Professional Education

  • Doctor of Philosophy, Eidgenossische Technische Hochschule (ETH Zurich) (2012)
  • Master of Science, Universitat Zurich (2007)

Stanford Advisors


All Publications

  • Ligand-based receptor identification on living cells and tissues using TRICEPS NATURE PROTOCOLS Frei, A. P., Moest, H., Novy, K., Wollscheid, B. 2013; 8 (7): 1321-1336


    Physiological responses to ligands such as peptides, proteins, pharmaceutical drugs or whole pathogens are generally mediated through interactions with specific cell surface protein receptors. Here we describe the application of TRICEPS, a specifically designed chemoproteomic reagent that can be coupled to a ligand of interest for the subsequent ligand-based capture of corresponding receptors on living cells and tissues. This is achieved by three orthogonal functionalities in TRICEPS-one that enables conjugation to an amino group containing ligands, a second for the ligand-based capture of glycosylated receptors on gently oxidized living cells and a biotin tag for purifying receptor peptides for analysis by quantitative mass spectrometry (MS). Specific receptors for the ligand of interest are identified through quantitative comparison of the identified peptides with a sample generated by a control probe with known (e.g., insulin) or no binding preferences (e.g., TRICEPS quenched with glycine). In combination with powerful statistical models, this ligand-based receptor capture (LRC) technology enables the unbiased and sensitive identification of one or several specific receptors for a given ligand under near-physiological conditions and without the need for genetic manipulations. LRC has been designed for applications with proteins but can easily be adapted for ligands ranging from peptides to intact viruses. In experiments with small ligands that bind to receptors with comparatively large extracellular domains, LRC can also reveal approximate ligand-binding sites owing to the defined spacer length of TRICEPS. Provided that sufficient quantities of the ligand and target cells are available, LRC can be carried out within 1 week.

    View details for DOI 10.1038/nprot.2013.072

    View details for Web of Science ID 000321004300005

    View details for PubMedID 23764939

  • Malfunctioning of adipocytes in obesity is linked to quantitative surfaceome changes BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS Moest, H., Frei, A. P., Bhattacharya, I., Geiger, M., Wollscheid, B., Wolfrum, C. 2013; 1831 (7): 1208-1216


    Increased triglyceride accumulation in adipocytes caused by a misbalance between energy intake and energy consumption, results in increased adipocyte size, excess adipose tissue, increased body weight and ultimately, obesity. It is well established that enlarged adipocytes exhibit malfunctions that contribute to whole body insulin resistance, a key factor for the development of type 2 diabetes. However, the underlying molecular cause for dysfunctional adipocyte behavior and signaling is poorly understood. Since the adipocyte cell surface proteome, or surfaceome, represents the cellular signaling gateway to the microenvironment, we studied the contribution of this subproteome to adipocyte malfunctions in obesity. By using the chemoproteomic Cell Surface Capture (CSC) technology, we established surfaceome maps of primary adipocytes derived from different mouse models for metabolic disorders. Relative quantitative comparison between these surfaceome maps revealed a set of cell surface glycoproteins with modulated location-specific abundance levels. RNAi mediated targeting of a subset of the detected obesity modulated cell surface glycoproteins in an in vitro model system provided functional evidence for their role in adiponectin secretion and the lipolytic activity of adipocytes. Thus, we conclude that the identified cell surface glycoproteins which exhibit obesity induced abundance changes and impact adipocyte function at the same time contribute to adipocyte malfunction in obesity. The regulation of their concerted activities could improve adipocyte function in obesity.

