Professional Education

  • Bachelor of Science, Zhongshan University (2004)
  • Doctor of Philosophy, University of Illinois Chicago (2010)

Stanford Advisors


All Publications

  • Autism-associated SHANK3 haploinsufficiency causes I-h channelopathy in human neurons SCIENCE Yi, F., Danko, T., Botelho, S. C., Patzke, C., Pak, C., Wernig, M., Sudhof, T. C. 2016; 352 (6286): 672-?


    Heterozygous SHANK3 mutations are associated with idiopathic autism and Phelan-McDermid syndrome. SHANK3 is a ubiquitously expressed scaffolding protein that is enriched in postsynaptic excitatory synapses. Here, we used engineered conditional mutations in human neurons and found that heterozygous and homozygous SHANK3 mutations severely and specifically impaired Ih channels. SHANK3 mutations caused alterations in neuronal morphology and synaptic connectivity; chronic pharmacological blockage of Ih channels reproduced these phenotypes, suggesting that they may be secondary to Ih-channel impairment. Moreover, mouse Shank3-deficient neurons also exhibited severe decreases in Ih currents. SHANK3 protein interacted with hyperpolarization-activated cyclic nucleotide-gated channel proteins (HCN proteins) forming Ih channels, indicating that SHANK3 functions to organize HCN channels. Our data suggest SHANK3 mutations predispose to autism, at least partially, by inducing an Ih channelopathy that may be amenable to pharmacological intervention.

    View details for DOI 10.1126/science.aaf2669

    View details for Web of Science ID 000375417100028

    View details for PubMedID 26966193

  • Human Neuropsychiatric Disease Modeling using Conditional Deletion Reveals Synaptic Transmission Defects Caused by Heterozygous Mutations in NRXN1. Cell stem cell Pak, C., Danko, T., Zhang, Y., Aoto, J., Anderson, G., Maxeiner, S., Yi, F., Wernig, M., Südhof, T. C. 2015; 17 (3): 316-328


    Heterozygous mutations of the NRXN1 gene, which encodes the presynaptic cell-adhesion molecule neurexin-1, were repeatedly associated with autism and schizophrenia. However, diverse clinical presentations of NRXN1 mutations in patients raise the question of whether heterozygous NRXN1 mutations alone directly impair synaptic function. To address this question under conditions that precisely control for genetic background, we generated human ESCs with different heterozygous conditional NRXN1 mutations and analyzed two different types of isogenic control and NRXN1 mutant neurons derived from these ESCs. Both heterozygous NRXN1 mutations selectively impaired neurotransmitter release in human neurons without changing neuronal differentiation or synapse formation. Moreover, both NRXN1 mutations increased the levels of CASK, a critical synaptic scaffolding protein that binds to neurexin-1. Our results show that, unexpectedly, heterozygous inactivation of NRXN1 directly impairs synaptic function in human neurons, and they illustrate the value of this conditional deletion approach for studying the functional effects of disease-associated mutations.

    View details for DOI 10.1016/j.stem.2015.07.017

    View details for PubMedID 26279266

  • Analysis of conditional heterozygous STXBP1 mutations in human neurons. journal of clinical investigation Patzke, C., Han, Y., Covy, J., Yi, F., Maxeiner, S., Wernig, M., Südhof, T. C. 2015; 125 (9): 3560-3571


    Heterozygous mutations in the syntaxin-binding protein 1 (STXBP1) gene, which encodes Munc18-1, a core component of the presynaptic membrane-fusion machinery, cause infantile early epileptic encephalopathy (Ohtahara syndrome), but it is unclear how a partial loss of Munc18-1 produces this severe clinical presentation. Here, we generated human ES cells designed to conditionally express heterozygous and homozygous STXBP1 loss-of-function mutations and studied isogenic WT and STXBP1-mutant human neurons derived from these conditionally mutant ES cells. We demonstrated that heterozygous STXBP1 mutations lower the levels of Munc18-1 protein and its binding partner, the t-SNARE-protein Syntaxin-1, by approximately 30% and decrease spontaneous and evoked neurotransmitter release by nearly 50%. Thus, our results confirm that using engineered human embryonic stem (ES) cells is a viable approach to studying disease-associated mutations in human neurons on a controlled genetic background, demonstrate that partial STXBP1 loss of function robustly impairs neurotransmitter release in human neurons, and suggest that heterozygous STXBP1 mutations cause early epileptic encephalopathy specifically through a presynaptic impairment.

