1
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Ngiow SF, Manne S, Huang YJ, Azar T, Chen Z, Mathew D, Chen Q, Khan O, Wu JE, Alcalde V, Flowers AJ, McClain S, Baxter AE, Kurachi M, Shi J, Huang AC, Giles JR, Sharpe AH, Vignali DAA, Wherry EJ. LAG-3 sustains TOX expression and regulates the CD94/NKG2-Qa-1b axis to govern exhausted CD8 T cell NK receptor expression and cytotoxicity. Cell 2024; 187:4336-4354.e19. [PMID: 39121847 PMCID: PMC11337978 DOI: 10.1016/j.cell.2024.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 11/20/2023] [Accepted: 07/10/2024] [Indexed: 08/12/2024]
Abstract
Exhausted CD8 T (Tex) cells in chronic viral infection and cancer have sustained co-expression of inhibitory receptors (IRs). Tex cells can be reinvigorated by blocking IRs, such as PD-1, but synergistic reinvigoration and enhanced disease control can be achieved by co-targeting multiple IRs including PD-1 and LAG-3. To dissect the molecular changes intrinsic when these IR pathways are disrupted, we investigated the impact of loss of PD-1 and/or LAG-3 on Tex cells during chronic infection. These analyses revealed distinct roles of PD-1 and LAG-3 in regulating Tex cell proliferation and effector functions, respectively. Moreover, these studies identified an essential role for LAG-3 in sustaining TOX and Tex cell durability as well as a LAG-3-dependent circuit that generated a CD94/NKG2+ subset of Tex cells with enhanced cytotoxicity mediated by recognition of the stress ligand Qa-1b, with similar observations in humans. These analyses disentangle the non-redundant mechanisms of PD-1 and LAG-3 and their synergy in regulating Tex cells.
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Affiliation(s)
- Shin Foong Ngiow
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, 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 and Immune Health, 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 and Immune Health, 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
| | - Tarek Azar
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Divij Mathew
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, 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
| | - Qingzhou Chen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, 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 and Immune Health, 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 and Immune Health, 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
| | - Victor Alcalde
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ahron J Flowers
- Tara Miller Melanoma Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sean McClain
- Tara Miller Melanoma Center, 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 and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Makoto Kurachi
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Junwei Shi
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander C Huang
- Institute for Immunology and Immune Health, 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, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, 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
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Gene Lay Institute of Immunology and Inflammation at Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, 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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2
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Ni L. Potential mechanisms of cancer stem-like progenitor T-cell bio-behaviours. Clin Transl Med 2024; 14:e1817. [PMID: 39169517 PMCID: PMC11338842 DOI: 10.1002/ctm2.1817] [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: 05/08/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024] Open
Abstract
In situations involving continuous exposure to antigens, such as chronic infections or cancer, antigen-specific CD8+ T cells can become dysfunctional or exhausted. This change is marked by increased expression levels of inhibitory receptors (PD-1 and Tim-3). Stem-like progenitor exhausted (Tpex) cells, a subset of exhausted cells that express TCF-1 and are mainly found in the lymph nodes, demonstrate the ability to self-renew and exhibit a high rate of proliferation. Tpex cells can further differentiate into transitional intermediate exhausted (Tex-int) cells and terminally exhausted (Tex-term) cells. Alternatively, they can directly differentiate into Tex-term cells. Tpex cells are the predominant subset that respond to immune checkpoint inhibitors (ICI), making them a prime candidate for improving the efficacy of ICI therapy. This review article aimed to present the latest developments in the field of Tpex formation, expansion, and differentiation in the context of cancer, as well as their responses to ICIs in cancer immunotherapy. Consequently, it may be possible to develop novel treatments that exclusively target Tpex cells, thus improving overall treatment outcomes. KEY POINTS: Tpex cells are located in lymph nodes and TLS. Several pathways control the differentiation trajectories of Tpex cells, including epigenetic factors, transcription factors, cytokines, age, sex, etc.
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Affiliation(s)
- Ling Ni
- Institute for Immunology and School of Basic MedicineTsinghua UniversityBeijingChina
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3
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Witkop EM, Diggins K, Wiedeman A, Serti E, Nepom G, Gersuk VH, Fuchs B, Long SA, Linsley PS. Interconnected lineage trajectories link conventional and natural killer (NK)-like exhausted CD8 + T cells beneficial in type 1 diabetes. Commun Biol 2024; 7:773. [PMID: 38937521 PMCID: PMC11211332 DOI: 10.1038/s42003-024-06456-3] [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: 08/17/2023] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
Distinct Natural Killer (NK)-like CD57+ and PD-1+ CD8+ exhausted-like T cell populations (Tex) have both been linked to beneficial immunotherapy response in autoimmune type 1 diabetes (T1D) patients. The origins and relationships between these cell types are poorly understood. Here we show that while PD-1+ and CD57+ Tex populations are epigenetically similar, CD57+ Tex cells display unique increased chromatin accessibility of inhibitory Killer Cell Immunoglobulin-like Receptor (iKIR) and other NK cell genes. PD-1+ and CD57+ Tex also show reciprocal expression of Inhibitory Receptors (IRs) and iKIRs accompanied by chromatin accessibility of Tcf1 and Tbet transcription factor target sites, respectively. CD57+ Tex show unappreciated gene expression heterogeneity and share clonal relationships with PD-1+ Tex, with these cells differentiating along four interconnected lineage trajectories: Tex-PD-1+, Tex-CD57+, Tex-Branching, and Tex-Fluid. Our findings demonstrate new relationships between Tex-like populations in human autoimmune disease and suggest that modulating common precursor populations may enhance response to autoimmune disease treatment.
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Affiliation(s)
- Erin M Witkop
- Benaroya Research Institute, Systems Immunology, Seattle, WA, USA
| | - Kirsten Diggins
- Benaroya Research Institute, Systems Immunology, Seattle, WA, USA
| | - Alice Wiedeman
- Benaroya Research Institute, Translational Immunology, Seattle, WA, USA
| | | | - Gerald Nepom
- Benaroya Research Institute, Translational Immunology, Seattle, WA, USA
- Immune Tolerance Network (ITN), Bethesda, MD, USA
| | - Vivian H Gersuk
- Benaroya Research Institute, Genomics Core, Seattle, WA, USA
| | - Bryce Fuchs
- Benaroya Research Institute, Translational Immunology, Seattle, WA, USA
| | - S Alice Long
- Benaroya Research Institute, Translational Immunology, Seattle, WA, USA
| | - Peter S Linsley
- Benaroya Research Institute, Systems Immunology, Seattle, WA, USA.
