Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies

Cell - Tập 181 - Trang 728-744.e21 - 2020
Theodore L. Roth1,2,3,4,5, P. Jonathan Li3,4,5, Franziska Blaeschke3,4,5, Jasper F. Nies3,4,5, Ryan Apathy3,4,5, Cody Mowery1,2,3,4,5, Ruby Yu3,4,5, Michelle L.T. Nguyen3,4,5, Youjin Lee3,4,5, Anna Truong3,4,5, Joseph Hiatt1,2,3,4,5, David Wu1,2, David N. Nguyen3,4,5,6, Daniel Goodman3,4,5, Jeffrey A. Bluestone4,7,8, Chun Jimmie Ye7,9,10,11,12,13, Kole Roybal3,9,8,14, Eric Shifrut3,4,5, Alexander Marson3,4,5,6,7,9,14
1Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
2Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
3Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
4Diabetes Center, University of California San Francisco, San Francisco, CA, USA
5Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
6Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
7Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
8Sean N. Parker Autoimmune Research Laboratory, University of California, San Francisco, San Francisco, CA, USA
9Chan Zuckerberg Biohub, San Francisco, CA, USA
10Institute for Human Genetics University of California–San Francisco San Francisco CA USA
11Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
12Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
13Department of Epidemiology and Biostatistics, University of California-San Francisco, San Francisco, CA, USA
14UCSF Helen Diller Family Comprehensive Cancer Center University of California–San Francisco San Francisco CA USA

Tài liệu tham khảo

Adamson, 2016, A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response, Cell, 167, 1867, 10.1016/j.cell.2016.11.048 Anderson, 2017, Obstacles Posed by the Tumor Microenvironment to T cell Activity: A Case for Synergistic Therapies, Cancer Cell, 31, 311, 10.1016/j.ccell.2017.02.008 Arber, 2017, Reprogramming cellular functions with engineered membrane proteins, Curr. Opin. Biotechnol., 47, 92, 10.1016/j.copbio.2017.06.009 Batlle, 2019, Transforming Growth Factor-β Signaling in Immunity and Cancer, Immunity, 50, 924, 10.1016/j.immuni.2019.03.024 Binnewies, 2018, Understanding the tumor immune microenvironment (TIME) for effective therapy, Nat. Med., 24, 541, 10.1038/s41591-018-0014-x Butler, 2018, Integrating single-cell transcriptomic data across different conditions, technologies, and species, Nat. Biotechnol., 36, 411, 10.1038/nbt.4096 Cavazzana-Calvo, 2010, Transfusion independence and HMGA2 activation after gene therapy of human β-thalassaemia, Nature, 467, 318, 10.1038/nature09328 Chavez, 2015, Highly efficient Cas9-mediated transcriptional programming, Nat. Methods, 12, 326, 10.1038/nmeth.3312 Chen, 2013, Oncology meets immunology: the cancer-immunity cycle, Immunity, 39, 1, 10.1016/j.immuni.2013.07.012 Chen, 2016, CAR T-cell intrinsic PD-1 checkpoint blockade: A two-in-one approach for solid tumor immunotherapy, Oncoimmunology, 6, e1273302, 10.1080/2162402X.2016.1273302 Dahmani, 2018, TGF-β in T cell biology: Implications for cancer immunotherapy, Cancers (Basel), 10, E194, 10.3390/cancers10060194 Datlinger, 2017, Pooled CRISPR screening with single-cell transcriptome readout, Nat. Methods, 14, 297, 10.1038/nmeth.4177 Dixit, 2016, Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens, Cell, 167, 1853, 10.1016/j.cell.2016.11.038 Dong, 2019, Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells, Cell, 178, 1189, 10.1016/j.cell.2019.07.044 Esensten, 2017, Engineering Therapeutic T Cells: From Synthetic Biology to Clinical Trials, Annu. Rev. Pathol., 12, 305, 10.1146/annurev-pathol-052016-100304 Eyquem, 2017, Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection, Nature, 543, 113, 10.1038/nature21405 Fabregat, 2018, The Reactome Pathway Knowledgebase, Nucleic Acids Res., 46, D649, 10.1093/nar/gkx1132 Feldman, 