Selected publications (* = Co-first author, † = Corresponding author):
(Full publications: https://scholar.google.com/citations?hl=en&user=gUqFuHMAAAAJ)
2024
Yuanfang Cao*, Xueting Li*, Yumu Pan*, Huahe Wang*, Siyu Yang*, Lingjuan Hong, Lupeng Ye†. CRISPR-based genetic screens advance cancer immunology. SCIENCE CHINA Life Sciences. 2024. (Review)
Peng L*, Renauer P*, Sferruzza G, Yang L, Zou Y, Fang Z, Park J, Chow R, Zhang Y, Lin Q, Bai M, Sanchez A, Zhang Y, Lam S, Ye L† and Chen S†. In vivo AAV-SB-CRISPR screens of tumor-infiltrating primary NK cells identify genetic checkpoints of CAR-NK therapy. Nature Biotechnology. 2024. (Highlighted in Nature Biotechnology etc.)(Corresponding Author)
https://www.nature.com/articles/s41587-024-02282-4
https://www.nature.com/articles/s41587-024-02319-8
2023
Ye L, Lam S, Yang L, Suzuki K, Zou Y, Lin Q, Zhang Y, Clark P, Peng L, Chen S†. AAV-mediated delivery of a Sleeping-Beauty transposon and an mRNA-encoded transposase for the engineering of therapeutic immune cells. Nature Biomedical Engineering. 2023. Cover Article https://www.nature.com/articles/s41551-023-01058-6
Renauer P, Park JJ, Bai M, Acosta A, Lee W, Lin G, Zhang Y, Dai X, Wang G, Errami Y, Wu T, Clark P, Ye L†, Yang Q†, Sidi Chen†. Immunogenetic metabolomics revealed key enzymes that modulate CAR-T metabolism and function. Cancer Immunology Research.2023. (Corresponding Author) https://aacrjournals.org/cancerimmunolres/article-abstract/11/8/1068/728057/Immunogenetic-Metabolomics-Reveals-Key-Enzymes?redirectedFrom=fulltext
2022
Hong, L, Ye, L†. The interferon-γ receptor pathway: a new way to regulate CAR T cell-solid tumor cell adhesion. Signal Transduction and Targeted Therapy. 7, 315 (2022). (Corresponding Author) https://www.nature.com/articles/s41392-022-01165-x
Ye L*, Park JJ*, Peng L*, Yang Q *, Chow RD, Dong M, Lam S, Guo J, Tang E, Zhang Y, Wang G, Dai X, Du Y, Kim H, Cao H, Errami Y, Clark P, Bersenev A, Montgomery RR, Chen S†. A genome-scale gain-of-function CRISPR screen in CD8 T cells identifies proline metabolism as a means to enhance CAR-T therapy. Cell Metabolism. 2022. doi.org/10.1016/j.cmet.2022.02.009. (Highlighted in Cancer Discovery, ScienceDaily, Fierce Biotech, EurekAlertAAAS, Technology Networks, YaleNews, Yale Scientific Magazine, YaleToday, Yale Daily News, TodayUKNews, ecancer, Medical Xpress etc.) (*Contributed equally) https://www.sciencedirect.com/science/article/pii/S1550413122000535
Park JJ*, Codina A*, Ye L*, Lam S, Guo J, Clark P, Zhou X, Peng L, Chen S†. Double knockout CRISPR screen for cancer resistance to T cell cytotoxicity. Journal of Hematology & Oncology. 2022. (*Contributed equally) https://jhoonline.biomedcentral.com/articles/10.1186/s13045-022-01389-y
2020
Wang G*, Chow RD*, Zhu L*, Bai Z*, Ye L, Zhang F, Renauer PA, Dong MB, Dai X, Zhang X, Du Y, Cheng Y, Niu L, Chu Z, Kim K, Liao C, Clark P, Errami Y, Chen S†. CRISPR-GEMM Pooled Mutagenic Screening Identifies KMT2D as a Major Modulator of Immune Checkpoint Blockade. Cancer Discovery. 2020 Dec;10(12):1912-1933. doi: 10.1158/2159-8290.CD-19-1448.
Sun N, Chen D, Ye L, Sheng G, Gong J, Chen B, Lu Y†, Han F†. CRISPR-Sunspot: Imaging of endogenous low-abundance RNA at the single-molecule level in live cells. Theranostics. 2020 Sep 2;10(24):10993-11012. doi: 10.7150/thno.43094.