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4
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Maxwell MB, Hom-Tedla MS, Yi J, Li S, Rivera SA, Yu J, Burns MJ, McRae HM, Stevenson BT, Coakley KE, Ho J, Gastelum KB, Bell JC, Jones AC, Eskander RN, Dykhuizen EC, Shadel GS, Kaech SM, Hargreaves DC. ARID1A suppresses R-loop-mediated STING-type I interferon pathway activation of anti-tumor immunity. Cell 2024; 187:3390-3408.e19. [PMID: 38754421 PMCID: PMC11193641 DOI: 10.1016/j.cell.2024.04.025] [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: 11/19/2022] [Revised: 02/26/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Clinical trials have identified ARID1A mutations as enriched among patients who respond favorably to immune checkpoint blockade (ICB) in several solid tumor types independent of microsatellite instability. We show that ARID1A loss in murine models is sufficient to induce anti-tumor immune phenotypes observed in ARID1A mutant human cancers, including increased CD8+ T cell infiltration and cytolytic activity. ARID1A-deficient cancers upregulated an interferon (IFN) gene expression signature, the ARID1A-IFN signature, associated with increased R-loops and cytosolic single-stranded DNA (ssDNA). Overexpression of the R-loop resolving enzyme, RNASEH2B, or cytosolic DNase, TREX1, in ARID1A-deficient cells prevented cytosolic ssDNA accumulation and ARID1A-IFN gene upregulation. Further, the ARID1A-IFN signature and anti-tumor immunity were driven by STING-dependent type I IFN signaling, which was required for improved responsiveness of ARID1A mutant tumors to ICB treatment. These findings define a molecular mechanism underlying anti-tumor immunity in ARID1A mutant cancers.
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Affiliation(s)
- Matthew B Maxwell
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92092, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Marianne S Hom-Tedla
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Gynecologic Oncology, University of California, San Diego, San Diego, CA, USA
| | - Jawoon Yi
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Shitian Li
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92092, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Samuel A Rivera
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92092, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jingting Yu
- Integrative Genomics and Bioinformatics Core, Salk Institute of Biological Studies, La Jolla, CA 92037, USA
| | - Mannix J Burns
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Helen M McRae
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Braden T Stevenson
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Katherine E Coakley
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Gynecologic Oncology, University of California, San Diego, San Diego, CA, USA
| | - Josephine Ho
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Joshua C Bell
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Alexander C Jones
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ramez N Eskander
- Center for Personalized Cancer Therapy and Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Gerald S Shadel
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Diana C Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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5
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Mazzoccoli L, Liu B. Dendritic Cells in Shaping Anti-Tumor T Cell Response. Cancers (Basel) 2024; 16:2211. [PMID: 38927916 PMCID: PMC11201542 DOI: 10.3390/cancers16122211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Among professional antigen-presenting cells, dendritic cells (DCs) orchestrate innate and adaptive immunity and play a pivotal role in anti-tumor immunity. DCs are a heterogeneous population with varying functions in the tumor microenvironment (TME). Tumor-associated DCs differentiate developmentally and functionally into three main subsets: conventional DCs (cDCs), plasmacytoid DCs (pDCs), and monocyte-derived DCs (MoDCs). There are two major subsets of cDCs in TME, cDC1 and cDC2. cDC1 is critical for cross-presenting tumor antigens to activate cytotoxic CD8+ T cells and is also required for priming earlier CD4+ T cells in certain solid tumors. cDC2 is vital for priming anti-tumor CD4+ T cells in multiple tumor models. pDC is a unique subset of DCs and produces type I IFN through TLR7 and TLR9. Studies have shown that pDCs are related to immunosuppression in the TME through the secretion of immunosuppressive cytokines and by promoting regulatory T cells. MoDCs differentiate separately from monocytes in response to inflammatory cues and infection. Also, MoDCs can cross-prime CD8+ T cells. In this review, we summarize the subsets and functions of DCs. We also discuss the role of different DC subsets in shaping T cell immunity in TME and targeting DCs for potential immunotherapeutic benefits against cancer.
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Affiliation(s)
- Luciano Mazzoccoli
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA;
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Bei Liu
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA;
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
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6
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Lan X, Mi T, Alli S, Guy C, Djekidel MN, Liu X, Boi S, Chowdhury P, He M, Zehn D, Feng Y, Youngblood B. Antitumor progenitor exhausted CD8 + T cells are sustained by TCR engagement. Nat Immunol 2024; 25:1046-1058. [PMID: 38816618 DOI: 10.1038/s41590-024-01843-8] [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: 04/30/2023] [Accepted: 04/16/2024] [Indexed: 06/01/2024]
Abstract
The durability of an antitumor immune response is mediated in part by the persistence of progenitor exhausted CD8+ T cells (Tpex). Tpex serve as a resource for replenishing effector T cells and preserve their quantity through self-renewal. However, it is unknown how T cell receptor (TCR) engagement affects the self-renewal capacity of Tpex in settings of continued antigen exposure. Here we use a Lewis lung carcinoma model that elicits either optimal or attenuated TCR signaling in CD8+ T cells to show that formation of Tpex in tumor-draining lymph nodes and their intratumoral persistence is dependent on optimal TCR engagement. Notably, attenuated TCR stimulation accelerates the terminal differentiation of optimally primed Tpex. This TCR-reinforced Tpex development and self-renewal is coupled to proximal positioning to dendritic cells and epigenetic imprinting involving increased chromatin accessibility at Egr2 and Tcf1 target loci. Collectively, this study highlights the critical function of TCR engagement in sustaining Tpex during tumor progression.
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MESH Headings
- Animals
- CD8-Positive T-Lymphocytes/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/immunology
- Mice
- Carcinoma, Lewis Lung/immunology
- Carcinoma, Lewis Lung/pathology
- Carcinoma, Lewis Lung/metabolism
- Mice, Inbred C57BL
- Hepatocyte Nuclear Factor 1-alpha/metabolism
- Cell Differentiation/immunology
- Dendritic Cells/immunology
- Signal Transduction/immunology
- Mice, Knockout
- Lymphocyte Activation/immunology
- Cell Self Renewal
- Mice, Transgenic
- Early Growth Response Protein 2
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Affiliation(s)
- Xin Lan
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Tian Mi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shanta Alli
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cliff Guy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Xueyan Liu
- Department of Mathematics, University of New Orleans, New Orleans, LA, USA
| | - Shannon Boi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Partha Chowdhury
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Minghong He
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Dietmar Zehn
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Yongqiang Feng
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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7
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Ojo OA, Shen H, Ingram JT, Bonner JA, Welner RS, Lacaud G, Zajac AJ, Shi LZ. Gfi1 controls the formation of effector CD8 T cells during chronic infection and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.579535. [PMID: 38659890 PMCID: PMC11042319 DOI: 10.1101/2024.04.18.579535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
During chronic infections and tumor progression, CD8 T cells gradually lose their effector functions and become exhausted. These exhausted CD8 T cells are heterogeneous and comprised of different subsets, including self-renewing progenitors that give rise to Ly108 - CX3CR1 + effector-like cells. Generation of these effector-like cells is essential for the control of chronic infections and tumors, albeit limited. However, the precise cues and mechanisms directing the formation and maintenance of exhausted effector-like are incompletely understood. Using genetic mouse models challenged with LCMV Clone 13 or syngeneic tumors, we show that the expression of a transcriptional repressor, growth factor independent 1 (Gfi1) is dynamically regulated in exhausted CD8 T cells, which in turn regulates the formation of exhausted effector-like cells. Gfi1 deletion in T cells dysregulates the chromatin accessibility and transcriptomic programs associated with the differentiation of LCMV Clone 13-specific CD8 T cell exhaustion, preventing the formation of effector-like and terminally exhausted cells while maintaining progenitors and a newly identified Ly108 + CX3CR1 + state. These Ly108 + CX3CR1 + cells have a distinct chromatin profile and may represent an alternative target for therapeutic interventions to combat chronic infections and cancer. In sum, we show that Gfi1 is a critical regulator of the formation of exhausted effector-like cells.
