PubMedID 1384166



    The HLA-A,B negative mutant cell line C1R is widely used as a transfection recipient in functional studies of class I MHC genes. It was derived from a normal B cell line, Hmy2, by three rounds of mutagenesis and immunoselection with anti-HLA mAb. Serology characterizes C1R to be negative for the HLA-A2, A3, B35, Bw62, and Cw3 Ag of the parental cell line while retaining expression of HLA-Cw4. We find, however, that CTL specific for HLA-B35 lyse C1R cells, suggesting that expression of HLA-B35 is also retained. To resolve this paradox we examined the expression of HLA-A,B,C genes and proteins in C1R cells. The results are consistent with deletion of the HLA-A3, Bw62, Cw3 haplotype and retention of the HLA-A2, B35, Cw4 haplotype in C1R. Although present, the HLA-A2 gene appears not to be transcribed. As expected, the HLA-Cw4 gene is transcribed and the protein expressed at normal levels. Transcription of the HLA-B35 gene is also normal and comparable to that of HLA-Cw4. However, expression of the HLA-B35 protein is reduced to a few percent of the parental level. Comparison of the nucleotide sequence of B35 alleles from C1R and Hmy2 revealed that reduced translation in C1R is caused by a point mutation (ATG to TTG) in the translation initiation codon. The HLA-B35 allele from C1R and Hmy2 represents a novel subtype, B*3503, differing from B*3501 by replacement of serine by phenylalanine at the peptide binding position 116. This study shows cell surface levels of a class I molecule which are insensitive to lysis by antibody and complement can be readily recognized by alloreactive T cells, further illustrating the relative sensitivity of Ag recognition by T cells.

    View details for Web of Science ID A1992HH74600050

    View details for PubMedID 1541831



    Dissection of the peptide binding grooves of seven subtypes of human histocompatibility leukocyte antigen (HLA)-B27 into the six specificity pockets defined by the 2.6-A structure of HLA-A*0201 revealed just one pocket, the B ("45") pocket, that is conserved among all the HLA-B27 subtypes. Functional studies of mutant HLA-B*2705 molecules with point substitutions in residues of the B pocket show that this structure, and the glutamine residue at position 45 in particular, plays a critical role in cell surface expression, peptide binding, and in the presentation of both exogenous and endogenous peptides by HLA-B*2705. We predict that the B pocket of HLA-B*2705 interacts with an amino acid side chain that anchors peptides in the binding groove, and that this peptide motif is present in most endogenously processed peptides that bind to all seven subtypes of HLA-B27.

    View details for Web of Science ID A1992HF64000019

    View details for PubMedID 1371304

  • HLA-BW22 - A FAMILY OF MOLECULES WITH IDENTITY TO HLA-B7 IN THE ALPHA-1-HELIX JOURNAL OF IMMUNOLOGY Hildebrand, W. H., Madrigal, J. A., Little, A. M., Parham, P. 1992; 148 (4): 1155-1162


    Various HLA-B molecules exhibit serologic cross-reactions with HLA-B7, including HLA-B27, B40, Bw42, and Bw22. Of this group, primary structures for the three serologic subdivisions of HLA-Bw22, HLA-Bw54, Bw55, and Bw56, have yet to be determined. Here, we describe the nucleotide sequences of five distinctive HLA-Bw22 alleles isolated from cells of different ethnic origins typed either for Bw54, Bw55, or Bw56. Heterogeneity in molecules typed as Bw55 and Bw56 was defined. The five HLA-Bw22 alleles form a closely related family that appears to have evolved by a series of simple gene conversion events, all of which alter the antigen recognition site of the encoded proteins. Of note, HLA-Bw54 is the product of a gene conversion between HLA-B and C alleles. All the Bw22 alleles encode an alpha 1-helix identical in amino acid sequence to that of HLA-B7 and Bw42, a feature almost certainly responsible for the serologic cross-reactivity of these molecules. Shared substitutions in the alpha 1-helix can also explain the cross-reactivity of Bw22 and B7 with B27. Patterns of amino acid substitution in the alpha 2-domain of Bw22 heavy chains correlate with certain antibody and T cell cross-reactivities, thereby implicating particular amino acids in their target epitopes.

    View details for Web of Science ID A1992HD97500026

    View details for PubMedID 1737933



    The close association of HLA-B27 with arthritic conditions has led to the suggestion that these diseases are mediated by cytotoxic T lymphocytes that recognize self-peptides presented by HLA-B27 molecules. The further association with enteric bacterial infections suggests that bacterial antigens may prime the CTL that later crossreacts on self. Bacterial infections do not usually generate CTL responses. We speculate here that unusual properties of HLA-B27 molecules may predispose to such responses. Thus, HLA-B27-related disease may be an unfortunate consequence of the generation of a suitable, self-mimicking HLA-B27-binding peptide by certain bacteria, plus an unusual propensity for the HLA-B27 molecule to bind and present such peptides.

