Stanford Advisors


All Publications


  • GSEApy: a comprehensive package for performing gene set enrichment analysis in Python. Bioinformatics (Oxford, England) Fang, Z., Liu, X., Peltz, G. 2022

    Abstract

    Gene Set enrichment analysis (GSEA) is a commonly used algorithm for characterizing gene expression changes. However, the currently available tools used to perform GSEA have a limited ability to analyze large datasets, which is particularly problematic for the analysis of single-cell data. To overcome this limitation, we developed a GSEA package in Python (GSEApy), which could efficiently analyze large single-cell datasets.We present a package (GSEApy) that performs GSEA in either the command line or Python environment. GSEApy uses a Rust implementation to enable it to calculate the same enrichment statistic as GSEA for a collection of pathways. The Rust implementation of GSEApy is 3-fold faster than the Numpy version of GSEApy (v0.10.8) and uses >4-fold less memory. GSEApy also provides an interface between Python and Enrichr web services, as well as for BioMart. The Enrichr API enables GSEApy to perform over-representation analysis for an input gene list. Furthermore, GSEApy consists of several tools, each designed to facilitate a particular type of enrichment analysis.The new GSEApy with Rust extension is deposited in PyPI: https://pypi.org/project/gseapy/. The GSEApy source code is freely available at https://github.com/zqfang/GSEApy. Also, the documentation website is available at https://gseapy.rtfd.io/.is available online.

    View details for DOI 10.1093/bioinformatics/btac757

    View details for PubMedID 36426870

  • An Automated Multi-Modal Graph-Based Pipeline for Mouse Genetic Discovery. Bioinformatics (Oxford, England) Fang, Z., Peltz, G. 2022

    Abstract

    Our ability to identify causative genetic factors for mouse genetic models of human diseases and biomedical traits has been limited by the difficulties associated with identifying true causative factors, which are often obscured by the many false positive genetic associations produced by a GWAS.To accelerate the pace of genetic discovery, we developed a graph neural network (GNN)-based automated pipeline (GNNHap) that could rapidly analyze mouse genetic model data and identify high probability causal genetic factors for analyzed traits. After assessing the strength of allelic associations with the strain response pattern; this pipeline analyzes 29M published papers to assess candidate gene-phenotype relationships; and incorporates the information obtained from a protein-protein interaction network and protein sequence features into the analysis. The GNN model produces markedly improved results relative to that of a simple linear neural network. We demonstrate that GNNHap can identify novel causative genetic factors for murine models of diabetes/obesity and for cataract formation, which were validated by the phenotypes appearing in previously analyzed gene knockout mice. The diabetes/obesity results indicate how characterization of the underlying genetic architecture enables new therapies to be discovered and tested by applying 'precision medicine' principles to murine models.The GNNHap source code is freely available at https://github.com/zqfang/gnnhap, and the new version of the HBCGM program is available at https://github.com/zqfang/haplomap.Supplementary information is available online.

    View details for DOI 10.1093/bioinformatics/btac356

    View details for PubMedID 35608290

  • A human multi-lineage hepatic organoid model for liver fibrosis. Nature communications Guan, Y., Enejder, A., Wang, M., Fang, Z., Cui, L., Chen, S., Wang, J., Tan, Y., Wu, M., Chen, X., Johansson, P. K., Osman, I., Kunimoto, K., Russo, P., Heilshorn, S. C., Peltz, G. 2021; 12 (1): 6138

    Abstract

    To investigate the pathogenesis of a congenital form of hepatic fibrosis, human hepatic organoids were engineered to express the most common causative mutation for Autosomal Recessive Polycystic Kidney Disease (ARPKD). Here we show that these hepatic organoids develop the key features of ARPKD liver pathology (abnormal bile ducts and fibrosis) in only 21 days. The ARPKD mutation increases collagen abundance and thick collagen fiber production in hepatic organoids, which mirrors ARPKD liver tissue pathology. Transcriptomic and other analyses indicate that the ARPKD mutation generates cholangiocytes with increased TGFbeta pathway activation, which are actively involved stimulating myofibroblasts to form collagen fibers. There is also an expansion of collagen-producing myofibroblasts with markedly increased PDGFRB protein expression and an activated STAT3 signaling pathway. Moreover, the transcriptome of ARPKD organoid myofibroblasts resemble those present in commonly occurring forms of liver fibrosis. PDGFRB pathway involvement was confirmed by the anti-fibrotic effect observed when ARPKD organoids were treated with PDGFRB inhibitors. Besides providing insight into the pathogenesis of congenital (and possibly acquired) forms of liver fibrosis, ARPKD organoids could also be used to test the anti-fibrotic efficacy of potential anti-fibrotic therapies.

