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Publications (selected)

2023 ~ present (as a PI): Stem Cells, Bioinformatics, and B-cell Homeostasis

  • Navarro-Corcuera A, Zhu Y, Ma F, Gupta N, Asplund H, et al. and Huang X#, Cai B#. (2024) Resolvin D1–mediated cellular crosstalk protects against MASH. JHEP Reports (#co-corresponding, accepted, preprint available at BioRxiv).​

  • Huang X#, Balmer S, Lyu C, Xiang Y, et al. and Wang J#. (2024) ZFP281 controls transcriptional and epigenetic changes promoting mouse pluripotent state transitions via DNMT3 and TET1. Developmental Cell 59(4), 465-481. (#co-corresponding).​​

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  • Malik V, Huang X, Zhou H, Bojar R, Soni RK, Landry DW, Jelic S, and Wang, J. (2025). Multomics reveal biomolecular shifts and ER-stress in sleep-restricted women affecting NSC functions. iScience (accepted).

  • Ma F, Longo M, Meroni M, et al, and Huang X, Yurdagul Jr A, Rom O, Wang L, Fried SK, Dongiovanni P, Friedman S, Cai B. (2025) EHBP1 suppresses liver fibrosis in metabolic dysfunction-associated steatohepatitis. Cell Metabolism (online, doi.org/10.1016 /j.cmet.2025.01.020)

  • Yuan F, Yang J, Ma F, Hu Z, Malik V, Zang R, Li D, Shi X, Huang X, Zhou H, and Wang J (2025) Pluripotency factor Tex10 finetunes Wnt signaling for spermatogenesis and primordial germ cell development. Nature Communications 16:1900

  • ​Yan XZ, Peng J, Liu YQ, et al. and Huang X, Tan SH, and Wang HL. (2025) Mixed exposure to PFOA and PFOS induces oocyte apoptosis and subfertility in mice by activating the Hippo signaling pathway. Reproductive Toxicology 132:108829. 

  • Shi X, Li Y, Zhou H, Hou X, Yang J, Malik V, et al. and Huang X, Chen Y, and Wang J. (2024). DDX18 coordinates nucleolus phase separation and chromatin organization to control the pluripotency of human embryonic stem cells. Nature Communications 15:10803

  • Zhang X, Zhang X, Huang X, Iqbal J, et al. and Fu K. (2024) MiR-17∼92 is involved in NF-κB activation via targeting the ubiquitin-editing proteins to mediate RIP1 complex polyubiquitinations in ABC-DLBCL. Clinical Immunology doi: 10.1016/j.clim.2024.110297. 

  • Ma F, Huang X, and Cai B. (2024) Linking MASLD to ACVD through Kupffer cells. Nature Cardiovascular Research 3:258–259.

2014 ~ 2022 (as a trainee): Epigenetics, Pluripotency, and Early Development

  • Huang X, Bashkenova N, Hong Y, C Lyu, et al. and Wang J. (2022) A TET1-PSPC1-Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency. Cell Reports 39 (10), 110928.

  • Huang X*, Park KM*, Gontarz P, Zhang B, Pan J, McKenzie Z, et al. and Wang J, Theunissen TW. (2021) OCT4 cooperates with distinct ATP dependent chromatin remodelers in naïve and primed pluripotent states in human. Nature Communications 12:5123 (*co-first).

  • Yang F*, Huang X*, Zang R*, Chen J, et al. and Gao S, Wang J. (2020) DUX-miR-344-ZMYM2-mediated activation of MERVL LTRs induces a totipotent 2C-like state. Cell Stem Cell 26, 234-250. (*co-first).

  • Huang X, Bashkenova N, Yang J, Li D, and Wang J. (2021) Zfp281 recruits polycomb repressive complex 2 to restrict extraembryonic endoderm potential in safeguarding embryonic stem cell pluripotency. Protein & Cell 12(3), 213-219.

  • Huang X, Balmer S, Yang F, et al. and Wang J. (2017) Zfp281 is essential for epiblast maturation through transcriptional control of Nodal Signaling in the mouse embryo. eLife 6:e33333.

  • Huang X, Wang J. (2017) Mitotic bookmarking: maintaining the stem cell identity during mitosis. Cell Stem Cell 20:741-42.

  • Huang X, Wang J. (2017) A determined "hesitation" on H3K27me3 empowers stem cells to differentiate. Molecular Cell 66:165–66.

  • Huang X, Wang J. (2014) The extended pluripotency protein interactome and its links to reprogramming. Current Opinion in Genetics & Development 28:16–24.

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  • Nobre AR, Dalla E, Yang J, Huang X, Wullkopf L, et al. and Wang J, Aguirre-Ghiso JA. (2022) ZFP281 drives a mesenchymal-like dormancy program in early disseminated breast cancer cells that prevents metastatic outgrowth in the lung. Nature Cancer 3(10): 1165-80.

