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He K, Xiao H, MacDonald WA, Mehta I, Kishore A, Vincent A, Xu Z, Ray A, Chen W, Weaver CT, Lambrecht BN, Das J, Poholek AC. Spatial microniches of IL-2 combine with IL-10 to drive lung migratory T H2 cells in response to inhaled allergen. Nat Immunol 2024:10.1038/s41590-024-01986-8. [PMID: 39394532 DOI: 10.1038/s41590-024-01986-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 09/12/2024] [Indexed: 10/13/2024]
Abstract
The mechanisms that guide T helper 2 (TH2) cell differentiation in barrier tissues are unclear. Here we describe the molecular pathways driving allergen-specific TH2 cells using temporal, spatial and single-cell transcriptomic tracking of house dust mite-specific T cells in mice. Differentiation and migration of lung allergen-specific TH2 cells requires early expression of the transcriptional repressor Blimp-1. Loss of Blimp-1 during priming in the lymph node ablated the formation of TH2 cells in the lung, indicating early Blimp-1 promotes TH2 cells with migratory capability. IL-2/STAT5 signals and autocrine/paracrine IL-10 from house dust mite-specific T cells were essential for Blimp-1 and subsequent GATA3 upregulation through repression of Bcl6 and Bach2. Spatial microniches of IL-2 in the lymph node supported the earliest Blimp-1+TH2 cells, demonstrating lymph node localization is a driver of TH2 initiation. Our findings identify an early requirement for IL-2-mediated spatial microniches that integrate with allergen-driven IL-10 from responding T cells to drive allergic asthma.
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Affiliation(s)
- Kun He
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Hanxi Xiao
- Center for Systems Immunology, Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - William A MacDonald
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Health Sciences Sequencing Core, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Isha Mehta
- Center for Systems Immunology, Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Akash Kishore
- Center for Systems Immunology, Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Augusta Vincent
- Center for Systems Immunology, Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zhongli Xu
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Anuradha Ray
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Wei Chen
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Biostatistics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Casey T Weaver
- Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Bart N Lambrecht
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Jishnu Das
- Center for Systems Immunology, Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amanda C Poholek
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Center for Systems Immunology, Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA.
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2
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Humblin E, Korpas I, Prokhnevska N, Vaidya A, Lu J, van der Heide V, Filipescu D, Bobrowski T, Marks A, Park MD, Bernstein E, Brown BD, Lujambio A, Dominguez-Sola D, Rosenberg BR, Kamphorst AO. ICOS limits memory-like properties and function of exhausted PD-1 + CD8 T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.611518. [PMID: 39345453 PMCID: PMC11429760 DOI: 10.1101/2024.09.16.611518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
During persistent antigen stimulation, PD-1 + CD8 T cells are maintained by progenitor exhausted PD-1 + TCF-1 + CD8 T cells (Tpex). Tpex respond to PD-1 blockade, and regulation of Tpex differentiation into more functional Tex is of major interest for cancer immunotherapies. Tpex express high levels of Inducible Costimulator (ICOS), but the role of ICOS for PD-1 + CD8 T cell responses has not been addressed. In chronic infection, ICOS-deficiency increased both number and quality of virus-specific CD8 T cells, with accumulation of effector-like Tex due to enhanced survival. Mechanistically, loss of ICOS signaling potentiated FoxO1 activity and memory-like features of Tpex. In mice with established chronic infection, ICOS-Ligand blockade resulted in expansion of effector-like Tex and reduction in viral load. In a mouse model of hepatocellular carcinoma, ICOS inhibition improved cytokine production by tumor-specific PD-1 + CD8 T cells and delayed tumor growth. Overall, we show that ICOS limits CD8 T cell responses during chronic antigen exposure.
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3
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Karginov TA, Ménoret A, Leclair NK, Harrison AG, Chandiran K, Suarez-Ramirez JE, Yurieva M, Karlinsey K, Wang P, O'Neill RJ, Murphy PA, Adler AJ, Cauley LS, Anczuków O, Zhou B, Vella AT. Autoregulated splicing of TRA2β programs T cell fate in response to antigen-receptor stimulation. Science 2024; 385:eadj1979. [PMID: 39265028 DOI: 10.1126/science.adj1979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 03/13/2024] [Accepted: 07/09/2024] [Indexed: 09/14/2024]
Abstract
T cell receptor (TCR) sensitivity to peptide-major histocompatibility complex (MHC) dictates T cell fate. Canonical models of TCR sensitivity cannot be fully explained by transcriptional regulation. In this work, we identify a posttranscriptional regulatory mechanism of TCR sensitivity that guides alternative splicing of TCR signaling transcripts through an evolutionarily ultraconserved poison exon (PE) in the RNA-binding protein (RBP) TRA2β in mouse and human. TRA2β-PE splicing, seen during cancer and infection, was required for TCR-induced effector T cell expansion and function. Tra2β-PE skipping enhanced T cell response to antigen by increasing TCR sensitivity. As antigen levels decreased, Tra2β-PE reinclusion allowed T cell survival. Finally, we found that TRA2β-PE was first included in the genome of jawed vertebrates that were capable of TCR gene rearrangements. We propose that TRA2β-PE splicing acts as a gatekeeper of TCR sensitivity to shape T cell fate.
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Affiliation(s)
- Timofey A Karginov
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
| | - Antoine Ménoret
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
| | - Nathan K Leclair
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Andrew G Harrison
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
| | - Karthik Chandiran
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
| | - Jenny E Suarez-Ramirez
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
| | - Marina Yurieva
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Keaton Karlinsey
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
| | - Penghua Wang
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
| | - Rachel J O'Neill
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Patrick A Murphy
- Center for Vascular Biology, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
| | - Adam J Adler
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
| | - Linda S Cauley
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
| | - Olga Anczuków
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Beiyan Zhou
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Anthony T Vella
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, Farmington, CT 06030, USA
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4
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Buquicchio FA, Fonseca R, Yan PK, Wang F, Evrard M, Obers A, Gutierrez JC, Raposo CJ, Belk JA, Daniel B, Zareie P, Yost KE, Qi Y, Yin Y, Nico KF, Tierney FM, Howitt MR, Lareau CA, Satpathy AT, Mackay LK. Distinct epigenomic landscapes underlie tissue-specific memory T cell differentiation. Immunity 2024; 57:2202-2215.e6. [PMID: 39043184 DOI: 10.1016/j.immuni.2024.06.014] [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] [Received: 12/18/2023] [Revised: 05/07/2024] [Accepted: 06/27/2024] [Indexed: 07/25/2024]
Abstract
The memory CD8+ T cell pool contains phenotypically and transcriptionally heterogeneous subsets with specialized functions and recirculation patterns. Here, we examined the epigenetic landscape of CD8+ T cells isolated from seven non-lymphoid organs across four distinct infection models, alongside their circulating T cell counterparts. Using single-cell transposase-accessible chromatin sequencing (scATAC-seq), we found that tissue-resident memory T (TRM) cells and circulating memory T (TCIRC) cells develop along distinct epigenetic trajectories. We identified organ-specific transcriptional regulators of TRM cell development, including FOSB, FOS, FOSL1, and BACH2, and defined an epigenetic signature common to TRM cells across organs. Finally, we found that although terminal TEX cells share accessible regulatory elements with TRM cells, they are defined by TEX-specific epigenetic features absent from TRM cells. Together, this comprehensive data resource shows that TRM cell development is accompanied by dynamic transcriptome alterations and chromatin accessibility changes that direct tissue-adapted and functionally distinct T cell states.
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Affiliation(s)
- Frank A Buquicchio
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Raissa Fonseca
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Patrick K Yan
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Fangyi Wang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Maximilien Evrard
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Andreas Obers
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jacob C Gutierrez
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Colin J Raposo
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Julia A Belk
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Pirooz Zareie
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Kathryn E Yost
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Yajie Yin
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Katherine F Nico
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Flora M Tierney
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Michael R Howitt
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA; Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA 94129, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA; Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA 94129, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.
| | - Laura K Mackay
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
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5
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Gubser PM, Wijesinghe S, Heyden L, Gabriel SS, de Souza DP, Hess C, McConville MM, Utzschneider DT, Kallies A. Aerobic glycolysis but not GLS1-dependent glutamine metabolism is critical for anti-tumor immunity and response to checkpoint inhibition. Cell Rep 2024; 43:114632. [PMID: 39159042 DOI: 10.1016/j.celrep.2024.114632] [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] [Received: 06/06/2023] [Revised: 07/04/2024] [Accepted: 07/30/2024] [Indexed: 08/21/2024] Open
Abstract
Tumor cells undergo uncontrolled proliferation driven by enhanced anabolic metabolism including glycolysis and glutaminolysis. Targeting these pathways to inhibit cancer growth is a strategy for cancer treatment. Critically, however, tumor-responsive T cells share metabolic features with cancer cells, making them susceptible to these treatments as well. Here, we assess the impact on anti-tumor T cell immunity and T cell exhaustion by genetic ablation of lactate dehydrogenase A (LDHA) and glutaminase1 (GLS1), key enzymes in aerobic glycolysis and glutaminolysis. Loss of LDHA severely impairs expansion of T cells in response to tumors and chronic infection. In contrast, T cells lacking GLS1 can compensate for impaired glutaminolysis by engaging alternative pathways, including upregulation of asparagine synthetase, and thus efficiently respond to tumor challenge and chronic infection as well as immune checkpoint blockade. Targeting GLS1-dependent glutaminolysis, but not aerobic glycolysis, may therefore be a successful strategy in cancer treatment, particularly in combination with immunotherapy.
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Affiliation(s)
- Patrick M Gubser
- The Peter Doherty Institute for Infection and Immunity and Department of Microbiology and Immunology, University of Melbourne, Parkville, VIC, Australia
| | - Sharanya Wijesinghe
- The Peter Doherty Institute for Infection and Immunity and Department of Microbiology and Immunology, University of Melbourne, Parkville, VIC, Australia
| | - Leonie Heyden
- The Peter Doherty Institute for Infection and Immunity and Department of Microbiology and Immunology, University of Melbourne, Parkville, VIC, Australia
| | - Sarah S Gabriel
- The Peter Doherty Institute for Infection and Immunity and Department of Microbiology and Immunology, University of Melbourne, Parkville, VIC, Australia
| | - David P de Souza
- Metabolomics Australia, Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Christoph Hess
- Department of Biomedicine, Immunobiology, University of Basel and University Hospital of Basel, 4031 Basel, Switzerland; Department of Medicine, CITIID, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Malcolm M McConville
- Metabolomics Australia, Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia; Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Daniel T Utzschneider
- The Peter Doherty Institute for Infection and Immunity and Department of Microbiology and Immunology, University of Melbourne, Parkville, VIC, Australia
| | - Axel Kallies
- The Peter Doherty Institute for Infection and Immunity and Department of Microbiology and Immunology, University of Melbourne, Parkville, VIC, Australia.
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6
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Sutton VR, Watt SV, Akhlaghi H, Cipolla DC, Chen KJ, LaSala D, McDonald PP, Beavis PA, Munoz I, Hodel AW, Noori T, Voskoboinik I, Trapani JA. Pharmacologic inhibition of dipeptidyl peptidase 1 (cathepsin C) does not block in vitro granzyme-mediated target cell killing by CD8 T or NK cells. Front Pharmacol 2024; 15:1396710. [PMID: 39021839 PMCID: PMC11251990 DOI: 10.3389/fphar.2024.1396710] [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: 03/06/2024] [Accepted: 05/15/2024] [Indexed: 07/20/2024] Open
Abstract
Recently developed small-molecule inhibitors of the lysosomal protease dipeptidyl peptidase 1 (DPP1), also known as cathepsin C (CatC), can suppress suppurative inflammation in vivo by blocking the processing of zymogenic (pro-) forms of neutrophil serine proteases (NSPs), including neutrophil elastase, proteinase 3, and cathepsin G. DPP1 also plays an important role in activating granzyme serine proteases that are expressed by cytotoxic T lymphocytes (CTL) and natural killer (NK) cells. Therefore, it is critical to determine whether DPP1 inhibition can also cause off-target suppression of CTL/NK-cell-mediated killing of virus-infected or malignant cells. Herein, we demonstrate that the processing of human granzymes A and B, transitioning from zymogen to active proteases, is not solely dependent on DPP1. Thus, the killing of target cells by primary human CD8+ T cells, NK cells, and gene-engineered anti-CD19 CAR T cells was not blocked in vitro even after prior exposure to high concentrations of the reversible DPP1 inhibitor brensocatib. Consistent with this observation, the turnover of model granzyme A/B peptide substrates in the human CTL/NK cell lysates was not significantly reduced by brensocatib. In contrast, preincubation with brensocatib almost entirely abolished (>90%) both the cytotoxic activity of mouse CD8+ T cells and granzyme substrate turnover. Overall, our finding that the effects of DPP1 inhibition on human cytotoxic lymphocytes are attenuated in comparison to those of mice indicates that granzyme processing/activation pathways differ between mice and humans. Moreover, the in vitro data suggest that human subjects treated with reversible DPP1 inhibitors, such as brensocatib, are unlikely to experience any appreciable deficits in CTL/NK-cell-mediated immunities.
