Personal Introduction

Education

• 2007-2011 Fuzhou University B.S. Biotechnology

• 2011-2016 Tongji University Ph.D. Bioinformatics

Career

• 20016-2017 University of Texas Health Science Center at Houston Research Associate

• 2017-2019 University of Texas Health Science Center at Houston Postdoctoral Fellow

• 2020-present Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine     Principal Investigator

Research Interests

• The research in my laboratory focuses on tumor microenvironment (TME) and immunotherapy. We take full advantage of the multi-omics data in human cancer, combine with innovative bioinformatics methods, basic experiments, clinical cohorts and other multi-scale methods to build an immunotherapy efficacy prediction model, to explore the regulatory roles of tumor (boundary) microenvironment on tumor progression and immune escape. We have revealed critical roles of tumor boundary, hypoxia, transcriptional and post-transcriptional regulation on TME and immunotherapy, providing new potential therapeutic strategies and predictive models for immunotherapy (Cancer Cell, 2020; Nature Metabolism, 2019; Nature Immunology, 2019; Nature Communications, 2020, 2022; etc.).

• The main research contents as follows: 1) combining multi-scale data such as spatial transcriptomics, single-cell multi-omics, pathological images, etc., to construct approaches to accurately study the regulation roles of tumor boundary microenvironment in tumor progression, and immunotherapy resistance, and to develop new therapeutic strategies based on the targets in tumor boundary microenvironment; 2) single-cell and other omics based clinical cohorts reveal tumor microenvironment-related characteristics to assist tumor immunotherapy.

Scientific Research Project

• Small-molecule MMP2/MMP9 inhibitor SB-3CT modulates tumor immune surveillance by regulating PD-L1, Funding Source: Natural Science Foundation of Shanghai, Grant Number: 20ZR1472900, 2020/07-2023/06.

• Single-cellTranscriptomics Reveal Potential Therapeutic Targets of Tumor Microenvironment in Colorectal Cancer, Funding Source: Natural Science Foundation of Shanghai, Grant Number: 20PJ1412800, 2020/11-2022/10.

• Bulk- and single-cells multi-omics characterize hypoxia-associated immune features to aid cancer immunotherapy. Funding Source: NSFC(General Program), Grant Number: 82073145, 2021/01-2023/12.

Publications

• Qi J., Sun H., Zhang Y., Wang Z., Xun Z., Li, Z., Ding X., Bao R., Hong L., Ji W., Fang, F., Li H., Chen L., Zhong J., Zou D., Liu L., Han L., Ginhoux F., Ye, Y.#, Su, B.#. Single-cell and spatial analysis reveal interaction of FAP+ fibroblasts and SPP1+ macrophages in colorectal cancer. Nature Communications (2022) 13:1742.

• Shen M., Du Y.#, Ye Y.#. Tumor-associated macrophages, dendritic cells, and neutrophils: biological roles, crosstalk, and therapeutic relevance. Medical Review. 2022;4710:1–22.

• Wang F; Zhang Y; Yu X; Teng X-L; Ding R; Hu Z; Wang A; Wang Z; Ye Y.#, Zou Q#. ZFP91 disturbs metabolic fitness and antitumor activity of tumor-infiltrating T cells. Journal of Clinical Investigation (2021) 131.

• Ye Y. *#, Kuang X. *, Xie Z. *, Liang L., Zhang Z., Zhang Y., Ma F., Gao, Q., Chang R., Zhao S., Su J., Li, H., Peng, J., Chen H., Yin M., Peng C., Yang N., Liu J., Liu H.#, Han L.#, Chen X#. Small-molecule MMP2/MMP9 inhibitor SB-3CT modulates tumor immune surveillance by regulating PD-L1. Genome Medicine (2020) 12:83.

• Liu Z.*, Ye Y. *, Liu Y., Liu Y., Chen H., Shen M., Wang Z., Huang S., Han L., Chen Z., He X. RNA helicase DHX37 facilitates liver cancer progression by cooperating with PLRG1 to drive super enhancer-mediated transcription of cyclin D1. Cancer Research (2022) 82:1937–52.