    View details for DOI 10.1038/s41467-021-26410-9

    View details for PubMedID 34686668

  • Calcineurin A gamma and NFATc3/SRPX2 axis contribute to human embryonic stem cell differentiation JOURNAL OF CELLULAR PHYSIOLOGY Chen, H., Zeng, Y., Shao, M., Zhao, H., Fang, Z., Gu, J., Liao, B., Jin, Y. 2021; 236 (8): 5698-5713

    Abstract

    Our understanding of signaling pathways regulating the cell fate of human embryonic stem cells (hESCs) is limited. Calcineurin-NFAT signaling is associated with a wide range of biological processes and diseases. However, its role in controlling hESC fate remains unclear. Here, we report that calcineurin A gamma and the NFATc3/SRPX2 axis control the expression of lineage and epithelial-mesenchymal transition (EMT) markers in hESCs. Knockdown of PPP3CC, the gene encoding calcineurin A gamma, or NFATC3, downregulates certain markers both at the self-renewal state and during differentiation of hESCs. Furthermore, NFATc3 interacts with c-JUN and regulates the expression of SRPX2, the gene encoding a secreted glycoprotein known as a ligand of uPAR. We show that SRPX2 is a downstream target of NFATc3. Both SRPX2 and uPAR participate in controlling expression of lineage and EMT markers. Importantly, SRPX2 knockdown diminishes the upregulation of multiple lineage and EMT markers induced by co-overexpression of NFATc3 and c-JUN in hESCs. Together, this study uncovers a previously unknown role of calcineurin A gamma and the NFATc3/SRPX2 axis in modulating the fate determination of hESCs.

    View details for DOI 10.1002/jcp.30255

    View details for Web of Science ID 000604253100001

    View details for PubMedID 33393109

  • The Effect of Population Structure on Murine Genome-Wide Association Studies. Frontiers in genetics Wang, M., Fang, Z., Yoo, B., Bejerano, G., Peltz, G. 2021; 12: 745361

    Abstract

    The ability to use genome-wide association studies (GWAS) for genetic discovery depends upon our ability to distinguish true causative from false positive association signals. Population structure (PS) has been shown to cause false positive signals in GWAS. PS correction is routinely used for analysis of human GWAS results, and it has been assumed that it also should be utilized for murine GWAS using inbred strains. Nevertheless, there are fundamental differences between murine and human GWAS, and the impact of PS on murine GWAS results has not been carefully investigated. To assess the impact of PS on murine GWAS, we examined 8223 datasets that characterized biomedical responses in panels of inbred mouse strains. Rather than treat PS as a confounding variable, we examined it as a response variable. Surprisingly, we found that PS had a minimal impact on datasets measuring responses in ≤20 strains; and had surprisingly little impact on most datasets characterizing 21 - 40 inbred strains. Moreover, we show that true positive association signals arising from haplotype blocks, SNPs or indels, which were experimentally demonstrated to be causative for trait differences, would be rejected if PS correction were applied to them. Our results indicate because of the special conditions created by GWAS (the use of inbred strains, small sample sizes) PS assessment results should be carefully evaluated in conjunction with other criteria, when murine GWAS results are evaluated.

    View details for DOI 10.3389/fgene.2021.745361

    View details for PubMedID 34589118

  • SOX1 Is Required for the Specification of Rostral Hindbrain Neural Progenitor Cells from Human Embryonic Stem Cells ISCIENCE Liu, X., Fang, Z., Wen, J., Tang, F., Liao, B., Jing, N., Lai, D., Jin, Y. 2020; 23 (9): 101475

    Abstract

    Region-specific neural progenitor cells (NPCs) can be generated from human embryonic stem cells (hESCs) by modulating signaling pathways. However, how intrinsic transcriptional factors contribute to the neural regionalization is not well characterized. Here, we generate region-specific NPCs from hESCs and find that SOX1 is highly expressed in NPCs with the rostral hindbrain identity. Moreover, we find that OTX2 inhibits SOX1 expression, displaying exclusive expression between the two factors. Furthermore, SOX1 knockout (KO) leads to the upregulation of midbrain genes and downregulation of rostral hindbrain genes, indicating that SOX1 is required for specification of rostral hindbrain NPCs. Our SOX1 chromatin immunoprecipitation sequencing analysis reveals that SOX1 binds to the distal region of GBX2 to activate its expression. Overexpression of GBX2 largely abrogates SOX1-KO-induced aberrant gene expression. Taken together, this study uncovers previously unappreciated role of SOX1 in early neural regionalization and provides new information for the precise control of the OTX2/GBX2 interface.