    View details for Web of Science ID A1992LA27600003

    View details for PubMedID 1561398

  • MOLECULAR DEFINITION OF AN ELUSIVE 3RD HLA-A9 MOLECULE - HLA-A9.3 IMMUNOGENETICS Little, A. M., Madrigal, J. A., Parham, P. 1992; 35 (1): 41-45


    The HLA-A9 family has been characterized as possessing two well defined specificities; HLA-A23 and A24. Serological studies have suggested the presence of a third member of this family HLA-A9.3, however there is doubt surrounding the existence of this specificity. HLA-A23, A24, and the putative A9.3 proteins were analyzed biochemically by immunoprecipitation and isoelectric focusing. Both HLA-A24 and A9.3 have identical isoelectric points whereas A23 is different. We have sequenced cDNA encoding HLA-A23, A24, and A9.3. From the observed protein sequences, we found A9.3 to differ from A24 by two amino acid substitutions located in the alpha 2 helix of the class I molecule. These substitutions are expected to significantly change the shape of the peptide binding cleft.

    View details for Web of Science ID A1992GU19800006

    View details for PubMedID 1729171



    14 gorilla class I major histocompatibility complex (MHC) alleles have been isolated, sequenced, and compared to their counterparts in humans and chimpanzees. Gorilla homologues of HLA-A, -B, and -C were readily identified, and four Gogo-A, four Gogo-B, and five Gogo-C alleles were defined. In addition, an unusual Gogo class I gene with features in common with HLA-A and its related pseudogene, HLA-H, is described. None of the gorilla alleles is identical or even closely related to known class I alleles and each encodes a unique antigen recognition site. However, the majority of polymorphic substitutions and sequence motifs of gorilla class I alleles are shared with the human or chimpanzee systems. In particular, elements shared with HLA-A2 and HLA-B27 are found in Gogo-A and -B alleles. Diversity at the Gogo-B locus is less than at the Gogo-A locus, a trend the opposite of that seen for HLA-A and -B. The Gogo-C locus also appears to have limited polymorphism compared to Gogo-A. Two basic Gogo-C motifs were found and they segregate with distinctive sets of HLA-C alleles. HLA-A allels are divided into five families derived from two ancient lineages. All chimpanzee A alleles derived from one of these lineages and all gorilla alleles derive from the other. Unlike chimpanzee Patr-A alleles, the Gogo-A alleles do not clearly partition with one of the HLA-A families but have similarities with two. Overall, gorilla class I diversity appears from this sampling to show more distinctions from class I HLA than found for chimpanzee class I.

    View details for Web of Science ID A1991GU64400023

    View details for PubMedID 1744581



    A monomoprhic monoclonal antibody (LA45 antibody) reactive with "a new activation-induced surface structure on human T lymphocytes" (LA45 antigen) that resembled free class I heavy chains has recently been described (Schnabl, E., H. Stockinger, O. Majdic, H. Gaugitsch, I.J.D. Lindley, D. Maurer, A. Hajek-Rosenmayr, and W. Knapp. 1990. J. Exp. Med. 171:1431). This antibody was used to clone a class I-like heavy chain (LA45 gene) from the HUT 102 tumor cell, which paradoxically did not give rise to the LA45 antigen on transfection into monkey COS cells. We show here that the LA45 gene is HLA-Aw66.2, a previously uncharacterized allele of the HLA-A locus. The previously determined LA45 sequence differs from that of HLA-Aw66.2, from HUT 102, and the CR-B B cell line derived from the same individual as HUT 102 by substitution of tryptophan for serine at position 4 in the alpha 1 domain. Transfection of HLA-Aw66.2, and of a mutant of this gene with serine 4 substituted for tryptophan, into a human B cell line (C1R) both resulted in expression of the LA45 epitope. Furthermore, we find expression of the LA45 epitope on Epstein Barr virus-transformed B cell lines as well as lectin-activated T cells, but not on long-term T cell lines or unstimulated peripheral blood T cells. The specificity of the LA45 antibody is polymorphic and the presence of the LA45 epitope is precisely correlated with the sequence arginine, asparagine (RN) at residues 62 and 63 of the helix of the alpha 1 domain. The LA45 epitope is broadly distributed, being associated with half the alleles of both HLA-A and -B loci but none of the HLA-C locus. All the results are consistent with the presence of pools of free HLA-A and -B heavy chains at the surfaces of certain cell types but not others. Such molecules are probably responsible for the HLA-associated class I alloantigens of lectin-activated T cells. We hypothesize the free heavy chains result from dissociation of beta 2-microglobulin from subpopulations of empty HLA-A,B molecules, or molecules with weakly bound peptides, that vary in size depending on cellular activation and peptide supply.