    View details for DOI 10.1016/j.bbalip.2013.04.001

    View details for Web of Science ID 000320497100003

    View details for PubMedID 23583721

  • A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis NATURE Picotti, P., Clement-Ziza, M., Lam, H., Campbell, D. S., Schmidt, A., Deutsch, E. W., Roest, H., Sun, Z., Rinner, O., Reiter, L., Shen, Q., Michaelson, J. J., Frei, A., Alberti, S., Kusebauch, U., Wollscheid, B., Moritz, R. L., Beyer, A., Aebersold, R. 2013; 494 (7436): 266-270


    Experience from different fields of life sciences suggests that accessible, complete reference maps of the components of the system under study are highly beneficial research tools. Examples of such maps include libraries of the spectroscopic properties of molecules, or databases of drug structures in analytical or forensic chemistry. Such maps, and methods to navigate them, constitute reliable assays to probe any sample for the presence and amount of molecules contained in the map. So far, attempts to generate such maps for any proteome have failed to reach complete proteome coverage. Here we use a strategy based on high-throughput peptide synthesis and mass spectrometry to generate an almost complete reference map (97% of the genome-predicted proteins) of the Saccharomyces cerevisiae proteome. We generated two versions of this mass-spectrometric map, one supporting discovery-driven (shotgun) and the other supporting hypothesis-driven (targeted) proteomic measurements. Together, the two versions of the map constitute a complete set of proteomic assays to support most studies performed with contemporary proteomic technologies. To show the utility of the maps, we applied them to a protein quantitative trait locus (QTL) analysis, which requires precise measurement of the same set of peptides over a large number of samples. Protein measurements over 78 S. cerevisiae strains revealed a complex relationship between independent genetic loci, influencing the levels of related proteins. Our results suggest that selective pressure favours the acquisition of sets of polymorphisms that adapt protein levels but also maintain the stoichiometry of functionally related pathway members.

    View details for DOI 10.1038/nature11835

    View details for Web of Science ID 000315137700046

    View details for PubMedID 23334424

  • Direct identification of ligand-receptor interactions on living cells and tissues NATURE BIOTECHNOLOGY Frei, A. P., Jeon, O., Kilcher, S., Moest, H., Henning, L. M., Jost, C., Plueckthun, A., Mercer, J., Aebersold, R., Carreira, E. M., Wollscheid, B. 2012; 30 (10): 997-?


    Many cellular responses are triggered by proteins, drugs or pathogens binding to cell-surface receptors, but it can be challenging to identify which receptors are bound by a given ligand. Here we describe TRICEPS, a chemoproteomic reagent with three moieties--one that binds ligands containing an amino group, a second that binds glycosylated receptors on living cells and a biotin tag for purifying the receptor peptides for identification by quantitative mass spectrometry. We validated this ligand-based, receptor-capture (LRC) technology using insulin, transferrin, apelin, epidermal growth factor, the therapeutic antibody trastuzumab and two DARPins targeting ErbB2. In some cases, we could also determine the approximate ligand-binding sites on the receptors. Using TRICEPS to label intact mature vaccinia viruses, we identified the cell surface proteins AXL, M6PR, DAG1, CSPG4 and CDH13 as binding factors on human cells. This technology enables the identification of receptors for many types of ligands under near-physiological conditions and without the need for genetic manipulations.

    View details for DOI 10.1038/nbt.2354

    View details for Web of Science ID 000309965500027

    View details for PubMedID 22983091

  • Proteomic Analysis Reveals Drug Accessible Cell Surface N-Glycoproteins of Primary and Established Glioblastoma Cell Lines JOURNAL OF PROTEOME RESEARCH Bock, T., Moest, H., Omasits, U., Dolski, S., Lundberg, E., Frei, A., Hofmann, A., Bausch-Fluck, D., Jacobs, A., Krayenbuehl, N., Uhlen, M., Aebersold, R., Frei, K., Wollscheid, B. 2012; 11 (10): 4885-4893


    Glioblastoma is the most common primary brain tumor in adults with low average survival time after diagnosis. In order to improve glioblastoma treatment, new drug-accessible targets need to be identified. Cell surface glycoproteins are prime drug targets due to their accessibility at the surface of cancer cells. To overcome the limited availability of suitable antibodies for cell surface protein detection, we performed a comprehensive mass spectrometric investigation of the glioblastoma surfaceome. Our combined cell surface capturing analysis of primary ex vivo glioblastoma cell lines in combination with established glioblastoma cell lines revealed 633 N-glycoproteins, which vastly extends the known data of surfaceome drug targets at subcellular resolution. We provide direct evidence of common glioblastoma cell surface glycoproteins and an approximate estimate of their abundances, information that could not be derived from genomic and/or transcriptomic glioblastoma studies. Apart from our pharmaceutically valuable repertoire of already and potentially drug-accessible cell surface glycoproteins, we built a mass-spectrometry-based toolbox enabling directed, sensitive, and repetitive glycoprotein measurements for clinical follow-up studies. The included Skyline Glioblastoma SRM assay library provides an elevated starting point for parallel testing of the abundance level of the detected glioblastoma surfaceome members in future drug perturbation experiments.