    View details for DOI 10.1172/JCI78612

    View details for PubMedID 26280581

  • Eliminate mitochondrial diseases by gene editing in germ-line cells and embryos PROTEIN & CELL Wang, S., Yi, F., Qu, J. 2015; 6 (7): 472-475


    Nuclease-based gene editing technologies have opened up opportunities for correcting human genetic diseases. For the first time, scientists achieved targeted gene editing of mitochondrial DNA in mouse oocytes fused with patient cells. This fascinating progression may encourage the development of novel therapy for human maternally inherent mitochondrial diseases.

    View details for DOI 10.1007/s13238-015-0177-x

    View details for Web of Science ID 000357486900002

    View details for PubMedID 26081469

  • Aging stem cells. A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging. Science Zhang, W., Li, J., Suzuki, K., Qu, J., Wang, P., Zhou, J., Liu, X., Ren, R., Xu, X., Ocampo, A., Yuan, T., Yang, J., Li, Y., Shi, L., Guan, D., Pan, H., Duan, S., Ding, Z., Li, M., Yi, F., Bai, R., Wang, Y., Chen, C., Yang, F., Li, X., Wang, Z., Aizawa, E., Goebl, A., Soligalla, R. D., Reddy, P., Esteban, C. R., Tang, F., Liu, G., Belmonte, J. C. 2015; 348 (6239): 1160-1163


    Werner syndrome (WS) is a premature aging disorder caused by WRN protein deficiency. Here, we report on the generation of a human WS model in human embryonic stem cells (ESCs). Differentiation of WRN-null ESCs to mesenchymal stem cells (MSCs) recapitulates features of premature cellular aging, a global loss of H3K9me3, and changes in heterochromatin architecture. We show that WRN associates with heterochromatin proteins SUV39H1 and HP1α and nuclear lamina-heterochromatin anchoring protein LAP2β. Targeted knock-in of catalytically inactive SUV39H1 in wild-type MSCs recapitulates accelerated cellular senescence, resembling WRN-deficient MSCs. Moreover, decrease in WRN and heterochromatin marks are detected in MSCs from older individuals. Our observations uncover a role for WRN in maintaining heterochromatin stability and highlight heterochromatin disorganization as a potential determinant of human aging.

    View details for DOI 10.1126/science.aaa1356

    View details for PubMedID 25931448

  • Modelling Fanconi anemia pathogenesis and therapeutics using integration-free patient-derived iPSCs NATURE COMMUNICATIONS Liu, G., Suzuki, K., Li, M., Qu, J., Montserrat, N., Tarantino, C., Gu, Y., Yi, F., Xu, X., Zhang, W., Ruiz, S., Plongthongkum, N., Zhang, K., Masuda, S., Nivet, E., Tsunekawa, Y., Soligalla, R. D., Goebl, A., Aizawa, E., Kim, N. Y., Kim, J., Dubova, I., Li, Y., Ren, R., Benner, C., del Sol, A., Bueren, J., Pablo Trujillo, J., Surralles, J., Cappelli, E., Dufour, C., Esteban, C. R., Belmonte, J. C. 2014; 5


    Fanconi anaemia (FA) is a recessive disorder characterized by genomic instability, congenital abnormalities, cancer predisposition and bone marrow (BM) failure. However, the pathogenesis of FA is not fully understood partly due to the limitations of current disease models. Here, we derive integration free-induced pluripotent stem cells (iPSCs) from an FA patient without genetic complementation and report in situ gene correction in FA-iPSCs as well as the generation of isogenic FANCA-deficient human embryonic stem cell (ESC) lines. FA cellular phenotypes are recapitulated in iPSCs/ESCs and their adult stem/progenitor cell derivatives. By using isogenic pathogenic mutation-free controls as well as cellular and genomic tools, our model serves to facilitate the discovery of novel disease features. We validate our model as a drug-screening platform by identifying several compounds that improve hematopoietic differentiation of FA-iPSCs. These compounds are also able to rescue the hematopoietic phenotype of FA patient BM cells.

    View details for DOI 10.1038/ncomms5330

    View details for Web of Science ID 000340615500021

    View details for PubMedID 24999918

  • Progressive degeneration of human neural stem cells caused by pathogenic LRRK2 NATURE Liu, G., Qu, J., Suzuki, K., Nivet, E., Li, M., Montserrat, N., Yi, F., Xu, X., Ruiz, S., Zhang, W., Wagner, U., Kim, A., Ren, B., Li, Y., Goebl, A., Kim, J., Soligalla, R. D., Dubova, I., Thompson, J., Yates, J., Esteban, C. R., Sancho-Martinez, I., Izpisua Belmonte, J. C. 2012; 491 (7425): 603-607