    View details for Web of Science ID A1991GM80300013

    View details for PubMedID 1940790


    View details for Web of Science ID A1991GP45700008

    View details for PubMedID 1801311


    View details for Web of Science ID A1991GK37900002

    View details for PubMedID 1785134



    The HLA class I sequences included in this compilation are taken from publications listed in the accompanying paper, Nomenclature for factors of the HLA system, 1990 (Bodmer et al., 1991), and also in Nomenclature for factors of the HLA system, 1989 (Bodmer et al., 1990). Where discrepancies have arisen between reported sequences the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments identity between residues is indicated by a hyphen (-). An unavailable sequence is indicated by a full point (.). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number.

    View details for Web of Science ID A1991GD51700005

    View details for PubMedID 1764432


    View details for Web of Science ID A1991FR18900007

    View details for PubMedID 1890021


    View details for Web of Science ID A1991GL67400011

    View details for PubMedID 1754718

  • HLA CLASS-I NUCLEOTIDE-SEQUENCES, 1991 IMMUNOBIOLOGY ZEMMOUR, J., Parham, P. 1991; 182 (3-4): 347-367


    The HLA Class I sequences included in this compilation are taken from publications listed in the accompanying paper, Nomenclature for factors of the HLA system, 1990 and Nomenclature for factors of the HLA system, 1989. Where discrepancies have arisen between reported sequences the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments identity between residues is indicated by a hyphen (-). Unavailable sequence is indicated by a period (.). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number.

    View details for Web of Science ID A1991FP85400013

    View details for PubMedID 1916881

  • PEPTIDE BINDING TO EMPTY HLA-B27 MOLECULES OF VIABLE HUMAN-CELLS NATURE Benjamin, R. J., Madrigal, J. A., Parham, P. 1991; 351 (6321): 74-77


    Intracellular binding of antigenic peptides by polymorphic class I major histocompatibility complex molecules creates the ligands recognized by receptors of CD8+ T cells. Previously described in vitro assays of peptide binding to class I molecules have been limited by either the low proportion of accessible binding sites or the lack of allelic specificity. Here we describe a system in which the human class I molecule HLA-B27 binds considerable amounts of an influenza peptide with precise allelic discrimination. Binding requires viable cells, is stimulated by gamma-interferon and is inhibited by brefeldin A. Our results are consistent with the presence of fairly stable 'empty' HLA-B27 molecules at the cell surface. By contrast, analysis of the binding of a second influenza peptide indicates that empty HLA-Aw68 molecules are relatively short-lived. We speculate that HLA-B27 might bind extracellular peptides in vivo and that this property could underlie its association with autoimmune disease.

    View details for Web of Science ID A1991FK19300064

    View details for PubMedID 2027387

  • HLA CLASS-I NUCLEOTIDE-SEQUENCES, 1991 IMMUNOGENETICS ZEMMOUR, J., Parham, P. 1991; 33 (5-6): 310-320


    The HLA class I sequences included in this compilation are taken from publications listed in the accompanying paper. Nomenclature for factors of the HLA system. 1990 (Bodmer et al. 1991) and Nomenclature for factors of the HLA system, 1989 (Bodmer et al. 1990). Where discrepancies have arisen between reported sequences the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments identity between residues is indicated by a hyphen (-). Unavailable sequence is indicated by a period (.). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number.

    View details for Web of Science ID A1991FQ20600003

    View details for PubMedID 2050388

  • HLA CLASS-I NUCLEOTIDE-SEQUENCES, 1991 TISSUE ANTIGENS ZEMMOUR, J., Parham, P. 1991; 37 (4): 174-180


    The HLA Class I sequences included in this compilation are taken from publications listed in the papers: Nomenclature for factors of the HLA system, 1990 (1) and Nomenclature for factors of the HLA system, 1989 (2). Where discrepancies have arisen between reported sequences, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments, identity between residues is indicated by a hyphen (-). An unavailable sequence is indicated by a period (.). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number.

    View details for Web of Science ID A1991FQ55000008

    View details for PubMedID 1926127

  • ANCIENT HLA GENES FROM 7,500-YEAR-OLD ARCHAEOLOGICAL REMAINS NATURE Lawlor, D. A., DICKEL, C. D., Hauswirth, W. W., Parham, P. 1991; 349 (6312): 785-788


    In the past decade there has been increasing interest in cloning DNA from ancient and preserved tissues. Most studies, however, have focused on mitochondrial or chloroplast genes, present at hundreds to thousands of copies per cell compared with one or two for each nuclear gene. With a probe containing Alu repeat sequences, Pääbo isolated a 3.4-kilobase DNA fragment from a 2,400-year-old Egyptian mummy which was subsequently shown to contain an intron of the nuclear gene HLA-DQA (ref. 11). Here we report a more targeted approach to the characterization of nuclear genes from archaeological specimens. The Windover pond of central Florida has provided skeletal and soft tissue remains from 165 humans, radiocarbon-dated to be 6,990-8,130 years old. Using DNA obtained from one individual we have characterized segments from six nuclear genes: that for beta 2-microglobulin and five members of the class I HLA heavy chain gene family. Distinctive patterns of nucleotide substitution in the cloned heavy chain gene segments permit tentative assignment of the HLA-A,B type of the ancient individual.