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Affiliation(s)
- Vivien R. Sutton
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Sally V. Watt
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Hedieh Akhlaghi
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | | | - Kuan-Ju Chen
- Insmed Incorporated, Bridgewater, NJ, United States
| | | | | | - Paul A. Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Isabelle Munoz
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Adrian W. Hodel
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Tahereh Noori
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Ilia Voskoboinik
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Joseph A. Trapani
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
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7
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Dahabieh MS, DeCamp LM, Oswald BM, Kitchen-Goosen SM, Fu Z, Vos M, Compton SE, Longo J, Williams KS, Ellis AE, Johnson A, Sodiya I, Vincent M, Lee H, Sheldon RD, Krawczyk CM, Yao C, Wu T, Jones RG. NRF2-dependent regulation of the prostacyclin receptor PTGIR drives CD8 T cell exhaustion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.23.600279. [PMID: 38979360 PMCID: PMC11230227 DOI: 10.1101/2024.06.23.600279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The progressive decline of CD8 T cell effector function-also known as terminal exhaustion-is a major contributor to immune evasion in cancer. Yet, the molecular mechanisms that drive CD8 T cell dysfunction remain poorly understood. Here, we report that the Kelch-like ECH-associated protein 1 (KEAP1)-Nuclear factor erythroid 2-related factor 2 (NRF2) signaling axis, which mediates cellular adaptations to oxidative stress, directly regulates CD8 T cell exhaustion. Transcriptional profiling of dysfunctional CD8 T cells from chronic infection and cancer reveals enrichment of NRF2 activity in terminally exhausted (Texterm) CD8 T cells. Increasing NRF2 activity in CD8 T cells (via conditional deletion of KEAP1) promotes increased glutathione production and antioxidant defense yet accelerates the development of terminally exhausted (PD-1+TIM-3+) CD8 T cells in response to chronic infection or tumor challenge. Mechanistically, we identify PTGIR, a receptor for the circulating eicosanoid prostacyclin, as an NRF2-regulated protein that promotes CD8 T cell dysfunction. Silencing PTGIR expression restores the anti-tumor function of KEAP1-deficient T cells. Moreover, lowering PTGIR expression in CD8 T cells both reduces terminal exhaustion and enhances T cell effector responses (i.e. IFN-γ and granzyme production) to chronic infection and cancer. Together, these results establish the KEAP1-NRF2 axis as a metabolic sensor linking oxidative stress to CD8 T cell dysfunction and identify the prostacyclin receptor PTGIR as an NRF2-regulated immune checkpoint that regulates CD8 T cell fate decisions between effector and exhausted states.
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Affiliation(s)
- Michael S Dahabieh
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Lisa M DeCamp
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Brandon M Oswald
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Susan M Kitchen-Goosen
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Zhen Fu
- Bioinformatics and Biostatistics Core Facility, Van Andel Institute, Grand Rapids, MI, USA
| | - Matthew Vos
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Shelby E Compton
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Joseph Longo
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Kelsey S Williams
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Abigail E Ellis
- Mass Spectrometry Core Facility, Van Andel Institute, Grand Rapids, MI, USA
| | - Amy Johnson
- Mass Spectrometry Core Facility, Van Andel Institute, Grand Rapids, MI, USA
| | - Ibukunoluwa Sodiya
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core Facility, Van Andel Institute, Grand Rapids, MI, USA
| | - Michael Vincent
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core Facility, Van Andel Institute, Grand Rapids, MI, USA
| | - Hyoungjoo Lee
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core Facility, Van Andel Institute, Grand Rapids, MI, USA
| | - Ryan D Sheldon
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core Facility, Van Andel Institute, Grand Rapids, MI, USA
| | - Connie M Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Chen Yao
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tuoqi Wu
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Russell G Jones
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
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8
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Wang L, Mishra S, Fan KKH, Quon S, Li G, Yu B, Liao W, Liu Y, Zhang X, Qiu Y, Li Y, Goldrath AW, Ma C, Zhang N. T-bet deficiency and Hic1 induction override TGF-β-dependency in the formation of CD103 + intestine-resident memory CD8 + T cells. Cell Rep 2024; 43:114258. [PMID: 38781073 PMCID: PMC11240284 DOI: 10.1016/j.celrep.2024.114258] [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: 02/28/2023] [Revised: 03/01/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Transforming growth factor β (TGF-β) represents a well-established signal required for tissue-resident memory T cell (TRM) formation at intestinal surfaces, regulating the expression of a large collection of genes coordinately promoting intestinal TRM differentiation. The functional contribution from each TGF-β-controlled transcription factor is not entirely known. Here, we find that TGF-β-induced T-bet downregulation and Hic1 induction represent two critical events during intestinal TRM differentiation. Importantly, T-bet deficiency significantly rescues intestinal TRM formation in the absence of the TGF-β receptor. Hic1 induction further strengthens TRM maturation in the absence of TGF-β and T-bet. Our results reveal that provision of certain TGF-β-induced molecular events can partially replace TGF-β signaling to promote the establishment of intestinal TRMs, which allows the functional dissection of TGF-β-induced transcriptional targets and molecular mechanisms for TRM differentiation.
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Affiliation(s)
- Liwen Wang
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of Hematology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Shruti Mishra
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Kenneth Ka-Ho Fan
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Sara Quon
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Guo Li
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, China; Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Clinical Research Center for Laryngopharyngeal and Voice Disorders in Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Bingfei Yu
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wei Liao
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Yong Liu
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, China; Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Clinical Research Center for Laryngopharyngeal and Voice Disorders in Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xin Zhang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, China; Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Clinical Research Center for Laryngopharyngeal and Voice Disorders in Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yuanzheng Qiu
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, China; Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Clinical Research Center for Laryngopharyngeal and Voice Disorders in Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yue Li
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Ananda W Goldrath
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Chaoyu Ma
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Nu Zhang
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; South Texas Veterans Health Care System, San Antonio, TX 78229, USA.
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9
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Van Der Byl W, Nüssing S, Peters TJ, Ahn A, Li H, Ledergor G, David E, Koh AS, Wagle MV, Deguit CDT, de Menezes MN, Travers A, Sampurno S, Ramsbottom KM, Li R, Kallies A, Beavis PA, Jungmann R, Bastings MMC, Belz GT, Goel S, Trapani JA, Crabtree GR, Chang HY, Amit I, Goodnow CC, Luciani F, Parish IA. The CD8 + T cell tolerance checkpoint triggers a distinct differentiation state defined by protein translation defects. Immunity 2024; 57:1324-1344.e8. [PMID: 38776918 DOI: 10.1016/j.immuni.2024.04.026] [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: 05/15/2023] [Revised: 02/01/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Peripheral CD8+ T cell tolerance is a checkpoint in both autoimmune disease and anti-cancer immunity. Despite its importance, the relationship between tolerance-induced states and other CD8+ T cell differentiation states remains unclear. Using flow cytometric phenotyping, single-cell RNA sequencing (scRNA-seq), and chromatin accessibility profiling, we demonstrated that in vivo peripheral tolerance to a self-antigen triggered a fundamentally distinct differentiation state separate from exhaustion, memory, and functional effector cells but analogous to cells defectively primed against tumors. Tolerant cells diverged early and progressively from effector cells, adopting a transcriptionally and epigenetically distinct state within 60 h of antigen encounter. Breaching tolerance required the synergistic actions of strong T cell receptor (TCR) signaling and inflammation, which cooperatively induced gene modules that enhanced protein translation. Weak TCR signaling during bystander infection failed to breach tolerance due to the uncoupling of effector gene expression from protein translation. Thus, tolerance engages a distinct differentiation trajectory enforced by protein translation defects.
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Affiliation(s)
- Willem Van Der Byl
- The Kirby Institute for Infection and Immunity, UNSW, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, NSW, Australia
| | - Simone Nüssing
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Timothy J Peters
- Garvan Institute of Medical Research, Sydney, NSW, Australia; University of New South Wales Sydney, Sydney, NSW, Australia
| | - Antonio Ahn
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Hanjie Li
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Guy Ledergor
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Andrew S Koh
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Mayura V Wagle
- Garvan Institute of Medical Research, Sydney, NSW, Australia; John Curtin School of Medical Research, ANU, Canberra, ACT, Australia
| | | | - Maria N de Menezes
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Avraham Travers
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Shienny Sampurno
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Kelly M Ramsbottom
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Axel Kallies
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, Australia
| | - Paul A Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany; Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maartje M C Bastings
- Institute of Materials, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Interfaculty Bioengineering Institute, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gabrielle T Belz
- The Frazer Institute, The University of Queensland, Brisbane, QLD, Australia; Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Shom Goel
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Joseph A Trapani
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Gerald R Crabtree
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA; Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Chris C Goodnow
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, NSW, Australia; Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Fabio Luciani
- The Kirby Institute for Infection and Immunity, UNSW, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, NSW, Australia.
| | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia; John Curtin School of Medical Research, ANU, Canberra, ACT, Australia.
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10
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Lin D, Najam SS, Liu Y, Murgia N, Vinnikov IA. Noodles, the all-in-one system for on-target efficiency analysis of CRISPR guide RNAs. MethodsX 2024; 12:102481. [PMID: 38162150 PMCID: PMC10757036 DOI: 10.1016/j.mex.2023.102481] [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: 08/31/2023] [Accepted: 11/09/2023] [Indexed: 01/03/2024] Open
Abstract
The efficiency of clustered regularly interspaced short palindromic repeats (CRISPR) guide RNA (gRNA) targeting is critical for CRISPR associated protein 9 (Cas9)-dependent genomic modifications. Here, we developed Noodles, an all-in-one system to test the on-target activity of gRNAs easily and efficiently. Single-strand annealing repair mechanism of the split luciferase gene allows a positive selection of gRNAs efficiently driving nuclease activity of Cas9 from Streptococcus pyogenes (SpCas9). Our system can reliably validate in silico-predicted gRNAs before implementing them for in vitro and in vivo applications. Altogether, Noodles might be an asset for researchers and bioengineers, saving their time and efforts, while keeping the screening efficient and sensitive. •All-in-one dual-luciferase system to easily probe on-target activity of gRNAs based on homology-directed repair mechanism.•Easy-to-subclone spCas9-based 2-plasmid system comprising Renilla luciferase for transfection efficiency control.
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Affiliation(s)
- Dongfa Lin
- Key Laboratory for Molecular Enzymology and Engineering, School of Life Sciences, Jilin University, Changchun, China
- Laboratory of Molecular Neurobiology, Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Syeda Sadia Najam
- Laboratory of Molecular Neurobiology, Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Liu
- Laboratory of Molecular Neurobiology, Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Nicola Murgia
- Laboratory of Molecular Neurobiology, Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ilya A. Vinnikov
- Laboratory of Molecular Neurobiology, Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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11
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Xue G, Li X, Kalim M, Fang J, Jiang Z, Zheng N, Wang Z, Li X, Abdelrahim M, He Z, Nikiforov M, Jin G, Lu Y. Clinical drug screening reveals clofazimine potentiates the efficacy while reducing the toxicity of anti-PD-1 and CTLA-4 immunotherapy. Cancer Cell 2024; 42:780-796.e6. [PMID: 38518774 DOI: 10.1016/j.ccell.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 01/17/2024] [Accepted: 03/01/2024] [Indexed: 03/24/2024]
Abstract
Emerging as the most potent and durable combinational immunotherapy, dual anti-PD-1 and CTLA-4 immune checkpoint blockade (ICB) therapy notoriously increases grade 3-5 immune-related adverse events (irAEs) in patients. Accordingly, attempts to improve the antitumor potency of anti-PD-1+CTLA-4 ICB by including additional therapeutics have been largely discouraged due to concerns of further increasing fatal toxicity. Here, we screened ∼3,000 Food and Drug Administration (FDA)-approved drugs and identified clofazimine as a potential third agent to optimize anti-PD-1+CTLA-4 ICB. Remarkably, clofazimine outperforms ICB dose reduction or steroid treatment in reversing lethality of irAEs, but unlike the detrimental effect of steroids on antitumor efficacy, clofazimine potentiates curative responses in anti-PD-1+CTLA-4 ICB. Mechanistically, clofazimine promotes E2F1 activation in CD8+ T cells to overcome resistance and counteracts pathogenic Th17 cells to abolish irAEs. Collectively, clofazimine potentiates the antitumor efficacy of anti-PD-1+CTLA-4 ICB, curbs intractable irAEs, and may fill a desperate clinical need to improve patient survival.