2018, Lentiviral co-packaging mitigates the effects of intermolecular recombination and multiple integrations in pooled genetic screens, bioRxiv Fesnak, 2016, Engineered T cells: the promise and challenges of cancer immunotherapy, Nat. Rev. Cancer, 16, 566, 10.1038/nrc.2016.97 Findlay, 2014, Saturation Editing of Genomic Regions by Multiplex Homology-Directed Repair, Nature, 513, 120, 10.1038/nature13695 Findlay, 2018, Accurate Classification of BRCA1 Variants With Saturation Genome Editing, Nature, 562, 217, 10.1038/s41586-018-0461-z Fischbach, 2013, Cell-based therapeutics: the next pillar of medicine, Sci. Transl. Med., 5, 179ps7, 10.1126/scitranslmed.3005568 Gigante, 2012, TGF-beta: a master switch in tumor immunity, Curr. Pharm. Des., 18, 4126, 10.2174/138161212802430378 Gilbert, 2013, CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes, Cell, 154, 442, 10.1016/j.cell.2013.06.044 Gilbert, 2014, Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation, Cell, 159, 647, 10.1016/j.cell.2014.09.029 Gorelik, 2000, Abrogation of TGFbeta signaling in T cells leads to spontaneous T cell differentiation and autoimmune disease, Immunity, 12, 171, 10.1016/S1074-7613(00)80170-3 Gwiazda, 2016, High Efficiency CRISPR/Cas9-mediated Gene Editing in Primary Human T-cells Using Mutant Adenoviral E4orf6/E1b55k “Helper” Proteins, Mol. Ther., 24, 1570, 10.1038/mt.2016.105 Hanna, 2018, A case of mistaken identity, Nat. Biotechnol., 36, 802, 10.1038/nbt.4208 Hegde, 2018, Uncoupling of sgRNAs from their associated barcodes during PCR amplification of combinatorial CRISPR screens, PLoS ONE, 13, e0197547, 10.1371/journal.pone.0197547 Hess, 2016, Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells, Nat. Methods, 13, 1036, 10.1038/nmeth.4038 Jaitin, 2016, Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq, Cell, 167, 1883, 10.1016/j.cell.2016.11.039 June, 2018, Chimeric Antigen Receptor Therapy, N. Engl. J. Med., 379, 64, 10.1056/NEJMra1706169 Khan, 2019, TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion, Nature, 571, 211, 10.1038/s41586-019-1325-x Kim, 2017, An engineered transforming growth factor β (TGF-β) monomer that functions as a dominant negative to block TGF-β signaling, J. Biol. Chem., 292, 7173, 10.1074/jbc.M116.768754 Kloss, 2018, Dominant-Negative TGF-β Receptor Enhances PSMA-Targeted Human CAR T Cell Proliferation And Augments Prostate Cancer Eradication, Mol. Ther., 26, 1855, 10.1016/j.ymthe.2018.05.003 Kurtulus, 2019, Checkpoint Blockade Immunotherapy Induces Dynamic Changes in PD-1-CD8+ Tumor-Infiltrating T Cells, Immunity, 50, 181, 10.1016/j.immuni.2018.11.014 Leen, 2014, Reversal of tumor immune inhibition using a chimeric cytokine receptor, Mol. Ther., 22, 1211, 10.1038/mt.2014.47 Liu, 2016, A chimeric switch-receptor targeting PD1 augments the efficacy of second-generation CAR T cells in advanced solid tumors, Cancer Res., 76, 1578, 10.1158/0008-5472.CAN-15-2524 Lynn, 2019, c-Jun overexpression in CAR T cells induces exhaustion resistance, Nature, 576, 293, 10.1038/s41586-019-1805-z Ma, 2016, Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells, Nat. Methods, 13, 1029, 10.1038/nmeth.4027 Morgan, 2009, ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data, Bioinformatics, 25, 2607, 10.1093/bioinformatics/btp450 Nguyen, 2020, A Cas9 nanoparticle system with truncated Cas9 target sequences on DNA repair templates enhances genome targeting in diverse human immune cell types, Nature Biotechnology Oda, 2017, A CD200R-CD28 fusion protein appropriates an inhibitory signal to enhance T-cell function and therapy of murine leukemia, Blood, 130, 2410, 10.1182/blood-2017-04-777052 Ostrand-Rosenberg, 2012, Cross-talk between myeloid-derived suppressor cells (MDSC), macrophages, and dendritic cells enhances tumor-induced immune