Publications

2025

2024

  • Lei Peng*, Giacomo Sferruzza*, Luojia Yang*, Liqun Zhou, Sidi Chen. CAR-T and CAR-NK as cellular cancer immunotherapy for solid tumors. Cellular & Molecular Immunology, 2024. https://www.nature.com/articles/s41423-024-01207-0. PDF
  • Lei Peng*, Paul A. Renauer*, Giacomo Sferruzza, Luojia Yang, Yongji Zou, Zhenghao Fang, Jonathan J. Park, Ryan D. Chow, Yueqi Zhang, Qianqian Lin, Meizhu Bai, Angelica Sanchez, Yongzhan Zhang, Stanley Z. Lam, Lupeng Ye† & Sidi Chen†. In vivo AAV–SB-CRISPR screens of tumor-infiltrating primary NK cells identify genetic checkpoints of CAR-NK therapy. Nature Biotechnology, 2024. https://www.nature.com/articles/s41587-024-02282-4. PDF
  • Hao Shi, Sidi Chen, Hongbo Chi. Immunometabolism of CD8+ T cell differentiation in cancer. Trends in Cancer, 2024. https://www.cell.com/trends/cancer/fulltext/S2405-8033(24)00059-1. PDF
  • Sidi Chen, Matthew Dong. Platform for T lymphocyte genome engineering and in vivo high-throughput screening thereof. Granted patent, 2024.
  • Jameson Crandell*, Valter Silva Monteiro*, Lauren Pischel*, Zhenhao Fang, Yi Zhong, Lauren Lawres, Luciana Conde, Gustavo Meira de Asis, Gabriela Maciel, Agnieszka Zaleski, Guilherme S. Lira, Luiza M. Higa, Mallery I. Breban, Chantal B. F. Vogels, Nathan D. Grubaugh, Lydia Aoun-Barakat, Alba Grifoni, Alessandro Sette, Terezinha M. Castineiras, Sidi Chen, Inci Yildirim, Andre M. Vale†, Saad B. Omer20† & Carolina Lucas†. The impact of antigenic distance on Orthopoxvirus Vaccination and Mpox Infection for cross-protective immunity. medRxiv 2024. https://www.medrxiv.org/content/medrxiv/early/2024/02/01/2024.01.31.24302065.full.pdf. PDF
  • Nipun Verma, Paul A Renauer, Chuanpeng Dong, Shan Xin, Qianqian Lin, Feifei Zhang, Peter M Glazer, Sidi Chen†. Genome scale CRISPR screens identify actin capping proteins as key modulators of therapeutic responses to radiation and immunotherapy. bioRxiv 2024. https://www.biorxiv.org/content/10.1101/2024.01.14.575614v1