2019
Ye L*, Park JJ*, Dong MB*, Yang Q, Chow RD, Peng L, Du Y, Guo J, Dai X, Wang G, Errami Y, Chen S†. In vivo CRISPR screening in CD8 T cells with AAV-Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma. Nature Biotechnology. 2019. doi: 10.1038/s41587-019-0246-4. (Highlighted in Yale News, Yale Scientific Magazine, Phys.Org, Environmental News Network, Health Canal, LongRoom News, Twitter etc.) (*Contributed equally) https://www.nature.com/articles/s41587-019-0246-4
Dong MB*, Wang G*, Chow RD*, Ye L*, Zhu L, Dai X, Park JJ, Kim HR, Errami Y, Guzman CD, Zhou X, Chen KY, Renauer PA, Du Y, Shen J, Lam SZ, Zhou JJ, Lannin DR, Herbst RS, Chen S†. Systematic Immunotherapy Target Discovery Using Genome-Scale In vivo CRISPR Screens in CD8 T Cells. Cell. 2019. doi: 10.1016/j.cell.2019.07.044. (Highlighted in Nature Reviews Cancer, Recommended by Faculty1000 etc.) (*Contributed equally) https://www.sciencedirect.com/science/article/pii/S009286741930844X
Chow RD*, Wang G*, Ye L*, Codina A, Kim HR, Shen L, Dong MB, Errami Y, Chen S†. In vivo profiling of metastatic double knockouts through CRISPR-Cpf1 screens. Nature Methods. 2019. doi: 10.1038/s41592-019-0371-5. (*Contributed equally) https://www.nature.com/articles/s41592-019-0371-5
Wang G*, Chow RD*, Bai Z, Zhu L, Errami Y, Dai X, Dong MB, Ye L, Zhang X, Renauer PA, Park JJ, Shen L, Ye H, Fuchs CS, Chen S†. Multiplexed activation of endogenous genes by CRISPRa elicits potent antitumor immunity. Nature Immunology. 2019. doi: 10.1038/s41590-019-0500-4.
Codina A*, Renauer P*, Wang G*, Chow RD*, Park JJ, Ye H, Zhang K, Dong M, Gassaway B, Ye L, Errami Y, Shen L, Chang A, Jain D, Herbst RS, Bosenberg M, Rinehart J, Fan R and Chen S†. Convergent identification and interrogation of tumor-intrinsic factors that modulate cancer immunity in vivo. Cell Systems. 2019 Feb 27;8(2):136-151.e7. doi: 10.1016/j.cels.2019.01.004. PMID: 30797773. (Cover story).
Before 2019
Ye L*, Wang C*, Hong L, Sun N, Chen D, Chen S†, Han F†. Programmable DNA repair with CRISPRa/i enhanced homology-directed repair efficiency with a single Cas9. Cell Discovery. 2018 Jul 24;4:46. doi:10.1038/s41421-018-0049-7. (*Contributed equally) https://www.nature.com/articles/s41421-018-0049-7
Wang G*, Chow RD*, Ye L, Guzman CD, Dai X, Dong MB, Zhang F, Sharp PA, Platt RJ†, Chen S†. Mapping a functional cancer genome atlas of tumor suppressors in mouse liver using AAV-CRISPR mediated direct in vivo screening. Science Advances. 2018 Feb 28;4(2). doi: 10.1126/sciadv.aao5508
Chow, R.D*, Guzman, C.D*, Wang, G*, Schmidt, F*, Youngblood, M.W**, Ye, L**, Errami, Y, Dong, M.B, Martinez, M.A, Zhang, S,Renauer, P, Bilguvar, K, Gunel, M, Sharp, P.A, Zhang, F, Platt, R.J†, Chen, S†. AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma. Nature Neuroscience. 20, 1329–1341 (2017). https://doi.org/10.1038/nn.4620
Ye, L, You, Z, Qian, Q, Zhang Y, Che J, Song J, Zhong B†. TAL effectors mediate high-efficiency transposition of the piggyBac transposon in silkworm Bombyx mori L. Scientific Reports 5, 17172 (2015) doi:10.1038/srep17172
Ye, L, Qian, Q, Zhang, Y, You Z, Che J, Song J, Zhong B†. Analysis of the sericin1 promoter and assisted detection of exogenous gene expression efficiency in the silkworm Bombyx mori L. Scientific Reports 5, 8301 (2015) doi:10.1038/srep08301
Li J*, Ye L*, Che J, Song J, You Z, Yun K, Wang S, Zhong B†. Comparative proteomic analysis of the silkworm middle silk gland reveals the importance of ribosome biogenesis in silk protein production. Journal of Proteomics, 2015, 126:109-120. doi.org/10.1016/j.jprot.2015.06.001
Ye L, Zhuang L, Li J, You Z, Liang J, Wei H, Lin J, Zhong B†. Analysis of the activity of virus internal ribosome entry site in silkworm Bombyx mori. Acta Bioch Bioph Sin, 2013, 45:534-539. doi.org/10.1093/abbs/gmt046
Ye Lab - Nanjing University 