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Affiliation(s)
- Gang Xue
- Comprehensive Cancer Center, Wake Forest Baptist Health, Winston-Salem, NC 27157, USA.
| | - Xin Li
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Muhammad Kalim
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Jing Fang
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Zhiwu Jiang
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Ningbo Zheng
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Ziyu Wang
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Xiaoyin Li
- Department of Mathematics and Statistics, St. Cloud State University, St Cloud, MN 56301, USA
| | - Maen Abdelrahim
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Zhiheng He
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA.
| | | | - Guangxu Jin
- Comprehensive Cancer Center, Wake Forest Baptist Health, Winston-Salem, NC 27157, USA.
| | - Yong Lu
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA.
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12
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Mittermüller D, Otto L, Kilian AL, Schnormeier AK, Littwitz-Salomon E, Hasenberg A, Dittmer U, Gunzer M. PD-1 knockout on cytotoxic primary murine CD8 + T cells improves their motility in retrovirus infected mice. Front Immunol 2024; 15:1338218. [PMID: 38742109 PMCID: PMC11089113 DOI: 10.3389/fimmu.2024.1338218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
Cytotoxic T lymphocyte (CTL) motility is an important feature of effective CTL responses and is impaired when CTLs become exhausted, e.g. during chronic retroviral infections. A prominent T cell exhaustion marker is programmed cell death protein 1 (PD-1) and antibodies against the interaction of PD-1 and PD-ligand 1 (PD-L1) are known to improve CTL functions. However, antibody blockade affects all PD-1/PD-L1-expressing cell types, thus, the observed effects cannot be attributed selectively to CTLs. To overcome this problem, we performed CRISPR/Cas9 based knockout of the PD-1 coding gene PDCD1 in naïve Friend Retrovirus (FV)-specific CTLs. We transferred 1,000 of these cells into mice where they proliferated upon FV-infection. Using intravital two-photon microscopy we visualized CTL motility in the bone marrow and evaluated cytotoxic molecule expression by flow cytometry. Knockout of PDCD1 improved the CTL motility at 14 days post infection and enhanced the expression of cytotoxicity markers. Our data show the potential of genetic tuning of naive antiviral CTLs and might be relevant for future designs of improved T cell-mediated therapies.
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Affiliation(s)
- Daniela Mittermüller
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute for Experimental Immunology and Imaging, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lucas Otto
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute for Experimental Immunology and Imaging, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Annika Loredana Kilian
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ann-Kathrin Schnormeier
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Elisabeth Littwitz-Salomon
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV and AIDS-Associated Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Anja Hasenberg
- Institute for Experimental Immunology and Imaging, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV and AIDS-Associated Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Matthias Gunzer
- Institute for Experimental Immunology and Imaging, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Leibniz-Institut für Analytische Wissenschaften - ISAS-e.V., Dortmund, Germany
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13
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Djajawi TM, Wichmann J, Vervoort SJ, Kearney CJ. Tumor immune evasion: insights from CRISPR screens and future directions. FEBS J 2024; 291:1386-1399. [PMID: 37971319 DOI: 10.1111/febs.17003] [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: 09/03/2023] [Revised: 11/02/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Despite the clinical success of cancer immunotherapies including immune checkpoint blockade and adoptive cellular therapies across a variety of cancer types, many patients do not respond or ultimately relapse; however, the molecular underpinnings of this are not fully understood. Thus, a system-level understating of the routes to tumor immune evasion is required to inform the design of the next generation of immunotherapy approaches. CRISPR screening approaches have proved extremely powerful in identifying genes that promote tumor immune evasion or sensitize tumor cells to destruction by the immune system. These large-scale efforts have brought to light decades worth of fundamental immunology and have uncovered the key immune-evasion pathways subverted in cancers in an acquired manner in patients receiving immune-modulatory therapies. The comprehensive discovery of the main pathways involved in immune evasion has spurred the development and application of novel immune therapies to target this process. Although successful, conventional CRISPR screening approaches are hampered by a number of limitations, which obfuscate a complete understanding of the precise molecular regulation of immune evasion in cancer. Here, we provide a perspective on screening approaches to interrogate tumor-lymphocyte interactions and their limitations, and discuss further development of technologies to improve such approaches and discovery capability.
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Affiliation(s)
- Tirta Mario Djajawi
- Olivia Newton-John Cancer Research Institute, Heidelberg, Vic., Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Vic., Australia
| | - Johannes Wichmann
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Stephin J Vervoort
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Conor J Kearney
- Olivia Newton-John Cancer Research Institute, Heidelberg, Vic., Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Vic., Australia
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14
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May JF, Kelly RG, Suen AYW, Kim J, Kim J, Anderson CC, Rayat GR, Baldwin TA. Establishment of CD8+ T Cell Thymic Central Tolerance to Tissue-Restricted Antigen Requires PD-1. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:271-283. [PMID: 37982696 DOI: 10.4049/jimmunol.2200775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/02/2023] [Indexed: 11/21/2023]
Abstract
Highly self-reactive T cells are censored from the repertoire by both central and peripheral tolerance mechanisms upon receipt of high-affinity TCR signals. Clonal deletion is considered a major driver of central tolerance; however, other mechanisms such as induction of regulatory T cells and functional impairment have been described. An understanding of the interplay between these different central tolerance mechanisms is still lacking. We previously showed that impaired clonal deletion to a model tissue-restricted Ag did not compromise tolerance. In this study, we determined that murine T cells that failed clonal deletion were rendered functionally impaired in the thymus. Programmed cell death protein 1 (PD-1) was induced in the thymus and was required to establish cell-intrinsic tolerance to tissue-restricted Ag in CD8+ thymocytes independently of clonal deletion. In bone marrow chimeras, tolerance was not observed in PD-L1-deficient recipients, but tolerance was largely maintained following adoptive transfer of tolerant thymocytes or T cells to PD-L1-deficient recipients. However, CRISPR-mediated ablation of PD-1 in tolerant T cells resulted in broken tolerance, suggesting different PD-1 signaling requirements for establishing versus maintaining tolerance. Finally, we showed that chronic exposure to high-affinity Ag supported the long-term maintenance of tolerance. Taken together, our study identifies a critical role for PD-1 in establishing central tolerance in autoreactive T cells that escape clonal deletion. It also sheds light on potential mechanisms of action of anti-PD-1 pathway immune checkpoint blockade and the development of immune-related adverse events.
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Affiliation(s)
- Julia F May
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Rees G Kelly
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Alexander Y W Suen
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Jeongbee Kim
- Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Jeongwoo Kim
- Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Colin C Anderson
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
- Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Gina R Rayat
- Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
- Ray Rajotte Surgical-Medical Research Institute, AB Diabetes and Transplant Institutes, University of Alberta, Edmonton, Alberta, Canada
| | - Troy A Baldwin
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
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15
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Ito Y, Inoue S, Nakashima T, Zhang H, Li Y, Kasuya H, Matsukawa T, Wu Z, Yoshikawa T, Kataoka M, Ishikawa T, Kagoya Y. Epigenetic profiles guide improved CRISPR/Cas9-mediated gene knockout in human T cells. Nucleic Acids Res 2024; 52:141-153. [PMID: 37985205 PMCID: PMC10783505 DOI: 10.1093/nar/gkad1076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/22/2023] Open
Abstract
Genetic modification of specific genes is emerging as a useful tool to enhance the functions of antitumor T cells in adoptive immunotherapy. Current advances in CRISPR/Cas9 technology enable gene knockout during in vitro preparation of infused T-cell products through transient transfection of a Cas9-guide RNA (gRNA) ribonucleoprotein complex. However, selecting optimal gRNAs remains a major challenge for efficient gene ablation. Although multiple in silico tools to predict the targeting efficiency have been developed, their performance has not been validated in cultured human T cells. Here, we explored a strategy to select optimal gRNAs using our pooled data on CRISPR/Cas9-mediated gene knockout in human T cells. The currently available prediction tools alone were insufficient to accurately predict the indel percentage in T cells. We used data on the epigenetic profiles of cultured T cells obtained from transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Combining the epigenetic information with sequence-based prediction tools significantly improved the gene-editing efficiency. We further demonstrate that epigenetically closed regions can be targeted by designing two gRNAs in adjacent regions. Finally, we demonstrate that the gene-editing efficiency of unstimulated T cells can be enhanced through pretreatment with IL-7. These findings enable more efficient gene editing in human T cells.
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Affiliation(s)
- Yusuke Ito
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Satoshi Inoue
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Takahiro Nakashima
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Haosong Zhang
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yang Li
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hitomi Kasuya
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Tetsuya Matsukawa
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Zhiwen Wu
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Toshiaki Yoshikawa
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Mirei Kataoka
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - Tetsuo Ishikawa
- Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Yokohama, Japan
- Collective Intelligence Research Laboratory, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuki Kagoya
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
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16
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Helms RS, Marin-Gonzalez A, Patel CH, Sun IH, Wen J, Leone RD, Duvall B, Gao RD, Ha T, Tsukamoto T, Slusher BS, Pomerantz JL, Powell JD. SIKs Regulate HDAC7 Stabilization and Cytokine Recall in Late-Stage T Cell Effector Differentiation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1767-1782. [PMID: 37947442 PMCID: PMC10842463 DOI: 10.4049/jimmunol.2300248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/05/2023] [Indexed: 11/12/2023]
Abstract
Understanding the mechanisms underlying the acquisition and maintenance of effector function during T cell differentiation is important to unraveling how these processes can be dysregulated in the context of disease and manipulated for therapeutic intervention. In this study, we report the identification of a previously unappreciated regulator of murine T cell differentiation through the evaluation of a previously unreported activity of the kinase inhibitor, BioE-1197. Specifically, we demonstrate that liver kinase B1 (LKB1)-mediated activation of salt-inducible kinases epigenetically regulates cytokine recall potential in effector CD8+ and Th1 cells. Evaluation of this phenotype revealed that salt-inducible kinase-mediated phosphorylation-dependent stabilization of histone deacetylase 7 (HDAC7) occurred during late-stage effector differentiation. HDAC7 stabilization increased nuclear HDAC7 levels, which correlated with total and cytokine loci-specific reductions in the activating transcription mark histone 3 lysine 27 acetylation (H3K27Ac). Accordingly, HDAC7 stabilization diminished transcriptional induction of cytokine genes upon restimulation. Inhibition of this pathway during differentiation produced effector T cells epigenetically poised for enhanced cytokine recall. This work identifies a previously unrecognized target for enhancing effector T cell functionality.
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Affiliation(s)
- Rachel S. Helms
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alberto Marin-Gonzalez
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Chirag H. Patel
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Im-Hong Sun
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jiayu Wen
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert D. Leone
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Run-Duo Gao
- Johns Hopkins Drug Discovery, Baltimore, MD, USA
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Taekjip Ha
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Takashi Tsukamoto
- Johns Hopkins Drug Discovery, Baltimore, MD, USA
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Barbara S. Slusher
- Johns Hopkins Drug Discovery, Baltimore, MD, USA
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joel L. Pomerantz
- Department of Biological Chemistry, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- These authors contributed equally to this work
| | - Jonathan D. Powell
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Calico Life Sciences LLC, South San Francisco, CA, USA
- These authors contributed equally to this work
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17
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Meibers HE, Warrick KA, VonHandorf A, Vallez CN, Kawarizadeh K, Saha I, Donmez O, Jain VG, Kottyan LC, Weirauch MT, Pasare C. Effector memory T cells induce innate inflammation by triggering DNA damage and a non-canonical STING pathway in dendritic cells. Cell Rep 2023; 42:113180. [PMID: 37794597 PMCID: PMC10654673 DOI: 10.1016/j.celrep.2023.113180] [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: 05/30/2023] [Revised: 08/09/2023] [Accepted: 09/12/2023] [Indexed: 10/06/2023] Open
Abstract
Cognate interaction between CD4+ effector memory T (TEM) cells and dendritic cells (DCs) induces innate inflammatory cytokine production, resulting in detrimental autoimmune pathology and cytokine storms. While TEM cells use tumor necrosis factor (TNF) superfamily ligands to activate DCs, whether TEM cells prompt other DC-intrinsic changes that influence the innate inflammatory response has never been investigated. We report the surprising discovery that TEM cells trigger double-strand DNA breaks via mitochondrial reactive oxygen species (ROS) production in interacting DCs. Initiation of the DNA damage response in DCs induces activation of a cyclic guanosine monophosphate (GMP)-AMP synthase (cGAS)-independent, non-canonical stimulator of interferon genes (STING)-TNF receptor-associated factor 6 (TRAF6)-nuclear factor κB (NF-κB) signaling axis. Consequently, STING-deficient DCs display reduced NF-κB activation and subsequent defects in transcriptional induction and functional production of interleukin-1β (IL-1β) and IL-6 following their interaction with TEM cells. The discovery of TEM cell-induced innate inflammation through DNA damage and a non-canonical STING-NF-κB pathway presents this pathway as a potential target to alleviate T cell-driven inflammation in autoimmunity and cytokine storms.