2023

  • Barish S, Berg K, Drozd J, Berglund-Brown I, Khizir L, Wasson LK, Seidman CE, Seidman JG, Chen S, Brueckner M. The H2Bub1-deposition complex is required for human and mouse cardiogenesis. Development 2023. doi: 10.1242/dev.201899. PDF
  • Ping Ren*, Yingxia Hu*, Lei Peng*, Luojia Yang, Kazushi Suzuki, Zhenhao Fang, Meizhu Bai, Liqun Zhou, Yanzhi Feng, Yongji Zou, Yong Xiong† & , Sidi Chen†. Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages. Signal Transduction and Targeted Therapy 2023. https://www.nature.com/articles/s41392-023-01509-1. PDF
  • Devarkar SC, Vetick M, Balaji S, Lomakin IB, Yang L, Jin D, Gilbert WV, Chen S, Xiong Y. Structural basis for translation inhibition by MERS-CoV Nsp1 reveals a conserved mechanism for betacoronaviruses. Cell Reports 2023. doi: 10.1016/j.celrep.2023.113156. PDF
  • Xiaoyu Zhou*, Hanbing Cao*, Shao-Yu Fang, Ryan D. Chow, Kaiyuan Tang, Medha Majety, Meizhu Bai, Matthew B. Dong, Paul A. Renauer, Xingbo Shang, Kazushi Suzuki, Andre Levchenko, Sidi Chen†. CTLA-4 tail fusion enhances CAR-T antitumor immunity. Nature Immunology 2023. Cover Article. https://www.nature.com/articles/s41590-023-01571-5. PDF
  • Ye L, Lam SZ, Yang L, Suzuki K, Zou Y, Lin Q, Zhang Y, Clark P, Peng L, Chen S†. Therapeutic immune cell engineering with an mRNA : AAV-Sleeping Beauty composite system. Nature Biomedical Engineering 2023. Cover Article. https://www.nature.com/articles/s41551-023-01058-6. PDF
  • Xiaoyu Zhou*, Paul Renauer*, Liqun Zhou, Shao-Yu Fang, Sidi Chen†. Applications of CRISPR technology in cellular immunotherapy. Immunological Reviews 2023 https://doi.org/10.1111/imr.13241. PDF
  • Liqun Zhou*, Luojia Yang*, Yanzhi Feng*, Sidi Chen†. Pooled screening with next-generation gene editing tools. Current Opinion in Biomedical Engineering 2023 https://doi.org/10.1016/j.cobme.2023.100479. PDF
  • Paul Renauer, Jonathan J. Park, Meizhu Bai, Arianny Acosta, Won-Ho Lee, Guang Han Lin, Yueqi Zhang, Xiaoyun Dai, Guangchuan Wang, Youssef Errami, Terence Wu, Paul Clark, Lupeng Ye†, Quanjun Yang†, Sidi Chen†. Immunogenetic metabolomics reveals key enzymes that modulate CAR T-cell metabolism and function. Cancer Immunology Research 2023 https://doi.org/10.1158/2326-6066.CIR-22-0565. PDF
  • Li Zhang, Jonathan J Park, Matthew B Dong, Deanna Arsala, Shengqian Xia, Jianhai Chen, Dylan Sosa, Jared E Atlas, Manyuan Long†, Sidi Chen†. Human gene age dating reveals an early and rapid evolutionary construction of the adaptive immune system. Genome Biology and Evolution 2023 https://doi.org/10.1093/gbe/evad081.
  • Wang G, Zhang F, Chow RD, He E, Zhu L, Han Q, Chen S†. Rational design of immune gene therapy combinations via in vivo CRISPR activation screen of tumor microenvironment modulators. bioRxiv 2023 https://doi.org/10.1101/2023.03.14.532665
  • Zhang F, Wang G,  Chow RD, He E, Majety M, Zhang Y,  Chen S†. Multiplexed repression of immunosuppressive genes as combinatorial cancer immunotherapy. bioRxiv 2023. https://doi.org/10.1101/2023.03.14.532668
  • Zhenhao Fang*, Valter S. Monteiro*, Paul A. Renauer, Xingbo Shang, Kazushi Suzuki, Xinyu Ling, Meizhu Bai, Yan Xiang, Andre Levchenko, Carmen J. Booth, Carolina Lucas† & Sidi Chen†. Polyvalent mRNA vaccination elicited potent immune response to monkeypox virus surface antigens. Cell Research 2023. https://www.nature.com/articles/s41422-023-00792-5. PDF
  • Park JJ*, Lee KV*, … Chen S. Machine learning identifies T cell receptor repertoire signatures associated with COVID-19 severity. Communications Biology 2023. https://www.nature.com/articles/s42003-023-04447-4 PDF

2022

2021

  • Chow RD, Majety M, Chen S. The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2. Nature Communications 2021. doi:10.1038/s41467-020-20323-9. https://rdcu.be/cc1O0. PDF
  • Park JJ, Chen S. Metaviromic identification of discriminative genomic features in SARS-CoV-2 using machine learning. Cell Patterns 2021. doi:10.1016/j.patter.2021.100407. PDF