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8
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Abdullah L, Emiliani FE, Vaidya CM, Stuart H, Kolling FW, Ackerman ME, Song L, McKenna A, Huang YH. Hierarchal single-cell lineage tracing reveals differential fate commitment of CD8 T-cell clones in response to acute infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586160. [PMID: 38585810 PMCID: PMC10996474 DOI: 10.1101/2024.03.21.586160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Generating balanced populations of CD8 effector and memory T cells is necessary for immediate and durable immunity to infections and cancer. Yet, a definitive understanding of CD8 differentiation remains unclear. We used CARLIN, a processive lineage recording mouse model with single-cell RNA-seq and TCR-seq to track endogenous antigen-specific CD8 T cells during acute viral infection. We identified a diverse repertoire of expanded T-cell clones represented by seven transcriptional states. TCR enrichment analysis revealed differential memory- or effector-fate biases within clonal populations. Shared Vb segments and amino acid motifs were found within biased categories despite high TCR diversity. Using single-cell CARLIN barcode-seq we tracked multi-generational clones and found that unlike unbiased or memory-biased clones, which stably retain their fate profiles, effector-biased clones could adopt memory- or effector-bias within subclones. Collectively, our study demonstrates that a heterogenous T-cell repertoire specific for a shared antigen is composed of clones with distinct TCR-intrinsic fate-biases.
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Affiliation(s)
- Leena Abdullah
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Francesco E. Emiliani
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Chinmay M. Vaidya
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Hannah Stuart
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | | | - Margaret E. Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Li Song
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Aaron McKenna
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Yina H. Huang
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
- Department of Pathology and Laboratory Medicine, Dartmouth Health, Lebanon, NH 03756, USA
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9
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Maymí VI, Zhu H, Jager M, Johnson S, Getchell R, Casey JW, Grenier JK, Wherry EJ, Smith NL, Grimson A, Rudd BD. Neonatal CD8+ T Cells Resist Exhaustion during Chronic Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:834-843. [PMID: 38231127 PMCID: PMC11298781 DOI: 10.4049/jimmunol.2300396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024]
Abstract
Chronic viral infections, such as HIV and hepatitis C virus, represent a major public health problem. Although it is well understood that neonates and adults respond differently to chronic viral infections, the underlying mechanisms remain unknown. In this study, we transferred neonatal and adult CD8+ T cells into a mouse model of chronic infection (lymphocytic choriomeningitis virus clone 13) and dissected out the key cell-intrinsic differences that alter their ability to protect the host. Interestingly, we found that neonatal CD8+ T cells preferentially became effector cells early in chronic infection compared with adult CD8+ T cells and expressed higher levels of genes associated with cell migration and effector cell differentiation. During the chronic phase of infection, the neonatal cells retained more immune functionality and expressed lower levels of surface markers and genes related to exhaustion. Because the neonatal cells protect from viral replication early in chronic infection, the altered differentiation trajectories of neonatal and adult CD8+ T cells is functionally significant. Together, our work demonstrates how cell-intrinsic differences between neonatal and adult CD8+ T cells influence key cell fate decisions during chronic infection.
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Affiliation(s)
- Viviana I. Maymí
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Hongya Zhu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Mason Jager
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Shawn Johnson
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Rodman Getchell
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - James W. Casey
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Jennifer K. Grenier
- Transcriptional Regulation and Expression Facility, Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - E. John Wherry
- Institute for Immunology and Immune Health, and Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Norah L. Smith
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Brian D. Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
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10
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Clutton GT, Weideman AMK, Mischell MA, Kallon S, Conrad SZ, Shaw FR, Warren JA, Lin L, Kuruc JD, Xu Y, Gay CM, Armistead PM, G. Hudgens M, Goonetilleke NP. CD3 downregulation identifies high-avidity human CD8 T cells. Clin Exp Immunol 2024; 215:279-290. [PMID: 37950348 PMCID: PMC10876116 DOI: 10.1093/cei/uxad124] [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: 06/27/2023] [Revised: 09/22/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
CD8 T cells recognize infected and cancerous cells via their T-cell receptor (TCR), which binds peptide-MHC complexes on the target cell. The affinity of the interaction between the TCR and peptide-MHC contributes to the antigen sensitivity, or functional avidity, of the CD8 T cell. In response to peptide-MHC stimulation, the TCR-CD3 complex and CD8 co-receptor are downmodulated. We quantified CD3 and CD8 downmodulation following stimulation of human CD8 T cells with CMV, EBV, and HIV peptides spanning eight MHC restrictions, observing a strong correlation between the levels of CD3 and CD8 downmodulation and functional avidity, regardless of peptide viral origin. In TCR-transduced T cells targeting a tumor-associated antigen, changes in TCR-peptide affinity were sufficient to modify CD3 and CD8 downmodulation. Correlation analysis and generalized linear modeling indicated that CD3 downmodulation was the stronger correlate of avidity. CD3 downmodulation, simply measured using flow cytometry, can be used to identify high-avidity CD8 T cells in a clinical context.
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Affiliation(s)
- Genevieve T Clutton
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ann Marie K Weideman
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa A Mischell
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sallay Kallon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shayla Z Conrad
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fiona R Shaw
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joanna A Warren
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lin Lin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - JoAnn D Kuruc
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yinyan Xu
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cynthia M Gay
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paul M Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael G. Hudgens
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nilu P Goonetilleke
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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11
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Hou B, Hu Y, Zhu Y, Wang X, Li W, Tang J, Jia X, Wang J, Cong Y, Quan M, Yang H, Zheng H, Bao Y, Chen XL, Wang HR, Xu B, Gascoigne NRJ, Fu G. SHP-1 Regulates CD8+ T Cell Effector Function but Plays a Subtle Role with SHP-2 in T Cell Exhaustion Due to a Stage-Specific Nonredundant Functional Relay. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:397-409. [PMID: 38088801 DOI: 10.4049/jimmunol.2300462] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/14/2023] [Indexed: 01/18/2024]
Abstract
SHP-1 (Src homology region 2 domain-containing phosphatase 1) is a well-known negative regulator of T cells, whereas its close homolog SHP-2 is the long-recognized main signaling mediator of the PD-1 inhibitory pathway. However, recent studies have challenged the requirement of SHP-2 in PD-1 signaling, and follow-up studies further questioned the alternative idea that SHP-1 may replace SHP-2 in its absence. In this study, we systematically investigate the role of SHP-1 alone or jointly with SHP-2 in CD8+ T cells in a series of gene knockout mice. We show that although SHP-1 negatively regulates CD8+ T cell effector function during acute lymphocytic choriomeningitis virus (LCMV) infection, it is dispensable for CD8+ T cell exhaustion during chronic LCMV infection. Moreover, in contrast to the mortality of PD-1 knockout mice upon chronic LCMV infection, mice double deficient for SHP-1 and SHP-2 in CD8+ T cells survived without immunopathology. Importantly, CD8+ T cells lacking both phosphatases still differentiate into exhausted cells and respond to PD-1 blockade. Finally, we found that SHP-1 and SHP-2 suppressed effector CD8+ T cell expansion at the early and late stages, respectively, during chronic LCMV infection.
