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Bussey-Sutton CR, Ward A, Fox JA, Turner AMW, Peterson JJ, Emery A, Longoria AR, Gomez-Martinez I, Jones C, Hepperla A, Margolis DM, Strahl BD, Browne EP. The histone methyltransferase SETD2 regulates HIV expression and latency. PLoS Pathog 2024; 20:e1012281. [PMID: 38848441 DOI: 10.1371/journal.ppat.1012281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 05/22/2024] [Indexed: 06/09/2024] Open
Abstract
Understanding the mechanisms that drive HIV expression and latency is a key goal for achieving an HIV cure. Here we investigate the role of the SETD2 histone methyltransferase, which deposits H3K36 trimethylation (H3K36me3), in HIV infection. We show that prevention of H3K36me3 by a potent and selective inhibitor of SETD2 (EPZ-719) leads to reduced post-integration viral gene expression and accelerated emergence of latently infected cells. CRISPR/Cas9-mediated knockout of SETD2 in primary CD4 T cells confirmed the role of SETD2 in HIV expression. Transcriptomic profiling of EPZ-719-exposed HIV-infected cells identified numerous pathways impacted by EPZ-719. Notably, depletion of H3K36me3 prior to infection did not prevent HIV integration but resulted in a shift of integration sites from highly transcribed genes to quiescent chromatin regions and to polycomb repressed regions. We also observed that SETD2 inhibition did not apparently affect HIV RNA levels, indicating a post-transcriptional mechanism affecting HIV expression. Viral RNA splicing was modestly reduced in the presence of EPZ-719. Intriguingly, EPZ-719 exposure enhanced responsiveness of latent HIV to the HDAC inhibitor vorinostat, suggesting that H3K36me3 can contribute to a repressive chromatin state at the HIV locus. These results identify SETD2 and H3K36me3 as novel regulators of HIV integration, expression and latency.
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Affiliation(s)
- Cameron R Bussey-Sutton
- Department of Biochemistry, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Airlie Ward
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joshua A Fox
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Anne-Marie W Turner
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jackson J Peterson
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ann Emery
- Lineberger Comprehensive Cancer Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Arturo R Longoria
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ismael Gomez-Martinez
- Department of Genetics, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Corbin Jones
- Department of Genetics, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Austin Hepperla
- Department of Genetics, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David M Margolis
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Brian D Strahl
- Department of Biochemistry, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Edward P Browne
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
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2
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Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, Steinhart Z, Satpathy AT, Pollard KS, Corn JE, Bernstein BE, Ye CJ, Marson A. Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nat Genet 2024:10.1038/s41588-024-01743-5. [PMID: 38811842 DOI: 10.1038/s41588-024-01743-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/04/2024] [Indexed: 05/31/2024]
Abstract
Cis-regulatory elements (CREs) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to characterize the CREs controlling dynamic expression of the adjacent costimulatory genes CD28, CTLA4 and ICOS, encoding regulators of T cell-mediated immunity. Tiling CRISPR interference (CRISPRi) screens in primary human T cells, both conventional and regulatory subsets, uncovered gene-, cell subset- and stimulation-specific CREs. Integration with CRISPR knockout screens and assay for transposase-accessible chromatin with sequencing (ATAC-seq) profiling identified trans regulators influencing chromatin states at specific CRISPRi-responsive elements to control costimulatory gene expression. We then discovered a critical CCCTC-binding factor (CTCF) boundary that reinforces CRE interaction with CTLA4 while also preventing promiscuous activation of CD28. By systematically mapping CREs and associated trans regulators directly in primary human T cell subsets, this work overcomes longstanding experimental limitations to decode context-dependent gene regulatory programs in a complex, multi-gene locus critical to immune homeostasis.
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Affiliation(s)
- Cody T Mowery
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob W Freimer
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Zeyu Chen
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Salvador Casaní-Galdón
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Jennifer M Umhoefer
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Maya M Arce
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ketrin Gjoni
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Bence Daniel
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA, USA
| | - Katalin Sandor
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Benjamin G Gowen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Vinh Nguyen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA
| | - Dimitre R Simeonov
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Christian M Garrido
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Gemma L Curie
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Zachary Steinhart
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Ansuman T Satpathy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Bradley E Bernstein
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Chun Jimmie Ye
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA.
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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3
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Cowan QT, Gu S, Gu W, Ranzau BL, Simonson TS, Komor AC. Development of multiplexed orthogonal base editor (MOBE) systems. Nat Biotechnol 2024:10.1038/s41587-024-02240-0. [PMID: 38773305 DOI: 10.1038/s41587-024-02240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 04/10/2024] [Indexed: 05/23/2024]
Abstract
Base editors (BEs) enable efficient, programmable installation of point mutations while avoiding the use of double-strand breaks. Simultaneous application of two or more different BEs, such as an adenine BE (which converts A·T base pairs to G·C) and a cytosine BE (which converts C·G base pairs to T·A), is not feasible because guide RNA crosstalk results in non-orthogonal editing, with all BEs modifying all target loci. Here we engineer both adenine BEs and cytosine BEs that can be orthogonally multiplexed by using RNA aptamer-coat protein systems to recruit the DNA-modifying enzymes directly to the guide RNAs. We generate four multiplexed orthogonal BE systems that enable rates of precise co-occurring edits of up to 7.1% in the same DNA strand without enrichment or selection strategies. The addition of a fluorescent enrichment strategy increases co-occurring edit rates up to 24.8% in human cells. These systems are compatible with expanded protospacer adjacent motif and high-fidelity Cas9 variants, function well in multiple cell types, have equivalent or reduced off-target propensities compared with their parental systems and can model disease-relevant point mutation combinations.
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Affiliation(s)
- Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Sifeng Gu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Wanjun Gu
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Brodie L Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Tatum S Simonson
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
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4
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Lin T, Liu D, Guan Z, Zhao X, Li S, Wang X, Hou R, Zheng J, Cao J, Shi M. CRISPR screens in mechanism and target discovery for AML. Heliyon 2024; 10:e29382. [PMID: 38660246 PMCID: PMC11040068 DOI: 10.1016/j.heliyon.2024.e29382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 03/20/2024] [Accepted: 04/07/2024] [Indexed: 04/26/2024] Open
Abstract
CRISPR-based screens have discovered novel functional genes involving in diverse tumor biology and elucidated the mechanisms of the cancer pathological states. Recently, with its randomness and unbiasedness, CRISPR screens have been used to discover effector genes with previously unknown roles for AML. Those novel targets are related to AML survival resembled cellular pathways mediating epigenetics, synthetic lethality, transcriptional regulation, mitochondrial and energy metabolism. Other genes that are crucial for pharmaceutical targeting and drug resistance have also been identified. With the rapid development of novel strategies, such as barcodes and multiplexed mosaic CRISPR perturbation, more potential therapeutic targets and mechanism in AML will be discovered. In this review, we present an overview of recent progresses in the development of CRISPR-based screens for the mechanism and target identification in AML and discuss the challenges and possible solutions in this rapidly growing field.
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Affiliation(s)
- Tian Lin
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, Jiangsu, 221002, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Dan Liu
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, Jiangsu, 221002, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Zhangchun Guan
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, Jiangsu, 221002, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Xuan Zhao
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, Jiangsu, 221002, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Sijin Li
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, Jiangsu, 221002, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Xu Wang
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, Jiangsu, 221002, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Rui Hou
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, Jiangsu, 221002, China
- College of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Junnian Zheng
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, Jiangsu, 221002, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Jiang Cao
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, Jiangsu, 221002, China
| | - Ming Shi
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, Jiangsu, 221002, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, China
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5
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Xiang M, Li H, Zhan Y, Ma D, Gao Q, Fang Y. Functional CRISPR screens in T cells reveal new opportunities for cancer immunotherapies. Mol Cancer 2024; 23:73. [PMID: 38581063 PMCID: PMC10996278 DOI: 10.1186/s12943-024-01987-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/25/2024] [Indexed: 04/07/2024] Open
Abstract
T cells are fundamental components in tumour immunity and cancer immunotherapies, which have made immense strides and revolutionized cancer treatment paradigm. However, recent studies delineate the predicament of T cell dysregulation in tumour microenvironment and the compromised efficacy of cancer immunotherapies. CRISPR screens enable unbiased interrogation of gene function in T cells and have revealed functional determinators, genetic regulatory networks, and intercellular interactions in T cell life cycle, thereby providing opportunities to revamp cancer immunotherapies. In this review, we briefly described the central roles of T cells in successful cancer immunotherapies, comprehensively summarised the studies of CRISPR screens in T cells, elaborated resultant master genes that control T cell activation, proliferation, fate determination, effector function, and exhaustion, and highlighted genes (BATF, PRDM1, and TOX) and signalling cascades (JAK-STAT and NF-κB pathways) that extensively engage in multiple branches of T cell responses. In conclusion, this review bridged the gap between discovering element genes to a specific process of T cell activities and apprehending these genes in the global T cell life cycle, deepened the understanding of T cell biology in tumour immunity, and outlined CRISPR screens resources that might facilitate the development and implementation of cancer immunotherapies in the clinic.
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Affiliation(s)
- Minghua Xiang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huayi Li
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Zhan
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ding Ma
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qinglei Gao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yong Fang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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6
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Peterson JJ, Lewis CA, Burgos SD, Manickam A, Xu Y, Rowley AA, Clutton G, Richardson B, Zou F, Simon JM, Margolis DM, Goonetilleke N, Browne EP. A histone deacetylase network regulates epigenetic reprogramming and viral silencing in HIV-infected cells. Cell Chem Biol 2023; 30:1617-1633.e9. [PMID: 38134881 PMCID: PMC10754471 DOI: 10.1016/j.chembiol.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/23/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023]
Abstract
A long-lived latent reservoir of HIV-1-infected CD4 T cells persists with antiretroviral therapy and prevents cure. We report that the emergence of latently infected primary CD4 T cells requires the activity of histone deacetylase enzymes HDAC1/2 and HDAC3. Data from targeted HDAC molecules, an HDAC3-directed PROTAC, and CRISPR-Cas9 knockout experiments converge on a model where either HDAC1/2 or HDAC3 targeting can prevent latency, whereas all three enzymes must be targeted to achieve latency reversal. Furthermore, HDACi treatment targets features of memory T cells that are linked to proviral latency and persistence. Latency prevention is associated with increased H3K9ac at the proviral LTR promoter region and decreased H3K9me3, suggesting that this epigenetic switch is a key proviral silencing mechanism that depends on HDAC activity. These findings support further mechanistic work on latency initiation and eventual clinical studies of HDAC inhibitors to interfere with latency initiation.
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Affiliation(s)
- Jackson J Peterson
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Catherine A Lewis
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Samuel D Burgos
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Ashokkumar Manickam
- University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Yinyan Xu
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Allison A Rowley
- University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Genevieve Clutton
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Brian Richardson
- Department of Biostatistics, UNC Gillings School of Global Public Health, Chapel Hill, NC 27514, USA
| | - Fei Zou
- Department of Biostatistics, UNC Gillings School of Global Public Health, Chapel Hill, NC 27514, USA
| | - Jeremy M Simon
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC 27514, USA; UNC Neuroscience Center, UNC School of Medicine, Chapel Hill, NC 27514, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - David M Margolis
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA; Department of Medicine, UNC School of Medicine, Chapel Hill, NC 27514, USA; Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, NC 27514, USA
| | - Nilu Goonetilleke
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Edward P Browne
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA.
