Stanford Advisors

All Publications

  • Deciphering pathogenicity of variants of uncertain significance with CRISPR-edited iPSCs. Trends in genetics : TIG Guo, H., Liu, L., Nishiga, M., Cong, L., Wu, J. C. 2021


    Genetic variants play an important role in conferring risk for cardiovascular diseases (CVDs). With the rapid development of next-generation sequencing (NGS), thousands of genetic variants associated with CVDs have been identified by genome-wide association studies (GWAS), but the function of more than 40% of genetic variants is still unknown. This gap of knowledge is a barrier to the clinical application of the genetic information. However, determining the pathogenicity of a variant of uncertain significance (VUS) is challenging due to the lack of suitable model systems and accessible technologies. By combining clustered regularly interspaced short palindromic repeats (CRISPR) and human induced pluripotent stem cells (iPSCs), unprecedented advances are now possible in determining the pathogenicity of VUS in CVDs. Here, we summarize recent progress and new strategies in deciphering pathogenic variants for CVDs using CRISPR-edited human iPSCs.

    View details for DOI 10.1016/j.tig.2021.08.009

    View details for PubMedID 34509299

  • Generation of three induced pluripotent stem cell lines, SCVIi003-A, SCVIi004-A, SCVIi005-A, from patients with ARVD/C caused by heterozygous mutations in the PKP2 gene. Stem cell research Jahng, J. W., Black, K. E., Liu, L., Bae, H. R., Perez, M., Ashley, E. A., Sallam, K., Wu, J. C. 2021; 53: 102284


    Arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C) is an inherited heart disease which can cause life-threatening ventricular arrhythmias and cardiac dysfunction. The autosomal dominant form of ARVD/C is caused by mutations in the cardiac desmosome, such as those in the plakoglobin plakophilin-2 (PKP2) gene. Here, we generated three human induced pluripotent stem cell (iPSC) lines from the peripheral blood mononuclear cells (PBMCs) of three ARVD/C patients carrying pathogenic variants in their PKP2 genes (c.2065_2070delinsG; c.235C>T; c.1725_1728dup). All lines show the typical morphology of pluripotent stem cells, demonstrate high expression of pluripotent markers, display normal karyotype, and differentiate into all three germ layers in vitro. These lines are valuable resources for studying the pathological mechanisms of ARVD/C caused by PKP2 mutation.

    View details for DOI 10.1016/j.scr.2021.102284

    View details for PubMedID 33743362

  • Generation of two heterozygous MYBPC3 mutation-carrying human iPSC lines, SCVIi001-A and SCVIi002-A, for modeling hypertrophic cardiomyopathy. Stem cell research Liu, L., Shenoy, S. P., Jahng, J. W., Liu, Y., Knowles, J. W., Zhuge, Y., Wu, J. C. 2021; 53: 102279


    Hypertrophic cardiomyopathy (HCM) is an inherited heart disease that can cause sudden cardiac death and heart failure. HCM often arises from mutations in sarcomeric genes, among which the MYBPC3 is the most frequently mutated. Here we generated two human induced pluripotent stem cell (iPSC) lines from a HCM patient who has a familial history of HCM and his daughter who carries the pathogenic non-coding mutation. All lines show the typical morphology of pluripotent cells, a high expression of pluripotency markers, normal karyotype, and in vitro capacity to differentiate into all three germ layers. These lines provide a valuable resource for studying the molecular basis of HCM and drug screening for HCM.

    View details for DOI 10.1016/j.scr.2021.102279

    View details for PubMedID 33743363

  • Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation CELL REPORTS Lu, J., Shao, W., Chang, L., Yin, Y., Li, T., Zhang, H., Hong, Y., Percharde, M., Guo, L., Wu, Z., Liu, L., Liu, W., Yan, P., Ramalho-Santos, M., Sun, Y., Shen, X. 2020; 30 (10): 3296-+


    Repetitive elements are abundantly distributed in mammalian genomes. Here, we reveal a striking association between repeat subtypes and gene function. SINE, L1, and low-complexity repeats demarcate distinct functional categories of genes and may dictate the time and level of gene expression by providing binding sites for different regulatory proteins. Importantly, imaging and sequencing analysis show that L1 repeats sequester a large set of genes with specialized functions in nucleolus- and lamina-associated inactive domains that are depleted of SINE repeats. In addition, L1 transcripts bind extensively to its DNA in embryonic stem cells (ESCs). Depletion of L1 RNA in ESCs leads to relocation of L1-enriched chromosomal segments from inactive domains to the nuclear interior and de-repression of L1-associated genes. These results demonstrate a role of L1 DNA and RNA in gene silencing and suggest a general theme of genomic repeats in orchestrating the function, regulation, and expression of their host genes.