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Affiliation(s)
- Hannah E Meibers
- Immunology Graduate Program, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH 45229, USA; Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kathrynne A Warrick
- Immunology Graduate Program, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH 45229, USA; Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrew VonHandorf
- Center for Autoimmune Genetics and Etiology and Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Charles N Vallez
- Immunology Graduate Program, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH 45229, USA; Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kiana Kawarizadeh
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Irene Saha
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Omer Donmez
- Center for Autoimmune Genetics and Etiology and Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Viral G Jain
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Leah C Kottyan
- Center for Autoimmune Genetics and Etiology and Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45267, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genetics and Etiology and Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45267, USA
| | - Chandrashekhar Pasare
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45267, USA.
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18
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Globig AM, Zhao S, Roginsky J, Maltez VI, Guiza J, Avina-Ochoa N, Heeg M, Araujo Hoffmann F, Chaudhary O, Wang J, Senturk G, Chen D, O'Connor C, Pfaff S, Germain RN, Schalper KA, Emu B, Kaech SM. The β 1-adrenergic receptor links sympathetic nerves to T cell exhaustion. Nature 2023; 622:383-392. [PMID: 37731001 PMCID: PMC10871066 DOI: 10.1038/s41586-023-06568-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 08/24/2023] [Indexed: 09/22/2023]
Abstract
CD8+ T cells are essential components of the immune response against viral infections and tumours, and are capable of eliminating infected and cancerous cells. However, when the antigen cannot be cleared, T cells enter a state known as exhaustion1. Although it is clear that chronic antigen contributes to CD8+ T cell exhaustion, less is known about how stress responses in tissues regulate T cell function. Here we show a new link between the stress-associated catecholamines and the progression of T cell exhaustion through the β1-adrenergic receptor ADRB1. We identify that exhausted CD8+ T cells increase ADRB1 expression and that exposure of ADRB1+ T cells to catecholamines suppresses their cytokine production and proliferation. Exhausted CD8+ T cells cluster around sympathetic nerves in an ADRB1-dependent manner. Ablation of β1-adrenergic signalling limits the progression of T cells towards the exhausted state in chronic infection and improves effector functions when combined with immune checkpoint blockade (ICB) in melanoma. In a pancreatic cancer model resistant to ICB, β-blockers and ICB synergize to boost CD8+ T cell responses and induce the development of tissue-resident memory-like T cells. Malignant disease is associated with increased catecholamine levels in patients2,3, and our results establish a connection between the sympathetic stress response, tissue innervation and T cell exhaustion. Here, we uncover a new mechanism by which blocking β-adrenergic signalling in CD8+ T cells rejuvenates anti-tumour functions.
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Affiliation(s)
- Anna-Maria Globig
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Steven Zhao
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jessica Roginsky
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Vivien I Maltez
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Juan Guiza
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Natalia Avina-Ochoa
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Maximilian Heeg
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Filipe Araujo Hoffmann
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Omkar Chaudhary
- Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Jiawei Wang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Gokhan Senturk
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Dan Chen
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Carolyn O'Connor
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
- Flow Cytometry Core Facility, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Samuel Pfaff
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Kurt A Schalper
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Brinda Emu
- Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA.
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19
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Allemailem KS, Alsahli MA, Almatroudi A, Alrumaihi F, Al Abdulmonem W, Moawad AA, Alwanian WM, Almansour NM, Rahmani AH, Khan AA. Innovative Strategies of Reprogramming Immune System Cells by Targeting CRISPR/Cas9-Based Genome-Editing Tools: A New Era of Cancer Management. Int J Nanomedicine 2023; 18:5531-5559. [PMID: 37795042 PMCID: PMC10547015 DOI: 10.2147/ijn.s424872] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/16/2023] [Indexed: 10/06/2023] Open
Abstract
The recent developments in the study of clustered regularly interspaced short palindromic repeats/associated protein 9 (CRISPR/Cas9) system have revolutionized the art of genome-editing and its applications for cellular differentiation and immune response behavior. This technology has further helped in understanding the mysteries of cancer progression and possible designing of novel antitumor immunotherapies. CRISPR/Cas9-based genome-editing is now often used to engineer universal T-cells, equipped with recombinant T-cell receptor (TCR) or chimeric antigen receptor (CAR). In addition, this technology is used in cytokine stimulation, antibody designing, natural killer (NK) cell transfer, and to overcome immune checkpoints. The innovative potential of CRISPR/Cas9 in preparing the building blocks of adoptive cell transfer (ACT) immunotherapy has opened a new window of antitumor immunotherapy and some of them have gained FDA approval. The manipulation of immunogenetic regulators has opened a new interface for designing, implementation and interpretation of CRISPR/Cas9-based screening in immuno-oncology. Several cancers like lymphoma, melanoma, lung, and liver malignancies have been treated with this strategy, once thought to be impossible. The safe and efficient delivery of CRISPR/Cas9 system within the immune cells for the genome-editing strategy is a challenging task which needs to be sorted out for efficient immunotherapy. Several targeting approaches like virus-mediated, electroporation, microinjection and nanoformulation-based methods have been used, but each procedure offers some limitations. Here, we elaborate the recent updates of cancer management through immunotherapy in partnership with CRISPR/Cas9 technology. Further, some innovative methods of targeting this genome-editing system within the immune system cells for reprogramming them, as a novel strategy of anticancer immunotherapy is elaborated. In addition, future prospects and clinical trials are also discussed.
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Affiliation(s)
- Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Mohammed A Alsahli
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Amira A Moawad
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Wanian M Alwanian
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Nahlah Makki Almansour
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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20
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Heidarian M, Jensen IJ, Kannan SK, Pewe LL, Hassert M, Park S, Xue HH, Harty JT, Badovinac VP. Sublethal whole-body irradiation induces permanent loss and dysfunction in pathogen-specific circulating memory CD8 T cell populations. Proc Natl Acad Sci U S A 2023; 120:e2302785120. [PMID: 37364124 PMCID: PMC10318958 DOI: 10.1073/pnas.2302785120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
The increasing use of nuclear energy sources inevitably raises the risk of accidental or deliberate radiation exposure and associated immune dysfunction. However, the extent to which radiation exposure impacts memory CD8 T cells, potent mediators of immunity to recurring intracellular infections and malignancies, remains understudied. Using P14 CD8 T cell chimeric mice (P14 chimeras) with an lymphocytic choriomeningitis virus (LCMV) infection model, we observed that sublethal (5Gy) whole-body irradiation (WBI) induced a rapid decline in the number of naive (TN) and P14 circulating memory CD8 T cells (TCIRCM), with the former being more susceptible to radiation-induced numeric loss. While TN cell numbers rapidly recovered, as previously described, the number of P14 TCIRCM cells remained low at least 9 mo after radiation exposure. Additionally, the remaining P14 TCIRCM in irradiated hosts exhibited an inefficient transition to a central memory (CD62L+) phenotype compared to nonirradiated P14 chimeras. WBI also resulted in long-lasting T cell intrinsic deficits in memory CD8 T cells, including diminished cytokine and chemokine production along with impaired secondary expansion upon cognate Ag reencounter. Irradiated P14 chimeras displayed significantly higher bacterial burden after challenge with Listeria monocytogenes expressing the LCMV GP33-41 epitope relative to nonirradiated controls, likely due to radiation-induced numerical and functional impairments. Taken together, our findings suggest that sublethal radiation exposure caused a long-term numerical, impaired differentiation, and functional dysregulation in preexisting TCIRCM, rendering previously protected hosts susceptible to reinfection.
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Affiliation(s)
| | - Isaac J. Jensen
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA52246
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY10032
| | - Shravan Kumar Kannan
- Department of Pathology, University of Iowa, Iowa City, IA52246
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA52246
| | - Lecia L. Pewe
- Department of Pathology, University of Iowa, Iowa City, IA52246
| | - Mariah Hassert
- Department of Pathology, University of Iowa, Iowa City, IA52246
| | - SungRye Park
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ07110
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ07110
| | - John T. Harty
- Department of Pathology, University of Iowa, Iowa City, IA52246
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA52246
| | - Vladimir P. Badovinac
- Department of Pathology, University of Iowa, Iowa City, IA52246
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA52246
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21
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Damo M, Hornick NI, Venkat A, William I, Clulo K, Venkatesan S, He J, Fagerberg E, Loza JL, Kwok D, Tal A, Buck J, Cui C, Singh J, Damsky WE, Leventhal JS, Krishnaswamy S, Joshi NS. PD-1 maintains CD8 T cell tolerance towards cutaneous neoantigens. Nature 2023; 619:151-159. [PMID: 37344588 PMCID: PMC10989189 DOI: 10.1038/s41586-023-06217-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 05/12/2023] [Indexed: 06/23/2023]
Abstract
The peripheral T cell repertoire of healthy individuals contains self-reactive T cells1,2. Checkpoint receptors such as PD-1 are thought to enable the induction of peripheral tolerance by deletion or anergy of self-reactive CD8 T cells3-10. However, this model is challenged by the high frequency of immune-related adverse events in patients with cancer who have been treated with checkpoint inhibitors11. Here we developed a mouse model in which skin-specific expression of T cell antigens in the epidermis caused local infiltration of antigen-specific CD8 T cells with an effector gene-expression profile. In this setting, PD-1 enabled the maintenance of skin tolerance by preventing tissue-infiltrating antigen-specific effector CD8 T cells from (1) acquiring a fully functional, pathogenic differentiation state, (2) secreting significant amounts of effector molecules, and (3) gaining access to epidermal antigen-expressing cells. In the absence of PD-1, epidermal antigen-expressing cells were eliminated by antigen-specific CD8 T cells, resulting in local pathology. Transcriptomic analysis of skin biopsies from two patients with cutaneous lichenoid immune-related adverse events showed the presence of clonally expanded effector CD8 T cells in both lesional and non-lesional skin. Thus, our data support a model of peripheral T cell tolerance in which PD-1 allows antigen-specific effector CD8 T cells to co-exist with antigen-expressing cells in tissues without immunopathology.
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Affiliation(s)
- Martina Damo
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Noah I Hornick
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Aarthi Venkat
- Departments of Genetics and of Computer Science, Yale University School of Medicine, New Haven, CT, USA
| | - Ivana William
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Kathryn Clulo
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Srividhya Venkatesan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jiaming He
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Fagerberg
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jennifer L Loza
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Darwin Kwok
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Aya Tal
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jessica Buck
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Can Cui
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jaiveer Singh
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - William E Damsky
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Jonathan S Leventhal
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Smita Krishnaswamy
- Departments of Genetics and of Computer Science, Yale University School of Medicine, New Haven, CT, USA
| | - Nikhil S Joshi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
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22
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Kharel A, Shen J, Brown R, Chen Y, Nguyen C, Alson D, Bluemn T, Fan J, Gai K, Zhang B, Kudek M, Zhu N, Cui W. Loss of PBAF promotes expansion and effector differentiation of CD8 + T cells during chronic viral infection and cancer. Cell Rep 2023; 42:112649. [PMID: 37330910 PMCID: PMC10592487 DOI: 10.1016/j.celrep.2023.112649] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/10/2023] [Accepted: 05/30/2023] [Indexed: 06/20/2023] Open
Abstract
During chronic viral infection and cancer, it has been established that a subset of progenitor CD8+ T cells continuously gives rise to terminally exhausted cells and cytotoxic effector cells. Although multiple transcriptional programs governing the bifurcated differentiation trajectories have been previously studied, little is known about the chromatin structure changes regulating CD8+ T cell-fate decision. In this study, we demonstrate that the chromatin remodeling complex PBAF restrains expansion and promotes exhaustion of CD8+ T cells during chronic viral infection and cancer. Mechanistically, transcriptomic and epigenomic analyses reveal the role of PBAF in maintaining chromatin accessibility of multiple genetic pathways and transcriptional programs to restrain proliferation and promote T cell exhaustion. Harnessing this knowledge, we demonstrate that perturbation of PBAF complex constrained exhaustion and promoted expansion of tumor-specific CD8+ T cells resulting in antitumor immunity in a preclinical melanoma model, implicating PBAF as an attractive target for cancer immunotherapeutic.
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Affiliation(s)
- Arjun Kharel
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jian Shen
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ryan Brown
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yao Chen
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Christine Nguyen
- Blood Research Institute, Versiti, Milwaukee, WI, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Donia Alson
- Blood Research Institute, Versiti, Milwaukee, WI, USA
| | - Theresa Bluemn
- Blood Research Institute, Versiti, Milwaukee, WI, USA; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jie Fan
- Department of Medicine/Hematology and Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Kexin Gai
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bin Zhang
- Department of Medicine/Hematology and Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Microbiology-Immunology, Northwestern University, Chicago, IL, USA
| | - Matthew Kudek
- Blood Research Institute, Versiti, Milwaukee, WI, USA
| | - Nan Zhu
- Blood Research Institute, Versiti, Milwaukee, WI, USA; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Weiguo Cui
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Blood Research Institute, Versiti, Milwaukee, WI, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.