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7
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Li YR, Lyu Z, Tian Y, Fang Y, Zhu Y, Chen Y, Yang L. Advancements in CRISPR screens for the development of cancer immunotherapy strategies. Mol Ther Oncolytics 2023; 31:100733. [PMID: 37876793 PMCID: PMC10591018 DOI: 10.1016/j.omto.2023.100733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
CRISPR screen technology enables systematic and scalable interrogation of gene function by using the CRISPR-Cas9 system to perturb gene expression. In the field of cancer immunotherapy, this technology has empowered the discovery of genes, biomarkers, and pathways that regulate tumor development and progression, immune reactivity, and the effectiveness of immunotherapeutic interventions. By conducting large-scale genetic screens, researchers have successfully identified novel targets to impede tumor growth, enhance anti-tumor immune responses, and surmount immunosuppression within the tumor microenvironment (TME). Here, we present an overview of CRISPR screens conducted in tumor cells for the purpose of identifying novel therapeutic targets. We also explore the application of CRISPR screens in immune cells to propel the advancement of cell-based therapies, encompassing T cells, natural killer cells, dendritic cells, and macrophages. Furthermore, we outline the crucial components necessary for the successful implementation of immune-specific CRISPR screens and explore potential directions for future research.
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Affiliation(s)
- Yan-Ruide Li
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zibai Lyu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yanxin Tian
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ying Fang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yichen Zhu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yuning Chen
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lili Yang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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8
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Schraivogel D, Steinmetz LM, Parts L. Pooled Genome-Scale CRISPR Screens in Single Cells. Annu Rev Genet 2023; 57:223-244. [PMID: 37562410 DOI: 10.1146/annurev-genet-072920-013842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Assigning functions to genes and learning how to control their expression are part of the foundation of cell biology and therapeutic development. An efficient and unbiased method to accomplish this is genetic screening, which historically required laborious clone generation and phenotyping and is still limited by scale today. The rapid technological progress on modulating gene function with CRISPR-Cas and measuring it in individual cells has now relaxed the major experimental constraints and enabled pooled screening with complex readouts from single cells. Here, we review the principles and practical considerations for pooled single-cell CRISPR screening. We discuss perturbation strategies, experimental model systems, matching the perturbation to the individual cells, reading out cell phenotypes, and data analysis. Our focus is on single-cell RNA sequencing and cell sorting-based readouts, including image-enabled cell sorting. We expect this transformative approach to fuel biomedical research for the next several decades.
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Affiliation(s)
- Daniel Schraivogel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany;
| | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany;
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA;
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, California, USA
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9
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Dai X, Park JJ, Du Y, Na Z, Lam SZ, Chow RD, Renauer PA, Gu J, Xin S, Chu Z, Liao C, Clark P, Zhao H, Slavoff S, Chen S. Massively parallel knock-in engineering of human T cells. Nat Biotechnol 2023; 41:1239-1255. [PMID: 36702900 DOI: 10.1038/s41587-022-01639-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/12/2022] [Indexed: 01/27/2023]
Abstract
The efficiency of targeted knock-in for cell therapeutic applications is generally low, and the scale is limited. In this study, we developed CLASH, a system that enables high-efficiency, high-throughput knock-in engineering. In CLASH, Cas12a/Cpf1 mRNA combined with pooled adeno-associated viruses mediate simultaneous gene editing and precise transgene knock-in using massively parallel homology-directed repair, thereby producing a pool of stably integrated mutant variants each with targeted gene editing. We applied this technology in primary human T cells and performed time-coursed CLASH experiments in blood cancer and solid tumor models using CD3, CD8 and CD4 T cells, enabling pooled generation and unbiased selection of favorable CAR-T variants. Emerging from CLASH experiments, a unique CRISPR RNA (crRNA) generates an exon3 skip mutant of PRDM1 in CAR-Ts, which leads to increased proliferation, stem-like properties, central memory and longevity in these cells, resulting in higher efficacy in vivo across multiple cancer models, including a solid tumor model. The versatility of CLASH makes it broadly applicable to diverse cellular and therapeutic engineering applications.
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Affiliation(s)
- Xiaoyun Dai
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Jonathan J Park
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- M.D.-Ph.D. Program, Yale University, West Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
| | - Yaying Du
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhenkun Na
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Stanley Z Lam
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Ryan D Chow
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- M.D.-Ph.D. Program, Yale University, West Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
| | - Paul A Renauer
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
| | - Jianlei Gu
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Shan Xin
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Zhiyuan Chu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Immunobiology Program, Yale University, New Haven, CT, USA
| | - Cun Liao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Paul Clark
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA
| | - Sarah Slavoff
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
- System Biology Institute, Yale University, West Haven, CT, USA.
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA.
- M.D.-Ph.D. Program, Yale University, West Haven, CT, USA.
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA.
- Immunobiology Program, Yale University, New Haven, CT, USA.
- Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA.
- Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA.
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA.
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA.
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA.
- Yale Liver Center, Yale University School of Medicine, New Haven, CT, USA.
- Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA.
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10
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Itell HL, Humes D, Overbaugh J. Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4 + T cells. Cell Rep 2023; 42:112556. [PMID: 37227817 PMCID: PMC10592456 DOI: 10.1016/j.celrep.2023.112556] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/30/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
Type I interferon (IFN) upregulates proteins that inhibit HIV within infected cells. Prior studies have identified IFN-stimulated genes (ISGs) that impede lab-adapted HIV in cell lines, yet the ISG(s) that mediate IFN restriction in HIV target cells, primary CD4+ T cells, are unknown. Here, we interrogate ISG restriction of primary HIV in CD4+ T cells by performing CRISPR-knockout screens with a custom library that specifically targets ISGs expressed in CD4+ T cells. Our investigation identifies previously undescribed HIV-restricting ISGs (HM13, IGFBP2, LAP3) and finds that two factors characterized in other HIV infection models (IFI16 and UBE2L6) mediate IFN restriction in T cells. Inactivation of these five ISGs in combination further diminishes IFN's protective effect against diverse HIV strains. This work demonstrates that IFN restriction of HIV is multifaceted, resulting from several effectors functioning collectively, and establishes a primary cell ISG screening model to identify both single and combinations of HIV-restricting ISGs.
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Affiliation(s)
- Hannah L Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA 98195, USA; Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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11
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Martin-Rufino JD, Castano N, Pang M, Grody EI, Joubran S, Caulier A, Wahlster L, Li T, Qiu X, Riera-Escandell AM, Newby GA, Al'Khafaji A, Chaudhary S, Black S, Weng C, Munson G, Liu DR, Wlodarski MW, Sims K, Oakley JH, Fasano RM, Xavier RJ, Lander ES, Klein DE, Sankaran VG. Massively parallel base editing to map variant effects in human hematopoiesis. Cell 2023; 186:2456-2474.e24. [PMID: 37137305 PMCID: PMC10225359 DOI: 10.1016/j.cell.2023.03.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/26/2023] [Accepted: 03/30/2023] [Indexed: 05/05/2023]
Abstract
Systematic evaluation of the impact of genetic variants is critical for the study and treatment of human physiology and disease. While specific mutations can be introduced by genome engineering, we still lack scalable approaches that are applicable to the important setting of primary cells, such as blood and immune cells. Here, we describe the development of massively parallel base-editing screens in human hematopoietic stem and progenitor cells. Such approaches enable functional screens for variant effects across any hematopoietic differentiation state. Moreover, they allow for rich phenotyping through single-cell RNA sequencing readouts and separately for characterization of editing outcomes through pooled single-cell genotyping. We efficiently design improved leukemia immunotherapy approaches, comprehensively identify non-coding variants modulating fetal hemoglobin expression, define mechanisms regulating hematopoietic differentiation, and probe the pathogenicity of uncharacterized disease-associated variants. These strategies will advance effective and high-throughput variant-to-function mapping in human hematopoiesis to identify the causes of diverse diseases.
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Affiliation(s)
- Jorge D Martin-Rufino
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; PhD Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole Castano
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael Pang
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Samantha Joubran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology PhD Program, Harvard Medical School, Boston, MA 02115, USA
| | - Alexis Caulier
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tongqing Li
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xiaojie Qiu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Gregory A Newby
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Aziz Al'Khafaji
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Susan Black
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chen Weng
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Glen Munson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David R Liu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Marcin W Wlodarski
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kacie Sims
- St. Jude Affiliate Clinic at Our Lady of the Lake Children's Health, Baton Rouge, LA 70809, USA
| | - Jamie H Oakley
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, GA 30322, USA
| | - Ross M Fasano
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, GA 30322, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daryl E Klein
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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12
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van der Veer H, van Aalen EA, Michielsen CMS, Hanckmann ETL, Deckers J, van Borren MMGJ, Flipse J, Loonen AJM, Schoeber JPH, Merkx M. Glow-in-the-Dark Infectious Disease Diagnostics Using CRISPR-Cas9-Based Split Luciferase Complementation. ACS CENTRAL SCIENCE 2023; 9:657-667. [PMID: 37122471 PMCID: PMC10141630 DOI: 10.1021/acscentsci.2c01467] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Indexed: 05/03/2023]
Abstract
Nucleic acid detection methods based on CRISPR and isothermal amplification techniques show great potential for point-of-care diagnostic applications. However, most current methods rely on fluorescent or lateral flow assay readout, requiring external excitation or postamplification reaction transfer. Here, we developed a bioluminescent nucleic acid sensor (LUNAS) platform in which target dsDNA is sequence-specifically detected by a pair of dCas9-based probes mediating split NanoLuc luciferase complementation. LUNAS is easily integrated with recombinase polymerase amplification (RPA), providing attomolar sensitivity in a rapid one-pot assay. A calibrator luciferase is included for a robust ratiometric readout, enabling real-time monitoring of the RPA reaction using a simple digital camera. We designed an RT-RPA-LUNAS assay that allows SARS-CoV-2 RNA detection without the need for cumbersome RNA isolation and demonstrated its diagnostic performance for COVID-19 patient nasopharyngeal swab samples. Detection of SARS-CoV-2 from samples with viral RNA loads of ∼200 cp/μL was achieved within ∼20 min, showing that RPA-LUNAS is attractive for point-of-care infectious disease testing.