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Affiliation(s)
- Bowen Hou
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Yanyan Hu
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuzhen Zhu
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaocui Wang
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Wanyun Li
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Jian Tang
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Xian Jia
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiayu Wang
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yu Cong
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Minxue Quan
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Hongying Yang
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Haiping Zheng
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yuzhou Bao
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Xiao Lei Chen
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Hong-Rui Wang
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Bing Xu
- Department of Hematology, The First Affiliated Hospital and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
| | - Nicholas R J Gascoigne
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Guo Fu
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- Department of Hematology, The First Affiliated Hospital and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
- Cancer Research Center of Xiamen University, Xiamen, China
- Laboratory Animal Center, Xiamen University; Xiamen, China
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12
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Zhu Z, Lou G, Teng XL, Wang H, Luo Y, Shi W, Yihunie K, Hao S, DeGolier K, Liao C, Huang H, Zhang Q, Fry T, Wang T, Yao C, Wu T. FOXP1 and KLF2 reciprocally regulate checkpoints of stem-like to effector transition in CAR T cells. Nat Immunol 2024; 25:117-128. [PMID: 38012417 PMCID: PMC10841689 DOI: 10.1038/s41590-023-01685-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 10/16/2023] [Indexed: 11/29/2023]
Abstract
In cancer and infections, self-renewing stem-like CD8+ T cells mediate the response of immunotherapies and replenish terminally exhausted T cells and effector-like T cells. However, the programs governing the lineage choice in chimeric antigen receptor (CAR) T cells are unclear. Here, by simultaneously profiling single-cell chromatin accessibility and transcriptome in the same CAR T cells, we identified heterogeneous chromatin states within CD8+ T cell subsets that foreshadowed transcriptional changes and were primed for regulation by distinct transcription factors. Transcription factors that controlled each CD8+ T cell subset were regulated by high numbers of enhancers and positioned as hubs of gene networks. FOXP1, a hub in the stem-like network, promoted expansion and stemness of CAR T cells and limited excessive effector differentiation. In the effector network, KLF2 enhanced effector CD8+ T cell differentiation and prevented terminal exhaustion. Thus, we identified gene networks and hub transcription factors that controlled the differentiation of stem-like CD8+ CAR T cells into effector or exhausted CD8+ CAR T cells.
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Affiliation(s)
- Ziang Zhu
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Immunology Ph.D. Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guohua Lou
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xiao-Lu Teng
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Haixia Wang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ying Luo
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wangke Shi
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kiddist Yihunie
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shumeng Hao
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kole DeGolier
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Chengheng Liao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huocong Huang
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qing Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Terry Fry
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 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.
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13
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Beltra JC, Abdel-Hakeem MS, Manne S, Zhang Z, Huang H, Kurachi M, Su L, Picton L, Ngiow SF, Muroyama Y, Casella V, Huang YJ, Giles JR, Mathew D, Belman J, Klapholz M, Decaluwe H, Huang AC, Berger SL, Garcia KC, Wherry EJ. Stat5 opposes the transcription factor Tox and rewires exhausted CD8 + T cells toward durable effector-like states during chronic antigen exposure. Immunity 2023; 56:2699-2718.e11. [PMID: 38091951 PMCID: PMC10752292 DOI: 10.1016/j.immuni.2023.11.005] [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: 08/29/2022] [Revised: 08/23/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
Rewiring exhausted CD8+ T (Tex) cells toward functional states remains a therapeutic challenge. Tex cells are epigenetically programmed by the transcription factor Tox. However, epigenetic remodeling occurs as Tex cells transition from progenitor (Texprog) to intermediate (Texint) and terminal (Texterm) subsets, suggesting development flexibility. We examined epigenetic transitions between Tex cell subsets and revealed a reciprocally antagonistic circuit between Stat5a and Tox. Stat5 directed Texint cell formation and re-instigated partial effector biology during this Texprog-to-Texint cell transition. Constitutive Stat5a activity antagonized Tox and rewired CD8+ T cells from exhaustion to a durable effector and/or natural killer (NK)-like state with superior anti-tumor potential. Temporal induction of Stat5 activity in Tex cells using an orthogonal IL-2:IL2Rβ-pair fostered Texint cell accumulation, particularly upon PD-L1 blockade. Re-engaging Stat5 also partially reprogrammed the epigenetic landscape of exhaustion and restored polyfunctionality. These data highlight therapeutic opportunities of manipulating the IL-2-Stat5 axis to rewire Tex cells toward more durably protective states.
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Affiliation(s)
- Jean-Christophe Beltra
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - Mohamed S Abdel-Hakeem
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini, Cairo 11562, Egypt
| | - Sasikanth Manne
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhen Zhang
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hua Huang
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Makoto Kurachi
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa 920-8640, Japan
| | - Leon Su
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lora Picton
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shin Foong Ngiow
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuki Muroyama
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Valentina Casella
- Infection Biology Laboratory, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Yinghui J Huang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - Divij Mathew
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan Belman
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Max Klapholz
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hélène Decaluwe
- Cytokines and Adaptive Immunity Laboratory, Sainte-Justine University Hospital Research Center, Montreal, QC, Canada; Department of Microbiology and Immunology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada; Immunology and Rheumatology Division, Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Alexander C Huang
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - K Christopher Garcia
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Parker Institute for Cancer Immunotherapy, 1 Letterman Drive, Suite D3500, San Francisco, CA 94129, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA.