    View details for DOI 10.1016/j.isci.2020.101475

    View details for Web of Science ID 000577096400002

    View details for PubMedID 32905879

    View details for PubMedCentralID PMC7486433

  • SOX21 Ensures Rostral Forebrain Identity by Suppression of WNT8B during Neural Regionalization of Human Embryonic Stem Cells STEM CELL REPORTS Fang, Z., Liu, X., Wen, J., Tang, F., Zhou, Y., Jing, N., Jin, Y. 2019; 13 (6): 1038-1052

    Abstract

    The generation of brain region-specific progenitors from human embryonic stem cells (hESCs) is critical for their application. However, transcriptional regulation of neural regionalization in humans is poorly understood. Here, we applied a rostrocaudal patterning system from hESCs to dissect global transcriptional networks controlling early neural regionalization. We found that SOX21 is required for rostral forebrain fate specification. SOX21 knockout led to activation of Wnt signaling, resulting in caudalization of regional identity of rostral forebrain neural progenitor cells. Moreover, we identified WNT8B as a SOX21 direct target. Deletion of WNT8B or inhibition of Wnt signaling in SOX21 knockout neural progenitor cells restored rostral forebrain identity. Furthermore, SOX21 interacted with β-catenin, interfering with the binding of TCF4/β-catenin complex to the WNT8B enhancer. Collectively, these results unveil the unknown role of SOX21 and shed light on how a transcriptional factor modulates early neural regionalization through crosstalk with a key component of Wnt signaling.

    View details for DOI 10.1016/j.stemcr.2019.10.013

    View details for Web of Science ID 000502098700008

    View details for PubMedID 31761677

    View details for PubMedCentralID PMC6915843

  • CDK11 safeguards the identity of human embryonic stem cells via fine-tuning signaling pathways JOURNAL OF CELLULAR PHYSIOLOGY Ding, J., Fang, Z., Liu, X., Zhu, Z., Wen, C., Wang, H., Gu, J., Li, Q., Zeng, R., Li, H., Jin, Y. 2020; 235 (5): 4279-4290

    Abstract

    Signaling pathways transmit extracellular cues into cells and regulate transcriptome and epigenome to maintain or change the cell identity. Protein kinases and phosphatases are critical for signaling transduction and regulation. Here, we report that CDK11, a member of the CDK family, is required for the maintenance of human embryonic stem cell (hESC) self-renewal. Our results show that, among the three main isoforms of CDK11, CDK11p46 is the main isoform safeguarding the hESC identity. Mechanistically, CDK11 constrains two important mitogen-activated protein kinase (MAPK) signaling pathways (JNK and p38 signaling) through modulating the activity of protein phosphatase 1. Furthermore, CDK11 knockdown activates transforming growth factor β (TGF-β)/SMAD2/3 signaling and upregulates certain nonneural differentiation-associated genes. Taken together, this study uncovers a kinase required for hESC self-renewal through fine-tuning MAPK and TGF-β signaling at appropriate levels. The kinase-phosphatase axis reported here may shed new light on the molecular mechanism sustaining the identity of hESCs.

    View details for DOI 10.1002/jcp.29305

    View details for Web of Science ID 000489904800001

    View details for PubMedID 31612516

  • Stk40 deletion elevates c-JUN protein level and impairs mesoderm differentiation JOURNAL OF BIOLOGICAL CHEMISTRY Hu, J., Li, S., Sun, X., Fang, Z., Wang, L., Xiao, F., Shao, M., Ge, L., Tang, F., Gu, J., Yu, H., Guo, Y., Guo, X., Liao, B., Jin, Y. 2019; 294 (25): 9959-9972
  • Transcription coactivator Cited1 acts as an inducer of trophoblast-like state from mouse embryonic stem cells through the activation of BMP signaling CELL DEATH & DISEASE Xu, Y., Luo, X., Fang, Z., Zheng, X., Zeng, Y., Zhu, C., Gu, J., Tang, F., Hu, Y., Hu, G., Jin, Y., Li, H. 2018; 9
  • Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos JOURNAL OF BIOLOGICAL CHEMISTRY Wen, J., Zeng, Y., Fang, Z., Gu, J., Ge, L., Tang, F., Qu, Z., Hu, J., Cui, Y., Zhang, K., Wang, J., Li, S., Sun, Y., Jin, Y. 2017; 292 (23): 9840-9854
  • Deletion of Stk40 impairs definitive erythropoiesis in the mouse fetal liver CELL DEATH & DISEASE Wang, L., Yu, H., Cheng, H., He, K., Fang, Z., Ge, L., Cheng, T., Jin, Y. 2017; 8
  • Itch, an E3 ligase of Oct4, is required for embryonic stem cell self-renewal and pluripotency induction JOURNAL OF CELLULAR PHYSIOLOGY Liao, B., Zhong, X., Xu, H., Xiao, F., Fang, Z., Gu, J., Chen, Y., Zhao, Y., Jin, Y. 2013; 228 (7): 1443-1451

    View details for DOI 10.1002/jcp.24297

    View details for Web of Science ID 000316681100010