    View details for Web of Science ID A1991EZ66600054

    View details for PubMedID 2000147


    View details for Web of Science ID A1991EW49800007

    View details for PubMedID 2022494



    Uncoating of clathrin-coated vesicles is mediated by the heat shock cognate protein, hsc70, and requires clathrin light chains (LCa and LCb) and ATP hydrolysis. We demonstrate that purified light chains and synthetic peptides derived from their sequences bind hsc70 to stimulate ATP hydrolysis. LCa is more effective than LCb in stimulating hsc70 ATPase and in inhibiting clathrin uncoating by hsc70. These differences correlate with high sequence divergence in the proline- and glycine-rich region (residues 47-71) that forms the hsc70 binding site. For LCa, but not LCb, this region undergoes reversible conformational changes upon perturbation of the ionic strength or the calcium ion concentration. Our results show that LCa is more important for interactions with hsc70 than is LCb and suggest a model in which the LCa conformation regulates coated vesicle uncoating.

    View details for Web of Science ID A1990DY10000007

    View details for PubMedID 1975516



    Human leukocytes were stimulated in vitro with peptides corresponding in sequence to the highly variable helix of the alpha 1 domain of various HLA-B and -C molecules. A CD4+ CD8- cytotoxic T cell line, CTL-AV, that is specific for the HLA-B7 peptide presented by HLA-DR11.1 was obtained. The HLA-DR11.2 molecule, which only differs at three residues from HLA-DR11.1, did not present the HLA-B7 peptide to CTL-AV. Peptides from the alpha 1 domain helix of other HLA-A and HLA-B molecules, but not HLA-C molecules, competed with the HLA-B7 peptide for binding to HLA-DR11.1. A cell line (WT50) that coexpresses HLA-B7 and HLA-DR11.1 was killed by CTL-AV in the absence of any added HLA-B7 peptide. The processing and presentation of HLA-B7 in these cells appears to be through the endogenous, and not the exogenous, pathway of antigen presentation. Thus, Brefeldin A inhibits presentation and chloroquine does not. Furthermore, introduction of purified HLA-B7 molecules into HLA-DR11.1+, HLA-B7- cells by cytoplasmic loading via osmotic lysis of pinosomes, but not by simple incubation, rendered them susceptible to CTL-AV killing. These results provide an example of class II major histocompatibility complex (MHC) presentation of a constitutively synthesized self protein that uses the endogenous pathway of antigen presentation. They also emphasize the capacity for presentation of MHC peptides by MHC molecules.

    View details for Web of Science ID A1990DW49100012

    View details for PubMedID 2117634



    The specificity of binding of solubilized, purified HLA-A,B molecules to solid-phase peptides has been examined using the assay described by Bouillet et al. [1989. Nature (Lond.). 339:473.] 64 peptides derived from the sequences of viral antigens, HLA-A,B,C heavy chains, and clathrin light chains were tested for binding to HLA-A2.1, Aw68.1, Aw69, B44, and B5, molecules that differ by 5-17 residues of the peptide binding groove. 15 of the peptides, including those known to be T cell epitopes, gave significant binding. The pattern of peptide binding for each of the five HLA-A,B molecules was not significantly different. Binding was demonstrated to be a property of native beta 2m-associated HLA-A,B molecules that preserved conformational antigenic determinants after binding to peptide. In comparison to our previous results from solution-based assays the proportion of HLA-A,B molecules that can bind solid-phase peptides is very high. This accessibility of solid-phase peptides to the binding site of MHC molecules may be directly related to the observed absence of MHC specificity in the binding.

    View details for Web of Science ID A1990DW49100027

    View details for PubMedID 1696957



    The human class I HLA molecules are composed of both polymorphic, or private, and conserved, or public, regions. The private regions are recognized by alloreactive T cells and also serve as restriction elements for peptide presentation to autologous cells. Although the ability of public determinants to elicit antibody responses is well documented, little is known of their role in T cell function. In this study we examine the ability of one of these public HLA determinants, designated Bw4, to serve as a target Ag for CTL. We show that for some individuals the HLA-Bw4 epitope can function as a restriction element for CTL. This finding has important implications for organ transplantation.

