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本課題組主要聚焦腫瘤微環(huán)境（TME）和免疫治療，圍繞腫瘤（邊界）微環(huán)境,，以生物大數(shù)據(jù)為驅(qū)動(dòng)，構(gòu)建算法、結(jié)合生信創(chuàng)新方法,、基礎(chǔ)實(shí)驗(yàn),、臨床隊(duì)列等多尺度手段闡釋TME中調(diào)控因子對(duì)腫瘤進(jìn)展和免疫逃逸機(jī)制、并利用多維數(shù)據(jù)構(gòu)建免疫治療療效預(yù)測模型，為免疫治療提供新治療策略（Cancer cell,，2020,；Nature Metabolism， 2019,；Nature Immunology,， 2019；Nature Communications, 2020, 2022; etc.）,。主要研究內(nèi)容為 1）利用單細(xì)胞組學(xué),、空間組學(xué)和病理圖片等多尺度數(shù)據(jù)構(gòu)建精準(zhǔn)研究腫瘤邊界微環(huán)境的工具，以研究腫瘤邊界微環(huán)境在不同腫瘤免疫微環(huán)境分型,、腫瘤轉(zhuǎn)移,、免疫治療耐受中調(diào)控機(jī)制，及開放基于邊界微環(huán)境調(diào)控因子的新腫瘤治療策略,；2）基于臨床隊(duì)列的單細(xì)胞等組學(xué)揭示腫瘤微環(huán)境相關(guān)特征以輔助腫瘤免疫治療,。

本課題組更多研究方向和科研成果訊息詳見實(shí)驗(yàn)室網(wǎng)站：http://www.yelab.site/

代表性論文

以*（共同）一作/#共同通訊發(fā)表的期刊

2024

1. Du Y#, Shi J#, Wang J, Xun Z, Yu Z, Sun H, Bao R, Zheng J, Li Z, Ye, Y. Integration of Pan-Cancer Single-Cell and Spatial Transcriptomics Reveals Stromal Cell Features and Therapeutic Targets in Tumor Microenvironment. Cancer Res 2024 Jan 16;84(2):192-210.

2. Shi J#, Wei X#, Xun Z, Ding X, Liu Y, Liu L, Ye, Y. The Web-Based Portal SpatialTME Integrates Histological Images with Single-Cell and Spatial Transcriptomics to Explore the Tumor Microenvironment Cancer Res 2024 Apr 15;84(8):1210-1220.

3. Chen W, He Y, Zhou G, Chen X *, Ye, Y *, Zhang G *, Liu H *. Multiomics characterization of pyroptosis in the tumor microenvironment and therapeutic relevance in metastatic melanoma. BMC Med 2024 Jan 17;22(1):24.

4. Ding R, Yu X, Hu Z, Dong Y, Huang H, Zhang Y, Han Q, Ni ZY *, Zhao R *, Ye, Y *, Zou Q *. Lactate modulates RNA splicing to promote CTLA-4 expression in tumor-infiltrating regulatory T cells. Immunity 2024 Mar 12;57(3):528-540.e6.

5. Xiao J, Wang S, Chen L, Ding X, Dang Y, Han M, Zheng Y, Shen H, Wu S, Wang M, Yang D, Li N, Dong C, Hu M, Su C, Li W, Hui L, Ye, Y *, Tang H *, Wei B *, Wang H *. 25-Hydroxycholesterol regulates lysosome AMP kinase activation and metabolic reprogramming to educate immunosuppressive macrophages. Immunity 2024 Apr 12:S1074-7613(24)00142-0.

2023

1. Dong Y, Gao Q, Chen Y, Zhang Z, Du Y, Liu Y, Zhang G, Li S, Wang G, Chen X#, Liu H#, Han L#, Ye Y#. Identification of CircRNA signature associated with tumor immune infiltration to predict therapeutic efficacy of immunotherapy. Nature Communications(2023) 14(1):2540.

2. Xun, Z., Ding, X., Yao Zhang, Zhang, B., Lai, S., Zou, D., Zheng, J., Chen, G., Su, B., Han, L.# & Ye, Y.# Reconstruction of the tumor spatial microenvironment along the malignant- boundary-nonmalignant axis. Nature Communications(2023) 14: 933.
   

3. Sun, C. *, Ye, Y. *, Tan, Z., Liu, Y., Li, Y., Hu, W., Liang, K., Egranov, S. D., Huang, L. A., Zhang, Z., Zhang, Y., Yao, J., Nguyen, T. K., Zhao, Z., Wu, A., Marks, J. R., Caudle, A. S., Sahin, A. A., Gao, J., et al. Tumor-associated nonmyelinating Schwann cell - expressed PVT1 promotes pancreatic cancer kynurenine pathway and tumor immune exclusion. Science Advances 6995, 1–17 (2023).
   

4. Liu Y., Xun Z., Ma K.,Liang S., Li X., Zhou S., Sun L., Liu Y., Du Y., Guo X., Cui T., Zhou H., Wang J., Yin D., Song R., Zhang S., Cai W., Meng F., Guo H., Zhang B., Yang D., Bao R., Hu Q., Wang J., Ye, Y#., Liu L#. Identification of a tumour immune barrier in the HCC microenvironment that determines the efficacy of immunotherapy. Journal of hepatology S0168-8278(23)00023-5. doi: 10.1016/j.jhep.2023.01.011.

2022

1. Mo J., Tan K., Dong Y., Lu W., Liu F., Mei Y., Huang H., Zhao K., Lv Z.#, Ye Y.#, Tang Y.#. Therapeutic targeting the oncogenic driver EWSR1::FLI1 in Ewing sarcoma through inhibition of the FACT complex. Oncogene(2022) 42(1):11-25.

2. Zhang, C., Wang, H., Yang, X., Fu, Z., Ji, X., Shi, Y., Zhong, J., Hu, W., Ye Y.#, Wang, Z.# & Ni, D#. Oral zero-valent-molybdenum nanodots for inflammatory bowel disease therapy. Science Advances8, 1–12 (2022).

3. Wang G., Xie Z., Su J., Chen M., Du Y., Gao Q., Zhang G., Zhang H., Chen X.#, Liu H.#, Han L.# & Ye Y#. Characterization of immune-related alternative polyadenylation events in cancer immunotherapy. Cancer Research CAN-22-1417 (2022) doi:10.1158/0008-5472.CAN-22-1417.

4. He, Y., Dong, Y., Chen, Y., Zhang, G., Zhang, H., Lei, G., Du, Y., Chen, X.#, Ye, Y#. & Liu, H#. Multi-omics characterization and therapeutic liability of ferroptosis in melanoma. Signal Transduction and Targeted Therapy. 7, (2022).

5. 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.# (lead contact), Su, B.#. Single-cell and spatial analysis reveal interaction of FAP+ fibroblasts and SPP1+ macrophages in colorectal cancer. Nature Communications (2022) 13:1742.

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

7. 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 (2022) 3 (1) 100194.

8. 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.

9. 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.

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

2021

1. 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.

2. 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.

3. 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

4. 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.

5. 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.

Before

1. 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")

2. 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.

3. 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.

4. 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)

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

6. 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.

7. 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.

專著章節(jié)(#: 共同通訊)

1. 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.

2. 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.

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