    Nuclear-architecture defects have been shown to correlate with the manifestation of a number of human diseases as well as ageing. It is therefore plausible that diseases whose manifestations correlate with ageing might be connected to the appearance of nuclear aberrations over time. We decided to evaluate nuclear organization in the context of ageing-associated disorders by focusing on a leucine-rich repeat kinase 2 (LRRK2) dominant mutation (G2019S; glycine-to-serine substitution at amino acid 2019), which is associated with familial and sporadic Parkinson's disease as well as impairment of adult neurogenesis in mice. Here we report on the generation of induced pluripotent stem cells (iPSCs) derived from Parkinson's disease patients and the implications of LRRK2(G2019S) mutation in human neural-stem-cell (NSC) populations. Mutant NSCs showed increased susceptibility to proteasomal stress as well as passage-dependent deficiencies in nuclear-envelope organization, clonal expansion and neuronal differentiation. Disease phenotypes were rescued by targeted correction of the LRRK2(G2019S) mutation with its wild-type counterpart in Parkinson's disease iPSCs and were recapitulated after targeted knock-in of the LRRK2(G2019S) mutation in human embryonic stem cells. Analysis of human brain tissue showed nuclear-envelope impairment in clinically diagnosed Parkinson's disease patients. Together, our results identify the nucleus as a previously unknown cellular organelle in Parkinson's disease pathology and may help to open new avenues for Parkinson's disease diagnoses as well as for the potential development of therapeutics targeting this fundamental cell structure.

    View details for DOI 10.1038/nature11557

    View details for Web of Science ID 000311339800054

    View details for PubMedID 23075850

  • Establishment of hepatic and neural differentiation platforms of Wilson's disease specific induced pluripotent stem cells PROTEIN & CELL Yi, F., Qu, J., Li, M., Suzuki, K., Kim, N. Y., Liu, G., Izpisua Belmonte, J. C. 2012; 3 (11): 855-863


    The combination of disease-specific human induced pluripotent stem cells (iPSC) and directed cell differentiation offers an ideal platform for modeling and studying many inherited human diseases. Wilson's disease (WD) is a monogenic disorder of toxic copper accumulation caused by pathologic mutations of the ATP7B gene. WD affects multiple organs with primary manifestations in the liver and central nervous system (CNS). In order to better investigate the cellular pathogenesis of WD and to develop novel therapies against various WD syndromes, we sought to establish a comprehensive platform to differentiate WD patient iPSC into both hepatic and neural lineages. Here we report the generation of patient iPSC bearing a Caucasian population hotspot mutation of ATP7B. Combining with directed cell differentiation strategies, we successfully differentiated WD iPSC into hepatocyte-like cells, neural stem cells and neurons. Gene expression analysis and cDNA sequencing confirmed the expression of the mutant ATP7B gene in all differentiated cells. Hence we established a platform for studying both hepatic and neural abnormalities of WD, which may provide a new tool for tissue-specific disease modeling and drug screening in the future.

    View details for DOI 10.1007/s13238-012-2064-z

    View details for Web of Science ID 000310970600008

    View details for PubMedID 22806248

  • Rejuvenating liver and pancreas through cell transdifferentiation CELL RESEARCH Yi, F., Liu, G., Izpisua Belmonte, J. C. 2012; 22 (4): 616-619

    View details for DOI 10.1038/cr.2012.33

    View details for Web of Science ID 000302351800003

    View details for PubMedID 22373548

  • Human induced pluripotent stem cells derived hepatocytes: rising promise for disease modeling, drug development and cell therapy PROTEIN & CELL Yi, F., Liu, G., Izpisua Belmonte, J. C. 2012; 3 (4): 246-250


    Recent advances in the study of human hepatocytes derived from induced pluripotent stem cells (iPSC) represent new promises for liver disease study and drug discovery. Human hepatocytes or hepatocyte-like cells differentiated from iPSC recapitulate many functional properties of primary human hepatocytes and have been demonstrated as a powerful and efficient tool to model human liver metabolic diseases and facilitate drug development process. In this review, we summarize the recent progress in this field and discuss the future perspective of the application of human iPSC derived hepatocytes.

