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Yiping Fan, PhD

Yiping Fan, PhD

  • Associate Director, Functional Genomics

Education

PhD, Bioengineering - University of California at San Diego, San Diego, CA
MS, Biophysics and Physiology - University of Illinois Urbana-Champaign, Urbana, IL
BS, Biomedical Engineering - Zhejiang University, Hangzhou, China

About

Dr. Yiping Fan got his Bioengineering PhD, in 2002 at the University of California at San Diego and MS degree in Biophysics at University of Illinois Urbana Champaign in 1999. His research interests include bioinformatics method development and optimization, biomedical application of machine learning, epigenetic regulation of T-cell functions and cancer immunotherapy.

Research Interests

  • Bioinformatics method development and optimization
  • Biomedical application of machine learning
  • Epigenetic regulation of T-cell functions
  • Cancer immunotherapy

Patents

  • Methods for identifying and improving T cell multipotency, Filed by St Jude, patent pending
  • Novel CAR-T targets for pediatric AML, Filed by St Jude, patent pending
  • Genomic DNA based normalization method for gene expression data analysis (Patent #: WO 03/062450 A2)

Selected Publications

Abdelsamed HA, Zebley CC, Nguyen H, Rutishauser RL, Fan Y, Ghoneim HE, Crawford JC, Alfei F, Alli S, Ribeiro SP, Castellaw AH, McGargill MA, Jin H, Boi SK, Speake C, Serti E, Turka LA, Busch ME, Stone M, Deeks SG, Sekaly RP, Zehn D, James EA, Nepom GT, Youngblood B. Beta cell-specific CD8+ T cells maintain stem cell memory-associated epigenetic programs during type 1 diabetes. Nat Immunol. 2020 May;21(5):578-587. doi: 10.1038/s41590-020-0633-5. PMID: 32231298

Fonseca R, Beura LK, Quarnstrom CF, Ghoneim HE, Fan Y, Zebley CC, Scott MC, Fares-Frederickson NJ, Wijeyesinghe S, Thompson EA, Borges da Silva H, Vezys V, Youngblood B, Masopust D. Developmental plasticity allows outside-in immune responses by resident memory T cells. Nat Immunol. 2020 Apr;21(4):412-421. doi: 10.1038/s41590-020-0607-7. PMID: 32066954

Jin H, Kasper LH, Larson JD, Wu G, Baker SJ, Zhang J, Fan Y. ChIPseqSpikeInFree: a ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in. Bioinformatics. 2020 Feb 15;36(4):1270-1272. doi: 10.1093/bioinformatics/btz720. PMID: 31566663

Alfei F, Kanev K, Hofmann M, Wu M, Ghoneim HE, Roelli P, Utzschneider DT, von Hoesslin M, Cullen JG, Fan Y, Eisenberg V, Wohlleber D, Steiger K, Merkler D, Delorenzi M, Knolle PA, Cohen CJ, Thimme R, Youngblood B, Zehn D. TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection. Nature. 2019 Jul;571(7764):265-269. doi: 10.1038/s41586-019-1326-9. PMID: 31207605.

Silveira AB, Kasper LH, Fan Y, Jin H, Wu G, Shaw TI, Zhu X, Larson JD, Easton J, Shao Y, Yergeau DA, Rosencrance C, Boggs K, Rusch MC, Ding L, Zhang J, Finkelstein D, Noyes RM, Russell BL, Xu B, Broniscer A, Wetmore C, Pounds SB, Ellison DW, Zhang J, Baker SJ. H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo. Acta Neuropathol. 2019 Apr;137(4):637-655. doi: 10.1007/s00401-019-01975-4. PMID: 30770999

Yang X, Xu B, Mulvey B, Evans M, Jordan S, Wang YD, Pagala V, Peng J, Fan Y, Patel A, Peng JC. Differentiation of human pluripotent stem cells into neurons or cortical organoids requires transcriptional co-regulation by UTX and 53BP1. Nat Neurosci. 2019 Mar;22(3):362-373. doi: 10.1038/s41593-018-0328-5. PMID: 30718900