2020

  • Yuan S*, Peng L*, Park JJ, Hu Y, Devarkar SC, Dong MB, Shen Q, Wu S, Chen S**, Lomakin I**, Xiong Y**. Nonstructural protein 1 of SARS-CoV-2 is a potent pathogenicity factor redirecting host protein synthesis machinery toward viral RNA. Molecular Cell 2020. doi: 10.1016/j.molcel.2020.10.034. PDF
  • Chow RD*, Chen JS*, Shen J, and Chen S. A web tool for the design of prime-editing guide RNAs. Nature Biomedical Engineering 2020. doi: 10.1038/s41551-020-00622-8. PDF
  • 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. doi: 10.1158/2159-8290.CD-19-1448. PDF

2019

  • 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. PDF
  • 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. PDF
  • 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. PDF.
    in vitro screen raw count table
    in vivo screen raw count table
  • 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. PDF
  • Dai X*, Park JJ*, Du Y, Kim HR, Wang G, Errami Y, Chen S. One-step generation of modular CAR-T with AAV-Cpf1. Nature Methods 2019. doi: 10.1038/s41592-019-0329. PDF
  • Codina A*, Renauer PA*, 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, Chen S. Convergent identification and interrogation of tumor-intrinsic factors that modulate cancer immunity in vivo. Cell Systems 2019. 10.1016/j.cels.2019.01.004. PDF

2018

  • Chow RD, Chen S. Sno-derived RNAs are prevalent molecular markers of cancer immunity. Oncogene. 2018 Aug 2. PDF
  • 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. PDF
  • Chow RD, Kim HR, Chen S. Programmable sequential mutagenesis by inducible Cpf1 crRNA array inversion. Nature Communications. 2018 May 15;9(1):1903. PDF
  • Chow RD, Chen S. Cancer CRISPR screens in vivo. Trends in Cancer. 2018 Mar 29. PDF
  • 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). PDF

2017

  • Chow RD*, Guzman CD*, Wang G*, Schmidt F*, Youngblood MW, Ye L, Errami Y, Dong MB, Martinez MA, Zhang S, Renauer P, Bilguvar K, Gunel M, Sharp PA, Zhang F, Platt RJ, Chen S. AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma. Nature Neuroscience. 2017 Aug 14. PDF

2015

  • Chen S*, Sanjana NE*, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, Lee H, Zhang F, Sharp PA. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell. 2015 Mar 12;160(6):1246-60. PDF Best of Cell in 2015

2014

  • Platt RJ*, Chen S*, Zhou Y, Yim MJ, Swiech L, Kempton HR, Dahlman JE, Parnas O, Eisenhaure TM, Jovanovic M, Graham DB, Jhunjhunwala S, Heidenreich M, Xavier RJ, Langer R, Anderson DG, Hacohen N, Regev A, Feng G, Sharp PA, Zhang F. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell. 2014 Oct 9;159(2):440-55. PDF Cover Article
  • Xue W*, Chen S*, Yin H*, Tammela T, Papagiannakopoulos T, Joshi NS, Cai W, Yang G, Bronson R, Crowley DG, Zhang F, Anderson DG, Sharp PA, Jacks T. CRISPR-mediated direct mutation of cancer genes in the mouse liver. Nature. 2014 Oct 16;514(7522):380-4. PDF
  • Chen S*, Xue Y*, Wu X, Le C, Bhutkar A, Bell EL, Zhang F, Langer R, Sharp PA. Global microRNA depletion suppresses tumor angiogenesis. Genes Dev. 2014 May 15;28(10):1054-67. PDF

2013

  • Chen S, Krinsky BH, Long M. New genes as drivers of phenotypic evolution. Nat Rev Genet. 2013 Sep;14(9):645-60. PDF

2012

  • Chen S*, Ni X*, Krinsky BH, Zhang YE, Vibranovski MD, White KP, Long M. Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene. EMBO J. 2012 Jun 13;31(12):2798-809. PDF
  • Chen S, Spletter M, Ni X, White KP, Luo L, Long M. Frequent recent origination of brain genes shaped the evolution of foraging behavior in Drosophila. Cell Rep. 2012 Feb 23;1(2):118-32. PDF

2010

  • Chen S, Zhang YE, Long M. New genes in Drosophila quickly become essential. Science. 2010 Dec 17;330(6011):1682-5. PDF
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