    View details for DOI 10.1021/pr300360a

    View details for Web of Science ID 000309441000011

    View details for PubMedID 22909291

  • RIP-chip-SRM a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans GENOME RESEARCH Jovanovic, M., Reiter, L., Clark, A., Weiss, M., Picotti, P., Rehrauer, H., Frei, A., Neukomm, L. J., Kaufman, E., Wollscheid, B., Simard, M. J., Miska, E. A., Aebersold, R., Gerber, A. P., Hengartner, M. O. 2012; 22 (7): 1360-1371


    MicroRNAs (miRNAs) are small, noncoding RNAs that negatively regulate gene expression. As miRNAs are involved in a wide range of biological processes and diseases, much effort has been invested in identifying their mRNA targets. Here, we present a novel combinatorial approach, RIP-chip-SRM (RNA-binding protein immunopurification + microarray + targeted protein quantification via selected reaction monitoring), to identify de novo high-confidence miRNA targets in the nematode Caenorhabditis elegans. We used differential RIP-chip analysis of miRNA-induced silencing complexes from wild-type and miRNA mutant animals, followed by quantitative targeted proteomics via selected reaction monitoring to identify and validate mRNA targets of the C. elegans bantam homolog miR-58. Comparison of total mRNA and protein abundance changes in mir-58 mutant and wild-type animals indicated that the direct bantam/miR-58 targets identified here are mainly regulated at the level of protein abundance, not mRNA stability.

    View details for DOI 10.1101/gr.133330.111

    View details for Web of Science ID 000306030000015

    View details for PubMedID 22454234

  • Loss of the RhoGAP SRGP-1 promotes the clearance of dead and injured cells in Caenorhabditis elegans (vol 13, pg 79, 2011) NATURE CELL BIOLOGY Neukomm, L. J., Frei, A. P., Cabello, J., Kinchen, J. M., Zaidel-Bar, R., Ma, Z., Haney, L. B., Hardin, J., Ravichandran, K. S., Moreno, S., Hengartner, M. O. 2011; 13 (2)
  • Loss of the RhoGAP SRGP-1 promotes the clearance of dead and injured cells in Caenorhabditis elegans NATURE CELL BIOLOGY Neukomm, L. J., Frei, A. P., Cabello, J., Kinchen, J. M., Zaidel-Bar, R., Ma, Z., Haney, L. B., Hardin, J., Ravichandran, K. S., Moreno, S., Hengartner, M. O. 2011; 13 (1): 79-U193


    Multicellular animals rapidly clear dying cells from their bodies. Many of the pathways that mediate this cell removal are conserved through evolution. Here, we identify srgp-1 as a negative regulator of cell clearance in both Caenorhabditis elegans and mammalian cells. Loss of srgp-1 function results in improved engulfment of apoptotic cells, whereas srgp-1 overexpression inhibits apoptotic cell corpse removal. We show that SRGP-1 functions in engulfing cells and functions as a GTPase activating protein (GAP) for CED-10 (Rac1). Interestingly, loss of srgp-1 function promotes not only the clearance of already dead cells, but also the removal of cells that have been brought to the verge of death through sublethal apoptotic, necrotic or cytotoxic insults. In contrast, impaired engulfment allows damaged cells to escape clearance, which results in increased long-term survival. We propose that C. elegans uses the engulfment machinery as part of a primitive, but evolutionarily conserved, survey mechanism that identifies and removes unfit cells within a tissue.

    View details for DOI 10.1038/ncb2138

    View details for Web of Science ID 000285502200014

    View details for PubMedID 21170032

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