• Ye Y. *, Zhang Y. *, Yang N. *, Gao Q. *, Ding X., Kuang X., Bao R., Zhang Z., Sun C., Zhou B., Wang L., Hu Q., Lin C., Gao J., Lou Y., Lin S.H., Diao L., Liu H., Chen X., Mills G.B., Han L. Profiling of immune features to predict immunotherapy efficacy. The Innovation (2021) 3 (1) 100194.

• Chen, H., Yao, J., Bao, R., Dong, Y., Zhang, T., Du, Y., Wang, G., Ni, D., Xun, Z., Niu, X., Ye Y.#, Li H#. Cross-talk of four types of RNA modification writers defines tumor microenvironment and pharmacogenomic landscape in colorectal cancer. Molecular. Cancer (2021) 20, 1–21.

• Shen L#, Ye Y#, Sun H#, Su B. ILC3 plasticity in microbiome-mediated tumor progression and immunotherapy. Cancer Cell (2021) 39, 10:1308-1310

• Ye Y., Jing Y., Li L., Mills G.B., Diao L., Liu H., Han L. Sex-associated molecular differences for cancer immunotherapy. Nature Communications (2020). 11.

• Chang G. *, Shi L. *, Ye Y. *, Shi H., Zeng L, Tiwary S., Chang G., Huse J.T., Huo L., Ma L., Ma Y., Zeng L., Zhang S., Zhu J., Han L., He C. & Huang S. Genetic and Epigenetic Changes in YTHDF3 Promote Multiple Steps of Breast Cancer Brain Metastasis. Cancer Cell (2020) 38:1-15

• Ye Y.*, Zhang Z.*, Liu Y., Han L. A multi-omics perspective for quantitative trait loci in precision medicine. Trends in Genetics (2020). 318-336.

• Hui L.*, Kuang X. *, Liang, L. *, Ye Y. *, Zhang Y, Li J., Ma F., Tao J., Lei G., Zhao S., Su J., Yang N., Peng C., Xu X., Hung.-C., Han., Liu H., Liu J., & Chen X. The beneficial role of Sunitinib in tumor immune surveillance by regulating tumor PD-L1. Advanced Science (2020)6, 1–16.

• Ye Y.*, Hu Q.*, Chen H., Liang K., Yuan Y., Xiang Y., Ruan H., Zhang Z., Song A., Zhang H., Liu L., Diao L., Lou Y., Zhou B., Wang L., Zhou S., Gao J., Jonasch E., Lin S.H. et al. Characterization of hypoxia-associated molecular features to aid hypoxia-targeted therapy. Nature Metabolism (2019). 1, 431–444.

Featured as Cover Story

Included in Nature Research Collection on “Nobel Prize in Physiology or Medicine 2019”

• Hu Q.*, Ye Y.*, Chan L.-C., Li Y., Liang K., Lin A., Egranov S.D., Zhang Y., Xia W., Gong J., Pan Y., Chatterjee S.S., Yao J., Evans K.W., Nguyen T.K., Park P.K., Liu J., Coarfa C., Donepudi S.R. et al. Oncogenic lncRNA downregulates cancer cell antigen presentation and intrinsic tumor suppression. Nature Immunology (2019). 20, 835–851.

• Xiang Y.*, Ye Y.*, Lou Y., Yang Y., Cai C., Zhang Z., Mills T., Chen N., Kim Y., Ozguc F.M., Diao L., Karmouty-quintana H., Xia Y., Kellems R., Chen Z., Yoo S., Shyu A., Mills G.B. & Han L. Comprehensive characterization of alternative polyadenylation in human cancer. Journal of the National Cancer Institute (2018). 110, 379–389.

• Ye Y., Xiang Y., Ozguc F.M., Kim Y., Liu C.J., Park P.K., Hu Q., Diao L., Lou Y., Lin C., Guo A.Y., Zhou B., Wang L., Chen Z., Takahashi J.S., Mills G.B., Yoo S.H. & Han L. The Genomic Landscape and Pharmacogenomic Interactions of Clock Genes in Cancer Chronotherapy. Cell Systems (2018). 6, 314-328.E2.

Highlighted by preview from Cell Systems.

• Xiang Y.*, Ye Y.*, Zhang Z. & Han L. Maximizing the utility of cancer transcriptomic data. Trends Cancer (2018). 4, 823–837.