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Affiliation(s)
- Harmen
J. van der Veer
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Eva A. van Aalen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Claire M. S. Michielsen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Eva T. L. Hanckmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Jeroen Deckers
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | | | - Jacky Flipse
- Laboratory
for Medical Microbiology and Immunology, Rijnstate Hospital, P.O. Box 8, Velp 6880 AA, The Netherlands
| | - Anne J. M. Loonen
- Research
Group Applied Natural Sciences, Fontys University
of Applied Sciences, Eindhoven 5612 AP, The Netherlands
- Pathologie-DNA,
Lab for Molecular Diagnostics, Location
Jeroen Bosch Hospital, ’s-Hertogenbosch 5223 GZ, The Netherlands
| | - Joost P. H. Schoeber
- Research
Group Applied Natural Sciences, Fontys University
of Applied Sciences, Eindhoven 5612 AP, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
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13
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Glaser V, Flugel C, Kath J, Du W, Drosdek V, Franke C, Stein M, Pruß A, Schmueck-Henneresse M, Volk HD, Reinke P, Wagner DL. Combining different CRISPR nucleases for simultaneous knock-in and base editing prevents translocations in multiplex-edited CAR T cells. Genome Biol 2023; 24:89. [PMID: 37095570 PMCID: PMC10123993 DOI: 10.1186/s13059-023-02928-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Multiple genetic modifications may be required to develop potent off-the-shelf chimeric antigen receptor (CAR) T cell therapies. Conventional CRISPR-Cas nucleases install sequence-specific DNA double-strand breaks (DSBs), enabling gene knock-out or targeted transgene knock-in. However, simultaneous DSBs provoke a high rate of genomic rearrangements which may impede the safety of the edited cells. RESULTS Here, we combine a non-viral CRISPR-Cas9 nuclease-assisted knock-in and Cas9-derived base editing technology for DSB free knock-outs within a single intervention. We demonstrate efficient insertion of a CAR into the T cell receptor alpha constant (TRAC) gene, along with two knock-outs that silence major histocompatibility complexes (MHC) class I and II expression. This approach reduces translocations to 1.4% of edited cells. Small insertions and deletions at the base editing target sites indicate guide RNA exchange between the editors. This is overcome by using CRISPR enzymes of distinct evolutionary origins. Combining Cas12a Ultra for CAR knock-in and a Cas9-derived base editor enables the efficient generation of triple-edited CAR T cells with a translocation frequency comparable to unedited T cells. Resulting TCR- and MHC-negative CAR T cells resist allogeneic T cell targeting in vitro. CONCLUSIONS We outline a solution for non-viral CAR gene transfer and efficient gene silencing using different CRISPR enzymes for knock-in and base editing to prevent translocations. This single-step procedure may enable safer multiplex-edited cell products and demonstrates a path towards off-the-shelf CAR therapeutics.
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Affiliation(s)
- Viktor Glaser
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Christian Flugel
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Jonas Kath
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Weijie Du
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Vanessa Drosdek
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Clemens Franke
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Maik Stein
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Axel Pruß
- Institute of Transfusion Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Charité Mitte, Charitéplatz 1, 10117, Berlin, Germany
| | - Michael Schmueck-Henneresse
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Hans-Dieter Volk
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- CheckImmune GmbH, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Petra Reinke
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Dimitrios L Wagner
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany.
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany.
- Institute of Transfusion Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Charité Mitte, Charitéplatz 1, 10117, Berlin, Germany.
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany.
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14
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Kim YH, Kim N, Okafor I, Choi S, Min S, Lee J, Bae SM, Choi K, Choi J, Harihar V, Kim Y, Kim JS, Kleinstiver BP, Lee JK, Ha T, Kim HH. Sniper2L is a high-fidelity Cas9 variant with high activity. Nat Chem Biol 2023:10.1038/s41589-023-01279-5. [PMID: 36894722 PMCID: PMC10374439 DOI: 10.1038/s41589-023-01279-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 02/02/2023] [Indexed: 03/11/2023]
Abstract
Although several high-fidelity SpCas9 variants have been reported, it has been observed that this increased specificity is associated with reduced on-target activity, limiting the applications of the high-fidelity variants when efficient genome editing is required. Here, we developed an improved version of Sniper-Cas9, Sniper2L, which represents an exception to this trade-off trend as it showed higher specificity with retained high activity. We evaluated Sniper2L activities at a large number of target sequences and developed DeepSniper, a deep learning model that can predict the activity of Sniper2L. We also confirmed that Sniper2L can induce highly efficient and specific editing at a large number of target sequences when it is delivered as a ribonucleoprotein complex. Mechanically, the high specificity of Sniper2L originates from its superior ability to avoid unwinding a target DNA containing even a single mismatch. We envision that Sniper2L will be useful when efficient and specific genome editing is required.
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Affiliation(s)
- Young-Hoon Kim
- Toolgen, Seoul, Republic of Korea.,Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea.,Graduate Program of Biomedical Engineering, Yonsei University College of Medicine, Seoul, Republic of Korea.,Graduate Program of NanoScience and Technology, Yonsei University, Seoul, Republic of Korea
| | - Nahye Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea.,Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ikenna Okafor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sungchul Choi
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | | | | | | | - Janice Choi
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Vinayak Harihar
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | | | - Jin-Soo Kim
- Department of Biochemistry and NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | | | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA. .,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA. .,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Howard Hughes Medical Institute, Baltimore, MD, USA.
| | - Hyongbum Henry Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea. .,Graduate Program of NanoScience and Technology, Yonsei University, Seoul, Republic of Korea. .,Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea. .,Center for Nanomedicine, Institute for Basic Science, Seoul, Republic of Korea. .,Yonsei-Institute for Basic Science Institute, Yonsei University, Seoul, Republic of Korea. .,Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea. .,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea.
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15
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Stankey CT, Lee JC. Translating non-coding genetic associations into a better understanding of immune-mediated disease. Dis Model Mech 2023; 16:297044. [PMID: 36897113 PMCID: PMC10040244 DOI: 10.1242/dmm.049790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Genome-wide association studies have identified hundreds of genetic loci that are associated with immune-mediated diseases. Most disease-associated variants are non-coding, and a large proportion of these variants lie within enhancers. As a result, there is a pressing need to understand how common genetic variation might affect enhancer function and thereby contribute to immune-mediated (and other) diseases. In this Review, we first describe statistical and experimental methods to identify causal genetic variants that modulate gene expression, including statistical fine-mapping and massively parallel reporter assays. We then discuss approaches to characterise the mechanisms by which these variants modulate immune function, such as clustered regularly interspaced short palindromic repeats (CRISPR)-based screens. We highlight examples of studies that, by elucidating the effects of disease variants within enhancers, have provided important insights into immune function and uncovered key pathways of disease.
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Affiliation(s)
- Christina T Stankey
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK
| | - James C Lee
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Institute of Liver and Digestive Health, Royal Free Hospital, University College London, London NW3 2PF, UK
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16
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Itell HL, Humes D, Overbaugh J. Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4 + T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527545. [PMID: 36798236 PMCID: PMC9934674 DOI: 10.1101/2023.02.07.527545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Type I interferon (IFN) upregulates proteins that inhibit HIV within infected cells. Prior studies have identified IFN-stimulated genes (ISGs) that impede lab-adapted HIV in cell lines, yet the ISG(s) that mediate IFN restriction in HIV target cells, primary CD4 + T cells, are unknown. Here, we interrogate ISG restriction of primary HIV in CD4 + T cells. We performed CRISPR-knockout screens using a custom library that specifically targets ISGs expressed in CD4 + T cells and validated top hits. Our investigation identified new HIV-restricting ISGs (HM13, IGFBP2, LAP3) and found that two previously studied factors (IFI16, UBE2L6) are IFN effectors in T cells. Inactivation of these five ISGs in combination further diminished IFN’s protective effect against six diverse HIV strains. This work demonstrates that IFN restriction of HIV is multifaceted, resulting from several effectors functioning collectively, and establishes a primary cell ISG screening model to identify both single and combinations of HIV-restricting ISGs.
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Affiliation(s)
- Hannah L. Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA, 98109, USA
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Present address: Tr1X Inc, La Jolla, CA, 92037, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
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17
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Trefny MP, Kirchhammer N, Auf der Maur P, Natoli M, Schmid D, Germann M, Fernandez Rodriguez L, Herzig P, Lötscher J, Akrami M, Stinchcombe JC, Stanczak MA, Zingg A, Buchi M, Roux J, Marone R, Don L, Lardinois D, Wiese M, Jeker LT, Bentires-Alj M, Rossy J, Thommen DS, Griffiths GM, Läubli H, Hess C, Zippelius A. Deletion of SNX9 alleviates CD8 T cell exhaustion for effective cellular cancer immunotherapy. Nat Commun 2023; 14:86. [PMID: 36732507 PMCID: PMC9895440 DOI: 10.1038/s41467-022-35583-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/12/2022] [Indexed: 02/04/2023] Open
Abstract
Tumor-specific T cells are frequently exhausted by chronic antigenic stimulation. We here report on a human antigen-specific ex vivo model to explore new therapeutic options for T cell immunotherapies. T cells generated with this model resemble tumor-infiltrating exhausted T cells on a phenotypic and transcriptional level. Using a targeted pooled CRISPR-Cas9 screen and individual gene knockout validation experiments, we uncover sorting nexin-9 (SNX9) as a mediator of T cell exhaustion. Upon TCR/CD28 stimulation, deletion of SNX9 in CD8 T cells decreases PLCγ1, Ca2+, and NFATc2-mediated T cell signaling and reduces expression of NR4A1/3 and TOX. SNX9 knockout enhances memory differentiation and IFNγ secretion of adoptively transferred T cells and results in improved anti-tumor efficacy of human chimeric antigen receptor T cells in vivo. Our findings highlight that targeting SNX9 is a strategy to prevent T cell exhaustion and enhance anti-tumor immunity.
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Affiliation(s)
- Marcel P Trefny
- Laboratory of Cancer Immunology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland.
| | - Nicole Kirchhammer
- Laboratory of Cancer Immunology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Priska Auf der Maur
- Laboratory of Tumor Heterogeneity, Metastasis and Resistance, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Marina Natoli
- Laboratory of Cancer Immunology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Dominic Schmid
- Laboratory of Cancer Immunology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Markus Germann
- Laboratory of Cancer Immunology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Laura Fernandez Rodriguez
- Laboratory of Cancer Immunology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Petra Herzig
- Laboratory of Cancer Immunology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Jonas Lötscher
- Laboratory of Immunobiology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Maryam Akrami
- Laboratory of Cancer Immunology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Jane C Stinchcombe
- Cambridge Institute for Medical Research, Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Michal A Stanczak
- Laboratory of Cancer Immunotherapy, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Andreas Zingg
- Laboratory of Cancer Immunotherapy, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Melanie Buchi
- Laboratory of Cancer Immunology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Julien Roux
- Bioinformatics Core Facility, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Romina Marone
- Laboratory of Molecular Immune Regulation, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland.,Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Leyla Don
- Laboratory of Cancer Immunology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Didier Lardinois
- Department of Surgery, University Hospital Basel, Basel, Switzerland
| | - Mark Wiese
- Department of Surgery, University Hospital Basel, Basel, Switzerland
| | - Lukas T Jeker
- Laboratory of Molecular Immune Regulation, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland.,Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Mohamed Bentires-Alj
- Laboratory of Tumor Heterogeneity, Metastasis and Resistance, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Jérémie Rossy
- Biotechnology Institute Thurgau, University of Konstanz, Kreuzlingen, Switzerland
| | - Daniela S Thommen
- Laboratory of Cancer Immunology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland.,Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gillian M Griffiths
- Cambridge Institute for Medical Research, Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Heinz Läubli
- Laboratory of Cancer Immunotherapy, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland.,Medical Oncology, University Hospital Basel, Basel, Switzerland
| | - Christoph Hess
- Laboratory of Immunobiology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland.,Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Alfred Zippelius
- Laboratory of Cancer Immunology, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland. .,Medical Oncology, University Hospital Basel, Basel, Switzerland.