    View details for DOI 10.1016/j.celrep.2020.02.048

    View details for Web of Science ID 000519189700010

    View details for PubMedID 32160538

    View details for PubMedCentralID PMC7195444

  • Tumor Repressor Circular RNA as a New Target for Preventative Gene Therapy Against Doxorubicin-Induced Cardiotoxicity. Circulation research Jahng, J. W., Liu, L. n., Wu, J. C. 2020; 127 (4): 483–85

    View details for DOI 10.1161/CIRCRESAHA.120.317568

    View details for PubMedID 32762533

  • IDH1 fine-tunes cap-dependent translation initiation JOURNAL OF MOLECULAR CELL BIOLOGY Liu, L., Lu, J., Li, F., Xing, X., Li, T., Yang, X., Shen, X. 2019; 11 (10): 816-828


    The metabolic enzyme isocitrate dehydrogenase 1 (IDH1) catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG). Its mutation often leads to aberrant gene expression in cancer. IDH1 was reported to bind thousands of RNA transcripts in a sequence-dependent manner; yet, the functional significance of this RNA-binding activity remains elusive. Here, we report that IDH1 promotes mRNA translation via direct associations with polysome mRNA and translation machinery. Comprehensive proteomic analysis in embryonic stem cells (ESCs) revealed striking enrichment of ribosomal proteins and translation regulators in IDH1-bound protein interactomes. We performed ribosomal profiling and analyzed mRNA transcripts that are associated with actively translating polysomes. Interestingly, knockout of IDH1 in ESCs led to significant downregulation of polysome-bound mRNA in IDH1 targets and subtle upregulation of ribosome densities at the start codon, indicating inefficient translation initiation upon loss of IDH1. Tethering IDH1 to a luciferase mRNA via the MS2-MBP system promotes luciferase translation, independently of the catalytic activity of IDH1. Intriguingly, IDH1 fails to enhance luciferase translation driven by an internal ribosome entry site. Together, these results reveal an unforeseen role of IDH1 in fine-tuning cap-dependent translation via the initiation step.

    View details for DOI 10.1093/jmcb/mjz082

    View details for Web of Science ID 000505828900003

    View details for PubMedID 31408165

    View details for PubMedCentralID PMC6884706

  • Insight into novel RNA-binding activities via large-scale analysis of lncRNA-bound proteome and IDH1-bound transcriptome NUCLEIC ACIDS RESEARCH Liu, L., Li, T., Song, G., He, Q., Yin, Y., Lu, J., Bi, X., Wang, K., Luo, S., Chen, Y., Yang, Y., Sun, B., Yang, Y., Wu, J., Zhu, H., Shen, X. 2019; 47 (5): 2244-2262


    RNA-binding proteins (RBPs) play pivotal roles in directing RNA fate and function. Yet the current annotation of RBPs is largely limited to proteins carrying known RNA-binding domains. To systematically reveal dynamic RNA-protein interactions, we surveyed the human proteome by a protein array-based approach and identified 671 proteins with RNA-binding activity. Among these proteins, 525 lack annotated RNA-binding domains and are enriched in transcriptional and epigenetic regulators, metabolic enzymes, and small GTPases. Using an improved CLIP (crosslinking and immunoprecipitation) method, we performed genome-wide target profiling of isocitrate dehydrogenase 1 (IDH1), a novel RBP. IDH1 binds to thousands of RNA transcripts with enriched functions in transcription and chromatin regulation, cell cycle and RNA processing. Purified IDH1, but not an oncogenic mutant, binds directly to GA- or AU-rich RNA that are also enriched in IDH1 CLIP targets. Our study provides useful resources of unconventional RBPs and IDH1-bound transcriptome, and convincingly illustrates, for the first time, the in vivo and in vitro RNA targets and binding preferences of IDH1, revealing an unanticipated complexity of RNA regulation in diverse cellular processes.

    View details for DOI 10.1093/nar/gkz032

    View details for Web of Science ID 000467963700015

    View details for PubMedID 30698743

    View details for PubMedCentralID PMC6412114

  • Mouse knockout models reveal largely dispensable but context-dependent functions of lncRNAs during development JOURNAL OF MOLECULAR CELL BIOLOGY Han, X., Luo, S., Peng, G., Lu, J., Cui, G., Liu, L., Yan, P., Yin, Y., Liu, W., Wang, R., Zhang, J., Ai, S., Chang, Z., Na, J., He, A., Jing, N., Shen, X. 2018; 10 (2): 175-178

    View details for DOI 10.1093/jmcb/mjy003

    View details for Web of Science ID 000432613200009

    View details for PubMedID 29420831

  • Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells CELL STEM CELL Luo, S., Lu, Y., Liu, L., Yin, Y., Chen, C., Han, X., Wu, B., Xu, R., Liu, W., Yan, P., Shao, W., Lu, Z., Li, H., Na, J., Tang, F., Wang, J., Zhang, Y. E., Shen, X. 2016; 18 (5): 637-652


    Divergent lncRNAs that are transcribed in the opposite direction to nearby protein-coding genes comprise a significant proportion (∼20%) of total lncRNAs in mammalian genomes. Through genome-wide analysis, we found that the distribution of this lncRNA class strongly correlates with essential developmental regulatory genes. In pluripotent cells, divergent lncRNAs regulate the transcription of nearby genes. As an example, the divergent lncRNA Evx1as promotes transcription of its neighbor gene, EVX1, and regulates mesendodermal differentiation. At a single-cell level, early broad expression of Evx1as is followed by a rapid, high-level transcription of EVX1, supporting the idea that Evx1as plays an upstream role to facilitate EVX1 transcription. Mechanistically, Evx1as RNA binds to regulatory sites on chromatin, promotes an active chromatin state, and interacts with Mediator. Based on our analyses, we propose that the biological function of thousands of uncharacterized lncRNAs of this class may be inferred from the role of their neighboring adjacent genes.

    View details for DOI 10.1016/j.stem.2016.01.024

    View details for Web of Science ID 000375594200014

    View details for PubMedID 26996597