    View details for Web of Science ID A1990DF84400013

    View details for PubMedID 2341716

  • A BINDING-SITE FOR THE T-CELL CO-RECEPTOR CD8 ON THE ALPHA-3 DOMAIN OF HLA-A2 NATURE Salter, R. D., Benjamin, R. J., WESLEY, P. K., BUXTON, S. E., Garrett, T. P., CLAYBERGER, C., KRENSKY, A. M., Norment, A. M., Littman, D. R., Parham, P. 1990; 345 (6270): 41-46


    Adhesion measurements between CD8 and 48 point mutants of HLA-A2.1 show that the CD8 alpha-chain binds to the alpha 3 domain of HLA-A2.1. Three clusters of alpha 3 residues contribute to the binding, with an exposed, negatively charged loop (residues 223-229) playing a dominant role. CD8 binding correlates with cytotoxic T-cell recognition and sensitivity to inhibition by anti-CD8 antibodies. Impaired alloreactive T-cell recognition of an HLA-A2.1 mutant with reduced affinity for CD8 is not restored by functional CD8 binding sites on an antigenically irrelevant class I molecule. Therefore, complexes of CD8 and the T-cell receptor bound to the same class I major histocompatibility complex molecule seem to be necessary for T-cell activation.

    View details for Web of Science ID A1990DB95700049

    View details for PubMedID 2109837



    The MHC contains many class I genes other than those known to present peptides to T lymphocytes. These additional class I genes vary between species and their functions are unknown. Genes involved in Ag presentation, HLA-A,B,C in humans, are highly diverse whereas other class I genes are of much more limited diversity. We have studied alleles of a gene, HLA-AR, that is closely linked and structurally related to HLA-A; properties consistent with these two loci having been formed by a gene duplication. Compared to HLA-A the diversity in HLA-AR is much less, and does not focus on residues of a putative Ag recognition site. However, the structure of HLA-AR alleles closely resembles those encoding Ag-presenting molecules, although the presence of one or two deleterious mutations prevents these alleles being active in Ag presentation. These results suggest HLA-AR derives from an Ag-presenting locus that became inactivated, possibly as a result of positive natural selection due to changing demands on T cell immunity. Thus absence of diversity may sometimes correlate with loss rather than preservation of function in class I MHC genes.

    View details for Web of Science ID A1990DA76500052

    View details for PubMedID 2329283



    The remarkable association between HLA-B27 and ankylosing spondylitis (AS) remains an enigma. While previous reviews have discussed the controversies surrounding the involvement of bacteria in the etiology of this disease and the sequence variability between subtypes of HLA-B27, concepts of disease mechanism remain ill-defined. In this article Richard Benjamin and Peter Parham synthesize new data on the structure and function of HLA class I molecules into possible mechanisms that might underly the pathogenesis of AS.

    View details for Web of Science ID A1990CX52700015

    View details for PubMedID 2187471



    A method for cloning full-length HLA-A,B cDNA (1.1 kilobases) by using the polymerase chain reaction (PCR) is described. Six HLA-A,B alleles (HLA-A2, -A25, -B7, -B37, -B51, and -B57) were cloned, and their structures were determined. Multiple PCR clones for each allele were sequenced to obtain both an accurate consensus sequence and an "authentic" clone having that sequence. Sequences from 50 clones encoding five different alleles permit assessment of the frequency and nature of PCR-produced errors. These include recombinations, deletions, and insertions in addition to point substitutions. Authentic clones were obtained at a frequency of between 30% and 70%, and analysis of three or four clones generally should be sufficient for characterization of an allele.

    View details for Web of Science ID A1990CX49700093

    View details for PubMedID 2320591



    The complete sequence of the beta adaptin subunit of the plasma membrane adaptor complex from coated vesicles has been elucidated. Complementary cDNA clones from human fibroblasts, rat lymphocytes, and bovine lymphocytes have been isolated, sequenced, and compared with each other and with beta adaptin sequences from rat brain (Kirchhausen, T., Nathanson, K.L., Matsui, W., Vaisberg, A., Chow, E.P., Burne, C., Keen, J.H., and Davis, A.E. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 2612-2616). Surprisingly, the 937-amino acid beta adaptin polypeptide is totally conserved between species. This remarkable homology contrasts with the absence of significant sequence similarity between the alpha (Robinson, M.S. (1989) J. Cell Biol. 108, 833-842) and beta adaptins of the plasma membrane adaptor complex. Diversity within each adaptin family is created by the expression of different genes and by tissue-specific differential splicing. The structures of the beta and alpha adaptins can both be divided into two globular domains interconnected by a variable and potentially flexible stalk domain.

    View details for Web of Science ID A1990CV58700010

    View details for PubMedID 1969413


    View details for Web of Science ID A1990CV32900001

    View details for PubMedID 2183407


    View details for Web of Science ID A1990CP69600005

    View details for PubMedID 2405272

  • COMPARISON OF CLASS-I MHC ALLELES IN HUMANS AND APES IMMUNOLOGICAL REVIEWS Lawlor, D. A., Warren, E., Ward, F. E., Parham, P. 1990; 113: 147-185

    View details for Web of Science ID A1990CT61100007

    View details for PubMedID 1690682



    In this introductory article, the structure and function of HLA class-I molecules is discussed. The differences between HLA-B27 and the other class-I molecules are described. It is suggested that HLA-B27 contributes to autoimmune phenomena, but little is known about the actual autoimmune mechanisms that cause the B27-associated disease.

