基本信息
葉幼瓊
電話：63846590-776772
郵箱：[email protected]
個人簡歷
葉幼瓊，博士，研究員，上海交通大學(xué)醫(yī)學(xué)院上海市免疫學(xué)研究所腫瘤多組學(xué)與免疫治療組課題組組長。2016年12月獲得同濟大學(xué)博士學(xué)位，2017-2019年德克薩斯大學(xué)休斯頓健康科學(xué)中心從事博士后研究。致力于腫瘤發(fā)生、腫瘤微環(huán)境與腫瘤免疫治療相關(guān)研究，從事包括基因組學(xué)、轉(zhuǎn)錄組學(xué)、蛋白質(zhì)組學(xué)、表觀基因組學(xué)和代謝組學(xué)在內(nèi)的癌癥多組學(xué)數(shù)據(jù)挖掘，以揭示癌癥的相關(guān)調(diào)節(jié)機制，為臨床治療提供參考，幫助個性化或精準化癌癥治療。系列研究成果以第一/共一、共同通訊作者發(fā)表在Nature Metabolism、Nature Immunology、Cancer Cell、Cell Systems、Nature Communications等國際知名期刊。
研究方向
以腫瘤為研究對象，利用生物信息學(xué)手段和實驗臨床相結(jié)合分析大規(guī)模多組學(xué)數(shù)據(jù)揭示腫瘤與免疫治療相關(guān)的調(diào)控機制，為腫瘤的臨床治療提供參考，以幫助個性化或精確化癌癥治療。主要研究內(nèi)容包括 (1)開發(fā)/應(yīng)用計算方法分析腫瘤多組學(xué)數(shù)據(jù)以識別腫瘤疾病標志物和藥物靶標，探索腫瘤的發(fā)生和發(fā)展機制。(2)基于腫瘤組織和單細胞的多組學(xué)揭示腫瘤微環(huán)境相關(guān)免疫特征以輔助腫瘤免疫治療。(3)基于靶向的藥物治療或化療的治療前后的組學(xué)數(shù)據(jù)，建立分析模型，篩選適用性強、療效好、副作用小的輔助藥物與免疫治療相結(jié)合以提高免疫治療效果。
科研項目
1) 20ZR1472900，MMP2 / 9的小分子抑制劑SB-3CT通過調(diào)節(jié)PD-L1以增強腫瘤免疫治療療效，上海市自然科學(xué)基金項目 (原創(chuàng)探索類)，2020.7-2023.6，50萬元，項目負責(zé)人
2) 20PJ1412800，基于單細胞測序等方法解析結(jié)直腸癌微環(huán)境細胞互作以探索潛在治療靶點，上海市浦江人才計劃， 2020.11-2022.10，30萬元，項目負責(zé)人
3) 82073145，基于腫瘤組織/單細胞的多組學(xué)揭示低氧相關(guān)免疫特征以 輔助腫瘤免疫治療，國家自然科學(xué)基金 (面上項目)，2021.01-2024.12，55萬元，項目負責(zé)人
論文與專著
代表性論著（第一或共同一作、共同通訊）
1) Ye Y. (第一/共同通訊作者), 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.
2) Ye Y. (第一作者), Jing Y., Li L., Mills G.B., Diao L., Liu H., Han L. Sex-associated molecular differences for cancer immunotherapy. Nature Communications, 2020,11:1779.
3) Chang G., Shi L., Ye Y. (共同第一作者), 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
4) Ye Y. (第一作者), Zhang Z., Liu Y., Han L. A multi-omics perspective for quantitative trait loci. Trends Genetics,2020.
5) Hui Li, Kuang X., Liang, L., Ye Y. (第一作者), 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.
6) Ye Y. (第一作者), 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. Characterization of hypoxia-associated molecular features to aid hypoxia-targeted therapy. Nature Metabolism, 2019,1, 431–444.
7) Zhang Z., Ye Y. (共同第一作者), 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.
8) Hu Q., Ye Y. (共同第一作者), 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. Oncogenic lncRNA downregulates cancer cell antigen presentation and intrinsic tumor suppression. Nature Immunology, 2019,20, 835–851.
9) Ye Y. (第一作者), 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 System, 2018,6, 314-328.E2.