Larson JD, Kasper LH, Paugh BS, Jin H, Wu G, Kwon CH, Fan Y, Shaw TI, Silveira AB, Qu C, Xu R, Zhu X, Zhang J, Russell HR, Peters JL, Finkelstein D, Xu B, Lin T, Tinkle CL, Patay Z, Onar-Thomas A, Pounds SB, McKinnon PJ, Ellison DW, Zhang J, Baker SJ. Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression. Cancer Cell. 2019 Jan 14;35(1):140-155.e7. doi: 10.1016/j.ccell.2018.11.015. PMID: 30595505

Karmaus PWF, Chen X, Lim SA, Herrada AA, Nguyen TM, Xu B, Dhungana Y, Rankin S, Chen W, Rosencrance C, Yang K, Fan Y, Cheng Y, Easton J, Neale G, Vogel P, Chi H. Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity. Nature. 2019 Jan;565(7737):101-105. doi: 10.1038/s41586-018-0806-7. PMID: 30568299

Stewart E, McEvoy J, Wang H, Chen X, Honnell V, Ocarz M, Gordon B, Dapper J, Blankenship K, Yang Y, Li Y, Shaw TI, Cho JH, Wang X, Xu B, Gupta P, Fan Y, Liu Y, Rusch M, Griffiths L, Jeon J, Freeman BB 3rd, Clay MR, Pappo A, Easton J, Shurtleff S, Shelat A, Zhou X, Boggs K, Mulder H, Yergeau D, Bahrami A, Mardis ER, Wilson RK, Zhang J, Peng J, Downing JR, Dyer MA. Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses. Cancer Cell. 2018 Sep 10;34(3):411-426.e19. doi: 10.1016/j.ccell.2018.07.012. PMID: 30146332

Youngblood B, Hale JS, Kissick HT, Ahn E, Xu X, Wieland A, Araki K, West EE, Ghoneim HE, Fan Y, Dogra P, Davis CW, Konieczny BT, Antia R, Cheng X, Ahmed R. Effector CD8 T cells dedifferentiate into long-lived memory cells. Nature. 2017 Dec 21;552(7685):404-409. doi: 10.1038/nature25144. PMID: 29236683

Pitre A, Ge Y, Lin W, Wang Y, Fukuda Y, Temirov J, Phillips AH, Peters JL, Fan Y, Ma J, Nourse A, Sinha C, Lin H, Kriwacki R, Downing JR, Gruber TA, Centonze VE, Naren AP, Chen T, Schuetz JD. An unexpected protein interaction promotes drug resistance in leukemia. Nat Commun. 2017 Nov 16;8(1):1547. doi: 10.1038/s41467-017-01678-y. PMID: 29146910

Fukuda Y, Wang Y, Lian S, Lynch J, Nagai S, Fanshawe B, Kandilci A, Janke LJ, Neale G, Fan Y, Sorrentino BP, Roussel MF, Grosveld G, Schuetz JD. Upregulated heme biosynthesis, an exploitable vulnerability in MYCN-driven leukemogenesis. JCI Insight. 2017 Aug 3;2(15). doi: 10.1172/jci.insight.92409. PMID: 28768907

Ghoneim HE, Fan Y, Moustaki A, Abdelsamed HA, Dash P, Dogra P, Carter R, Awad W, Neale G, Thomas PG, Youngblood B. De Novo Epigenetic Programs Inhibit PD-1 Blockade-Mediated T Cell Rejuvenation. Cell. 2017 Jun 29;170(1):142-157.e19. doi: 10.1016/j.cell.2017.06.007. PMID: 28648661

Abdelsamed HA, Moustaki A, Fan Y, Dogra P, Ghoneim HE, Zebley CC, Triplett BM, Sekaly RP, Youngblood B. Human memory CD8 T cell effector potential is epigenetically preserved during in vivo homeostasis. J Exp Med. 2017 Jun 5;214(6):1593-1606. doi: 10.1084/jem.20161760. PMID: 28490440

Vo BT, Li C, Morgan MA, Theurillat I, Finkelstein D, Wright S, Hyle J, Smith SMC, Fan Y, Wang YD, Wu G, Orr BA, Northcott PA, Shilatifard A, Sherr CJ, Roussel MF. Inactivation of Ezh2 Upregulates Gfi1 and Drives Aggressive Myc-Driven Group 3 Medulloblastoma. Cell Rep. 2017 Mar 21;18(12):2907-2917. doi: 10.1016/j.celrep.2017.02.073. PMID: 28329683