• Zhang Z.*, Ye Y.*, Gong J., Ruan H., Liu C., Xiang Y., Cai C., Guo A., Ling J., Diao L., Weinstein J.N. & Han L. Global analysis of tRNA and translation factor expression reveals a dynamic landscape of translational regulation in human cancers. Communications Biology (2018). 1, 234.

• Ye Y.*, Li M.*, Gu L., Chen X., Shi J., Zhang X. & Jiang C. Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos. Cell Death and Differentiation (2017). 24, 409–420.

• Zhang T, Ding C, Chen H, Zhao J, Chen Z, Chen B, Mao K, Hao Y, Roulis M, Xu H, Kluger Y, Zou Q, Ye Y, Zhan M, Flavell RA, Li HB. m(6)A mRNA modification maintains colonic epithelial cell homeostasis via NF-κB-mediated antiapoptotic pathway Sci Adv. 2022 Mar 25;8(12):eabl5723.

• Zhang Z, Luo M, Li Q, Liu Y, Lussier C, Zhang J, Ye Y, Guo AY, Han L. Genetic, Pharmacogenomic, and Immune Landscapes of Enhancer RNAs Across Human Cancers Cancer Res. 2022 Mar 1;82(5):785-790.

• Chen B, Hu J, Hu X, Chen H, Bao R, Zhou Y, Ye Y, Zhan M, Cai W, Li H, Li HB. DENR controls JAK2 translation to induce PD-L1 expression for tumor immune evasion Nat Commun. 2022 Apr 19;13(1):2059.

• Wu Z, Huang H, Han Q, Hu Z, Teng XL, Ding R, Ye Y, Yu X, Zhao R, Wang Z, Zou Q. SENP7 senses oxidative stress to sustain metabolic fitness and antitumor functions of CD8+ T cells J Clin Invest. 2022 Apr 1;132(7):e155224.

• Li Y, Tan Z, Zhang Y, Zhang Z, Hu Q, Liang K, Jun Y, Ye Y, Li YC, Li C, Liao L, Xu J, Xing Z, Pan Y, Chatterjee SS, Nguyen TK, Hsiao H, Egranov SD, Putluri N, Coarfa C, Hawke DH, Gunaratne PH, Tsai KL, Han L, Hung MC, Calin GA, Namour F, Guéant JL, Muntau AC, Blau N, Sutton VR, Schiff M, Feillet F, Zhang S, Lin C, Yang L. A noncoding RNA modulator potentiates phenylalanine metabolism in mice Science. 2021 Aug 6;373(6555):662-673.

• Wu N, Sun H, Zhao X, Zhang Y, Tan J, Qi Y, Wang Q, Ng M, Liu Z, He L, Niu X, Chen L, Liu Z, Li HB, Zeng YA, Roulis M, Liu D, Cheng J, Zhou B, Ng LG, Zou D, Ye Y, Flavell RA, Ginhoux F, Su B. MAP3K2-regulated intestinal stromal cells define a distinct stem cell niche Nature. 2021 Apr;592(7855):606-610.

• Fang R, Chen X, Zhang S, Shi H, Ye Y, Shi H, Zou Z, Li P, Guo Q, Ma L, He C, Huang S. EGFR/SRC/ERK-stabilized YTHDF2 promotes cholesterol dysregulation and invasive growth of glioblastoma Nat Commun. 2021 Jan 8;12(1):177.

• Zhou J, Zhang X, Hu J, Qu R, Yu Z, Xu H, Chen H, Yan L, Ding C, Zou Q, Ye Y, Wang Z, Flavell RA, Li HB. m(6)A demethylase ALKBH5 controls CD4(+) T cell pathogenicity and promotes autoimmunity Sci Adv. 2021 Jun 16;7(25):eabg0470.

• Yang Y, Wu M, Cao D, Yang C, Jin J, Wu L, Hong X, Li W, Lu L, Li J, Wang X, Meng X, Zhang Z, Cheng J, Ye Y, Xiao H, Yu J, Deng L. ZBP1-MLKL necroptotic signaling potentiates radiation-induced antitumor immunity via intratumoral STING pathway activation Sci Adv. 2021 Oct 8;7(41):eabf6290.