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23
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Baxter AE, Huang H, Giles JR, Chen Z, Wu JE, Drury S, Dalton K, Park SL, Torres L, Simone BW, Klapholz M, Ngiow SF, Freilich E, Manne S, Alcalde V, Ekshyyan V, Berger SL, Shi J, Jordan MS, Wherry EJ. The SWI/SNF chromatin remodeling complexes BAF and PBAF differentially regulate epigenetic transitions in exhausted CD8 + T cells. Immunity 2023; 56:1320-1340.e10. [PMID: 37315535 DOI: 10.1016/j.immuni.2023.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/28/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023]
Abstract
CD8+ T cell exhaustion (Tex) limits disease control during chronic viral infections and cancer. Here, we investigated the epigenetic factors mediating major chromatin-remodeling events in Tex-cell development. A protein-domain-focused in vivo CRISPR screen identified distinct functions for two versions of the SWI/SNF chromatin-remodeling complex in Tex-cell differentiation. Depletion of the canonical SWI/SNF form, BAF, impaired initial CD8+ T cell responses in acute and chronic infection. In contrast, disruption of PBAF enhanced Tex-cell proliferation and survival. Mechanistically, PBAF regulated the epigenetic and transcriptional transition from TCF-1+ progenitor Tex cells to more differentiated TCF-1- Tex subsets. Whereas PBAF acted to preserve Tex progenitor biology, BAF was required to generate effector-like Tex cells, suggesting that the balance of these factors coordinates Tex-cell subset differentiation. Targeting PBAF improved tumor control both alone and in combination with anti-PD-L1 immunotherapy. Thus, PBAF may present a therapeutic target in cancer immunotherapy.
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Affiliation(s)
- Amy E Baxter
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hua Huang
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Josephine R Giles
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zeyu Chen
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jennifer E Wu
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sydney Drury
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Katherine Dalton
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Simone L Park
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Leonel Torres
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Brandon W Simone
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Max Klapholz
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Radiation Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shin Foong Ngiow
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Elizabeth Freilich
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sasikanth Manne
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Victor Alcalde
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Viktoriya Ekshyyan
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Junwei Shi
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Martha S Jordan
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - E John Wherry
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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24
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Kurzhagen JT, Noel S, Lee K, Sadasivam M, Gharaie S, Ankireddy A, Lee SA, Newman-Rivera A, Gong J, Arend LJ, Hamad AR, Reddy SP, Rabb H. T Cell Nrf2/Keap1 Gene Editing Using CRISPR/Cas9 and Experimental Kidney Ischemia-Reperfusion Injury. Antioxid Redox Signal 2023; 38:959-973. [PMID: 36734409 PMCID: PMC10171956 DOI: 10.1089/ars.2022.0058] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 12/21/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023]
Abstract
Aims: T cells play pathophysiologic roles in kidney ischemia-reperfusion injury (IRI), and the nuclear factor erythroid 2-related factor 2/kelch-like ECH-associated protein 1 (Nrf2/Keap1) pathway regulates T cell responses. We hypothesized that clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated Keap1-knockout (KO) augments Nrf2 antioxidant potential of CD4+ T cells, and that Keap1-KO CD4+ T cell immunotherapy protects from kidney IRI. Results: CD4+ T cell Keap1-KO resulted in significant increase of Nrf2 target genes NAD(P)H quinone dehydrogenase 1, heme oxygenase 1, glutamate-cysteine ligase catalytic subunit, and glutamate-cysteine ligase modifier subunit. Keap1-KO cells displayed no signs of exhaustion, and had significantly lower levels of interleukin 2 (IL2) and IL6 in normoxic conditions, but increased interferon gamma in hypoxic conditions in vitro. In vivo, adoptive transfer of Keap1-KO CD4+ T cells before IRI improved kidney function in T cell-deficient nu/nu mice compared with mice receiving unedited control CD4+ T cells. Keap1-KO CD4+ T cells isolated from recipient kidneys 24 h post IR were less activated compared with unedited CD4+ T cells, isolated from control kidneys. Innovation: Editing Nrf2/Keap1 pathway in murine T cells using CRISPR/Cas9 is an innovative and promising immunotherapy approach for kidney IRI and possibly other solid organ IRI. Conclusion: CRISPR/Cas9-mediated Keap1-KO increased Nrf2-regulated antioxidant gene expression in murine CD4+ T cells, modified responses to in vitro hypoxia and in vivo kidney IRI. Gene editing targeting the Nrf2/Keap1 pathway in T cells is a promising approach for immune-mediated kidney diseases.
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Affiliation(s)
- Johanna T. Kurzhagen
- Division of Nephrology and Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sanjeev Noel
- Division of Nephrology and Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kyungho Lee
- Division of Nephrology and Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mohanraj Sadasivam
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sepideh Gharaie
- Division of Nephrology and Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Aparna Ankireddy
- Department of Pediatrics, University of Illinois, Chicago, Illinois, USA
| | - Sul A. Lee
- Division of Nephrology and Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrea Newman-Rivera
- Division of Nephrology and Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jing Gong
- Division of Nephrology and Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lois J. Arend
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Abdel R.A. Hamad
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sekhar P. Reddy
- Department of Pediatrics, University of Illinois, Chicago, Illinois, USA
- Department of Pathology, and University of Illinois, Chicago, Illinois, USA
- University of Illinois Cancer Center, University of Illinois, Chicago, Illinois, USA
| | - Hamid Rabb
- Division of Nephrology and Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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25
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Tsai HC, Pietrobon V, Peng M, Wang S, Zhao L, Marincola FM, Cai Q. Current strategies employed in the manipulation of gene expression for clinical purposes. J Transl Med 2022; 20:535. [PMID: 36401279 PMCID: PMC9673226 DOI: 10.1186/s12967-022-03747-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
Abstract
Abnormal gene expression level or expression of genes containing deleterious mutations are two of the main determinants which lead to genetic disease. To obtain a therapeutic effect and thus to cure genetic diseases, it is crucial to regulate the host's gene expression and restore it to physiological conditions. With this purpose, several molecular tools have been developed and are currently tested in clinical trials. Genome editing nucleases are a class of molecular tools routinely used in laboratories to rewire host's gene expression. Genome editing nucleases include different categories of enzymes: meganucleses (MNs), zinc finger nucleases (ZFNs), clustered regularly interspaced short palindromic repeats (CRISPR)- CRISPR associated protein (Cas) and transcription activator-like effector nuclease (TALENs). Transposable elements are also a category of molecular tools which includes different members, for example Sleeping Beauty (SB), PiggyBac (PB), Tol2 and TcBuster. Transposons have been used for genetic studies and can serve as gene delivery tools. Molecular tools to rewire host's gene expression also include episomes, which are divided into different categories depending on their molecular structure. Finally, RNA interference is commonly used to regulate gene expression through the administration of small interfering RNA (siRNA), short hairpin RNA (shRNA) and bi-functional shRNA molecules. In this review, we will describe the different molecular tools that can be used to regulate gene expression and discuss their potential for clinical applications. These molecular tools are delivered into the host's cells in the form of DNA, RNA or protein using vectors that can be grouped into physical or biochemical categories. In this review we will also illustrate the different types of payloads that can be used, and we will discuss recent developments in viral and non-viral vector technology.
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Affiliation(s)
| | | | - Maoyu Peng
- Kite Pharma Inc, Santa Monica, CA, 90404, USA
| | - Suning Wang
- Kite Pharma Inc, Santa Monica, CA, 90404, USA
| | - Lihong Zhao
- Kite Pharma Inc, Santa Monica, CA, 90404, USA
| | | | - Qi Cai
- Kite Pharma Inc, Santa Monica, CA, 90404, USA.
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26
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Giles JR, Ngiow SF, Manne S, Baxter AE, Khan O, Wang P, Staupe R, Abdel-Hakeem MS, Huang H, Mathew D, Painter MM, Wu JE, Huang YJ, Goel RR, Yan PK, Karakousis GC, Xu X, Mitchell TC, Huang AC, Wherry EJ. Shared and distinct biological circuits in effector, memory and exhausted CD8 + T cells revealed by temporal single-cell transcriptomics and epigenetics. Nat Immunol 2022; 23:1600-1613. [PMID: 36271148 PMCID: PMC10408358 DOI: 10.1038/s41590-022-01338-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 09/13/2022] [Indexed: 01/13/2023]
Abstract
Naïve CD8+ T cells can differentiate into effector (Teff), memory (Tmem) or exhausted (Tex) T cells. These developmental pathways are associated with distinct transcriptional and epigenetic changes that endow cells with different functional capacities and therefore therapeutic potential. The molecular circuitry underlying these developmental trajectories and the extent of heterogeneity within Teff, Tmem and Tex populations remain poorly understood. Here, we used the lymphocytic choriomeningitis virus model of acute-resolving and chronic infection to address these gaps by applying longitudinal single-cell RNA-sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) analyses. These analyses uncovered new subsets, including a subpopulation of Tex cells expressing natural killer cell-associated genes that is dependent on the transcription factor Zeb2, as well as multiple distinct TCF-1+ stem/progenitor-like subsets in acute and chronic infection. These data also revealed insights into the reshaping of Tex subsets following programmed death 1 (PD-1) pathway blockade and identified a key role for the cell stress regulator, Btg1, in establishing the Tex population. Finally, these results highlighted how the same biological circuits such as cytotoxicity or stem/progenitor pathways can be used by CD8+ T cell subsets with highly divergent underlying chromatin landscapes generated during different infections.
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Affiliation(s)
- Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shin Foong Ngiow
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sasikanth Manne
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy E Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Omar Khan
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ping Wang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan Staupe
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Infectious Disease & Vaccines, MRL, Merck & Co. Inc., West Point, PA, USA
| | - Mohamed S Abdel-Hakeem
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Hua Huang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Divij Mathew
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark M Painter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer E Wu
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yinghui Jane Huang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rishi R Goel
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick K Yan
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Immunology Graduate Program, Stanford University, Stanford, CA, USA
| | | | - Xiaowei Xu
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Tara C Mitchell
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander C Huang
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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27
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Tsui C, Kretschmer L, Rapelius S, Gabriel SS, Chisanga D, Knöpper K, Utzschneider DT, Nüssing S, Liao Y, Mason T, Torres SV, Wilcox SA, Kanev K, Jarosch S, Leube J, Nutt SL, Zehn D, Parish IA, Kastenmüller W, Shi W, Buchholz VR, Kallies A. MYB orchestrates T cell exhaustion and response to checkpoint inhibition. Nature 2022; 609:354-360. [PMID: 35978192 PMCID: PMC9452299 DOI: 10.1038/s41586-022-05105-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 07/13/2022] [Indexed: 12/29/2022]
Abstract
CD8+ T cells that respond to chronic viral infections or cancer are characterized by the expression of inhibitory receptors such as programmed cell death protein 1 (PD-1) and by the impaired production of cytokines. This state of restrained functionality—which is referred to as T cell exhaustion1,2—is maintained by precursors of exhausted T (TPEX) cells that express the transcription factor T cell factor 1 (TCF1), self-renew and give rise to TCF1− exhausted effector T cells3–6. Here we show that the long-term proliferative potential, multipotency and repopulation capacity of exhausted T cells during chronic infection are selectively preserved in a small population of transcriptionally distinct CD62L+ TPEX cells. The transcription factor MYB is not only essential for the development of CD62L+ TPEX cells and maintenance of the antiviral CD8+ T cell response, but also induces functional exhaustion and thereby prevents lethal immunopathology. Furthermore, the proliferative burst in response to PD-1 checkpoint inhibition originates exclusively from CD62L+ TPEX cells and depends on MYB. Our findings identify CD62L+ TPEX cells as a stem-like population that is central to the maintenance of long-term antiviral immunity and responsiveness to immunotherapy. Moreover, they show that MYB is a transcriptional orchestrator of two fundamental aspects of exhausted T cell responses: the downregulation of effector function and the long-term preservation of self-renewal capacity. CD62L+ precursors of exhausted T cells retain long-term proliferative potential, multipotency and repopulation capacity, and the transcription factor MYB is essential for the development and function of this population of cells.