    View details for Web of Science ID A1990EQ49900002

    View details for PubMedID 2259878


    View details for Web of Science ID A1990DA09800002

    View details for PubMedID 2188663


    View details for Web of Science ID A1989AQ98300002

    View details for PubMedID 2479625

  • DIVERSITY AND DIVERSIFICATION OF HLA-A,B,C ALLELES JOURNAL OF IMMUNOLOGY Parham, P., Lawlor, D. A., LOMEN, C. E., Ennis, P. D. 1989; 142 (11): 3937-3950


    The nucleotide sequences encoding 14 HLA-A,B,C and 5 ChLA-A,B,C molecules have been determined. Combining these sequences with published data has enabled the polymorphism in 40 HLA-A,B,C and 9 ChLA-A,B,C alleles to be analyzed. Diversity is generated through assortment of point mutations by recombinational mechanisms including gene and allelic conversions. The distribution and frequency of silent and replacement substitutions indicate that there has been positive selection for allelic diversity in the 5' part of the gene (exons 1 to 3) and for allelic homogenization and locus specificity in the 3' part of the gene (exons 4 to 8). These differences may correlate with the lengths of converted sequences in the two parts of the gene and frequency of the CpG dinucleotide. Locus-specific divergence of HLA-A,B, and C demonstrates that recombinational events involving alleles of a locus have been more important than conversion between loci. This contrasts with the predominance of gene conversion events in the evolution of mutants of the H-2Kb gene. However, a striking example of gene conversion involving HLA-B and C alleles of an oriental haplotype has been found. Comparison of human and chimpanzee alleles reveals extensive sharing of polymorphisms, confirming that diversification is a slow process, and that much of contemporary polymorphism originated in ancestral primate species before the emergence of Homo sapiens. There is less polymorphism at the HLA-A locus compared to HLA-B, with greater similarity also being seen between HLA-A and ChLA-A alleles than between HLA-B and ChLA-B alleles. Although greater diversity is seen in the 5' "variable" exons of HLA-B compared to HLA-A, there is increased heterogeneity in the 3' "conserved" exons of HLA-A compared to HLA-B.

    View details for Web of Science ID A1989U688300030

    View details for PubMedID 2715640

  • POLYMORPHISM IN THE ALPHA-3 DOMAIN OF HLA-A MOLECULES AFFECTS BINDING TO CD8 NATURE Salter, R. D., Norment, A. M., Chen, B. P., CLAYBERGER, C., KRENSKY, A. M., Littman, D. R., Parham, P. 1989; 338 (6213): 345-347


    Cytotoxic T lymphocytes (CTL) expressing the CD8 glycoprotein recognize peptide antigens presented by class I major histocompatibility complex (MHC) molecules. This correlation and the absence of CD8 polymorphism led to the hypothesis that CD8 binds to a conserved site of class I MHC molecules. Using a cell-cell binding assay we previously demonstrated specific interaction between human class I MHC (HLA-A,B,C) molecules and CD8. Subsequent analysis of the products of 17 HLA-A,B alleles revealed a natural polymorphism for CD8 binding in the human population. Two molecules, HLA-Aw68.1 and HLA-Aw68.2, which do not bind CD8, have a valine residue at position 245 whereas all other HLA-A,B,C molecules have alanine. Site-directed mutagenesis shows that this single substitution in the alpha 3 domain is responsible for the CD8 binding phenotype and also affects recognition by alloreactive and influenza-specific CTL. Our results indicate that CD8 binds to the alpha 3 domain of class I MHC molecules.

    View details for Web of Science ID A1989T800800061

    View details for PubMedID 2784196



    Activation of T lymphocytes requires the intracellular fragmentation of foreign antigens and their presentation by class I or class II major histocompatibility complex (MHC) glycoproteins. The direct binding of peptides to class II molecules has been demonstrated using equilibrium dialysis, gel filtration and fluorescence energy transfer at planar membranes, and its specificity compared to that of T-cell activation. In contrast, direct binding of peptides to class I molecules has been difficult to detect; although peptide sensitization experiments and the crystallographic structure of HLA-A2 (ref. 9) persuasively argue for its occurrence and importance. Here we describe a gel filtration assay from which we derive direct evidence for selective binding of an influenza matrix peptide to HLA-A2 and for binding of an influenza nucleoprotein peptide to HLA-B37. These two peptides have previously been shown to act respectively as targets for certain HLA-A2 or HLA-B37 restricted influenza-specific cytotoxic T lymphocytes (CTL). In addition we demonstrate binding to some, but not all, HLA allospecificities that cannot present these peptides to CTL. We estimate that less than 0.3% of the HLA molecules present in any given purified preparation were able to bind the added peptides.