• Jing Y, Zhang Y, Wang J, Li K, Chen X, Heng J, Gao Q, Ye Y, Zhang Z, Liu Y, Lou Y, Lin SH, Diao L, Liu H, Chen X, Mills GB, Han L. Association Between Sex and Immune-Related Adverse Events During Immune Checkpoint Inhibitor Therapy J Natl Cancer Inst. 2021 Oct 1;113(10):1396-1404.

• Qi J, Crinier A, Escalière B, Ye Y, Wang Z, Zhang T, Batista L, Liu H, Hong L, Wu N, Zhang M, Chen L, Liu Y, Shen L, Narni-Mancinelli E, Vivier E, Su B. Single-cell transcriptomic landscape reveals tumor specific innate lymphoid cells associated with colorectal cancer progression Cell Rep Med. 2021 Jul 27;2(8):100353.

• Jing Y, Liu Y, Li Q, Ye Y, Diao L, Huang Y, Zhou Y, Green MR, Mills GB, Han L. Expression of chimeric antigen receptor therapy targets detected by single-cell sequencing of normal cells may contribute to off-tumor toxicity Cancer Cell. 2021 Dec 13;39(12):1558-1559.

• Yang B, Li X, Fu Y, Guo E, Ye Y, Li F, Liu S, Xiao R, Liu C, Lu F, Huang J, Qin T, Han L, Peng G, Mills GB, Sun C, Chen G. MEK Inhibition Remodels the Immune Landscape of Mutant KRAS Tumors to Overcome Resistance to PARP and Immune Checkpoint Inhibitors Cancer Res. 2021 May 15;81(10):2714-2729.

• Liang H, Lin Z, Ye Y, Luo R, Zeng L. ARRB2 promotes colorectal cancer growth through triggering WTAP Acta Biochim Biophys Sin (Shanghai). 2021 Jan 12;53(1):85-93.

• Fang W, Liao C, Shi R, Simon JM, Ptacek TS, Zurlo G, Ye Y, Han L, Fan C, Bao L, Ortiz CL, Lin HR, Manocha U, Luo W, Peng Y, Kim WY, Yang LW, Zhang Q. ZHX2 promotes HIF1α oncogenic signaling in triple-negative breast cancer Elife. 2021 Nov 15;10:e70412.

• Shi Z, Gan G, Xu X, Zhang J, Yuan Y, Bi B, Gao X, Xu P, Zeng W, Li J, Ye Y, Zhou A, Zhang N, Liu W, Lin S, Mi J. Kynurenine derivative 3-HAA is an agonist ligand for transcription factor YY1 J Hematol Oncol. 2021 Sep 25;14(1):153.

• Ma J, Han M, Yang D, Zheng T, Hu R, Wang B, Ye Y, Liu J, Huang G. Vps33B in Dendritic Cells Regulates House Dust Mite-Induced Allergic Lung Inflammation J Immunol. 2021 Dec 1;207(11):2649-2659.

• Li Y, Zhang Y, Hu Q, Egranov SD, Xing Z, Zhang Z, Liang K, Ye Y, Pan Y, Chatterjee SS, Mistretta B, Nguyen TK, Hawke DH, Gunaratne PH, Hung MC, Han L, Yang L, Lin C. Functional significance of gain-of-function H19 lncRNA in skeletal muscle differentiation and anti-obesity effects Genome Med. 2021 Aug 28;13(1):137.

• Liu H, Kuang X, Zhang Y, Ye Y, Li J, Liang L, Xie Z, Weng L, Guo J, Li H, Ma F, Chen X, Zhao S, Su J, Yang N, Fang F, Xie Y, Tao J, Zhang J, Chen M, Peng C, Sun L, Zhang X, Liu J, Han L, Xu X, Hung MC, Chen X. ADORA1 Inhibition Promotes Tumor Immune Evasion by Regulating the ATF3-PD-L1 Axis Cancer Cell. 2020 Mar 16;37(3):324-339.e8.

• Jing Y, Liu J, Ye Y, Pan L, Deng H, Wang Y, Yang Y, Diao L, Lin SH, Mills GB, Zhuang G, Xue X, Han L. Multi-omics prediction of immune-related adverse events during checkpoint immunotherapy Nat Commun. 2020 Oct 2;11(1):4946.