    View details for DOI 10.1007/s13238-012-2918-4

    View details for Web of Science ID 000310527600002

    View details for PubMedID 22441839

  • Opposing effects of Tcf3 and Tcf1 control Wnt stimulation of embryonic stem cell self-renewal NATURE CELL BIOLOGY Yi, F., Pereira, L., Hoffman, J. A., Shy, B. R., Yuen, C. M., Liu, D. R., Merrill, B. J. 2011; 13 (7): 762-U383


    The co-occupancy of Tcf3 with Oct4, Sox2 and Nanog on embryonic stem cell (ESC) chromatin indicated that Tcf3 has been suggested to play an integral role in a poorly understood mechanism underlying Wnt-dependent stimulation of mouse ESC self-renewal of mouse ESCs. Although the conventional view of Tcf proteins as the β-catenin-binding effectors of Wnt signalling suggested Tcf3-β-catenin activation of target genes would stimulate self-renewal, here we show that an antagonistic relationship between Wnt3a and Tcf3 on gene expression regulates ESC self-renewal. Genetic ablation of Tcf3 replaced the requirement for exogenous Wnt3a or GSK3 inhibition for ESC self-renewal, demonstrating that inhibition of Tcf3 repressor is the necessary downstream effect of Wnt signalling. Interestingly, both Tcf3-β-catenin and Tcf1-β-catenin interactions contributed to Wnt stimulation of self-renewal and gene expression, and the combination of Tcf3 and Tcf1 recruited Wnt-stabilized β-catenin to Oct4 binding sites on ESC chromatin. This work elucidates the molecular link between the effects of Wnt and the regulation of the Oct4/Sox2/Nanog network.

    View details for DOI 10.1038/ncb2283

    View details for Web of Science ID 000292305700006

    View details for PubMedID 21685894

  • Targeted Gene Correction of Laminopathy-Associated LMNA Mutations in Patient-Specific iPSCs CELL STEM CELL Liu, G., Suzuki, K., Qu, J., Sancho-Martinez, I., Yi, F., Li, M., Kumar, S., Nivet, E., Kim, J., Soligalla, R. D., Dubova, I., Goebl, A., Plongthongkum, N., Fung, H., Zhang, K., Loring, J. F., Laurent, L. C., Izpisua Belmonte, J. C. 2011; 8 (6): 688-694


    Combination of stem cell-based approaches with gene-editing technologies represents an attractive strategy for studying human disease and developing therapies. However, gene-editing methodologies described to date for human cells suffer from technical limitations including limited target gene size, low targeting efficiency at transcriptionally inactive loci, and off-target genetic effects that could hamper broad clinical application. To address these limitations, and as a proof of principle, we focused on homologous recombination-based gene correction of multiple mutations on lamin A (LMNA), which are associated with various degenerative diseases. We show that helper-dependent adenoviral vectors (HDAdVs) provide a highly efficient and safe method for correcting mutations in large genomic regions in human induced pluripotent stem cells and can also be effective in adult human mesenchymal stem cells. This type of approach could be used to generate genotype-matched cell lines for disease modeling and drug discovery and potentially also in therapeutics.

    View details for DOI 10.1016/j.stem.2011.04.019

    View details for Web of Science ID 000291844100016

    View details for PubMedID 21596650

  • Canonical Wnt/beta-Catenin Regulation of Liver Receptor Homolog-1 Mediates Pluripotency Gene Expression STEM CELLS Wagner, R. T., Xu, X., Yi, F., Merrill, B. J., Cooney, A. J. 2010; 28 (10): 1794-1804


    Delineating the signaling pathways that underlie ESC pluripotency is paramount for development of ESC applications in both the research and clinical settings. In culture pluripotency is maintained by leukemia inhibitory factor (LIF) stimulation of two separate signaling axes: Stat3/Klf4/Sox2 and PI3K/Tbx3/Nanog, which converge in the regulation of Oct4 expression. However, LIF signaling is not required in vivo for self-renewal, thus alternate signaling axes likely mediate these pathways. Additional factors that promote pluripotency gene expression have been identified, including the direct regulation of Oct4 by liver receptor homolog-1 (Lrh-1) and β-catenin regulation of Nanog. Here, we present genetic, molecular, and pharmacological studies identifying a signaling axis in which β-catenin promotes pluripotency gene expression in an Lrh-1-dependent manner. Furthermore, Lrh-1 was identified as a novel β-catenin target gene, and Lrh-1 regulation is required for maintaining proper levels of Oct4, Nanog, and Tbx3. Elucidation of this pathway provides an alternate mechanism by which the primary pluripotency axis may be regulated in vivo and may pave the way for small molecule applications to manipulate pluripotency or improve the efficiency of somatic cell reprogramming.