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18
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Huang S, Baskin JM. Adding a Chemical Biology Twist to CRISPR Screening. Isr J Chem 2023; 63:e202200056. [PMID: 37588264 PMCID: PMC10427134 DOI: 10.1002/ijch.202200056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Indexed: 11/09/2022]
Abstract
In less than a decade, CRISPR screening has revolutionized forward genetics and cell and molecular biology. Advances in screening technologies, including sgRNA libraries, Cas9-expressing cell lines, and streamlined sequencing pipelines, have democratized pooled CRISPR screens at genome-wide scale. Initially, many such screens were survival-based, identifying essential genes in physiological or perturbed processes. With the application of new chemical biology tools to CRISPR screening, the phenotypic space is no longer limited to live/dead selection or screening for levels of conventional fluorescent protein reporters. Further, the resolution has been increased from cell populations to single cells or even the subcellular level. We highlight advances in pooled CRISPR screening, powered by chemical biology, that have expanded phenotypic space, resolution, scope, and scalability as well as strengthened the CRISPR/Cas enzyme toolkit to enable biological hypothesis generation and discovery.
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Affiliation(s)
- Shiying Huang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853 USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853 USA
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19
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Biederstädt A, Manzar GS, Daher M. Multiplexed engineering and precision gene editing in cellular immunotherapy. Front Immunol 2022; 13:1063303. [PMID: 36483551 PMCID: PMC9723254 DOI: 10.3389/fimmu.2022.1063303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
Abstract
The advent of cellular immunotherapy in the clinic has entirely redrawn the treatment landscape for a growing number of human cancers. Genetically reprogrammed immune cells, including chimeric antigen receptor (CAR)-modified immune effector cells as well as T cell receptor (TCR) therapy, have demonstrated remarkable responses across different hard-to-treat patient populations. While these novel treatment options have had tremendous success in providing long-term remissions for a considerable fraction of treated patients, a number of challenges remain. Limited in vivo persistence and functional exhaustion of infused immune cells as well as tumor immune escape and on-target off-tumor toxicities are just some examples of the challenges which restrain the potency of today's genetically engineered cell products. Multiple engineering strategies are being explored to tackle these challenges.The advent of multiplexed precision genome editing has in recent years provided a flexible and highly modular toolkit to specifically address some of these challenges by targeted genetic interventions. This class of next-generation cellular therapeutics aims to endow engineered immune cells with enhanced functionality and shield them from immunosuppressive cues arising from intrinsic immune checkpoints as well as the hostile tumor microenvironment (TME). Previous efforts to introduce additional genetic modifications into immune cells have in large parts focused on nuclease-based tools like the CRISPR/Cas9 system or TALEN. However, nuclease-inactive platforms including base and prime editors have recently emerged and promise a potentially safer route to rewriting genetic sequences and introducing large segments of transgenic DNA without inducing double-strand breaks (DSBs). In this review, we discuss how these two exciting and emerging fields-cellular immunotherapy and precision genome editing-have co-evolved to enable a dramatic expansion in the possibilities to engineer personalized anti-cancer treatments. We will lay out how various engineering strategies in addition to nuclease-dependent and nuclease-inactive precision genome editing toolkits are increasingly being applied to overcome today's limitations to build more potent cellular therapeutics. We will reflect on how novel information-rich unbiased discovery approaches are continuously deepening our understanding of fundamental mechanisms governing tumor biology. We will conclude with a perspective of how multiplexed-engineered and gene edited cell products may upend today's treatment paradigms as they evolve into the next generation of more potent cellular immunotherapies.
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Affiliation(s)
- Alexander Biederstädt
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Medicine III, Hematology and Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Gohar Shahwar Manzar
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - May Daher
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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20
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Holcomb EA, Pearson AN, Jungles KM, Tate A, James J, Jiang L, Huber AK, Green MD. High-content CRISPR screening in tumor immunology. Front Immunol 2022; 13:1041451. [PMID: 36479127 PMCID: PMC9721350 DOI: 10.3389/fimmu.2022.1041451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/21/2022] [Indexed: 11/22/2022] Open
Abstract
CRISPR screening is a powerful tool that links specific genetic alterations to corresponding phenotypes, thus allowing for high-throughput identification of novel gene functions. Pooled CRISPR screens have enabled discovery of innate and adaptive immune response regulators in the setting of viral infection and cancer. Emerging methods couple pooled CRISPR screens with parallel high-content readouts at the transcriptomic, epigenetic, proteomic, and optical levels. These approaches are illuminating cancer immune evasion mechanisms as well as nominating novel targets that augment T cell activation, increase T cell infiltration into tumors, and promote enhanced T cell cytotoxicity. This review details recent methodological advances in high-content CRISPR screens and highlights the impact this technology is having on tumor immunology.
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Affiliation(s)
- Erin A. Holcomb
- Graduate Program in Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Ashley N. Pearson
- Graduate Program in Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Kassidy M. Jungles
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Department of Pharmacology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Akshay Tate
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Jadyn James
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Long Jiang
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China
| | - Amanda K. Huber
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Michael D. Green
- Graduate Program in Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States,Department of Microbiology and Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Department of Radiation Oncology, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, MI, United States,*Correspondence: Michael D. Green,
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21
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Bäckström A, Yudovich D, Žemaitis K, Nilsén Falck L, Subramaniam A, Larsson J. Combinatorial gene targeting in primary human hematopoietic stem and progenitor cells. Sci Rep 2022; 12:18169. [PMID: 36307542 PMCID: PMC9616885 DOI: 10.1038/s41598-022-23118-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/25/2022] [Indexed: 12/31/2022] Open
Abstract
The CRISPR/Cas9 system offers enormous versatility for functional genomics but many applications have proven to be challenging in primary human cells compared to cell lines or mouse cells. Here, to establish a paradigm for multiplexed gene editing in primary human cord blood-derived hematopoietic stem and progenitor cells (HSPCs), we used co-delivery of lentiviral sgRNA vectors expressing either Enhanced Green Fluorescent Protein (EGFP) or Kusabira Orange (KuO), together with Cas9 mRNA, to simultaneously edit two genetic loci. The fluorescent markers allow for tracking of either single- or double-edited cells, and we could achieve robust double knockout of the cell surface molecules CD45 and CD44 with an efficiency of ~ 70%. As a functional proof of concept, we demonstrate that this system can be used to model gene dependencies for cell survival, by simultaneously targeting the cohesin genes STAG1 and STAG2. Moreover, we show combinatorial effects with potential synergy for HSPC expansion by targeting the Aryl Hydrocarbon Receptor (AHR) in conjunction with members of the CoREST complex. Taken together, our traceable multiplexed CRISPR/Cas9 system enables studies of genetic dependencies and cooperation in primary HSPCs, and has important implications for modelling polygenic diseases, as well as investigation of the underlying mechanisms of gene interactions.
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Affiliation(s)
- Alexandra Bäckström
- grid.4514.40000 0001 0930 2361Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
| | - David Yudovich
- grid.4514.40000 0001 0930 2361Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
| | - Kristijonas Žemaitis
- grid.4514.40000 0001 0930 2361Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
| | - Ludvig Nilsén Falck
- grid.4514.40000 0001 0930 2361Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
| | - Agatheeswaran Subramaniam
- grid.4514.40000 0001 0930 2361Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
| | - Jonas Larsson
- grid.4514.40000 0001 0930 2361Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
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22
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Abstract
Natural killer (NK) cells comprise a unique population of innate lymphoid cells endowed with intrinsic abilities to identify and eliminate virally infected cells and tumour cells. Possessing multiple cytotoxicity mechanisms and the ability to modulate the immune response through cytokine production, NK cells play a pivotal role in anticancer immunity. This role was elucidated nearly two decades ago, when NK cells, used as immunotherapeutic agents, showed safety and efficacy in the treatment of patients with advanced-stage leukaemia. In recent years, following the paradigm-shifting successes of chimeric antigen receptor (CAR)-engineered adoptive T cell therapy and the advancement in technologies that can turn cells into powerful antitumour weapons, the interest in NK cells as a candidate for immunotherapy has grown exponentially. Strategies for the development of NK cell-based therapies focus on enhancing NK cell potency and persistence through co-stimulatory signalling, checkpoint inhibition and cytokine armouring, and aim to redirect NK cell specificity to the tumour through expression of CAR or the use of engager molecules. In the clinic, the first generation of NK cell therapies have delivered promising results, showing encouraging efficacy and remarkable safety, thus driving great enthusiasm for continued innovation. In this Review, we describe the various approaches to augment NK cell cytotoxicity and longevity, evaluate challenges and opportunities, and reflect on how lessons learned from the clinic will guide the design of next-generation NK cell products that will address the unique complexities of each cancer.
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Affiliation(s)
- Tamara J Laskowski
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander Biederstädt
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
- Department of Medicine III: Hematology and Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.
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23
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Verhagen HJMP, Kuijk C, Rutgers L, Kokke AM, van der Meulen SA, van Mierlo G, Voermans C, van den Akker E. Optimized Guide RNA Selection Improves Streptococcus pyogenes Cas9 Gene Editing of Human Hematopoietic Stem and Progenitor Cells. CRISPR J 2022; 5:702-716. [PMID: 36169633 DOI: 10.1089/crispr.2021.0112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Ribonucleoproteins (RNPs) are frequently applied for therapeutic gene editing as well as fundamental research because the method is fast, viral free, and shows fewest off target effects. We evaluated various parameters to genetically engineer human hematopoietic stem and progenitor cells (HSPCs) using Streptococcus pyogenes Cas9 (spCas9) RNPs, and achieve gene editing efficiencies up to 80%. We find that guide RNA (gRNA) design is critical to achieve high gene editing efficiencies. However, finding effective gRNAs for HSPCs can be challenging, while the contribution of numerous in silico models is unclear. By screening more than 120 gRNAs, our data demonstrate that in silico gRNA prediction models are ineffective. In this study, we established a time- and cost-efficient in vitro transcribed gRNA screening model in K562 cells that predicts effective gRNAs for HSPCs. RNP based screening thus outperforms in silico modeling and we report that gene editing is equally efficient in distinct CD34+ HSPC subpopulations. Furthermore, no effects on cell proliferation, differentiation, or in vitro hematopoietic lineage commitment were observed. Finally, no upregulation of p21 expression was found, suggesting unperturbed HSPC homeostasis.