Klein JD, Qu C, Yang X, Fan Y, Tang C, Peng JC. c-Fos Repression by Piwi Regulates Drosophila Ovarian Germline Formation and Tissue Morphogenesis. PLoS Genet. 2016 Sep;12(9):e1006281. doi: 10.1371/journal.pgen.1006281. PMID: 27622269

Diouf B, Devaraju P, Janke LJ, Fan Y, Frase S, Eddins D, Peters JL, Kim J, Pei D, Cheng C, Zakharenko SS, Evans WE. Msh2 deficiency leads to dysmyelination of the corpus callosum, impaired locomotion, and altered sensory function in mice. Sci Rep. 2016 Aug 1;6:30757. doi: 10.1038/srep30757. PMID: 27476972

Fan Y, Lee S, Wu G, Easton J, Yergeau D, Dummer R, Vogel P, Kirkwood JM, Barnhill RL, Pappo A, Bahrami A. Telomerase Expression by Aberrant Methylation of the TERT Promoter in Melanoma Arising in Giant Congenital Nevi. J Invest Dermatol. 2016 Jan;136(1):339-342. doi: 10.1038/JID.2015.374. PMID: 26763461

Mullighan CG, Jeha S, Pei D, Payne-Turner D, Coustan-Smith E, Roberts KG, Waanders E, Choi JK, Ma X, Raimondi SC, Fan Y, Yang W, Song G, Yang JJ, Inaba H, Downing JR, Leung WH, Bowman WP, Relling MV, Evans WE, Zhang J, Campana D, Pui CH. Outcome of children with hypodiploid ALL treated with risk-directed therapy based on MRD levels. Blood. 2015 Dec 24;126(26):2896-9. doi: 10.1182/blood-2015-09-671131. PMID: 26527677

Hiler D, Chen X, Hazen J, Kupriyanov S, Carroll PA, Qu C, Xu B, Johnson D, Griffiths L, Frase S, Rodriguez AR, Martin G, Zhang J, Jeon J, Fan Y, Finkelstein D, Eisenman RN, Baldwin K, Dyer MA. Quantification of Retinogenesis in 3D Cultures Reveals Epigenetic Memory and Higher Efficiency in iPSCs Derived from Rod Photoreceptors. Cell Stem Cell. 2015 Jul 2;17(1):101-15. doi: 10.1016/j.stem.2015.05.015. PMID: 26140606

Paugh SW, Bonten EJ, Savic D, Ramsey LB, Thierfelder WE, Gurung P, Malireddi RK, Actis M, Mayasundari A, Min J, Coss DR, Laudermilk LT, Panetta JC, McCorkle JR, Fan Y, Crews KR, Stocco G, Wilkinson MR, Ferreira AM, Cheng C, Yang W, Karol SE, Fernandez CA, Diouf B, Smith C, Hicks JK, Zanut A, Giordanengo A, Crona D, Bianchi JJ, Holmfeldt L, Mullighan CG, den Boer ML, Pieters R, Jeha S, Dunwell TL, Latif F, Bhojwani D, Carroll WL, Pui CH, Myers RM, Guy RK, Kanneganti TD, Relling MV, Evans WE. NALP3 inflammasome upregulation and CASP1 cleavage of the glucocorticoid receptor cause glucocorticoid resistance in leukemia cells. Nat Genet. 2015 Jun;47(6):607-14. doi: 10.1038/ng.3283. PMID: 25938942

Diouf B, Crews KR, Lew G, Pei D, Cheng C, Bao J, Zheng JJ, Yang W, Fan Y, Wheeler HE, Wing C, Delaney SM, Komatsu M, Paugh SW, McCorkle JR, Lu X, Winick NJ, Carroll WL, Loh ML, Hunger SP, Devidas M, Pui CH, Dolan ME, Relling MV, Evans WE. Association of an inherited genetic variant with vincristine-related peripheral neuropathy in children with acute lymphoblastic leukemia. JAMA. 2015 Feb 24;313(8):815-23. doi: 10.1001/jama.2015.0894. PMID: 25710658

Full Publications List

Last update: June 2020