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Affiliation(s)
- Carlson Tsui
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Lorenz Kretschmer
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Svenja Rapelius
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Sarah S Gabriel
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - David Chisanga
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia.,The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Konrad Knöpper
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Daniel T Utzschneider
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Simone Nüssing
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Yang Liao
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia.,The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Teisha Mason
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Santiago Valle Torres
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen A Wilcox
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Krystian Kanev
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Justin Leube
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Dietmar Zehn
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Ian A Parish
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Wolfgang Kastenmüller
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Wei Shi
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia.,The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany.
| | - Axel Kallies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
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28
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Lelliott EJ, Ramsbottom KM, Dowling MR, Shembrey C, Noori T, Kearney CJ, Michie J, Parish IA, Jordan MA, Baxter AG, Young ND, Brennan AJ, Oliaro J. NKG7 Enhances CD8+ T Cell Synapse Efficiency to Limit Inflammation. Front Immunol 2022; 13:931630. [PMID: 35874669 PMCID: PMC9299089 DOI: 10.3389/fimmu.2022.931630] [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: 04/29/2022] [Accepted: 06/06/2022] [Indexed: 12/01/2022] Open
Abstract
Cytotoxic lymphocytes are essential for anti-tumor immunity, and for effective responses to cancer immunotherapy. Natural killer cell granule protein 7 (NKG7) is expressed at high levels in cytotoxic lymphocytes infiltrating tumors from patients treated with immunotherapy, but until recently, the role of this protein in cytotoxic lymphocyte function was largely unknown. Unexpectedly, we found that highly CD8+ T cell-immunogenic murine colon carcinoma (MC38-OVA) tumors grew at an equal rate in Nkg7+/+ and Nkg7-/- littermate mice, suggesting NKG7 may not be necessary for effective CD8+ T cell anti-tumor activity. Mechanistically, we found that deletion of NKG7 reduces the ability of CD8+ T cells to degranulate and kill target cells in vitro. However, as a result of inefficient cytotoxic activity, NKG7 deficient T cells form a prolonged immune synapse with tumor cells, resulting in increased secretion of inflammatory cytokines, including tumor necrosis factor alpha (TNF). By deleting the TNF receptor, TNFR1, from MC38-OVA tumors, we demonstrate that this hyper-secretion of TNF compensates for reduced synapse-mediated cytotoxic activity against MC38-OVA tumors in vivo, via increased TNF-mediated tumor cell death. Taken together, our results demonstrate that NKG7 enhances CD8+ T cell immune synapse efficiency, which may serve as a mechanism to accelerate direct cytotoxicity and limit potentially harmful inflammatory responses.
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Affiliation(s)
- Emily J Lelliott
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kelly M Ramsbottom
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Mark R Dowling
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Carolyn Shembrey
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Tahereh Noori
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Conor J Kearney
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Jessica Michie
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Ian A Parish
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Margaret A Jordan
- College of Public Health, Medical & Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Alan G Baxter
- College of Public Health, Medical & Veterinary Sciences, James Cook University, Townsville, QLD, Australia.,Central Clinical School, Monash University, Prahran, VIC, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Amelia J Brennan
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Jane Oliaro
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
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29
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Pfenninger P, Yerly L, Abe J. Naïve Primary Mouse CD8+ T Cells Retain In Vivo Immune Responsiveness After Electroporation-Based CRISPR/Cas9 Genetic Engineering. Front Immunol 2022; 13:777113. [PMID: 35844563 PMCID: PMC9280190 DOI: 10.3389/fimmu.2022.777113] [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: 09/14/2021] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
CRISPR/Cas9 technology has revolutionized genetic engineering of primary cells. Although its use is gaining momentum in studies on CD8+ T cell biology, it remains elusive to what extent CRISPR/Cas9 affects in vivo function of CD8+ T cells. Here, we optimized nucleofection-based CRISPR/Cas9 genetic engineering of naïve and in vitro-activated primary mouse CD8+ T cells and tested their in vivo immune responses. Nucleofection of naïve CD8+ T cells preserved their in vivo antiviral immune responsiveness to an extent that is indistinguishable from non-nucleofected cells, whereas nucleofection of in vitro-activated CD8+ T cells led to slightly impaired expansion/survival at early time point after adoptive transfer and more pronounced contraction. Of note, different target proteins displayed distinct decay rates after gene editing. This is in stark contrast to a comparable period of time required to complete gene inactivation. Thus, for optimal experimental design, it is crucial to determine the kinetics of the loss of target gene product to adapt incubation period after gene editing. In sum, nucleofection-based CRISPR/Cas9 genome editing achieves efficient and rapid generation of mutant CD8+ T cells without imposing detrimental constraints on their in vivo functions.
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30
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Karginov TA, Ménoret A, Vella AT. Optimal CD8 + T cell effector function requires costimulation-induced RNA-binding proteins that reprogram the transcript isoform landscape. Nat Commun 2022; 13:3540. [PMID: 35725727 PMCID: PMC9209503 DOI: 10.1038/s41467-022-31228-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/25/2022] [Indexed: 11/11/2022] Open
Abstract
Boosting T cell activation through costimulation directs defense against cancer and viral infections. Despite multiple studies targeting costimulation in clinical trials, the increased potency and reprogramming of T cells endowed by costimulation is poorly understood. Canonical dogma states that transcription mediates T cell activation. Here, we show that the spliceosome, controlling post-transcriptional alternative splicing and alternative polyadenylation, is the most enriched pathway in T cells after CD134/CD137 costimulation. Costimulation of CD8+ T cells significantly increases expression of 29 RNA-binding proteins while RNA-seq uncovers over 1000 differential alternative splicing and polyadenylation events. Using in vivo mouse and in vitro human models, we demonstrate that RNA-binding protein Tardbp is required for effector cytokine production, CD8+ T cell clonal expansion, and isoform regulation after costimulation. The prospect of immune response optimization through reprogramming of mRNA isoform production offered herein opens new avenues for experimentally and therapeutically tuning the activities of T cells.
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Affiliation(s)
- Timofey A Karginov
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Antoine Ménoret
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Anthony T Vella
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, 263 Farmington Avenue, Farmington, CT, 06030, USA.
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31
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Guan X, Polesso F, Wang C, Sehrawat A, Hawkins RM, Murray SE, Thomas GV, Caruso B, Thompson RF, Wood MA, Hipfinger C, Hammond SA, Graff JN, Xia Z, Moran AE. Androgen receptor activity in T cells limits checkpoint blockade efficacy. Nature 2022; 606:791-796. [PMID: 35322234 PMCID: PMC10294141 DOI: 10.1038/s41586-022-04522-6] [Citation(s) in RCA: 181] [Impact Index Per Article: 90.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/04/2022] [Indexed: 12/16/2022]
Abstract
Immune checkpoint blockade has revolutionized the field of oncology, inducing durable anti-tumour immunity in solid tumours. In patients with advanced prostate cancer, immunotherapy treatments have largely failed1-5. Androgen deprivation therapy is classically administered in these patients to inhibit tumour cell growth, and we postulated that this therapy also affects tumour-associated T cells. Here we demonstrate that androgen receptor (AR) blockade sensitizes tumour-bearing hosts to effective checkpoint blockade by directly enhancing CD8 T cell function. Inhibition of AR activity in CD8 T cells prevented T cell exhaustion and improved responsiveness to PD-1 targeted therapy via increased IFNγ expression. AR bound directly to Ifng and eviction of AR with a small molecule significantly increased cytokine production in CD8 T cells. Together, our findings establish that T cell intrinsic AR activity represses IFNγ expression and represents a novel mechanism of immunotherapy resistance.
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Affiliation(s)
- Xiangnan Guan
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
- Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
- Genentech, Inc., South San Francisco, CA, USA
| | - Fanny Polesso
- Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Chaojie Wang
- Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
- Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Archana Sehrawat
- Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Reed M Hawkins
- Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Susan E Murray
- Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
- Department of Biology, University of Portland, Portland, OR, USA
| | - George V Thomas
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Department of Pathology and Laboratory Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Breanna Caruso
- Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Reid F Thompson
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Department of Radiation Medicine, Oregon Health and Science University, Portland, OR, USA
- VA Portland Health Care System, Portland, OR, USA
| | - Mary A Wood
- VA Portland Health Care System, Portland, OR, USA
| | - Christina Hipfinger
- Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Scott A Hammond
- Clinical IO Discovery, Oncology R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Julie N Graff
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- VA Portland Health Care System, Portland, OR, USA
| | - Zheng Xia
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
- Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Amy E Moran
- Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA.
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
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32
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Rezalotfi A, Fritz L, Förster R, Bošnjak B. Challenges of CRISPR-Based Gene Editing in Primary T Cells. Int J Mol Sci 2022; 23:ijms23031689. [PMID: 35163611 PMCID: PMC8835901 DOI: 10.3390/ijms23031689] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/29/2022] [Indexed: 12/30/2022] Open
Abstract
Adaptive T-cell immunotherapy holds great promise for the successful treatment of leukemia, as well as other types of cancers. More recently, it was also shown to be an effective treatment option for chronic virus infections in immunosuppressed patients. Autologous or allogeneic T cells used for immunotherapy are usually genetically modified to express novel T-cell or chimeric antigen receptors. The production of such cells was significantly simplified with the CRISPR/Cas system, allowing for the deletion or insertion of novel genes at specific locations within the genome. In this review, we describe recent methodological breakthroughs that were important for the conduction of these genetic modifications, summarize crucial points to be considered when conducting such experiments, and highlight the potential pitfalls of these approaches.
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Affiliation(s)
- Alaleh Rezalotfi
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.R.); (L.F.); (R.F.)
| | - Lea Fritz
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.R.); (L.F.); (R.F.)
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.R.); (L.F.); (R.F.)
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover, 30625 Hannover, Germany
| | - Berislav Bošnjak
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.R.); (L.F.); (R.F.)
- Correspondence: ; Tel.: +49-511-532-9731
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33
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Severely impaired CTL killing is a feature of the neurological disorder Niemann-Pick Syndrome type C1. Blood 2022; 139:1833-1849. [PMID: 35081253 DOI: 10.1182/blood.2021013477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/18/2022] [Indexed: 11/20/2022] Open
Abstract
Niemann-Pick disease type C1 (NP-C1) is a rare lysosomal storage disorder resulting from mutations in an endo-lysosomal cholesterol transporter, NPC1. Despite typically presenting with pronounced neurological manifestations, NP-C1 also resembles long-term congenital immunodeficiencies that arise due to impairment of cytotoxic T lymphocyte (CTL) effector function. CTLs kill their targets through exocytosis of the contents of lysosome-like secretory cytotoxic granules (CGs) that store, and ultimately release the essential pore-forming protein perforin and pro-apoptotic serine proteases, granzymes, into the synapse formed between the CTL and a target cell. We have discovered that NPC1 deficiency increases CG lipid burden, impairs autophagic flux due to stalled trafficking of the transcription factor EB (TFEB), and dramatically reduces CTL cytotoxicity. Using a variety of immunological and cell biology techniques, we show that the cytotoxic defect arises specifically due to impaired perforin pore-formation. We demonstrated defects of CTL function of varying severity in NP-C1 patients, with the greatest loss of function associated with the most florid and/or earliest disease presentations. Remarkably, perforin function and CTL cytotoxicity were restored in vitro by promoting lipid clearance with therapeutic 2-hydroxypropyl-b-cyclodextrin (HPbCD), whereas restoring autophagy through TFEB over-expression was ineffective. Overall, our study revealed that NPC1 deficiency has a deleterious impact on CTL (but not natural killer cell) cytotoxicity that, in the long term, may predispose NP-C1 patients to atypical infections and impaired immune surveillance more generally.
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34
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Evrard M, Wynne-Jones E, Peng C, Kato Y, Christo SN, Fonseca R, Park SL, Burn TN, Osman M, Devi S, Chun J, Mueller SN, Kannourakis G, Berzins SP, Pellicci DG, Heath WR, Jameson SC, Mackay LK. Sphingosine 1-phosphate receptor 5 (S1PR5) regulates the peripheral retention of tissue-resident lymphocytes. J Exp Med 2022; 219:e20210116. [PMID: 34677611 PMCID: PMC8546662 DOI: 10.1084/jem.20210116] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 08/16/2021] [Accepted: 10/01/2021] [Indexed: 11/05/2022] Open
Abstract
Tissue-resident memory T (TRM) cells provide long-lasting immune protection. One of the key events controlling TRM cell development is the local retention of TRM cell precursors coupled to downregulation of molecules necessary for tissue exit. Sphingosine-1-phosphate receptor 5 (S1PR5) is a migratory receptor with an uncharted function in T cells. Here, we show that S1PR5 plays a critical role in T cell infiltration and emigration from peripheral organs, as well as being specifically downregulated in TRM cells. Consequentially, TRM cell development was selectively impaired upon ectopic expression of S1pr5, whereas loss of S1pr5 enhanced skin TRM cell formation by promoting peripheral T cell sequestration. Importantly, we found that T-bet and ZEB2 were required for S1pr5 induction and that local TGF-β signaling was necessary to promote coordinated Tbx21, Zeb2, and S1pr5 downregulation. Moreover, S1PR5-mediated control of tissue residency was conserved across innate and adaptive immune compartments. Together, these results identify the T-bet-ZEB2-S1PR5 axis as a previously unappreciated mechanism modulating the generation of tissue-resident lymphocytes.