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Affiliation(s)
- Han J M P Verhagen
- Department of Hematopoiesis and Sanquin Research, Landsteiner Laboratory, Department of Molecular Hematology, Amsterdam UMC, University of Amsterdam, The Netherlands
| | - Carlijn Kuijk
- Department of Hematopoiesis and Sanquin Research, Landsteiner Laboratory, Department of Molecular Hematology, Amsterdam UMC, University of Amsterdam, The Netherlands
| | - Laurens Rutgers
- Department of Hematopoiesis and Sanquin Research, Landsteiner Laboratory, Department of Molecular Hematology, Amsterdam UMC, University of Amsterdam, The Netherlands
| | - Anne M Kokke
- Department of Hematopoiesis and Sanquin Research, Landsteiner Laboratory, Department of Molecular Hematology, Amsterdam UMC, University of Amsterdam, The Netherlands
| | - Santhe A van der Meulen
- Department of Hematopoiesis and Sanquin Research, Landsteiner Laboratory, Department of Molecular Hematology, Amsterdam UMC, University of Amsterdam, The Netherlands
| | - Gerard van Mierlo
- Department of Immunopathology, Sanquin Research, Landsteiner Laboratory, Department of Molecular Hematology, Amsterdam UMC, University of Amsterdam, The Netherlands
| | - Carlijn Voermans
- Department of Hematopoiesis and Sanquin Research, Landsteiner Laboratory, Department of Molecular Hematology, Amsterdam UMC, University of Amsterdam, The Netherlands
| | - Emile van den Akker
- Department of Hematopoiesis and Sanquin Research, Landsteiner Laboratory, Department of Molecular Hematology, Amsterdam UMC, University of Amsterdam, The Netherlands
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24
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Molony RD, Funk T, Trabucco G, Corcoran E, Ruddy D, Varadarajan M, Elliot G, Piquet M, Lam J, Meyer MJ, Wang HQ, Kurtulus S, Lu H. CRISPR screening identifies T cell-intrinsic regulators of CD3-bispecific antibody responses. Front Immunol 2022; 13:909979. [PMID: 35990699 PMCID: PMC9388929 DOI: 10.3389/fimmu.2022.909979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
CD3-engaging bispecific antibodies (BsAbs) enable the formation of an immune synapse between T cells and tumor cells, resulting in robust target cell killing not dependent on a preexisting tumor specific T cell receptor. While recent studies have shed light on tumor cell-specific factors that modulate BsAb sensitivity, the T cell-intrinsic determinants of BsAb efficacy and response durability are poorly understood. To better clarify the genes that shape BsAb-induced T cell responses, we conducted targeted analyses and a large-scale unbiased in vitro CRISPR/Cas9-based screen to identify negative regulators of BsAb-induced T cell proliferation. These analyses revealed that CD8+ T cells are dependent on CD4+ T cell-derived signaling factors in order to achieve sustained killing in vitro. Moreover, the mammalian target of rapamycin (mTOR) pathway and several other candidate genes were identified as intrinsic regulators of BsAb-induced T cell proliferation and/or activation, highlighting promising approaches to enhancing the utility of these potent therapeutics.
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25
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Freimer JW, Shaked O, Naqvi S, Sinnott-Armstrong N, Kathiria A, Garrido CM, Chen AF, Cortez JT, Greenleaf WJ, Pritchard JK, Marson A. Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks. Nat Genet 2022; 54:1133-1144. [PMID: 35817986 PMCID: PMC10035359 DOI: 10.1038/s41588-022-01106-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 05/26/2022] [Indexed: 12/14/2022]
Abstract
Gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression is sufficiently perturbed, it can lead to disease. To understand how gene expression disruptions percolate through a network, we must first map connections between regulatory genes and their downstream targets. However, we lack comprehensive knowledge of the upstream regulators of most genes. Here, we developed an approach for systematic discovery of upstream regulators of critical immune factors-IL2RA, IL-2 and CTLA4-in primary human T cells. Then, we mapped the network of the target genes of these regulators and putative cis-regulatory elements using CRISPR perturbations, RNA-seq and ATAC-seq. These regulators form densely interconnected networks with extensive feedback loops. Furthermore, this network is enriched for immune-associated disease variants and genes. These results provide insight into how immune-associated disease genes are regulated in T cells and broader principles about the structure of human gene regulatory networks.
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Affiliation(s)
- Jacob W Freimer
- Department of Genetics, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Oren Shaked
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California, San Francisco, CA, USA
| | - Sahin Naqvi
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, USA
| | | | - Arwa Kathiria
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Amy F Chen
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Jessica T Cortez
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
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26
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Ye L, Park JJ, Peng L, Yang Q, Chow RD, Dong MB, Lam SZ, Guo J, Tang E, Zhang Y, Wang G, Dai X, Du Y, Kim HR, 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 Metab 2022; 34:595-614.e14. [PMID: 35276062 PMCID: PMC8986623 DOI: 10.1016/j.cmet.2022.02.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/15/2021] [Accepted: 02/17/2022] [Indexed: 02/07/2023]
Abstract
Chimeric antigen receptor (CAR)-T cell-based immunotherapy for cancer and immunological diseases has made great strides, but it still faces multiple hurdles. Finding the right molecular targets to engineer T cells toward a desired function has broad implications for the armamentarium of T cell-centered therapies. Here, we developed a dead-guide RNA (dgRNA)-based CRISPR activation screen in primary CD8+ T cells and identified gain-of-function (GOF) targets for CAR-T engineering. Targeted knockin or overexpression of a lead target, PRODH2, enhanced CAR-T-based killing and in vivo efficacy in multiple cancer models. Transcriptomics and metabolomics in CAR-T cells revealed that augmenting PRODH2 expression reshaped broad and distinct gene expression and metabolic programs. Mitochondrial, metabolic, and immunological analyses showed that PRODH2 engineering enhances the metabolic and immune functions of CAR-T cells against cancer. Together, these findings provide a system for identification of GOF immune boosters and demonstrate PRODH2 as a target to enhance CAR-T efficacy.
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Affiliation(s)
- Lupeng Ye
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA
| | - Jonathan J Park
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA; Yale M.D.-Ph.D. Program, 367 Cedar Street, New Haven, CT 06510, USA; Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT 06510, USA; MCGD Program, Yale University, New Haven, CT 06510, USA
| | - Lei Peng
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA
| | - Quanjun Yang
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA
| | - Ryan D Chow
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA; Yale M.D.-Ph.D. Program, 367 Cedar Street, New Haven, CT 06510, USA; Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT 06510, USA; MCGD Program, Yale University, New Haven, CT 06510, USA
| | - Matthew B Dong
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA; Yale M.D.-Ph.D. Program, 367 Cedar Street, New Haven, CT 06510, USA; Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT 06510, USA; MCGD Program, Yale University, New Haven, CT 06510, USA; Immunobiology Program, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Stanley Z Lam
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA; The College, Yale University, New Haven, CT 06520, USA
| | - Jianjian Guo
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA; Yale M.D.-Ph.D. Program, 367 Cedar Street, New Haven, CT 06510, USA; Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT 06510, USA; MCGD Program, Yale University, New Haven, CT 06510, USA
| | - Erting Tang
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA
| | - Yueqi Zhang
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA
| | - Guangchuan Wang
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA
| | - Xiaoyun Dai
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA
| | - Yaying Du
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA
| | - Hyunu R Kim
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA
| | - Hanbing Cao
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA
| | - Youssef Errami
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA
| | - Paul Clark
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA
| | - Alexey Bersenev
- Advanced Cell Therapy Laboratory, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ruth R Montgomery
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Epidemiology of Microbial Diseases, Yale University School of Public Health, New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Rheumatology, Yale University School of Medicine, New Haven, CT 06520, USA; Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA; Comprehensive Cancer Center, Yale University, New Haven, CT 06510, USA
| | - Sidi Chen
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT 06516, USA; Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT 06510, USA; MCGD Program, Yale University, New Haven, CT 06510, USA; Immunobiology Program, Yale University, New Haven, CT 06520, USA; Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA; Comprehensive Cancer Center, Yale University, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Liver Center, Yale University School of Medicine, New Haven, CT, USA; Center for RNA Science and Medicine, Yale University, New Haven, CT 06510, USA.
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27
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Bernard BE, Landmann E, Jeker LT, Schumann K. CRISPR/Cas-based Human T cell Engineering: Basic Research and Clinical Application. Immunol Lett 2022; 245:18-28. [DOI: 10.1016/j.imlet.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/08/2022] [Accepted: 03/15/2022] [Indexed: 11/05/2022]
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28
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Schmidt R, Steinhart Z, Layeghi M, Freimer JW, Bueno R, Nguyen VQ, Blaeschke F, Ye CJ, Marson A. CRISPR activation and interference screens decode stimulation responses in primary human T cells. Science 2022; 375:eabj4008. [PMID: 35113687 DOI: 10.1126/science.abj4008] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Regulation of cytokine production in stimulated T cells can be disrupted in autoimmunity, immunodeficiencies, and cancer. Systematic discovery of stimulation-dependent cytokine regulators requires both loss-of-function and gain-of-function studies, which have been challenging in primary human cells. We now report genome-wide CRISPR activation (CRISPRa) and interference (CRISPRi) screens in primary human T cells to identify gene networks controlling interleukin-2 (IL-2) and interferon-γ (IFN-γ) production. Arrayed CRISPRa confirmed key hits and enabled multiplexed secretome characterization, revealing reshaped cytokine responses. Coupling CRISPRa screening with single-cell RNA sequencing enabled deep molecular characterization of screen hits, revealing how perturbations tuned T cell activation and promoted cell states characterized by distinct cytokine expression profiles. These screens reveal genes that reprogram critical immune cell functions, which could inform the design of immunotherapies.
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Affiliation(s)
- Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Zachary Steinhart
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Madeline Layeghi
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Jacob W Freimer
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.,Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Raymund Bueno
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Vinh Q Nguyen
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Franziska Blaeschke
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Chun Jimmie Ye
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.,Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, CA 94129, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.,Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA.,Diabetes Center, University of California San Francisco, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA.,UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA.,Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, CA 94129, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
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29
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Ramadier S, Chalumeau A, Felix T, Othman N, Aknoun S, Casini A, Maule G, Masson C, De Cian A, Frati G, Brusson M, Concordet JP, Cavazzana M, Cereseto A, El Nemer W, Amendola M, Wattellier B, Meneghini V, Miccio A. Combination of lentiviral and genome editing technologies for the treatment of sickle cell disease. Mol Ther 2022; 30:145-163. [PMID: 34418541 PMCID: PMC8753569 DOI: 10.1016/j.ymthe.2021.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 01/07/2023] Open
Abstract
Sickle cell disease (SCD) is caused by a mutation in the β-globin gene leading to polymerization of the sickle hemoglobin (HbS) and deformation of red blood cells. Autologous transplantation of hematopoietic stem/progenitor cells (HSPCs) genetically modified using lentiviral vectors (LVs) to express an anti-sickling β-globin leads to some clinical benefit in SCD patients, but it requires high-level transgene expression (i.e., high vector copy number [VCN]) to counteract HbS polymerization. Here, we developed therapeutic approaches combining LV-based gene addition and CRISPR-Cas9 strategies aimed to either knock down the sickle β-globin and increase the incorporation of an anti-sickling globin (AS3) in hemoglobin tetramers, or to induce the expression of anti-sickling fetal γ-globins. HSPCs from SCD patients were transduced with LVs expressing AS3 and a guide RNA either targeting the endogenous β-globin gene or regions involved in fetal hemoglobin silencing. Transfection of transduced cells with Cas9 protein resulted in high editing efficiency, elevated levels of anti-sickling hemoglobins, and rescue of the SCD phenotype at a significantly lower VCN compared to the conventional LV-based approach. This versatile platform can improve the efficacy of current gene addition approaches by combining different therapeutic strategies, thus reducing the vector amount required to achieve a therapeutic VCN and the associated genotoxicity risk.