  • Li D, Yang J, Malik V, Huang Y, Huang X, and Wang J. (2022) An RNAi screen of RNA helicases identifies eIF4A3 as a regulator of embryonic stem cell identity. Nucleic Acids Research 50(21) 12462-79.

  • Li D, Yang J, Huang X, Zhou H, and Wang J. (2022) eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of stem cell pluripotency. Science Advances 8(13):eabm0478

  • Guallar D, Bi X*, Pardavilam JA*, Huang X*, Saenz C, et al. and Wang J. (2018) RNA-dependent chromatin targeting of Tet2 for endogenous retrovirus control in pluripotent stem cells. Nature Genetics 50:443-451 (*equal contribution).

  • Saunders A, Huang X, Fidalgo M, Reimer M, et al. and Wang J. (2017) The SIN3A/HDAC corepressor complex functionally cooperates with NANOG in promoting pluripotency. Cell Reports 18, 1713-26.

  • Fidalgo M, Huang X, Guallar D, Sanchez-Priego C, et al. and Wang J. (2016) Zfp281 Coordinates opposite functions of Tet1 and Tet2 for alternative pluripotent states. Cell Stem Cell 19:355–69.

  • Ding J, Huang X, Shao N, Zhou H, et al. and Wang J. (2015) Tex10 coordinates epigenetic control of super-enhancer activity in pluripotency and reprogramming. Cell Stem Cell 16:653-68.

  • Gingold JA, Fidalgo M, Guallar D, Lau Z, Sun Z, Zhou H, Faiola F, Huang X, et al. and Lemischka IR, Wang J. (2014) A genome-wide RNAi screen identifies opposing functions of Snai1 and Snai2 on the Nanog dependency in reprogramming. Molecular Cell 56(1), 140-152

2008 ~ 2013 (as a student): Cancer Genetics, Lymphoma, and Mass Spectrometry

  • ​Iqbal J*, Shen Y*, Huang X*, Liu Y, Wake L, et al. and Fu K, Chan WC. (2015) Global microRNA expression profiling uncovers molecular markers for classification and prognosis in aggressive B cell lymphoma. Blood 125:1137-45 (*co-first).

  • Huang X, Meng B, Iqbal J, et al. and Chan WC, Fu K. (2013) Activation of STAT3 signaling pathway is associated with the poor survival in diffuse large B-cell lymphoma patients treated with R-CHOP. Journal of Clinical Oncology 31:4520-28.

    • ​Comment in: David A. Frank. (2013) Transcription Factor STAT3 As a Prognostic Marker and Therapeutic Target in Cancer. Journal of Clinical Oncology, 31:4560–61

  • Huang X, Shen Y, Bi C, et al. and Fu K. (2012) Quantitative proteomics reveals microRNA-155 regulates PI3K/AKT pathway in diffuse large B cell lymphoma. American Journal of Pathology 181:26-33.

  • Huang X, Huang L, et al. and Fu K, Ding SJ. (2013) ISPTM: an iterative search approach for systematic identification of post-translational modifications from complex proteome mixtures. Journal of Proteome Research 12:3831-42.

  • Huang X, Tian C, Liu M, et al. and Fu K Ding SJ. (2012) Quantitative proteomic analysis of mouse embryonic fibroblasts and induced pluripotent stem cells using 16O/18O labeling. Journal of Proteome Research 11:2091-102.

  • Huang X, Liu M, Nold MJ, et al. and Fu K, Ding SJ. (2011) Software for quantitative proteomic analysis using stable isotope labeling and data independent acquisition. Analytical Chemistry 83:6971-79.

  • Huang X, Tolmachev AV, Shen Y, et al. and Fu K, Ding SJ. (2011) UNiquant, a program for quantitative proteomics analysis using stable isotope labeling. Journal of Proteome Research 10:1228-37.

  • Huang X, Shao L, Gong Y, Mao Y, Liu C, Qu H, Cheng YY. (2008) A metabonomic characterization of CCl4-induced acute liver failure using partial least square regression based on the GC/MS metabolic profiles of plasma in mice. Journal of Chromatography B 870:178-185​​

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  • Rao E, Jiang C, Ji M, Huang X, et al. and Fu K. (2012) The miRNA-17-92 cluster mediates chemoresistance and enhances tumor growth in mantle cell lymphoma via PI3K/AKT pathway. Leukemia 26:1064-72.

  • Liu M, Hou J, Huang L, Huang X, et al. and Ding SJ. (2010) Site-specific proteomics approach for study protein S-nitrosylation. Analytical Chemistry 82:7160-68.

Copyright © 2024 Xin Huang Lab @Columbia University

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