suppression, Semin. Cancer Biol., 22, 275, 10.1016/j.semcancer.2012.01.011 Paquet, 2016, Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9, Nature, 533, 125, 10.1038/nature17664 Prosser, 2012, Tumor PD-L1 co-stimulates primary human CD8(+) cytotoxic T cells modified to express a PD1:CD28 chimeric receptor, Mol. Immunol., 51, 263, 10.1016/j.molimm.2012.03.023 Rafiq, 2020, Engineering strategies to overcome the current roadblocks in CAR T cell therapy, Nat. Rev. Clin. Oncol., 17, 147, 10.1038/s41571-019-0297-y Ren, 2017, Multiplex genome editing to generate universal CAR T cells resistant to PD1 inhibition, Clin. Cancer Res., 23, 2255, 10.1158/1078-0432.CCR-16-1300 Romero, 2013, β-globin gene transfer to human bone marrow for sickle cell disease, J. Clin. Invest., 67930 Roth, 2018, Reprogramming human T cell function and specificity with non-viral genome targeting, Nature, 559, 405, 10.1038/s41586-018-0326-5 Rupp, 2017, CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells, Sci. Rep., 7, 737, 10.1038/s41598-017-00462-8 Sack, 2016, Sources of error in mammalian genetic screens, G3 (Bethesda), 6, 2781, 10.1534/g3.116.030973 Sadelain, 2017, Therapeutic T cell engineering, Nature, 545, 423, 10.1038/nature22395 Sanjana, 2017, Genome-scale CRISPR pooled screens, Anal. Biochem., 532, 95, 10.1016/j.ab.2016.05.014 Sergushichev, 2016, An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation, bioRxiv Shalem, 2014, Genome-scale CRISPR-Cas9 Knockout Screening in Human Cells, Science, 343, 84, 10.1126/science.1247005 Shifrut, 2018, Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function, Cell, 175, 1958, 10.1016/j.cell.2018.10.024 Shin, 2012, Positive conversion of negative signaling of CTLA4 potentiates antitumor efficacy of adoptive T-cell therapy in murine tumor models, Blood, 119, 5678, 10.1182/blood-2011-09-380519 Shin, 2016, Enhanced anti-tumor reactivity of cytotoxic T lymphocytes expressing PD-1 decoy, Immune Netw., 16, 134, 10.4110/in.2016.16.2.134 Siddiqui, 2019, Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy, Immunity, 50, 195, 10.1016/j.immuni.2018.12.021 Stadtmauer, 2020, CRISPR-engineered T cells in patients with refractory cancer, Science, 367, 80, 10.1126/science.aba7365 Strasser, 2009, The many roles of FAS receptor signaling in the immune system, Immunity, 30, 180, 10.1016/j.immuni.2009.01.001 Su, 2016, CRISPR-Cas9 mediated efficient PD-1 disruption on human primary T cells from cancer patients, Sci. Rep., 6, 20070, 10.1038/srep20070 Tay, 2017, Chimeric switch receptor: switching for improved adoptive T-cell therapy against cancers, Immunotherapy, 9, 1339, 10.2217/imt-2017-0103 Thomas, 2005, TGF-β directly targets cytotoxic T cell functions during tumor evasion of immune surveillance, Cancer Cell, 8, 369, 10.1016/j.ccr.2005.10.012 Wang, 2014, Genetic Screens in Human Cells Using the CRISPR-Cas9 System, Science, 343, 80, 10.1126/science.1246981 Wei, 2019, Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy, Nature, 576, 471, 10.1038/s41586-019-1821-z Weiner, 2010, Monoclonal antibodies: versatile platforms for cancer immunotherapy, Nat. Rev. Immunol., 10, 317, 10.1038/nri2744 Wherry, 2011, T cell exhaustion, Nat. Immunol., 12, 492, 10.1038/ni.2035 Wu, 2016, The TCF1-Bcl6 axis counteracts type I interferon to repress exhaustion and maintain T cell stemness, Sci. Immunol., 1, eaai8593, 10.1126/sciimmunol.aai8593 Yamamoto, 2019, T cells genetically engineered to overcome death signaling enhance adoptive cancer immunotherapy, J. Clin. Invest., 129, 1551, 10.1172/JCI121491 Zaretsky, 2016, Mutations Associated With Acquired Resistance to PD-1 Blockade in Melanoma, N. Engl. J. Med., 375, 819, 10.1056/NEJMoa1604958 Zheng, 2017, Massively parallel digital transcriptional profiling of single cells, Nat. Commun., 8, 14049, 10.1038/ncomms14049