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Affiliation(s)
- Sophie Ramadier
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France; Phasics, Bâtiment Explorer, Espace Technologique, Route de l'Orme des Merisiers, 91190 St. Aubin, France
| | - Anne Chalumeau
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France
| | - Tristan Felix
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France
| | - Nadia Othman
- Phasics, Bâtiment Explorer, Espace Technologique, Route de l'Orme des Merisiers, 91190 St. Aubin, France
| | - Sherazade Aknoun
- Phasics, Bâtiment Explorer, Espace Technologique, Route de l'Orme des Merisiers, 91190 St. Aubin, France
| | | | - Giulia Maule
- CIBIO, University of Trento, 38100 Trento, Italy
| | - Cecile Masson
- Paris-Descartes Bioinformatics Platform, Imagine Institute, 75015 Paris, France
| | - Anne De Cian
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, 75015 Paris, France
| | - Giacomo Frati
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France
| | - Megane Brusson
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France
| | - Jean-Paul Concordet
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, 75015 Paris, France
| | - Marina Cavazzana
- Université de Paris, 75015 Paris, France; Imagine Institute, 75015 Paris, France; Biotherapy Department and Clinical Investigation Center, Assistance Publique Hôpitaux de Paris, INSERM, 75015 Paris, France
| | | | - Wassim El Nemer
- Etablissement Français du Sang PACA-Corse, Marseille, France; Aix Marseille Université, EFS, CNRS, ADES, "Biologie des Groupes Sanguins," 13000 Marseille, France; Laboratoire d'Excellence GR-Ex, Paris, France
| | | | - Benoit Wattellier
- Phasics, Bâtiment Explorer, Espace Technologique, Route de l'Orme des Merisiers, 91190 St. Aubin, France
| | - Vasco Meneghini
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France.
| | - Annarita Miccio
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France.
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30
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Lee BC, Lozano RJ, Dunbar CE. Understanding and overcoming adverse consequences of genome editing on hematopoietic stem and progenitor cells. Mol Ther 2021; 29:3205-3218. [PMID: 34509667 DOI: 10.1016/j.ymthe.2021.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/25/2021] [Accepted: 09/03/2021] [Indexed: 12/12/2022] Open
Abstract
Hematopoietic stem and progenitor cell (HSPC) gene therapies have recently moved beyond gene-addition approaches to encompass targeted genome modification or correction, based on the development of zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR-Cas technologies. Advances in ex vivo HSPC manipulation techniques have greatly improved HSPC susceptibility to genetic modification. Targeted gene-editing techniques enable precise modifications at desired genomic sites. Numerous preclinical studies have already demonstrated the therapeutic potential of gene therapies based on targeted editing. However, several significant hurdles related to adverse consequences of gene editing on HSPC function and genomic integrity remain before broad clinical potential can be realized. This review summarizes the status of HSPC gene editing, focusing on efficiency, genomic integrity, and long-term engraftment ability related to available genetic editing platforms and HSPC delivery methods. The response of long-term engrafting HSPCs to nuclease-mediated DNA breaks, with activation of p53, is a significant challenge, as are activation of innate and adaptive immune responses to editing components. Lastly, we propose alternative strategies that can overcome current hurdles to HSPC editing at various stages from cell collection to transplantation to facilitate successful clinical applications.
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Affiliation(s)
- Byung-Chul Lee
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard J Lozano
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cynthia E Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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31
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Gutierrez-Guerrero A, Abrey Recalde MJ, Mangeot PE, Costa C, Bernadin O, Périan S, Fusil F, Froment G, Martinez-Turtos A, Krug A, Martin F, Benabdellah K, Ricci EP, Giovannozzi S, Gijsbers R, Ayuso E, Cosset FL, Verhoeyen E. Baboon Envelope Pseudotyped "Nanoblades" Carrying Cas9/gRNA Complexes Allow Efficient Genome Editing in Human T, B, and CD34 + Cells and Knock-in of AAV6-Encoded Donor DNA in CD34 + Cells. Front Genome Ed 2021; 3:604371. [PMID: 34713246 PMCID: PMC8525375 DOI: 10.3389/fgeed.2021.604371] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/18/2021] [Indexed: 12/26/2022] Open
Abstract
Programmable nucleases have enabled rapid and accessible genome engineering in eukaryotic cells and living organisms. However, their delivery into human blood cells can be challenging. Here, we have utilized "nanoblades," a new technology that delivers a genomic cleaving agent into cells. These are modified murine leukemia virus (MLV) or HIV-derived virus-like particle (VLP), in which the viral structural protein Gag has been fused to Cas9. These VLPs are thus loaded with Cas9 protein complexed with the guide RNAs. Highly efficient gene editing was obtained in cell lines, IPS and primary mouse and human cells. Here, we showed that nanoblades were remarkably efficient for entry into human T, B, and hematopoietic stem and progenitor cells (HSPCs) thanks to their surface co-pseudotyping with baboon retroviral and VSV-G envelope glycoproteins. A brief incubation of human T and B cells with nanoblades incorporating two gRNAs resulted in 40 and 15% edited deletion in the Wiskott-Aldrich syndrome (WAS) gene locus, respectively. CD34+ cells (HSPCs) treated with the same nanoblades allowed 30-40% exon 1 drop-out in the WAS gene locus. Importantly, no toxicity was detected upon nanoblade-mediated gene editing of these blood cells. Finally, we also treated HSPCs with nanoblades in combination with a donor-encoding rAAV6 vector resulting in up to 40% of stable expression cassette knock-in into the WAS gene locus. Summarizing, this new technology is simple to implement, shows high flexibility for different targets including primary immune cells of human and murine origin, is relatively inexpensive and therefore gives important prospects for basic and clinical translation in the area of gene therapy.
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Affiliation(s)
- Alejandra Gutierrez-Guerrero
- CIRI-International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Maria Jimena Abrey Recalde
- CIRI-International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France.,Laboratory of Lentiviral Vectors and Gene Therapy, University Institute of Italian Hospital, National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
| | - Philippe E Mangeot
- CIRI-International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Caroline Costa
- CIRI-International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Ornellie Bernadin
- CIRI-International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Séverine Périan
- CIRI-International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Floriane Fusil
- CIRI-International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Gisèle Froment
- CIRI-International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | | | - Adrien Krug
- Université Côte d'Azur, INSERM, Nice, France
| | - Francisco Martin
- Centre for Genomics and Oncological Research (GENYO), Genomic Medicine Department, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Karim Benabdellah
- Centre for Genomics and Oncological Research (GENYO), Genomic Medicine Department, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Emiliano P Ricci
- CIRI-International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France.,Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, Ecole Normale Supérieure de Lyon (ENS de Lyon), Université Claude Bernard, Inserm, U1210, CNRS, UMR5239, Lyon, France
| | - Simone Giovannozzi
- Laboratory for Viral Vector Technology & Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, Katholieke Universiteit Leuven, Leuven, Belgium.,KU Leuven, Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, Leuven, Belgium
| | - Rik Gijsbers
- Laboratory for Viral Vector Technology & Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Eduard Ayuso
- INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| | - François-Loïc Cosset
- CIRI-International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Els Verhoeyen
- CIRI-International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France.,Université Côte d'Azur, INSERM, Nice, France
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32
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Ray-Jones H, Spivakov M. Transcriptional enhancers and their communication with gene promoters. Cell Mol Life Sci 2021; 78:6453-6485. [PMID: 34414474 PMCID: PMC8558291 DOI: 10.1007/s00018-021-03903-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
Abstract
Transcriptional enhancers play a key role in the initiation and maintenance of gene expression programmes, particularly in metazoa. How these elements control their target genes in the right place and time is one of the most pertinent questions in functional genomics, with wide implications for most areas of biology. Here, we synthesise classic and recent evidence on the regulatory logic of enhancers, including the principles of enhancer organisation, factors that facilitate and delimit enhancer-promoter communication, and the joint effects of multiple enhancers. We show how modern approaches building on classic insights have begun to unravel the complexity of enhancer-promoter relationships, paving the way towards a quantitative understanding of gene control.
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Affiliation(s)
- Helen Ray-Jones
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK
| | - Mikhail Spivakov
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
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33
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Abstract
The past 25 years of genomics research first revealed which genes are encoded by the human genome and then a detailed catalogue of human genome variation associated with many diseases. Despite this, the function of many genes and gene regulatory elements remains poorly characterized, which limits our ability to apply these insights to human disease. The advent of new CRISPR functional genomics tools allows for scalable and multiplexable characterization of genes and gene regulatory elements encoded by the human genome. These approaches promise to reveal mechanisms of gene function and regulation, and to enable exploration of how genes work together to modulate complex phenotypes.
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34
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Rao S, Yao Y, Soares de Brito J, Yao Q, Shen AH, Watkinson RE, Kennedy AL, Coyne S, Ren C, Zeng J, Serbin AV, Studer S, Ballotti K, Harris CE, Luk K, Stevens CS, Armant M, Pinello L, Wolfe SA, Chiarle R, Shimamura A, Lee B, Newburger PE, Bauer DE. Dissecting ELANE neutropenia pathogenicity by human HSC gene editing. Cell Stem Cell 2021; 28:833-845.e5. [PMID: 33513358 PMCID: PMC8106646 DOI: 10.1016/j.stem.2020.12.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/15/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023]
Abstract
Severe congenital neutropenia (SCN) is a life-threatening disorder most often caused by dominant mutations of ELANE that interfere with neutrophil maturation. We conducted a pooled CRISPR screen in human hematopoietic stem and progenitor cells (HSPCs) that correlated ELANE mutations with neutrophil maturation potential. Highly efficient gene editing of early exons elicited nonsense-mediated decay (NMD), overcame neutrophil maturation arrest in HSPCs from ELANE-mutant SCN patients, and produced normal hematopoietic engraftment function. Conversely, terminal exon frameshift alleles that mimic SCN-associated mutations escaped NMD, recapitulated neutrophil maturation arrest, and established an animal model of ELANE-mutant SCN. Surprisingly, only -1 frame insertions or deletions (indels) impeded neutrophil maturation, whereas -2 frame late exon indels repressed translation and supported neutrophil maturation. Gene editing of primary HSPCs allowed faithful identification of variant pathogenicity to clarify molecular mechanisms of disease and encourage a universal therapeutic approach to ELANE-mutant neutropenia, returning normal neutrophil production and preserving HSPC function.
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Affiliation(s)
- Shuquan Rao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Yao Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Josias Soares de Brito
- Departments of Pediatrics and of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Qiuming Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, MA 02129, USA
| | - Anne H Shen
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Ruth E Watkinson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alyssa L Kennedy
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Steven Coyne
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Chunyan Ren
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Victoria Serbin
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard College, Cambridge, MA 02138, USA
| | - Sabine Studer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Kaitlyn Ballotti
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Chad E Harris
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Christian S Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myriam Armant
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Luca Pinello
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, MA 02129, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Akiko Shimamura
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter E Newburger
- Departments of Pediatrics and of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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35
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Jost M, Jacobson AN, Hussmann JA, Cirolia G, Fischbach MA, Weissman JS. CRISPR-based functional genomics in human dendritic cells. eLife 2021; 10:e65856. [PMID: 33904395 PMCID: PMC8104964 DOI: 10.7554/elife.65856] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/26/2021] [Indexed: 12/12/2022] Open
Abstract
Dendritic cells (DCs) regulate processes ranging from antitumor and antiviral immunity to host-microbe communication at mucosal surfaces. It remains difficult, however, to genetically manipulate human DCs, limiting our ability to probe how DCs elicit specific immune responses. Here, we develop a CRISPR-Cas9 genome editing method for human monocyte-derived DCs (moDCs) that mediates knockouts with a median efficiency of >94% across >300 genes. Using this method, we perform genetic screens in moDCs, identifying mechanisms by which DCs tune responses to lipopolysaccharides from the human microbiome. In addition, we reveal donor-specific responses to lipopolysaccharides, underscoring the importance of assessing immune phenotypes in donor-derived cells, and identify candidate genes that control this specificity, highlighting the potential of our method to pinpoint determinants of inter-individual variation in immunity. Our work sets the stage for a systematic dissection of the immune signaling at the host-microbiome interface and for targeted engineering of DCs for neoantigen vaccination.