10) Xiang Y., Ye Y. (共同第一作者), Zhang Z. & Han L. Maximizing the Utility of Cancer Transcriptomic Data. Trends in Cancer, 2018,4, 823–837.
11) Xiang Y., Ye Y. (共同第一作者), 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.
12) Ye Y. (第一作者), 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.
共同作者
13) 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, X. ADORA1 Inhibition Promotes Tumor Immune Evasion by Regulating the ATF3-PD-L1 Axis. Cancer Cell, 37(3), (2020). 324-339.e8.
14) Jing, Y., Liu, J., Ye, Y., Pan, L., Deng, H., Wang, Y., Yang, Y., Diao, L., Lin, S. H., Mills, G. B., Zhuang, G., Xue, X., & Han, L. (2020). Multi-omics prediction of immune-related adverse events during checkpoint immunotherapy. Nature Communications, 11(1), 1–7.
15) Hong, W., Ruan, H., Zhang, Z., Ye, Y., Liu, Y., Li, S., Jing, Y., Zhang, H., Diao, L., Liang, H., & Han, L. (2020). APAatlas: Decoding alternative polyadenylation across human tissues. Nucleic Acids Research, 48(D1), D34–D39.
16) 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 effcts of heat shock proteins (HSPs) in cancer hallmarks to aid development of HSP inhibitors. Genome Medicine (2020). 12(1)
17) 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. Molecular Cancer (2020). 19(1), 1–7.
18) Zhang, Z., Lee, J., Ruan H., Ye Y., Krakowiak, J., Hu, Q., Xiang, X., Gong, J., et al. Dr. Bingying Zhou, Li Wang, Chunru Lin, Dr. Lixia Diao, Mills G., Li W., HanL. Nature Communications (2019). 10 (1), 1-15.
19) 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 (2019). gkz876.
20) Ruan H., Xiang Y., Ko J., Li S., Jing Y., Zhu X., Ye Y., Zhang Z., Mills T., Feng J., Liu C.-J., Jing J., Cao J., Zhou B., Wang L., Zhou Y., Lin C., Guo A.-Y., Chen X. et al. Comprehensive characterization of circular RNAs in ~1000 human cancer cell lines. Genome Medicine (2019). 1–14.
21) Chen X., Ye Y., Gu L., Sun J., Du Y., Liu W., Li W., Zhang X. & Jiang C. H3K27me3 signal in the cis regulatory elements reveals the differentiation potential of progenitors in Drosophila neuroglial development. Genomics, Proteomics & Bioinformatics (2019).
22) 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). 9, 986–1000.
23) 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. et al. PTPN3 acts as a tumor suppressor and boosts TGF‐β signaling independent of its phosphatase activity. The EMBO Journal (2019). e99945.
24) Nohara K., Mallampalli V., Nemkov T., Wirianto M., Yang J., Ye Y., Sun Y., Han L., Esser K.A., Mileykovskaya E., D’Alessandro A., Green C.B., Takahashi J.S., Dowhan W., Yoo S.-H. & Chen Z. Nobiletin fortifies mitochondrial respiration in skeletal muscle to promote healthy aging against metabolic challenge. Nature Communications (2019). 10, 3923.
25) Adebiyi M.G., Zhao Z., Ye Y., Manalo J., Hong Y., Lee C.C., Xian W., McKeon F., Culp-Hill R., D’ Alessandro A., Kellems R.E., Yoo S.-H., Han L. & Xia Y. Circadian period 2: a missing beneficial factor in sickle cell disease by lowering pulmonary inflammation, iron overload, and mortality. The FASEB Journal (2019). fj.201900246RR.
26) Zhang Z., Ruan H., Liu C.-J., Ye Y., Gong J., Diao L., Guo A.-Y. & Han L. tRic: A user-friendly data portal to explore the expression landscape of tRNAs in human cancers. RNA biology (2019). 1.
27) Neve, I., Sowa, J., Lin, C., Sivaramakrishnan,P., Ye, Y., Han, L., Herman, C., Wang, M. Escherichia coli Metabolite Profiling Leads to the Development of an RNA Interference Strain for Caenorhabditis elegans. Genes, Genomes, Genetics (2019).