    View details for DOI 10.1002/stem.502

    View details for Web of Science ID 000284104100009

    View details for PubMedID 20734354

  • Non-cell-autonomous stimulation of stem cell proliferation following ablation of Tcf3 EXPERIMENTAL CELL RESEARCH Yi, F., Merrill, B. J. 2010; 316 (6): 1050-1060


    A combination of cell intrinsic factors and extracellular signals determine whether mouse embryonic stem cells (ESC) divide, self-renew, and differentiate. Here, we report a new interaction between cell intrinsic aspects of the canonical Wnt/Tcf/beta-catenin signaling pathway and extracellular Lif/Jak/Stat3 stimulation that combines to promote self-renewal and proliferation of ESC. Mutant ESC lacking the Tcf3 transcriptional repressor continue to self-renew in the absence of exogenous Lif and through pharmacological inhibition of Lif/Jak/Stat3 signaling; however, proliferation rates of TCF3-/- ESC were significantly decreased by inhibiting Jak/Stat3 activity. Cell mixing experiments showed that stimulation of Stat3 phosphorylation in TCF3-/- ESC was mediated through secretion of paracrine acting factors, but did not involve elevated Lif or LifR transcription. The new interaction between Wnt and Lif/Jak/Stat3 signaling pathways has potential for new insights into the growth of tumors caused by aberrant activity of Wnt/Tcf/beta-catenin signaling.

    View details for DOI 10.1016/j.yexcr.2009.12.005

    View details for Web of Science ID 000275986000016

    View details for PubMedID 20006604

  • Tcf3 functions as a steady-state limiter of transcriptional programs of mouse embryonic stem cell self-renewal STEM CELLS Yi, F., Pereira, L., Merrill, B. J. 2008; 26 (8): 1951-1960


    Elucidating the underlying transcriptional control of pluripotent cells is necessary for the development of new methods of inducing and maintaining pluripotent cells in vitro. Three transcription factors, Nanog, Oct4, and Sox2, have been reported to form a feedforward circuit promoting pluripotent cell self-renewal in embryonic stem cells (ESC). Previously, we found that a transcriptional repressor activity of Tcf3, a DNA-binding effector of Wnt signaling, reduced Nanog promoter activity and Nanog levels in mouse embryonic stem cells (mESC). The objective of this study was to determine the scope of Tcf3 effects on gene expression and self-renewal beyond the regulation of Nanog levels. We show that Tcf3 acts broadly on a genome-wide scale to reduce the levels of several promoters of self-renewal (Nanog, Tcl1, Tbx3, Esrrb) while not affecting other ESC genes (Oct4, Sox2, Fgf4). Comparing effects of Tcf3 ablation with Oct4 or Nanog knockdown revealed that Tcf3 counteracted effects of both Nanog and Oct4. Interestingly, the effects of Tcf3 were more strongly correlated with Oct4 than with Nanog, despite the normal levels of Oct4 in TCF3-/- mESC. The deranged gene expression allowed TCF3-/- mESC self-renewal even in the absence of leukemia inhibitory factor and delayed differentiation in embryoid bodies. These findings identify Tcf3 as a cell-intrinsic inhibitor of pluripotent cell self-renewal that functions by limiting steady-state levels of self-renewal factors. Disclosure of potential conflicts of interest is found at the end of this article.

    View details for DOI 10.1634/stemcells.2008-0229

    View details for Web of Science ID 000258297500004

    View details for PubMedID 18483421

  • Repression of Nanog gene transcription by Tcf3 limits embryonic stem cell self-renewal MOLECULAR AND CELLULAR BIOLOGY Pereira, L., Yi, F., Merrill, B. J. 2006; 26 (20): 7479-7491


    The dual function of stem cells requires them not only to form new stem cells through self-renewal but also to form lineage-committed cells through differentiation. Embryonic stem cells (ESC), which are derived from the blastocyst inner cell mass, retain properties of self-renewal and the potential for lineage commitment. To balance self-renewal and differentiation, ESC must carefully control the levels of several transcription factors, including Nanog, Sox2, and Oct4. While molecular mechanisms promoting transcription of these genes have been described, mechanisms preventing excessive levels in self-renewing ESC remain unknown. By examining the function of the TCF family of transcription factors in ESC, we have found that Tcf3 is necessary to limit the steady-state levels of Nanog mRNA, protein, and promoter activity in self-renewing ESC. Chromatin immunoprecipitation and promoter reporter assays showed that Tcf3 bound to a promoter regulatory region of the Nanog gene and repressed its transcriptional activity in ESC through a Groucho interaction domain-dependent process. The absence of Tcf3 caused delayed differentiation of ESC in vitro as elevated Nanog levels persisted through 5 days of embryoid body formation. These new data support a model wherein Tcf3-mediated control of Nanog levels allows stem cells to balance the creation of lineage-committed and undifferentiated cells.

    View details for DOI 10.1128/MCB.00368-06

    View details for Web of Science ID 000241252300012

    View details for PubMedID 16894029