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Affiliation(s)
- Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Howard Hughes Medical Institute, University of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Microbiology and Immunology, University of California, San FranciscoSan FranciscoUnited States
| | - Amy N Jacobson
- Department of Bioengineering, Stanford UniversityStanfordUnited States
- ChEM-H, Stanford UniversityStanfordUnited States
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Howard Hughes Medical Institute, University of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Microbiology and Immunology, University of California, San FranciscoSan FranciscoUnited States
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
| | | | - Michael A Fischbach
- Department of Bioengineering, Stanford UniversityStanfordUnited States
- ChEM-H, Stanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Howard Hughes Medical Institute, University of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biosciences, University of California, San FranciscoSan FranciscoUnited States
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
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36
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Buquicchio FA, Satpathy AT. Interrogating immune cells and cancer with CRISPR-Cas9. Trends Immunol 2021; 42:432-446. [PMID: 33812776 DOI: 10.1016/j.it.2021.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas9 technologies have transformed the study of genetic pathways governing cellular differentiation and function. Recent advances have adapted these methods to immune cells, which has accelerated the pace of functional genomics in immunology and enabled new avenues for the design of cellular immunotherapies for cancer. In this review, we summarize recent developments in CRISPR-Cas9 technology and discuss how they have been leveraged to discover and manipulate novel genetic regulators of the immune system. We envision that these results will provide a valuable resource to aid in the design, implementation, and interpretation of CRISPR-Cas9-based screens in immunology and immuno-oncology.
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Affiliation(s)
- Frank A Buquicchio
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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37
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Humes D, Rainwater S, Overbaugh J. The TOP vector: a new high-titer lentiviral construct for delivery of sgRNAs and transgenes to primary T cells. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 20:30-38. [PMID: 33335945 PMCID: PMC7732963 DOI: 10.1016/j.omtm.2020.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/21/2020] [Indexed: 11/01/2022]
Abstract
Efficient delivery of nucleic acids for the engineering of primary T cells is central to the study of the basic biology of these key immune effector cells and has clinical implications. To date, lentiviral vectors delivering guide RNAs for CRISPR-Cas9 editing are not optimal for use in primary cells. Herein, we describe the T cell optimized for packaging (TOP) vector for delivering guide RNAs and transgenes into primary T cells. The TOP vector produces high-titer virus compared to a routinely used guide RNA vector, resulting in a ~10-fold increase in transduction in T cells. Moreover, a TOP vector expressing a chimeric antigen receptor and a guide RNA targeting the T cell receptor showed an ~5- to 9-fold increased transduction efficiency with ~2- to 3-fold higher expression compared to the commonly used epHIV7 vector and was simultaneously able to mediate efficient knockout of the endogenous T cell receptor in >71% of transduced cells upon Cas9 electroporation. The increased packaging of the TOP vector genome into viral particles appears to contribute to its higher transduction efficiency. The TOP vector represents an optimal tool for tandem delivery of transgenes and guide RNAs to primary T cells for use in functional screens and immunotherapy applications.
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Affiliation(s)
- Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie Rainwater
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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38
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Fix SM, Jazaeri AA, Hwu P. Applications of CRISPR Genome Editing to Advance the Next Generation of Adoptive Cell Therapies for Cancer. Cancer Discov 2021; 11:560-574. [PMID: 33563662 PMCID: PMC8193798 DOI: 10.1158/2159-8290.cd-20-1083] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/21/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022]
Abstract
Adoptive cell therapy (ACT) for cancer shows tremendous potential; however, several challenges preclude its widespread use. These include poor T-cell function in hostile tumor microenvironments, a lack of tumor-specific target antigens, and the high cost and poor scalability of cell therapy manufacturing. Creative genome-editing strategies are beginning to emerge to address each of these limitations, which has initiated the next generation of cell therapy products now entering clinical trials. CRISPR is at the forefront of this revolution, offering a simple and versatile platform for genetic engineering. This review provides a comprehensive overview of CRISPR applications that have advanced ACT. SIGNIFICANCE: The clinical impact of ACT for cancer can be expanded by implementing specific genetic modifications that enhance the potency, safety, and scalability of cellular products. Here we provide a detailed description of such genetic modifications, highlighting avenues to enhance the therapeutic efficacy and accessibility of ACT for cancer. Furthermore, we review high-throughput CRISPR genetic screens that have unveiled novel targets for cell therapy enhancement.
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MESH Headings
- Animals
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- CRISPR-Cas Systems
- Cell- and Tissue-Based Therapy/adverse effects
- Cell- and Tissue-Based Therapy/methods
- Clinical Trials as Topic
- Combined Modality Therapy
- Disease Management
- Drug Evaluation, Preclinical
- Gene Editing/methods
- Genetic Engineering
- Genetic Therapy
- Humans
- Immunotherapy, Adoptive/adverse effects
- Immunotherapy, Adoptive/methods
- Neoplasms/therapy
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Treatment Outcome
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Affiliation(s)
- Samantha M Fix
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amir A Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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39
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Combined lentiviral- and RNA-mediated CRISPR/Cas9 delivery for efficient and traceable gene editing in human hematopoietic stem and progenitor cells. Sci Rep 2020; 10:22393. [PMID: 33372184 PMCID: PMC7769964 DOI: 10.1038/s41598-020-79724-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 12/11/2020] [Indexed: 12/17/2022] Open
Abstract
The CRISPR/Cas9 system is a versatile tool for functional genomics and forward genetic screens in mammalian cells. However, it has been challenging to deliver the CRISPR components to sensitive cell types, such as primary human hematopoietic stem and progenitor cells (HSPCs), partly due to lentiviral transduction of Cas9 being extremely inefficient in these cells. Here, to overcome these hurdles, we developed a combinatorial system using stable lentiviral delivery of single guide RNA (sgRNA) followed by transient transfection of Cas9 mRNA by electroporation in human cord blood-derived CD34+ HSPCs. We further applied an optimized sgRNA structure, that significantly improved editing efficiency in this context, and we obtained knockout levels reaching 90% for the cell surface proteins CD45 and CD44 in sgRNA transduced HSPCs. Our combinatorial CRISPR/Cas9 delivery approach had no negative influence on CD34 expression or colony forming capacity in vitro compared to non-treated HSPCs. Furthermore, gene edited HSPCs showed intact in vivo reconstitution capacity following transplantation to immunodeficient mice. Taken together, we developed a paradigm for combinatorial CRISPR/Cas9 delivery that enables efficient and traceable gene editing in primary human HSPCs, and is compatible with high functionality both in vitro and in vivo.
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40
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Kotowski M, Sharma S. CRISPR-Based Editing Techniques for Genetic Manipulation of Primary T Cells. Methods Protoc 2020; 3:mps3040079. [PMID: 33217926 PMCID: PMC7720142 DOI: 10.3390/mps3040079] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/15/2022] Open
Abstract
While clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing techniques have been widely adapted for use in immortalised immune cells, efficient manipulation of primary T cells has proved to be more challenging. Nonetheless, the rapid expansion of the CRISPR toolbox accompanied by the development of techniques for delivery of CRISPR components into primary T cells now affords the possibility to genetically manipulate primary T cells both with precision and at scale. Here, we review the key features of the techniques for primary T cell editing and discuss how the new generation of CRISPR-based tools may advance genetic engineering of these immune cells. This improved ability to genetically manipulate primary T cells will further enhance our fundamental understanding of cellular signalling and transcriptional networks in T cells and more importantly has the potential to revolutionise T cell-based therapies.
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41
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Functional CRISPR dissection of gene networks controlling human regulatory T cell identity. Nat Immunol 2020; 21:1456-1466. [PMID: 32989329 PMCID: PMC7577958 DOI: 10.1038/s41590-020-0784-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 08/12/2020] [Indexed: 12/13/2022]
Abstract
Human regulatory T (Treg) cells are essential for immune homeostasis. The transcription factor (TF) FOXP3 maintains Treg cell identity, yet the complete set of key TFs that control Treg cell gene expression remains unknown. Here, we used pooled and arrayed Cas9 ribonucleoprotein (RNP) screens to identify TFs that regulate critical proteins in primary human Treg cells under basal and pro-inflammatory conditions. We then generated 54,424 single-cell transcriptomes from Treg cells subjected to genetic perturbations and cytokine stimulation, which revealed distinct gene networks individually regulated by FOXP3 and PRDM1, in addition to a network co-regulated by FOXO1 and IRF4. We also discovered that HIVEP2, not previously implicated in Treg cell function, co-regulates another gene network with SATB1 and is important for Treg cell-mediated immunosuppression. By integrating CRISPR screens and scRNA-seq profiling, we have uncovered novel transcriptional regulators and downstream gene networks in human Treg cells that could be targeted for immunotherapies.
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42
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Coelho MA, De Braekeleer E, Firth M, Bista M, Lukasiak S, Cuomo ME, Taylor BJM. CRISPR GUARD protects off-target sites from Cas9 nuclease activity using short guide RNAs. Nat Commun 2020; 11:4132. [PMID: 32807781 PMCID: PMC7431537 DOI: 10.1038/s41467-020-17952-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/23/2020] [Indexed: 11/16/2022] Open
Abstract
Precise genome editing using CRISPR-Cas9 is a promising therapeutic avenue for genetic diseases, although off-target editing remains a significant safety concern. Guide RNAs shorter than 16 nucleotides in length effectively recruit Cas9 to complementary sites in the genome but do not permit Cas9 nuclease activity. Here we describe CRISPR Guide RNA Assisted Reduction of Damage (CRISPR GUARD) as a method for protecting off-targets sites by co-delivery of short guide RNAs directed against off-target loci by competition with the on-target guide RNA. CRISPR GUARD reduces off-target mutagenesis while retaining on-target editing efficiencies with Cas9 and base editor. However, we discover that short guide RNAs can also support base editing if they contain cytosines within the deaminase activity window. We explore design rules and the universality of this method through in vitro studies and high-throughput screening, revealing CRISPR GUARD as a rapidly implementable strategy to improve the specificity of genome editing for most genomic loci. Finally, we create an online tool for CRISPR GUARD design.
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Affiliation(s)
- Matthew A Coelho
- Discovery Sciences, R&D, AstraZeneca, Cambridge, UK.
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1RQ, UK.
| | | | - Mike Firth
- Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Michal Bista
- Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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43
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Abstract
PURPOSE OF REVIEW T cell-based cellular and antibody immunotherapies have dramatically altered the landscape of cancer treatment over the past decade. Over the same time span, gene editing technologies have enabled unprecedented degrees of genetic control. RECENT FINDINGS Knock-outs of endogenous genes, especially based on electroporation of targetable nucleases such as CRISPR/Cas9, have rapidly proliferated. Simultaneous introduction of large DNA sequences can integrate new synthetic genetic instructions with specific endogenous loci to alter T cell function and specificity. Recently developed discovery technologies to perform genome-wide knock-out and large-scale knock-in screens in T cells can rapidly identify endogenous gene targets and therapeutic knock-in programs. Endogenous gene knock-outs and targeted knock-ins may offer the chance to expand beyond the current limitations of randomly integrating viral vector-based T cell therapies, and extend immunotherapies' therapeutic advances to wider hematologic and solid tumor indications.