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Affiliation(s)
- Maximilien Evrard
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Erica Wynne-Jones
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Changwei Peng
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Yu Kato
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Susan N. Christo
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Raissa Fonseca
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Simone L. Park
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Thomas N. Burn
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Maleika Osman
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sapna Devi
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Scott N. Mueller
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - George Kannourakis
- Federation University Australia and Fiona Elsey Cancer Research Institute, Ballarat, Victoria, Australia
| | - Stuart P. Berzins
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Federation University Australia and Fiona Elsey Cancer Research Institute, Ballarat, Victoria, Australia
| | - Daniel G. Pellicci
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
- Cellular Immunology Group, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - William R. Heath
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Stephen C. Jameson
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Laura K. Mackay
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
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35
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Johansen KH. How CRISPR/Cas9 Gene Editing Is Revolutionizing T Cell Research. DNA Cell Biol 2022; 41:53-57. [PMID: 34939826 PMCID: PMC8787706 DOI: 10.1089/dna.2021.0579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/05/2021] [Accepted: 09/19/2021] [Indexed: 11/12/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 allows for precise gene targeting in mammalian cells, including T cells, allowing scientists to disrupt or edit specific genes of interest. This has enabled immunologists to investigate T cell functions as well as opened the path for novel therapeutics involving gene editing of T cells ex vivo before transferring these back to patients to increase T cell efficacy. This review outlines how CRISPR/Cas9 has transformed T cell research allowing immunologists to rapidly probe the roles of genes in T cells thus paving the way for novel therapeutics. Furthermore, this review describes how these tools reduce the requirement for genetic mouse models, while increasing the translational potential of T cell research.
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Affiliation(s)
- Kristoffer Haurum Johansen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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36
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Mori D, Grégoire C, Voisinne G, Celis-Gutierrez J, Aussel R, Girard L, Camus M, Marcellin M, Argenty J, Burlet-Schiltz O, Fiore F, Gonzalez de Peredo A, Malissen M, Roncagalli R, Malissen B. The T cell CD6 receptor operates a multitask signalosome with opposite functions in T cell activation. J Exp Med 2021; 218:211516. [PMID: 33125054 PMCID: PMC7608068 DOI: 10.1084/jem.20201011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/19/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022] Open
Abstract
To determine the respective contribution of the LAT transmembrane adaptor and CD5 and CD6 transmembrane receptors to early TCR signal propagation, diversification, and termination, we describe a CRISPR/Cas9-based platform that uses primary mouse T cells and permits establishment of the composition of their LAT, CD5, and CD6 signalosomes in only 4 mo using quantitative mass spectrometry. We confirmed that positive and negative functions can be solely assigned to the LAT and CD5 signalosomes, respectively. In contrast, the TCR-inducible CD6 signalosome comprised both positive (SLP-76, ZAP70, VAV1) and negative (UBASH3A/STS-2) regulators of T cell activation. Moreover, CD6 associated independently of TCR engagement to proteins that support its implication in inflammatory pathologies necessitating T cell transendothelial migration. The multifaceted role of CD6 unveiled here accounts for past difficulties in classifying it as a coinhibitor or costimulator. Congruent with our identification of UBASH3A within the CD6 signalosome and the view that CD6 constitutes a promising target for autoimmune disease treatment, single-nucleotide polymorphisms associated with human autoimmune diseases have been found in the Cd6 and Ubash3a genes.
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Affiliation(s)
- Daiki Mori
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France.,Centre d'Immunophénomique, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France
| | - Claude Grégoire
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France
| | - Guillaume Voisinne
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France
| | - Javier Celis-Gutierrez
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France.,Centre d'Immunophénomique, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France
| | - Rudy Aussel
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France
| | - Laura Girard
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France.,Centre d'Immunophénomique, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France
| | - Mylène Camus
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
| | - Marlène Marcellin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
| | - Jérémy Argenty
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
| | - Frédéric Fiore
- Centre d'Immunophénomique, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France
| | - Anne Gonzalez de Peredo
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
| | - Marie Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France.,Centre d'Immunophénomique, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France
| | - Romain Roncagalli
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France.,Centre d'Immunophénomique, Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Marseille, France
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37
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Majumder S, Jugovic I, Saul D, Bell L, Hundhausen N, Seal R, Beilhack A, Rosenwald A, Mougiakakos D, Berberich-Siebelt F. Rapid and Efficient Gene Editing for Direct Transplantation of Naive Murine Cas9 + T Cells. Front Immunol 2021; 12:683631. [PMID: 34367143 PMCID: PMC8335400 DOI: 10.3389/fimmu.2021.683631] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/06/2021] [Indexed: 01/10/2023] Open
Abstract
Gene editing of primary T cells is a difficult task. However, it is important for research and especially for clinical T-cell transfers. CRISPR/Cas9 is the most powerful gene-editing technique. It has to be applied to cells by either retroviral transduction or electroporation of ribonucleoprotein complexes. Only the latter is possible with resting T cells. Here, we make use of Cas9 transgenic mice and demonstrate nucleofection of pre-stimulated and, importantly, of naive CD3+ T cells with guideRNA only. This proved to be rapid and efficient with no need of further selection. In the mixture of Cas9+CD3+ T cells, CD4+ and CD8+ conventional as well as regulatory T cells were targeted concurrently. IL-7 supported survival and naivety in vitro, but T cells were also transplantable immediately after nucleofection and elicited their function like unprocessed T cells. Accordingly, metabolic reprogramming reached normal levels within days. In a major mismatch model of GvHD, not only ablation of NFATc1 and/or NFATc2, but also of the NFAT-target gene IRF4 in naïve primary murine Cas9+CD3+ T cells by gRNA-only nucleofection ameliorated GvHD. However, pre-activated murine T cells could not achieve long-term protection from GvHD upon single NFATc1 or NFATc2 knockout. This emphasizes the necessity of gene-editing and transferring unstimulated human T cells during allogenic hematopoietic stem cell transplantation.
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Affiliation(s)
- Snigdha Majumder
- Institute of Pathology, University of Wuerzburg, Wuerzburg, Germany
| | - Isabelle Jugovic
- Institute of Pathology, University of Wuerzburg, Wuerzburg, Germany
| | - Domenica Saul
- Department of Internal Medicine 5, Hematology and Oncology, Friedrich-Alexander University (FAU) of Erlangen-Nuremberg, Erlangen, Wuerzburg, Germany
| | - Luisa Bell
- Institute of Pathology, University of Wuerzburg, Wuerzburg, Germany
| | | | - Rishav Seal
- Institute of Pathology, University of Wuerzburg, Wuerzburg, Germany
| | - Andreas Beilhack
- Department of Medicine II, Center for Interdisciplinary Clinical Research (IZKF), University Hospital Wuerzburg, Wuerzburg, Germany
| | - Andreas Rosenwald
- Institute of Pathology, University of Wuerzburg, Wuerzburg, Germany.,Comprehensive Cancer Centre Mainfranken, University of Wuerzburg, Wuerzburg, Germany
| | - Dimitrios Mougiakakos
- Department of Internal Medicine 5, Hematology and Oncology, Friedrich-Alexander University (FAU) of Erlangen-Nuremberg, Erlangen, Wuerzburg, Germany.,Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander University (FAU) of Erlangen-Nuremberg, Erlangen, Germany
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38
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Rose SA, Wroblewska A, Dhainaut M, Yoshida H, Shaffer JM, Bektesevic A, Ben-Zvi B, Rhoads A, Kim EY, Yu B, Lavin Y, Merad M, Buenrostro JD, Brown BD. A microRNA expression and regulatory element activity atlas of the mouse immune system. Nat Immunol 2021; 22:914-927. [PMID: 34099919 PMCID: PMC8480231 DOI: 10.1038/s41590-021-00944-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
To better define the control of immune system regulation, we generated an atlas of microRNA (miRNA) expression from 63 mouse immune cell populations and connected these signatures with assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation followed by sequencing (ChIP-seq) and nascent RNA profiles to establish a map of miRNA promoter and enhancer usage in immune cells. miRNA complexity was relatively low, with >90% of the miRNA compartment of each population comprising <75 miRNAs; however, each cell type had a unique miRNA signature. Integration of miRNA expression with chromatin accessibility revealed putative regulatory elements for differentially expressed miRNAs, including miR-21a, miR-146a and miR-223. The integrated maps suggest that many miRNAs utilize multiple promoters to reach high abundance and identified dominant and divergent miRNA regulatory elements between lineages and during development that may be used by clustered miRNAs, such as miR-99a/let-7c/miR-125b, to achieve distinct expression. These studies, with web-accessible data, help delineate the cis-regulatory elements controlling miRNA signatures of the immune system.
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Affiliation(s)
- Samuel A Rose
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksandra Wroblewska
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maxime Dhainaut
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hideyuki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | | | - Anela Bektesevic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Ben-Zvi
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Rhoads
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Edy Y Kim
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bingfei Yu
- Division of Biology, University of California San Diego, La Jolla, CA, USA
| | - Yonit Lavin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Brian D Brown
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Ramirez-Phillips AC, Liu D. Therapeutic Genome Editing and In Vivo Delivery. AAPS JOURNAL 2021; 23:80. [PMID: 34080099 DOI: 10.1208/s12248-021-00613-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/20/2021] [Indexed: 11/30/2022]
Abstract
Improvements in the understanding of human genetics and its roles in disease development and prevention have led to an increased interest in therapeutic genome editing via the use of engineered nucleases. Various approaches have been explored in the past focusing on the development of an effective and safe system for sequence-specific editing. Compared to earlier nucleases such as zinc finger nuclease and transcription activator-like effector nuclease, the relatively low cost and ease of producing clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR/Cas9) systems have made therapeutic genome editing significantly more feasible. CRISPR/Cas9 genome editing has shown great potential to correct genetic mutations implicated in monogenic diseases and to eradicate latent or chronic viral infections in preclinical studies. Several CRISPR/Cas9-based therapeutics have reached the clinical stage, including treatments for inherited red blood cell disorders and Leber Congenital Amaurosis 10, as well as CRISPR/Cas9-edited T cells designed to target and destroy cancer cells. Further advances in therapeutic genome editing will rely on a safe and more efficient method of in vivo CRISPR/Cas9 delivery and improved efficiency of homology-directed repair for site-specific gene insertion or replacement. While other reviews have focused on one or two aspects of CRISPR/Cas9 genome editing, this review aims to provide a summary of the mechanisms of genome editing, the reasons for the emerging interest in CRISPR/Cas9 compared to other engineered nucleases, the current progress in developing CRISPR/Cas9 delivery systems, and the current preclinical and clinical applications of CRISPR/Cas9 genome editing.
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Affiliation(s)
| | - Dexi Liu
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, 30602, USA.
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CRISPR/Cas9 mediated deletion of the adenosine A2A receptor enhances CAR T cell efficacy. Nat Commun 2021; 12:3236. [PMID: 34050151 PMCID: PMC8163771 DOI: 10.1038/s41467-021-23331-5] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 04/22/2021] [Indexed: 12/16/2022] Open
Abstract
Adenosine is an immunosuppressive factor that limits anti-tumor immunity through the suppression of multiple immune subsets including T cells via activation of the adenosine A2A receptor (A2AR). Using both murine and human chimeric antigen receptor (CAR) T cells, here we show that targeting A2AR with a clinically relevant CRISPR/Cas9 strategy significantly enhances their in vivo efficacy, leading to improved survival of mice. Effects evoked by CRISPR/Cas9 mediated gene deletion of A2AR are superior to shRNA mediated knockdown or pharmacological blockade of A2AR. Mechanistically, human A2AR-edited CAR T cells are significantly resistant to adenosine-mediated transcriptional changes, resulting in enhanced production of cytokines including IFNγ and TNF, and increased expression of JAK-STAT signaling pathway associated genes. A2AR deficient CAR T cells are well tolerated and do not induce overt pathologies in mice, supporting the use of CRISPR/Cas9 to target A2AR for the improvement of CAR T cell function in the clinic.
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41
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Freen-van Heeren JJ. Using CRISPR to enhance T cell effector function for therapeutic applications. Cytokine X 2021; 3:100049. [PMID: 33604565 PMCID: PMC7885876 DOI: 10.1016/j.cytox.2020.100049] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
T cells are critical to fight pathogenic microbes and combat malignantly transformed cells in the fight against cancer. To exert their effector function, T cells produce effector molecules, such as the pro-inflammatory cytokines IFN-γ, TNF-α and IL-2. Tumors possess many inhibitory mechanisms that dampen T cell effector function, limiting the secretion of cytotoxic molecules. As a result, the control and elimination of tumors is impaired. Through recent advances in genomic editing, T cells can now be successfully modified via CRISPR/Cas9 technology. For instance, engaging (post-)transcriptional mechanisms to enhance T cell cytokine production, the retargeting of T cell antigen specificity or rendering T cells refractive to inhibitory receptor signaling can augment T cell effector function. Therefore, CRISPR/Cas9-mediated genome editing might provide novel strategies for cancer immunotherapy. Recently, the first-in-patient clinical trial was successfully performed with CRISPR/Cas9-modified human T cell therapy. In this review, a brief overview of currently available techniques is provided, and recent advances in T cell genomic engineering for the enhancement of T cell effector function for therapeutic purposes are discussed.