• Zhang Z, Jing J, Ye Y, Chen Z, Jing Y, Li S, Hong W, Ruan H, Liu Y, Hu Q, Wang J, Li W, Lin C, Diao L, Zhou Y, Han L. Characterization of the dual functional effects of heat shock proteins (HSPs) in cancer hallmarks to aid development of HSP inhibitors Genome Med. 2020 Nov 23;12(1):101.

• Hong W, Ruan H, Zhang Z, Ye Y, Liu Y, Li S, Jing Y, Zhang H, Diao L, Liang H, Han L. APAatlas: decoding alternative polyadenylation across human tissues Nucleic Acids Res. 2020 Jan 8;48(D1):D34-D39.

• Liu Y, Ruan H, Li S, Ye Y, Hong W, Gong J, Zhang Z, Jing Y, Zhang X, Diao L, Han L. The genetic and pharmacogenomic landscape of snoRNAs in human cancer Mol Cancer. 2020 Jun 23;19(1):108.

• Liu Y, Ye Y, Gong J, Han L. Expression Quantitative Trait Loci (eQTL) Analysis in Cancer Methods Mol Biol. 2020;2082:189-199.

• Zhang Z, Ruan H, Liu CJ, Ye Y, Gong J, Diao L, Guo AY, Han L. tRic: a user-friendly data portal to explore the expression landscape of tRNAs in human cancers RNA Biol. 2020 Nov;17(11):1674-1679.

• Neve IAA, Sowa JN, Lin CJ, Sivaramakrishnan P, Herman C, Ye Y, Han L, Wang MC. Escherichia coli Metabolite Profiling Leads to the Development of an RNA Interference Strain for Caenorhabditis elegans G3 (Bethesda). 2020 Jan 7;10(1):189-198.

• Zhang Z, Lee JH, Ruan H, Ye Y, Krakowiak J, Hu Q, Xiang Y, Gong J, Zhou B, Wang L, Lin C, Diao L, Mills GB, Li W, Han L. Transcriptional landscape and clinical utility of enhancer RNAs for eRNA-targeted therapy in cancer Nat Commun. 2019 Oct 8;10(1):4562.

• Tan P, Ye Y, Mao J, He L. Autophagy and Immune-Related Diseases Adv Exp Med Biol. 2019;1209:167-179.

• Hu Q, Li C, Wang S, Li Y, Wen B, Zhang Y, Liang K, Yao J, Ye Y, Hsiao H, Nguyen TK, Park PK, Egranov SD, Hawke DH, Marks JR, Han L, Hung MC, Zhang B, Lin C, Yang L. LncRNAs-directed PTEN enzymatic switch governs epithelial-mesenchymal transition Cell Res. 2019 Apr;29(4):286-304.

• Ruan H, Xiang Y, Ko J, Li S, Jing Y, Zhu X, Ye Y, Zhang Z, Mills T, Feng J, Liu CJ, Jing J, Cao J, Zhou B, Wang L, Zhou Y, Lin C, Guo AY, Chen X, Diao L, Li W, Chen Z, He X, Mills GB, Blackburn MR, Han L. Comprehensive characterization of circular RNAs in ~ 1000 human cancer cell lines Genome Med. 2019 Aug 26;11(1):55.

• Yuan B, Liu J, Cao J, Yu Y, Zhang H, Wang F, Zhu Y, Xiao M, Liu S, Ye Y, Ma L, Xu D, Xu N, Li Y, Zhao B, Xu P, Jin J, Xu J, Chen X, Shen L, Lin X, Feng XH. PTPN3 acts as a tumor suppressor and boosts TGF-β signaling independent of its phosphatase activity EMBO J. 2019 Jul 15;38(14):e99945.

• Nohara K, Mallampalli V, Nemkov T, Wirianto M, Yang J, Ye Y, Sun Y, Han L, Esser KA, Mileykovskaya E, D'Alessandro A, Green CB, Takahashi JS, Dowhan W, Yoo SH, Chen Z. Nobiletin fortifies mitochondrial respiration in skeletal muscle to promote healthy aging against metabolic challenge Nat Commun. 2019 Aug 28;10(1):3923.