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14
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Chung HK, Liu C, Sun M, Casillas E, Chen T, Chick B, Wang J, Ma S, Mcdonald B, He P, Yang Q, Varanasi SK, Mann T, Chen D, Hoffmann F, Tripple V, Hang Y, Ho J, Cho UH, Williams A, Wang Y, Hargreaves D, Kaech SM, Wang W. Multiomics atlas-assisted discovery of transcription factors enables specific cell state programming. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522354. [PMID: 36711632 PMCID: PMC9881845 DOI: 10.1101/2023.01.03.522354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The same types of cells can assume diverse states with varying functionalities. Effective cell therapy can be achieved by specifically driving a desirable cell state, which requires the elucidation of key transcription factors (TFs). Here, we integrated epigenomic and transcriptomic data at the systems level to identify TFs that define different CD8 + T cell states in an unbiased manner. These TF profiles can be used for cell state programming that aims to maximize the therapeutic potential of T cells. For example, T cells can be programmed to avoid a terminal exhaustion state (Tex Term ), a dysfunctional T cell state that is often found in tumors or chronic infections. However, Tex Term exhibits high similarity with the beneficial tissue-resident memory T states (T RM ) in terms of their locations and transcription profiles. Our bioinformatic analysis predicted Zscan20 , a novel TF, to be uniquely active in Tex Term . Consistently, Zscan20 knock-out thwarted the differentiation of Tex Term in vivo , but not that of T RM . Furthermore, perturbation of Zscan20 programs T cells into an effector-like state that confers superior tumor and virus control and synergizes with immune checkpoint therapy. We also identified Jdp2 and Nfil3 as powerful Tex Term drivers. In short, our multiomics-based approach discovered novel TFs that enhance anti-tumor immunity, and enable highly effective cell state programming. One sentence summary Multiomics atlas enables the systematic identification of cell-state specifying transcription factors for therapeutic cell state programming.
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15
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Abstract
T cells can acquire a broad spectrum of differentiation states following activation. At the extreme ends of this continuum are short-lived cells equipped with effector machinery and more quiescent, long-lived cells with heightened proliferative potential and stem cell-like developmental plasticity. The latter encompass stem-like exhausted T cells and memory T cells, both of which have recently emerged as key determinants of cancer immunity and response to immunotherapy. Here, we discuss key similarities and differences in the regulation and function of stem-like exhausted CD8+ T cells and memory CD8+ T cells, and consider their context-specific contributions to protective immunity in diverse outcomes of cancer, including tumour escape, long-term control and eradication. Finally, we emphasize how recent advances in the understanding of the molecular regulation of stem-like exhausted T cells and memory T cells are being explored for clinical benefit in cancer immunotherapies such as checkpoint inhibition, adoptive cell therapy and vaccination.
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Affiliation(s)
- Thomas Gebhardt
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Simone L Park
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.
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16
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Bonté PE, Metoikidou C, Heurtebise-Chretien S, Arribas YA, Sutra Del Galy A, Ye M, Niborski LL, Zueva E, Piaggio E, Seguin-Givelet A, Girard N, Alanio C, Burbage M, Goudot C, Amigorena S. Selective control of transposable element expression during T cell exhaustion and anti-PD-1 treatment. Sci Immunol 2023; 8:eadf8838. [PMID: 37889984 DOI: 10.1126/sciimmunol.adf8838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 09/01/2023] [Indexed: 10/29/2023]
Abstract
In chronic infections and cancer, T cells are exposed to prolonged antigen stimulation, resulting in loss of function (or exhaustion) and impairment of effective immunological protection. Exhausted T cells are heterogeneous and include early progenitors (Tpex) and terminally exhausted cells (Tex). Here, we used bulk and single-cell transcriptomics to analyze expression of transposable elements (TEs) in subpopulations of mouse and human CD8+ tumor-infiltrating T lymphocytes (TILs). We show that in mice, members of the virus-like murine VL30 TE family (mostly intact, evolutionary young ERV1s) are strongly repressed in terminally exhausted CD8+ T cells in both tumor and viral models of exhaustion. Tpex expression of these VL30s, which are mainly intergenic and transcribed independently of their closest gene neighbors, was driven by Fli1, a transcription factor involved in progression from Tpex to Tex. Immune checkpoint blockade (ICB) in both mice and patients with cancer increased TE expression (including VL30 in mice), demonstrating that TEs may be applicable as ICB response biomarkers. We conclude that expression of TEs is tightly regulated in TILs during establishment of exhaustion and reprogramming by ICB. Analyses of TE expression on single cells and bulk populations open opportunities for understanding immune cell identity and heterogeneity, as well as for defining cellular gene expression signatures and disease biomarkers.
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Affiliation(s)
- Pierre-Emmanuel Bonté
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | - Christina Metoikidou
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | | | - Yago A Arribas
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | | | - Mengliang Ye
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | | | - Elina Zueva
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | - Eliane Piaggio
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | | | - Nicolas Girard
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
- Institut Curie, Institut du Thorax Curie Montsouris, Paris 75005, France
- Paris Saclay, UVSQ, UFR Simmone Veil, Versailles 78000, France
| | - Cécile Alanio
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
- Laboratoire d'immunologie clinique, Institut Curie, Paris 75005, France
- Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA
| | - Marianne Burbage
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | - Christel Goudot
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | - Sebastian Amigorena
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
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17
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Kasmani MY, Topchyan P, Brown AK, Brown RJ, Wu X, Chen Y, Khatun A, Alson D, Wu Y, Burns R, Lin CW, Kudek MR, Sun J, Cui W. A spatial sequencing atlas of age-induced changes in the lung during influenza infection. Nat Commun 2023; 14:6597. [PMID: 37852965 PMCID: PMC10584893 DOI: 10.1038/s41467-023-42021-y] [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: 06/06/2022] [Accepted: 09/26/2023] [Indexed: 10/20/2023] Open
Abstract
Influenza virus infection causes increased morbidity and mortality in the elderly. Aging impairs the immune response to influenza, both intrinsically and because of altered interactions with endothelial and pulmonary epithelial cells. To characterize these changes, we performed single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and bulk RNA sequencing (bulk RNA-seq) on lung tissue from young and aged female mice at days 0, 3, and 9 post-influenza infection. Our analyses identified dozens of key genes differentially expressed in kinetic, age-dependent, and cell type-specific manners. Aged immune cells exhibited altered inflammatory, memory, and chemotactic profiles. Aged endothelial cells demonstrated characteristics of reduced vascular wound healing and a prothrombotic state. Spatial transcriptomics identified novel profibrotic and antifibrotic markers expressed by epithelial and non-epithelial cells, highlighting the complex networks that promote fibrosis in aged lungs. Bulk RNA-seq generated a timeline of global transcriptional activity, showing increased expression of genes involved in inflammation and coagulation in aged lungs. Our work provides an atlas of high-throughput sequencing methodologies that can be used to investigate age-related changes in the response to influenza virus, identify novel cell-cell interactions for further study, and ultimately uncover potential therapeutic targets to improve health outcomes in the elderly following influenza infection.
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Affiliation(s)
- Moujtaba Y Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Paytsar Topchyan
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Ashley K Brown
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Ryan J Brown
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Xiaopeng Wu
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Yao Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Achia Khatun
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Donia Alson
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Yue Wu
- Carter Immunology Center, University of Virginia, Charlottesville, VA, 22908, USA
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22908, USA
| | - Robert Burns
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Chien-Wei Lin
- Department of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Matthew R Kudek
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Jie Sun
- Carter Immunology Center, University of Virginia, Charlottesville, VA, 22908, USA
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22908, USA
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA.