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Key Words
- AP-1, activator protein 1
- ARE, AU-rich element
- ARE-Del, deletion of the 3′UTR AREs from the Ifng/IFNG gene
- CAR T cells
- CAR, Chimeric Antigen Receptor
- CRISPR
- CRISPR, Clustered Regularly Interspaced Short Palindromic Repeat
- CRS, cytokine release syndrome
- CTLA-4, cytotoxic T-lymphocyte-associated protein 4
- Cas, CRISPR-associated
- Cas9
- Cytokines
- DGK, Diacylglycerol kinase
- DHX37, DEAH-box helicase 37
- EBV, Epstein Barr virus
- FOXP3, Forkhead box P3
- GATA, GATA binding protein
- Genome editing
- IFN, interferon
- IL, interleukin
- LAG-3, Lymphocyte Activating 3
- NF-κB, nuclear factor of activated B cells
- PD-1, Programmed cell Death 1
- PD-L1, Programmed Death Ligand 1
- PTPN2, Protein Tyrosine Phosphatase Non-Receptor 2
- Pdia3, Protein Disulfide Isomerase Family A Member 3
- RBP, RNA-binding protein
- RNP, ribonuclear protein
- T cell effector function
- T cells
- TCR, T cell receptor
- TGF, transforming growth factor
- TIL, Tumor Infiltrating Lymphocyte
- TLRs, Toll-like receptors
- TNF, tumor necrosis factor
- TRAC, TCR-α chain
- TRBC, TCR-β chain
- UTR, untranslated region
- tTCR, transgenic TCR
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Zhang S, Shen J, Li D, Cheng Y. Strategies in the delivery of Cas9 ribonucleoprotein for CRISPR/Cas9 genome editing. Theranostics 2021; 11:614-648. [PMID: 33391496 PMCID: PMC7738854 DOI: 10.7150/thno.47007] [Citation(s) in RCA: 183] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/31/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas9 genome editing has gained rapidly increasing attentions in recent years, however, the translation of this biotechnology into therapy has been hindered by efficient delivery of CRISPR/Cas9 materials into target cells. Direct delivery of CRISPR/Cas9 system as a ribonucleoprotein (RNP) complex consisting of Cas9 protein and single guide RNA (sgRNA) has emerged as a powerful and widespread method for genome editing due to its advantages of transient genome editing and reduced off-target effects. In this review, we summarized the current Cas9 RNP delivery systems including physical approaches and synthetic carriers. The mechanisms and beneficial roles of these strategies in intracellular Cas9 RNP delivery were reviewed. Examples in the development of stimuli-responsive and targeted carriers for RNP delivery are highlighted. Finally, the challenges of current Cas9 RNP delivery systems and perspectives in rational design of next generation materials for this promising field will be discussed.
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Affiliation(s)
- Song Zhang
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Jiangtao Shen
- The Second People's Hospital of Taizhou affiliated to Yangzhou University, Taizhou, 225500, China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, East China Normal University, Shanghai 200241, China
| | - Yiyun Cheng
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Shanghai Key Laboratory of Regulatory Biology, East China Normal University, Shanghai 200241, China
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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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44
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Targeting the epigenetic regulation of antitumour immunity. Nat Rev Drug Discov 2020; 19:776-800. [PMID: 32929243 DOI: 10.1038/s41573-020-0077-5] [Citation(s) in RCA: 293] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2020] [Indexed: 01/10/2023]
Abstract
Dysregulation of the epigenome drives aberrant transcriptional programmes that promote cancer onset and progression. Although defective gene regulation often affects oncogenic and tumour-suppressor networks, tumour immunogenicity and immune cells involved in antitumour responses may also be affected by epigenomic alterations. This could have important implications for the development and application of both epigenetic therapies and cancer immunotherapies, and combinations thereof. Here, we review the role of key aberrant epigenetic processes - DNA methylation and post-translational modification of histones - in tumour immunogenicity, as well as the effects of epigenetic modulation on antitumour immune cell function. We emphasize opportunities for small-molecule inhibitors of epigenetic regulators to enhance antitumour immune responses, and discuss the challenges of exploiting the complex interplay between cancer epigenetics and cancer immunology to develop treatment regimens combining epigenetic therapies with immunotherapies.
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45
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Kurup SP, Moioffer SJ, Pewe LL, Harty JT. p53 Hinders CRISPR/Cas9-Mediated Targeted Gene Disruption in Memory CD8 T Cells In Vivo. THE JOURNAL OF IMMUNOLOGY 2020; 205:2222-2230. [PMID: 32887747 DOI: 10.4049/jimmunol.2000654] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/11/2020] [Indexed: 01/14/2023]
Abstract
CRISPR/Cas9 technology has revolutionized rapid and reliable gene editing in cells. Although many cell types have been subjected to CRISPR/Cas9-mediated gene editing, there is no evidence of success in genetic alteration of Ag-experienced memory CD8 T cells. In this study, we show that CRISPR/Cas9-mediated gene editing in memory CD8 T cells precludes their proliferation after Ag re-encounter in vivo. This defect is mediated by the proapoptotic transcription factor p53, a sensor of DNA damage. Temporarily inhibiting p53 function offers a window of opportunity for the memory CD8 T cells to repair the DNA damage, facilitating robust recall responses on Ag re-encounter. We demonstrate this by functionally altering memory CD8 T cells using CRISPR/Cas9-mediated targeted gene disruption under the aegis of p53siRNA in the mouse model. Our approach thus adapts the CRISPR/Cas9 technology for memory CD8 T cells to undertake gene editing in vivo, for the first time, to our knowledge.
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Affiliation(s)
- Samarchith P Kurup
- Department of Cellular Biology, University of Georgia, Athens, GA 30602.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602
| | - Steven J Moioffer
- Department of Pathology, University of Iowa, Iowa City, IA 52242; and
| | - Lecia L Pewe
- Department of Pathology, University of Iowa, Iowa City, IA 52242; and
| | - John T Harty
- Department of Pathology, University of Iowa, Iowa City, IA 52242; and .,Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242
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46
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Chiappell F. Putative Natural History of CoViD-19. Bioinformation 2020; 16:398-403. [PMID: 32831521 PMCID: PMC7434958 DOI: 10.6026/97320630016398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 12/22/2022] Open
Abstract
The Severe Acute Respiratory Syndrome Corona Virus2 (SARS-CoV2) is responsible for Corona Virus Disease 2019 (CoViD-19), the pandemic that has afflicted close to two million people worldwide, and has taken the lives of over 120,000 patients since its first report in late December 2019. Per million people globally, the infection rate is close to 250 with a death rate of close to 14 (death rate average global death rate: 6.06%; for comparison, revised estimate of the 1918 influenza pandemic had an average global death rate of 5.4% [1]). About 400,000 SARS-CoV2-positive patients have been declared 'recovered', although it is not clear to date what exactly that entails. To be clear, the natural history of SARS-CoV2 infection and of the patho-physiology of CoViD-19 remains shrouded in relative confusion, in part due to the exceedingly virulent nature of the virus, as manifest by its elevated morbidity and mortality, and the fast accumulation of clinical observations and research evidence. Many pieces of a complex puzzle are emerging all at once and their organization into a coherent and cogent picture of the natural history of CoViD-19 is arduous and still wanting. Here, we discuss the recent findings in the context of the available evidence. We propose a putative prediction model of the natural history of CoViD-19. We highlight putative loci and modes of therapeutic intervention that may become beneficial preventive and treatment modalities for individuals at risk of SARS-CoV2 infection and CoViD-19 patients.
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47
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Kurniawan H, Franchina DG, Guerra L, Bonetti L, -Baguet LS, Grusdat M, Schlicker L, Hunewald O, Dostert C, Merz MP, Binsfeld C, Duncan GS, Farinelle S, Nonnenmacher Y, Haight J, Das Gupta D, Ewen A, Taskesen R, Halder R, Chen Y, Jäger C, Ollert M, Wilmes P, Vasiliou V, Harris IS, Knobbe-Thomsen CB, Turner JD, Mak TW, Lohoff M, Meiser J, Hiller K, Brenner D. Glutathione Restricts Serine Metabolism to Preserve Regulatory T Cell Function. Cell Metab 2020; 31:920-936.e7. [PMID: 32213345 PMCID: PMC7265172 DOI: 10.1016/j.cmet.2020.03.004] [Citation(s) in RCA: 124] [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: 06/20/2019] [Revised: 12/26/2019] [Accepted: 03/02/2020] [Indexed: 01/03/2023]
Abstract
Regulatory T cells (Tregs) maintain immune homeostasis and prevent autoimmunity. Serine stimulates glutathione (GSH) synthesis and feeds into the one-carbon metabolic network (1CMet) essential for effector T cell (Teff) responses. However, serine's functions, linkage to GSH, and role in stress responses in Tregs are unknown. Here, we show, using mice with Treg-specific ablation of the catalytic subunit of glutamate cysteine ligase (Gclc), that GSH loss in Tregs alters serine import and synthesis and that the integrity of this feedback loop is critical for Treg suppressive capacity. Although Gclc ablation does not impair Treg differentiation, mutant mice exhibit severe autoimmunity and enhanced anti-tumor responses. Gclc-deficient Tregs show increased serine metabolism, mTOR activation, and proliferation but downregulated FoxP3. Limitation of cellular serine in vitro and in vivo restores FoxP3 expression and suppressive capacity of Gclc-deficient Tregs. Our work reveals an unexpected role for GSH in restricting serine availability to preserve Treg functionality.
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Affiliation(s)
- Henry Kurniawan
- Experimental & Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, Esch-sur-Alzette, Luxembourg
| | - Davide G Franchina
- Experimental & Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, Esch-sur-Alzette, Luxembourg
| | - Luana Guerra
- Experimental & Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, Esch-sur-Alzette, Luxembourg
| | - Lynn Bonetti
- Experimental & Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, Esch-sur-Alzette, Luxembourg
| | - Leticia Soriano -Baguet
- Experimental & Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, Esch-sur-Alzette, Luxembourg
| | - Melanie Grusdat
- Experimental & Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, Esch-sur-Alzette, Luxembourg
| | - Lisa Schlicker
- Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Oliver Hunewald
- Allergy and Clinical Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Catherine Dostert
- Experimental & Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, Esch-sur-Alzette, Luxembourg
| | - Myriam P Merz
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg
| | - Carole Binsfeld
- Experimental & Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, Esch-sur-Alzette, Luxembourg
| | - Gordon S Duncan
- The Campbell Family Cancer Research Institute, Ontario Cancer Institute University Health Network, Toronto, ON, Canada
| | - Sophie Farinelle
- Experimental & Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, Esch-sur-Alzette, Luxembourg
| | - Yannic Nonnenmacher
- Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Jillian Haight
- The Campbell Family Cancer Research Institute, Ontario Cancer Institute University Health Network, Toronto, ON, Canada
| | - Dennis Das Gupta
- Institute for Medical Microbiology and Hospital Hygiene, University of Marburg, Marburg, Germany
| | - Anouk Ewen
- Experimental & Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, Esch-sur-Alzette, Luxembourg
| | - Rabia Taskesen
- Departments of Medical Biophysics and Immunology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, Esch-sur-Alzette, Luxembourg
| | - Ying Chen
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Christian Jäger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, Esch-sur-Alzette, Luxembourg
| | - Markus Ollert
- Allergy and Clinical Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; Odense Research Center for Anaphylaxis (ORCA), Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, Esch-sur-Alzette, Luxembourg
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Isaac S Harris
- Department of Biomedical Genetics and Wilmot Cancer Institute, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, New York, USA
| | - Christiane B Knobbe-Thomsen
- Departments of Medical Biophysics and Immunology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Jonathan D Turner
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg
| | - Tak W Mak
- The Campbell Family Cancer Research Institute, Ontario Cancer Institute University Health Network, Toronto, ON, Canada; Departments of Medical Biophysics and Immunology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; The University of Hong Kong, Hong Kong SAR, China
| | - Michael Lohoff
- Institute for Medical Microbiology and Hospital Hygiene, University of Marburg, Marburg, Germany
| | - Johannes Meiser
- Cancer Metabolism Group, Department of Oncology, 84 Val Fleuri, Luxembourg, Luxembourg
| | - Karsten Hiller
- Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Dirk Brenner
- Experimental & Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, Esch-sur-Alzette, Luxembourg; Odense Research Center for Anaphylaxis (ORCA), Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark; Immunology & Genetics, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, Esch-sur-Alzette, Luxembourg.
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