• Zhang Q, Zhang Q, Jiang X, Ye Y, Liao H, Zhu F, Yan J, Luo L, Tian L, Jiang C, Chen Y, Liang X, Sun Y. Collaborative ISL1/GATA3 interaction in controlling neuroblastoma oncogenic pathways overlapping with but distinct from MYCN Theranostics. 2019 Jan 30;9(4):986-1000.

• Ruan H, Liao Y, Ren Z, Mao L, Yao F, Yu P, Ye Y, Zhang Z, Li S, Xu H, Liu J, Diao L, Zhou B, Han L, Wang L. Single-cell reconstruction of differentiation trajectory reveals a critical role of ETS1 in human cardiac lineage commitment BMC Biol. 2019 Nov 13;17(1):89.

• Chen X, Ye Y, Gu L, Sun J, Du Y, Liu WJ, Li W, Zhang X, Jiang C. H3K27me3 Signal in the Cis Regulatory Elements Reveals the Differentiation Potential of Progenitors During Drosophila Neuroglial Development Genomics Proteomics Bioinformatics. 2019 Jun;17(3):297-304.

• Adebiyi MG, Zhao Z, Ye Y, Manalo J, Hong Y, Lee CC, Xian W, McKeon F, Culp-Hill R, D' Alessandro A, Kellems RE, Yoo SH, Han L, Xia Y. Circadian period 2: a missing beneficial factor in sickle cell disease by lowering pulmonary inflammation, iron overload, and mortality FASEB J. 2019 Sep;33(9):10528-10537.

• Gong J, Mei S, Liu C, Xiang Y, Ye Y, Zhang Z, Feng J, Liu R, Diao L, Guo AY, Miao X, Han L. PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types Nucleic Acids Res. 2018 Jan 4;46(D1):D971-D976.

• Zhang Q, Huang R, Ye Y, Guo X, Lu J, Zhu F, Gong X, Zhang Q, Yan J, Luo L, Zhuang S, Chen Y, Zhao X, Evans SM, Jiang C, Liang X, Sun Y. Temporal requirements for ISL1 in sympathetic neuron proliferation, differentiation, and diversification Cell Death Dis. 2018 Feb 14;9(2):247.

• Tan P, Ye Y, He L, Xie J, Jing J, Ma G, Pan H, Han L, Han W, Zhou Y. TRIM59 promotes breast cancer motility by suppressing p62-selective autophagic degradation of PDCD10 PLoS Biol. 2018 Nov 8;16(11):e3000051.

• Hu J, Gu L, Ye Y, Zheng M, Xu Z, Lin J, Du Y, Tian M, Luo L, Wang B, Zhang X, Weng Z, Jiang C. Dynamic placement of the linker histone H1 associated with nucleosome arrangement and gene transcription in early Drosophila embryonic development Cell Death Dis. 2018 Jul 9;9(7):765.

• Gong J, Li Y, Liu CJ, Xiang Y, Li C, Ye Y, Zhang Z, Hawke DH, Park PK, Diao L, Putkey JA, Yang L, Guo AY, Lin C, Han L. A Pan-cancer Analysis of the Expression and Clinical Relevance of Small Nucleolar RNAs in Human Cancer Cell Rep. 2017 Nov 14;21(7):1968-1981.

• Fu Y, Huang C, Xu X, Gu H, Ye Y, Jiang C, Qiu Z, Xie X. Direct reprogramming of mouse fibroblasts into cardiomyocytes with chemical cocktails Cell Res. 2015 Sep;25(9):1013-24.

• Shi J, Zheng M, Ye Y, Li M, Chen X, Hu X, Sun J, Zhang X, Jiang C. Drosophila Brahma complex remodels nucleosome organizations in multiple aspects Nucleic Acids Res. 2014 Sep;42(15):9730-9.

Chapter

• Tan P. #, Ye Y.#, Mao J., He L: Autophagy- and Immune-Related Diseases. In: Cui J Ed. Autophagy Regulation of Innate Immunity, Advances in Experimental Medicine and Biology. 2019.

• Liu Y., Ye Y., Gong J., Han L: Expression Quantitative Trait Loci (eQTL) Analysis in Cancer. In Walker J Ed. Methods in Molecular Biology ISSN: 1064-3745. 2019.

Patent

• Youqiong Ye, Zhenzhen Xun, Software of Construct of tumor transition zone microenvironment [Cottrazm] V1.0