- Department of Pathology, Northwestern University, Chicago, IL, 60611, USA.
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18
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Giles JR, Globig AM, Kaech SM, Wherry EJ. CD8 + T cells in the cancer-immunity cycle. Immunity 2023; 56:2231-2253. [PMID: 37820583 PMCID: PMC11237652 DOI: 10.1016/j.immuni.2023.09.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023]
Abstract
CD8+ T cells are end effectors of cancer immunity. Most forms of effective cancer immunotherapy involve CD8+ T cell effector function. Here, we review the current understanding of T cell function in cancer, focusing on key CD8+ T cell subtypes and states. We discuss factors that influence CD8+ T cell differentiation and function in cancer through a framework that incorporates the classic three-signal model and a fourth signal-metabolism-and also consider the impact of the tumor microenvironment from a T cell perspective. We argue for the notion of immunotherapies as "pro-drugs" that act to augment or modulate T cells, which ultimately serve as the drug in vivo, and for the importance of overall immune health in cancer treatment and prevention. The progress in understanding T cell function in cancer has and will continue to improve harnessing of the immune system across broader tumor types to benefit more patients.
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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 and Immune Health, 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
| | - Anna-Maria Globig
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, 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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19
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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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20
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Baysoy A, Bai Z, Satija R, Fan R. The technological landscape and applications of single-cell multi-omics. Nat Rev Mol Cell Biol 2023; 24:695-713. [PMID: 37280296 PMCID: PMC10242609 DOI: 10.1038/s41580-023-00615-w] [Citation(s) in RCA: 114] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 06/08/2023]
Abstract
Single-cell multi-omics technologies and methods characterize cell states and activities by simultaneously integrating various single-modality omics methods that profile the transcriptome, genome, epigenome, epitranscriptome, proteome, metabolome and other (emerging) omics. Collectively, these methods are revolutionizing molecular cell biology research. In this comprehensive Review, we discuss established multi-omics technologies as well as cutting-edge and state-of-the-art methods in the field. We discuss how multi-omics technologies have been adapted and improved over the past decade using a framework characterized by optimization of throughput and resolution, modality integration, uniqueness and accuracy, and we also discuss multi-omics limitations. We highlight the impact that single-cell multi-omics technologies have had in cell lineage tracing, tissue-specific and cell-specific atlas production, tumour immunology and cancer genetics, and in mapping of cellular spatial information in fundamental and translational research. Finally, we discuss bioinformatics tools that have been developed to link different omics modalities and elucidate functionality through the use of better mathematical modelling and computational methods.
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Affiliation(s)
- Alev Baysoy
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Rahul Satija
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
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21
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Borys SM, Reilly SP, Magill I, Zemmour D, Brossay L. PD-1 Mediated Regulation of Unique Activated CD8 + T Cells by NK Cells in the Submandibular Gland. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.557930. [PMID: 37745414 PMCID: PMC10515922 DOI: 10.1101/2023.09.15.557930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The increasing utilization of anti-PD-1 immune checkpoint blockade (ICB) has led to the emergence of immune-related adverse events (irAEs), including sicca syndrome. Interestingly, we found that the submandibular gland (SMG) of PD-1 deficient mice harbors a large population of CD8 + T cells, reminiscing ICB induced sicca. This phenotype was also observed in the SMG of both NK cell-depleted C57BL/6 animals and NK cell-deficient animals. Mechanistically, using mice conditionally deficient for PD-L1 in the NK cell lineage, we discovered that NK cells regulate CD8 + T cell homeostasis via the PD-1/PD-L1 axis in this organ. Importantly, single-cell RNA sequencing of PD-1 deficient SMG CD8 + T cells reveals a unique transcriptional profile consistent with TCR activation. These cells have limited TCR diversity and phenotypically overlap with GzmK + CD8 + T autoimmune cells identified in primary Sjögren's syndrome patients. These insights into NK cell immunoregulation in the SMG, and the consequences of disrupted CD8 + T cell homeostasis, provide opportunities for preventing the development of irAEs. Highlights Elevated CD8 + T cells in the submandibular gland (SMG) of PD-1 deficient mice parallel sicca-like irAEs seen in ICB patients. In addition to their previously described hyporesponsive phenotype, NK cells in the SMG regulate CD8 + T cell homeostasis through the PD-L1/PD-1 axis. PD-1 deficient SMG CD8 + T cells display unique transcriptional profiles associated with proinflammatory functions, TCR activation, interferon stimulation, and exhaustion. Oligoclonal expansion and similarities in TCR sequences indicate T cell activation and a preference for recognizing specific antigens.
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22
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Lan X, Zebley CC, Youngblood B. Cellular and molecular waypoints along the path of T cell exhaustion. Sci Immunol 2023; 8:eadg3868. [PMID: 37656775 PMCID: PMC10618911 DOI: 10.1126/sciimmunol.adg3868] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/09/2023] [Indexed: 09/03/2023]
Abstract
Thirty years of foundational research investigating molecular and cellular mechanisms promoting T cell exhaustion are now enabling rational design of T cell-based therapies for the treatment of chronic infections and cancer. Once described as a static cell fate, it is now well appreciated that the developmental path toward exhaustion is composed of a heterogeneous pool of cells with varying degrees of effector potential that ultimately converge on a terminally differentiated state. Recent description of the developmental stages along the differentiation trajectory of T cell exhaustion has provided insight into past immunotherapeutic success and future opportunities. Here, we discuss the hallmarks of distinct developmental stages occurring along the path to T cell dysfunction and the impact of these discrete CD8+ T cell fates on cancer immunotherapy.
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Affiliation(s)
- Xin Lan
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Caitlin C. Zebley
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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23
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McClory SE, Bardhan O, Rome KS, Giles JR, Baxter AE, Xu L, Gimotty PA, Faryabi RB, Wherry EJ, Pear WS, Jordan MS. The pseudokinase Trib1 regulates the transition of exhausted T cells to a KLR + CD8 + effector state, and its deletion improves checkpoint blockade. Cell Rep 2023; 42:112905. [PMID: 37527035 PMCID: PMC10540077 DOI: 10.1016/j.celrep.2023.112905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/22/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023] Open
Abstract
CD8+ T cell exhaustion (TEX) impairs the ability of T cells to clear chronic infection or cancer. While TEX are hypofunctional, some TEX retain effector gene signatures, a feature associated with killer lectin-like receptor (KLR) expression. Although KLR+ TEX (TKLR) may improve control of chronic antigen, the signaling molecules regulating this population are poorly understood. Using single-cell RNA sequencing (scRNA-seq), flow cytometry, RNA velocity, and single-cell T cell receptor sequencing (scTCR-seq), we demonstrate that deleting the pseudokinase Trib1 shifts TEX toward CX3CR1+ intermediates with robust enrichment of TKLR via clonal T cell expansion. Adoptive transfer studies demonstrate this shift toward CD8+ TKLR in Trib1-deficient cells is CD8 intrinsic, while CD4-depletion studies demonstrate CD4+ T cells are required for improved viral control in Trib1 conditional knockout mice. Further, Trib1 loss augments anti-programmed death-ligand 1 (PD-L1) blockade to improve viral clearance. These data identify Trib1 as an important regulator of CD8+ TEX whose targeting enhances the TKLR effector state and improves checkpoint inhibitor therapy.