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Affiliation(s)
- Theodore L Roth
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA.
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44
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Freund EC, Lock JY, Oh J, Maculins T, Delamarre L, Bohlen CJ, Haley B, Murthy A. Efficient gene knockout in primary human and murine myeloid cells by non-viral delivery of CRISPR-Cas9. J Exp Med 2020; 217:e20191692. [PMID: 32357367 PMCID: PMC7336301 DOI: 10.1084/jem.20191692] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 02/17/2020] [Accepted: 04/07/2020] [Indexed: 12/11/2022] Open
Abstract
Myeloid cells play critical and diverse roles in mammalian physiology, including tissue development and repair, innate defense against pathogens, and generation of adaptive immunity. As cells that show prolonged recruitment to sites of injury or pathology, myeloid cells represent therapeutic targets for a broad range of diseases. However, few approaches have been developed for gene editing of these cell types, likely owing to their sensitivity to foreign genetic material or virus-based manipulation. Here we describe optimized strategies for gene disruption in primary myeloid cells of human and murine origin. Using nucleofection-based delivery of Cas9-ribonuclear proteins (RNPs), we achieved near population-level genetic knockout of single and multiple targets in a range of cell types without selection or enrichment. Importantly, we show that cellular fitness and response to immunological stimuli is not significantly impacted by the gene editing process. This provides a significant advance in the study of myeloid cell biology, thus enabling pathway discovery and drug target validation across species in the field of innate immunity.
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Affiliation(s)
- Emily C. Freund
- Department of Molecular Biology, Genentech, South San Francisco, CA
| | - Jaclyn Y. Lock
- Department of Cancer Immunology, Genentech, South San Francisco, CA
| | - Jaehak Oh
- Department of Cancer Immunology, Genentech, South San Francisco, CA
| | - Timurs Maculins
- Department of Cancer Immunology, Genentech, South San Francisco, CA
| | - Lelia Delamarre
- Department of Cancer Immunology, Genentech, South San Francisco, CA
| | | | - Benjamin Haley
- Department of Molecular Biology, Genentech, South San Francisco, CA
| | - Aditya Murthy
- Department of Cancer Immunology, Genentech, South San Francisco, CA
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45
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Liu D, Zhao X, Tang A, Xu X, Liu S, Zha L, Ma W, Zheng J, Shi M. CRISPR screen in mechanism and target discovery for cancer immunotherapy. Biochim Biophys Acta Rev Cancer 2020; 1874:188378. [PMID: 32413572 DOI: 10.1016/j.bbcan.2020.188378] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022]
Abstract
CRISPR/Cas-based genetic perturbation screens have emerged as powerful tools for large-scale identification of new targets for cancer immunotherapy. Various strategies of CRISPR screen have been used for immune-oncology (IO) target discovery. The genomic sequences targeted by CRISPR/Cas system range from coding sequences to non-coding RNA/DNA, including miRNAs, LncRNAs, circRNAs, promoters, and enhancers, which may be potential targets for future pharmacological and therapeutic interventions. Rapid progresses have been witnessed in finding novel targets for enhancing tumor antigen presentation, sensitizing of tumor cells to immune-mediated cytotoxicity, and reinvigorating tumor-specific T cells by using CRISPR technologies. In combination with other strategies, the detailed characteristics of the targets for immunotherapy have been obtained by CRISPR screen. In this review, we present an overview of recent progresses in the development of CRISPR-based screens for IO target identification and discuss the challenges and possible solutions in this rapidly growing field.
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Affiliation(s)
- Dan Liu
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Xuan Zhao
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Anqun Tang
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Xiyue Xu
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Shuci Liu
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Li Zha
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Wen Ma
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Junnian Zheng
- Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China.
| | - Ming Shi
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China.
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46
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Huang B, Liu Z, Vonk A, Zeng Z, Li Z. Epigenetic regulation of kidney progenitor cells. Stem Cells Transl Med 2020; 9:655-660. [PMID: 32163228 PMCID: PMC7214665 DOI: 10.1002/sctm.19-0289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/26/2020] [Accepted: 02/17/2020] [Indexed: 12/15/2022] Open
Abstract
The reciprocal interactions among the different embryonic kidney progenitor populations lay the basis for proper kidney organogenesis. During kidney development, three types of progenitor cells, including nephron progenitor cells, ureteric bud progenitor cells, and interstitial progenitor cells, generate the three major kidney structures—the nephrons, the collecting duct network, and the stroma, respectively. Epigenetic mechanisms are well recognized for playing important roles in organism development, in fine‐tuned control of physiological activities, and in responses to environment stimuli. Recently, evidence supporting the importance of epigenetic mechanisms underlying kidney organogenesis has emerged. In this perspective, we summarize the research progress and discuss the potential contribution of novel stem cell, organoid, and next‐generation sequencing tools in advancing this field in the future.
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Affiliation(s)
- Biao Huang
- Division of Nephrology and Hypertension, Department of Medicine and USC/UKRO Kidney Research Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.,Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Zhenqing Liu
- Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, California, USA
| | - Ariel Vonk
- Division of Nephrology and Hypertension, Department of Medicine and USC/UKRO Kidney Research Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.,Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Zipeng Zeng
- Division of Nephrology and Hypertension, Department of Medicine and USC/UKRO Kidney Research Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.,Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Zhongwei Li
- Division of Nephrology and Hypertension, Department of Medicine and USC/UKRO Kidney Research Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.,Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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47
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Abstract
Recent advances in the development of gene editing technologies, especially the CRISPR/Cas 9 system, have substantially enhanced our ability to make precise and efficient changes in the genomes of various cells. In particular, the genetic engineering of T cells holds huge potential to improve the efficacy and safety of T cells-based cancer therapy. Due to its ease of use and high efficiency, CRISPR/Cas9 enables efficient gene knockout, site-specific knock-in, and genome-wide screen in T cells. Here we review the current progress of applying gene editing to T-cell therapy, focusing on the technical aspects of the CRISPR/Cas9 platform. We also discuss the challenges and future prospects.
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Affiliation(s)
- Xingying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Chen Cheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wen Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
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48
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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. Nat Biotechnol 2019; 37:1302-1313. [PMID: 31548728 PMCID: PMC6834896 DOI: 10.1038/s41587-019-0246-4] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 08/01/2019] [Indexed: 12/14/2022]
Abstract
Targeting membrane proteins could improve the efficacy of T cell-based immunotherapies. To facilitate the identification of T cell targets, we developed a hybrid genetic screening system where the Sleeping Beauty (SB) transposon and single guide RNA cassette are nested in an adeno-associated virus (AAV). SB-mediated genomic integration of the single guide RNA cassette enables efficient gene editing in primary murine T cells as well as a screen readout. We performed in vivo AAV-SB-CRISPR screens for membrane protein targets in CD8+ T cells in mouse models of glioblastoma (GBM). We validated screen hits by demonstrating that adoptive transfer of CD8+ T cells with Pdia3, Mgat5, Emp1 or Lag3 gene editing enhances the survival of GBM-bearing mice in both syngeneic and T-cell receptor transgenic models. Transcriptome profiling, single cell sequencing, cytokine assays and T cell signaling analysis showed that Pdia3 editing in T cells enhances effector functions. Engineered PDIA3 mutant EGFRvIII chimeric antigen T cells are more potent in antigen-specific killing of human GBM cells.
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Affiliation(s)
- Lupeng Ye
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Jonathan J Park
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
- Yale M.D.-Ph.D. Program, Yale University School of Medicine, New Haven, CT, USA
| | - Matthew B Dong
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
- Yale M.D.-Ph.D. Program, Yale University School of Medicine, New Haven, CT, USA
- Immunobiology Program, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Quanjun Yang
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Ryan D Chow
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
- Yale M.D.-Ph.D. Program, Yale University School of Medicine, New Haven, CT, USA
| | - Lei Peng
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Yaying Du
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Jianjian Guo
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Xiaoyun Dai
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Guangchuan Wang
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Youssef Errami
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Sidi Chen
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA.
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA.
- Yale M.D.-Ph.D. Program, Yale University School of Medicine, New Haven, CT, USA.
- Immunobiology Program, Yale University School of Medicine, New Haven, CT, USA.
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA.
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA.
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA.
- Yale Liver Center, Yale University School of Medicine, New Haven, CT, USA.
- Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA.
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49
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Balboa D, Prasad RB, Groop L, Otonkoski T. Genome editing of human pancreatic beta cell models: problems, possibilities and outlook. Diabetologia 2019; 62:1329-1336. [PMID: 31161346 PMCID: PMC6647170 DOI: 10.1007/s00125-019-4908-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/25/2019] [Indexed: 12/14/2022]
Abstract
Understanding the molecular mechanisms behind beta cell dysfunction is essential for the development of effective and specific approaches for diabetes care and prevention. Physiological human beta cell models are needed for this work. We review the possibilities and limitations of currently available human beta cell models and how they can be dramatically enhanced using genome-editing technologies. In addition to the gold standard, primary isolated islets, other models now include immortalised human beta cell lines and pluripotent stem cell-derived islet-like cells. The scarcity of human primary islet samples limits their use, but valuable gene expression and functional data from large collections of human islets have been made available to the scientific community. The possibilities for studying beta cell physiology using immortalised human beta cell lines and stem cell-derived islets are rapidly evolving. However, the functional immaturity of these cells is still a significant limitation. CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) has enabled precise engineering of specific genetic variants, targeted transcriptional modulation and genome-wide genetic screening. These approaches can now be exploited to gain understanding of the mechanisms behind coding and non-coding diabetes-associated genetic variants, allowing more precise evaluation of their contribution to diabetes pathogenesis. Despite all the progress, genome editing in primary pancreatic islets remains difficult to achieve, an important limitation requiring further technological development.
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Affiliation(s)
- Diego Balboa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rashmi B Prasad
- Genomics, Diabetes and Endocrinology, Lund University Diabetes Centre, CRC, Malmö, Sweden
| | - Leif Groop
- Genomics, Diabetes and Endocrinology, Lund University Diabetes Centre, CRC, Malmö, Sweden
- Institute of Molecular Medicine, Centre of Excellence in Complex Disease Genetics, University of Helsinki, Helsinki, Finland
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.
- Children's Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland.
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50
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CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases. Semin Cell Dev Biol 2019; 96:32-43. [PMID: 31112800 DOI: 10.1016/j.semcdb.2019.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/21/2022]
Abstract
Recent developments in the nucleic acid editing technologies have provided a powerful tool to precisely engineer the genome and epigenome for studying many aspects of immune cell differentiation and development as well as several immune mediated diseases (IMDs) including autoimmunity and cancer. Here, we discuss the recent technological achievements of the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based RNA-guided genome and epigenome editing toolkit and provide an insight into how CRISPR/Cas9 (CRISPR Associated Protein 9) toolbox could be used to examine genetic and epigenetic mechanisms underlying IMDs. In addition, we will review the progress in CRISPR/Cas9-based genome-wide genome and epigenome screens in various cell types including immune cells. Finally, we will discuss the potential of CRISPR/Cas9 in defining the molecular function of disease associated SNPs overlapping gene regulatory elements.
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