    View details for Web of Science ID A1989T371500063

    View details for PubMedID 2918908



    Three forms of clathrin light chain contain two cysteine residues. These are the predominant brain-specific forms of LCa and LCb and the non-brain form of LCb. After purification in the absence of thiols they contain intramolecular disulphide bonds. The reduced and the oxidized forms show differences in electrophoretic mobility, explaining the variable and heterogeneous patterns observed on electrophoresis. Accessibility of the thiol groups in the free light chains is greater than when they are associated with the heavy chain. In contrast the cysteine residues of the clathrin heavy chain are completely inaccessible in the absence of denaturants and are not found in disulphide bonds. The antigenic properties of the oxidized and the reduced forms of the clathrin light chains are similar, as is their capacity to bind to the clathrin heavy chain. After isolation in the presence of 10 mM-iodoacetamide, the light-chain cysteine residues are fully alkylated. The results are consistent with the reduced form being the native state and the light-chain disulphide bonds an artifact of isolation.

    View details for Web of Science ID A1989T075000023

    View details for PubMedID 2930486


    View details for Web of Science ID A1989JX74500061

    View details for PubMedID 2700944

  • HLA-B51 AND HLA-BW52 DIFFER BY ONLY 2 AMINO-ACIDS WHICH ARE IN THE HELICAL REGION OF THE ALPHA-1 DOMAIN JOURNAL OF IMMUNOLOGY Hayashi, H., Ennis, P. D., Ariga, H., Salter, R. D., Parham, P., Kano, K., Takiguchi, M. 1989; 142 (1): 306-311


    Genes encoding the serologically cross-reactive HLA-B51 and HLA-Bw52 molecules were isolated and the exons sequenced. HLA-B51 genes obtained from Caucasian and Oriental individuals were identical. HLA-Bw52 differs from HLA-B51 by four nucleotide substitutions in exon 2 encoding the alpha 1 domain. These comprise one isolated silent substitution in codon 23 and a cluster of three coding substitutions in codons 63 and 67. Amino acid substitutions of N----E at position 63 and F----S at position 67 are the only differences between HLA-B51 and HLA-Bw52 and these residues are postulated to form HLA-B51 specific epitopes. HLA-B51 could have been formed from HLA-Bw52 by the combination of a genetic exchange with HLA-B8 and a point mutation. Similarity of HLA-B51 and HLA-Bw52 with HLA-Bw58 suggest they also share a common ancestor.

    View details for Web of Science ID A1989R577700045

    View details for PubMedID 2909619



    Human class I major histocompatibility complex, human leukocyte antigen (HLA)-A,B,C molecules are peptide-binding proteins that present degraded fragments of antigens to cytotoxic T lymphocytes. HLA-A,B,C loci are highly polymorphic and their products are strong alloantigens. Comparison of the primary structure of 39 HLA-A,B,C molecules shows that variation is found at many positions in the extracellular domains (alpha 1, alpha 2, and alpha 3). Positions with high variability are concentrated in and around the peptide-binding groove formed by the alpha 1- and alpha 2-domains and defined by crystallographic analysis of HLA-A2. It is likely that the polymorphic differences serve to alter both the peptide-binding specificity and the interaction with T cell receptors. This in turn may result in differences in immune responsiveness, susceptibility, and resistance to disease, and in alloantigenicity.

    View details for Web of Science ID A1988R586200002

    View details for PubMedID 2462346



    Complementary DNAs (cDNA) encoding the brain and non-brain forms of the human clathrin light chains LCa and LCb have been isolated, sequenced, and compared with their homologues in cow and rat. The significant differences that distinguish LCa from LCb and the brain from non-brain forms show remarkable preservation in all three species. These features include the position and sequence of the brain-specific inserts, a totally conserved region of 22 residues near the amino terminus, the LCb-specific phosphorylation site, the heavy chain binding site, and a distinctive pattern of cysteine residues near the carboxyl terminus. Unorthodox sequences for translation initiation and polyadenylation are found for LCb contrasting with LCa which exhibits orthodox regulatory sequences. Small insertions in human LCa revealed a duplicated sequence of 13 residues that flank the 22-residue conserved region. Only the carboxyl-terminal copy of this sequence is present in LCb. All sequences are consistent with the heavy chain binding site comprising an alpha-helical central region of the light chains. The hydrophobic face of this helix, which is presumed to interact with the heavy chain, is highly conserved between LCa and LCb, whereas the hydrophilic face shows considerable divergence. To help define the carboxyl-terminal limit of the heavy chain binding region, the epitope recognized by the CVC.6 monoclonal antibody was localized to residues 192-208 of LCa with glutamic acid 198 being of most importance. The faithful preservation of clathrin light chain polymorphism in three mammalian species provides evidence supporting a functional diversification of the brain and non-brain forms of LCa and LCb.