28) Hu Q., Li C., Wang S., Li Y., Wen B., Zhang Y., Liang K., Yao J., Ye Y., Hsiao H., Nguyen T.K., Park P.K., Egranov S.D., Hawke D.H., Marks J.R., Han L., Hung M.-C., Zhang B., Lin C. et al. LncRNAs-directed PTEN enzymatic switch governs epithelial–mesenchymal transition. Cell Research (2019). 29, 286–304.
29) 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 biology (2018). 16, e3000051.
30) 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 & Disease (2018). 9, 765.
31) 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 S.M. & Jiang C. Temporal requirements for ISL1 in sympathetic neuron proliferation, differentiation, and diversi fi cation. Cell Death and Disease (2018).
32) Gong J., Mei S., Liu C., Xiang Y., Ye Y., Zhang Z., Feng J., Liu R., Diao L., Guo A.-Y., Miao X. & Han L. PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types. Nucleic Acids Research (2017). 46, D971–D976.
33) Gong J., Li Y., Liu C. jie, Xiang Y., Li C., Ye Y., Zhang Z., Hawke D.H., Park P.K., Diao L., Putkey J.A., Yang L., Guo A.Y., Lin C. & Han L. A Pan-cancer Analysis of the Expression and Clinical Relevance of Small Nucleolar RNAs in Human Cancer. Cell Reports (2017). 21, 1968–1981.
34) 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 research (2014). 42, 9730–9.
35) 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 Research (2015). 25, 1013–1024.
章節(jié)論著（#共同通訊）
36) 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.
37) 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.
榮譽與獎勵
2020年上半年上海市海外高層次人才計劃
2020年上海市浦江人才A類(科研開發(fā))
團隊介紹
本課題組形成由課題組長、助理研究員、實驗師、博士后、博士和碩士研究生組成的富有活力的科研研究團隊。本團隊致力于利用多組學(xué)大數(shù)據(jù)和生物信息學(xué)手段揭示腫瘤微環(huán)境與腫瘤治療相關(guān)的調(diào)控機制，并與生物學(xué)家及臨床醫(yī)生協(xié)同合作，實現(xiàn)生物信息數(shù)據(jù)分析的實驗和臨床驗證。
成員組成
杜艷華，博士，助理研究員
2017年6月至2020年6月，在同濟大學(xué)醫(yī)學(xué)院進行博士后訓(xùn)練；2011年9月至2017年5月就讀于同濟大學(xué)生命與科學(xué)技術(shù)學(xué)院生物信息學(xué)專業(yè)，獲博士學(xué)位。主要研究領(lǐng)域為利用多組學(xué)高通量測序技術(shù)（scRNA-seq；ChIP-seq；ATAC-seq；WGBS；Exon-seq等）研究神經(jīng)發(fā)育過程中的表觀調(diào)控機制，研究成果發(fā)表于Cell Death Differ，iScience，Cell Research ，Stem Cell Reports，Stem Cells 等雜志。
包汝娟，碩士，實驗師
于2016年7月在西安交通大學(xué)醫(yī)學(xué)院取得生物化學(xué)與分子生物學(xué)專業(yè)碩士學(xué)位。目前在團隊中承擔(dān)基于不同轉(zhuǎn)錄組平臺和病人隊列構(gòu)建結(jié)直腸癌預(yù)后模型及蛋白組學(xué)數(shù)據(jù)分析的工作。
董宇，博士后
2015年9月至2020年3月就讀于上海交通大學(xué)系統(tǒng)生物醫(yī)學(xué)研究院生物信息學(xué)專業(yè)，獲博士學(xué)位。主要從事腫瘤相關(guān)的研究，利用高通量多組學(xué)數(shù)據(jù)和單細胞測序(RNAseq、WGS、WES, ChIP-seq、Proteomics、scRNAseq)，為臨床診斷和治療提供線索，后續(xù)研究將聚焦于腫瘤與免疫治療相關(guān)方向。研究成果發(fā)表于proteomics，frontier in genetics等雜志
王高陽，2019級碩士研究生
荀臻臻，2020級博士研究生
聯(lián)系方式
辦公室地址： 上海市重慶南路280號5號樓6樓607室
辦公室電話： 021-63846590-776772
實驗室地址： 上海市重慶南路280號5號樓6樓607室
實驗室電話： 021-63846590-776772
郵 箱： [email protected]