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Affiliation(s)
- Susan E McClory
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Oishi Bardhan
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kelly S Rome
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amy E Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lanwei Xu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Phyllis A Gimotty
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Martha S Jordan
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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24
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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: 6] [Impact Index Per Article: 6.0] [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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25
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Chandiran K, Cauley LS. The diverse effects of transforming growth factor-β and SMAD signaling pathways during the CTL response. Front Immunol 2023; 14:1199671. [PMID: 37426662 PMCID: PMC10327426 DOI: 10.3389/fimmu.2023.1199671] [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: 04/03/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
Cytotoxic T lymphocytes (CTLs) play an important role in defense against infections with intracellular pathogens and anti-tumor immunity. Efficient migration is required to locate and destroy infected cells in different regions of the body. CTLs accomplish this task by differentiating into specialized subsets of effector and memory CD8 T cells that traffic to different tissues. Transforming growth factor-beta (TGFβ) belongs to a large family of growth factors that elicit diverse cellular responses via canonical and non-canonical signaling pathways. Canonical SMAD-dependent signaling pathways are required to coordinate changes in homing receptor expression as CTLs traffic between different tissues. In this review, we discuss the various ways that TGFβ and SMAD-dependent signaling pathways shape the cellular immune response and transcriptional programming of newly activated CTLs. As protective immunity requires access to the circulation, emphasis is placed on cellular processes that are required for cell-migration through the vasculature.
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Affiliation(s)
- Karthik Chandiran
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Linda S. Cauley
- Department of Immunology, UCONN Health, Farmington, CT, United States
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26
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Shen Y, Voigt A, Leng X, Rodriguez AA, Nguyen CQ. A current and future perspective on T cell receptor repertoire profiling. Front Genet 2023; 14:1159109. [PMID: 37408774 PMCID: PMC10319011 DOI: 10.3389/fgene.2023.1159109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
T cell receptors (TCR) play a vital role in the immune system's ability to recognize and respond to foreign antigens, relying on the highly polymorphic rearrangement of TCR genes. The recognition of autologous peptides by adaptive immunity may lead to the development and progression of autoimmune diseases. Understanding the specific TCR involved in this process can provide insights into the autoimmune process. RNA-seq (RNA sequencing) is a valuable tool for studying TCR repertoires by providing a comprehensive and quantitative analysis of the RNA transcripts. With the development of RNA technology, transcriptomic data must provide valuable information to model and predict TCR and antigen interaction and, more importantly, identify or predict neoantigens. This review provides an overview of the application and development of bulk RNA-seq and single-cell (SC) RNA-seq to examine the TCR repertoires. Furthermore, discussed here are bioinformatic tools that can be applied to study the structural biology of peptide/TCR/MHC (major histocompatibility complex) and predict antigenic epitopes using advanced artificial intelligence tools.
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Affiliation(s)
- Yiran Shen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Xuebing Leng
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Amy A. Rodriguez
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Cuong Q. Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, United States
- Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, United States
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27
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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: 16] [Impact Index Per Article: 16.0] [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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28
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Yan C, Zheng L, Jiang S, Yang H, Guo J, Jiang LY, Li T, Zhang H, Bai Y, Lou Y, Zhang Q, Liang T, Schamel W, Wang H, Yang W, Wang G, Zhu ZJ, Song BL, Xu C. Exhaustion-associated cholesterol deficiency dampens the cytotoxic arm of antitumor immunity. Cancer Cell 2023:S1535-6108(23)00142-3. [PMID: 37244259 DOI: 10.1016/j.ccell.2023.04.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 02/17/2023] [Accepted: 04/25/2023] [Indexed: 05/29/2023]
Abstract
The concept of targeting cholesterol metabolism to treat cancer has been widely tested in clinics, but the benefits are modest, calling for a complete understanding of cholesterol metabolism in intratumoral cells. We analyze the cholesterol atlas in the tumor microenvironment and find that intratumoral T cells have cholesterol deficiency, while immunosuppressive myeloid cells and tumor cells display cholesterol abundance. Low cholesterol levels inhibit T cell proliferation and cause autophagy-mediated apoptosis, particularly for cytotoxic T cells. In the tumor microenvironment, oxysterols mediate reciprocal alterations in the LXR and SREBP2 pathways to cause cholesterol deficiency of T cells, subsequently leading to aberrant metabolic and signaling pathways that drive T cell exhaustion/dysfunction. LXRβ depletion in chimeric antigen receptor T (CAR-T) cells leads to improved antitumor function against solid tumors. Since T cell cholesterol metabolism and oxysterols are generally linked to other diseases, the new mechanism and cholesterol-normalization strategy might have potential applications elsewhere.
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Affiliation(s)
- Chengsong Yan
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lin Zheng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shutan Jiang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Haochen Yang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jun Guo
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lu-Yi Jiang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Tongzhou Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Haosong Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yibing Bai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu Lou
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wolfgang Schamel
- Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Haopeng Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Weiwei Yang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guangchuan Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Bao-Liang Song
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.
| | - Chenqi Xu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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29
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Tang J, Jia X, Li J, Dong J, Wang J, Li W, Zhu Y, Hu Y, Hou B, Lin C, Cong Y, Ren T, Yan C, Yang H, Lai Q, Zheng H, Bao Y, Gautam N, Wang HR, Xu B, Chen XL, Li Q, Gascoigne NRJ, Fu G. Themis suppresses the effector function of CD8 + T cells in acute viral infection. Cell Mol Immunol 2023; 20:512-524. [PMID: 36977779 PMCID: PMC10203318 DOI: 10.1038/s41423-023-00997-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
CD8+ T cells play a central role in antiviral immune responses. Upon infection, naive CD8+ T cells differentiate into effector cells to eliminate virus-infected cells, and some of these effector cells further differentiate into memory cells to provide long-term protection after infection is resolved. Although extensively investigated, the underlying mechanisms of CD8+ T-cell differentiation remain incompletely understood. Themis is a T-cell-specific protein that plays critical roles in T-cell development. Recent studies using Themis T-cell conditional knockout mice also demonstrated that Themis is required to promote mature CD8+ T-cell homeostasis, cytokine responsiveness, and antibacterial responses. In this study, we used LCMV Armstrong infection as a probe to explore the role of Themis in viral infection. We found that preexisting CD8+ T-cell homeostasis defects and cytokine hyporesponsiveness do not impair viral clearance in Themis T-cell conditional knockout mice. Further analyses showed that in the primary immune response, Themis deficiency promoted the differentiation of CD8+ effector cells and increased their TNF and IFNγ production. Moreover, Themis deficiency impaired memory precursor cell (MPEC) differentiation but promoted short-lived effector cell (SLEC) differentiation. Themis deficiency also enhanced effector cytokine production in memory CD8+ T cells while impairing central memory CD8+ T-cell formation. Mechanistically, we found that Themis mediates PD-1 expression and its signaling in effector CD8+ T cells, which explains the elevated cytokine production in these cells when Themis is disrupted.