    View details for Web of Science ID A1988Q882600028

    View details for PubMedID 3267234

  • HLA-A AND HLA-B POLYMORPHISMS PREDATE THE DIVERGENCE OF HUMANS AND CHIMPANZEES NATURE Lawlor, D. A., Ward, F. E., Ennis, P. D., Jackson, A. P., Parham, P. 1988; 335 (6187): 268-271


    Major histocompatibility complex (MHC) glycoproteins bind processed fragments of proteins and present them to the receptors of T lymphocytes. The extraordinary polymorphism of class I MHC molecules in man (HLA-A, B and C) and mouse (H-2 K, D and L) poses many questions concerning their diversification and evolution. Comparison of allelic sequences within a species suggests diversity is generated by the assortment of point mutations into varied combinations by mechanisms of recombination and gene conversion. We have now compared class I MHC alleles in two closely related species: humans (Homo sapiens) and chimpanzees (Pan troglodytes). Chimpanzee homologues of HLA-A, HLA-B and a non-classical gene have been identified. No features distinguishing human and chimpanzee alleles could be found. Individual HLA-A or B alleles are more closely related to individual chimpanzee alleles than to other HLA-A or B alleles. These results show that a considerable proportion of contemporary HLA-A and B polymorphism existed before divergence of the chimpanzee and human lines. The stability of the polymorphism indicates that hyper-mutational mechanisms are not necessary to account for HLA-A, B and C diversity.

    View details for Web of Science ID A1988Q047700065

    View details for PubMedID 3412487

  • MOLECULAR-CLONING OF BOVINE CLASS-I MHC CDNA JOURNAL OF IMMUNOLOGY Ennis, P. D., Jackson, A. P., Parham, P. 1988; 141 (2): 642-651


    Two cDNA cloned from a Hereford cow B cell line (BL-3) have allowed the determination of the complete coding region for two class I molecules encoded by the bovine MHC (BoLA). The predicted protein sequences have all the features expected of expressed class I molecules that present peptide Ag to cytotoxic T cells. Comparison with class I molecules from other species strongly suggests these cDNA are derived from different genes and provides evidence for the existence of a second expressed class I BoLA locus. The BoLA proteins show greater similarity to HLA than to H-2 molecules, correlating with the cross-reactions of W6/32 and other murine anti-HLA-A,B,C mAb with BoLA molecules. The basis for the W6/32 epitope and the preferential association of H-2 class I H chains with bovine beta 2-m is examined.

    View details for Web of Science ID A1988P121200043

    View details for PubMedID 3133413



    Diversity in 39 HLA-A, -B, and -C molecules is derived from 20 amino acid positions of high variability and 71 positions of low variability. Variation in the structurally homologous alpha 1 and alpha 2 domains is distinct and may correlate with partial segregation of peptide and T-cell receptor binding functions. Comparison of 15 HLA-A with 20 HLA-B molecules reveals considerable locus-specific character, due primarily to differences at polymorphic residues. The results indicate that genetic exchange between alleles of the same locus has been a more important mechanism in the generation of HLA-A, -B, and -C diversity than genetic exchange events between alleles of different loci.

    View details for Web of Science ID A1988N799900073

    View details for PubMedID 3375250



    Clathrin light chains, LCa and LCb, are products of two closely related genes whose mRNAs undergo differential splicing to result in at least four different light chain isoforms. The physiological significance of clathrin light chain diversity remains unclear. To date, the only evidence for a functional distinction of LCa and LCb is the preferential phosphorylation of LCb, which takes place at serine residues and is mediated by coated vesicle-associated casein kinase II. As a first step toward determining the function of light chain diversity, we have mapped the in vitro phosphorylation sites on LCb. We use [32P]ATP to phosphorylate LCb within coated vesicles, followed by sequencing of 32P-labeled chymotryptic peptides thereof, to identify serine residues at positions 11 and 13 as the phosphorylation sites. We find that phosphorylation of LCb within coated vesicles can be inhibited by four monoclonal antibodies specific for different epitopes of the clathrin light chains.

    View details for Web of Science ID A1988N089800003

    View details for PubMedID 3128543



    The class-I and class-II molecules encoded by the major histocompatibility complex (MHC) are homologous proteins which allow cytotoxic and helper T cells to recognize foreign antigens. Recent studies have shown that the form of the antigen recognized by T cells is generally not a native protein but rather a short peptide fragment and that class-II molecules specifically bind antigenic peptides. Furthermore, the three-dimensional structure of the human MHC class-I molecule, HLA-A2, is consistent with a peptide-binding function for MHC class-I molecules. An outstanding question concerns the molecular nature and involvement of MHC-bound peptides in antigens recognized by alloreactive T cells. In this study the effects of peptides derived from HLA-A2 on cytolysis of alloreactive cytotoxic T cells (TC) cells are presented. Peptides can inhibit lysis by binding to the T cell or sensitize to lysis by binding an HLA-A2-related class-I molecule (HLA-Aw69) on the target cell. Thus, allospecific TC cells can recognize HLA-derived peptides in the context of the MHC.

    View details for Web of Science ID A1987L431600073

    View details for PubMedID 3501071


    View details for Web of Science ID A1987K095700022

    View details for PubMedID 2443449


    View details for Web of Science ID A1987K331400002

    View details for PubMedID 2445879

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