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Affiliation(s)
- Jian Tang
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Xian Jia
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Jian Li
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Junchen Dong
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiayu Wang
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Wanyun Li
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yuzhen Zhu
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Yanyan Hu
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Bowen Hou
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Chunjie Lin
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Yu Cong
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Tong Ren
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Changsheng Yan
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Hongying Yang
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Qian Lai
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Haiping Zheng
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yuzhou Bao
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Namrata Gautam
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hong-Rui Wang
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Bing Xu
- Department of Hematology, The First Affiliated Hospital and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
| | - Xiao Lei Chen
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
| | - Qing Li
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
| | - Nicholas R J Gascoigne
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Guo Fu
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
- Department of Hematology, The First Affiliated Hospital and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China.
- Cancer Research Center of Xiamen University, Xiamen, China.
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30
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Zander R, Cui W. Exhausted CD8 + T cells face a developmental fork in the road. Trends Immunol 2023; 44:276-286. [PMID: 36907685 PMCID: PMC10569258 DOI: 10.1016/j.it.2023.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 03/13/2023]
Abstract
Reinvigorating the function of exhausted CD8+ T cells during chronic viral infection and cancer is a major goal of current immunotherapy regimens. Here, we discuss recent advances in our understanding of exhausted CD8+ T cell heterogeneity as well as the potential differentiation trajectories that exhausted T cells follow during chronic infection and/or cancer. We highlight surmounting evidence suggesting that some T cell clones are divergent in nature and can develop into either terminally differentiated effector or exhausted CD8+ T cells. Lastly, we consider the potential therapeutic implications of such a bifurcation model of CD8+ T cell differentiation, including the intriguing hypothesis that redirecting progenitor CD8+ T cell differentiation along an effector pathway may serve as a novel approach to mitigate T cell exhaustion.
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Affiliation(s)
- Ryan Zander
- Department of Microbiology and Immunology, University of Iowa, 431 Newton Road, Iowa City, IA 52242, USA.
| | - Weiguo Cui
- Department of Pathology, Feinberg School of Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA.
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31
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Ford BR, Poholek AC. Regulation and Immunotherapeutic Targeting of the Epigenome in Exhausted CD8 T Cell Responses. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:869-879. [PMID: 36947818 PMCID: PMC10037537 DOI: 10.4049/jimmunol.2200681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/04/2023] [Indexed: 03/24/2023]
Abstract
Exhaustion is a state of CD8 T cell differentiation that occurs in settings of chronic Ag such as tumors, chronic viral infection, and autoimmunity. Cellular differentiation is driven by a series of environmental signals that promote epigenetic landscapes that set transcriptomes needed for function. For CD8 T cells, the epigenome that underlies exhaustion is distinct from effector and memory cell differentiation, suggesting that signals early on set in motion a process where the epigenome is modified to promote a trajectory toward a dysfunctional state. Although we know many signals that promote exhaustion, putting this in the context of the epigenetic changes that occur during differentiation has been less clear. In this review, we aim to summarize the epigenetic changes associated with exhaustion in the context of signals that promote it, highlighting immunotherapeutic studies that support these observations or areas for future therapeutic opportunities.
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Affiliation(s)
- B Rhodes Ford
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA; and Department of Immunology, University of Pittsburgh, Pittsburgh, PA
| | - Amanda C Poholek
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA; and Department of Immunology, University of Pittsburgh, Pittsburgh, PA
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32
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McClory SE, Bardhan O, Rome KS, Giles JR, Baxter AE, Xu L, Gimotty PA, Faryabi RB, Wherry EJ, Pear WS, Jordan MS. The pseudokinase Trib1 regulates the transition of exhausted T cells to a KLR + CD8 + effector state and its deletion improves checkpoint blockade. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528833. [PMID: 36824931 PMCID: PMC9948998 DOI: 10.1101/2023.02.16.528833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
T cell exhaustion (T EX ) impairs the ability of T cells to clear chronic infection or cancer. While exhausted T cells are hypofunctional, some exhausted T cells retain effector gene signatures, a feature that is associated with expression of KLRs (killer lectin-like receptors). Although KLR + T cells may improve control of chronic antigen, the signaling molecules regulating this population are poorly understood. Using scRNA-seq, flow cytometry, RNA velocity, and scTCR-seq, we demonstrate that deleting the pseudokinase Trib1 shifts T EX towards CX3CR1 + intermediates (T INT ) with robust enrichment of KLR + CD8 + T cells (T KLR ) via clonal T cell expansion. These changes are associated with globally increased KLR gene expression throughout the exhaustion program. Further, Trib1 loss augments anti-PD-L1 blockade to improve viral clearance by expanding the T KLR population. Together, these data identify Trib1 as an important regulator of T cell exhaustion whose targeting enhances the KLR + effector state and improves the response to checkpoint inhibitor therapy.
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Affiliation(s)
- Susan E. McClory
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Oishi Bardhan
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kelly S. Rome
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - 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 19104, 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
| | - Lanwei Xu
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Phyllis A. Gimotty
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert B. Faryabi
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School 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 19104, USA
| | - Warren S. Pear
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martha S. Jordan
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, 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 19104, USA
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33
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Topchyan P, Zander R, Kasmani MY, Nguyen C, Brown A, Lin S, Burns R, Cui W. Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection. Cell Rep 2022; 41:111736. [PMID: 36450262 PMCID: PMC9792173 DOI: 10.1016/j.celrep.2022.111736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/08/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
CD4 T cell help is critical to sustain effector CD8 T cell responses during chronic infection, notably via T follicular helper (Tfh)-derived interleukin-21 (IL-21). Conversely, CD4 depletion results in severe CD8 T cell dysfunction and lifelong viremia despite CD4 T cell reemergence following transient depletion. These observations suggest that repopulating CD4 subsets are functionally or numerically insufficient to orchestrate a robust CD8 response. We utilize spatial transcriptomics and single-cell RNA sequencing (scRNA-seq) to investigate CD4 T cell heterogeneity under CD4-replete and -deplete conditions and explore cellular interactions during chronic infection. Although IL-21-producing Tfh cells repopulate following transient CD4 depletion, they are outnumbered by immunomodulatory CD4 T cells. Moreover, the splenic architecture appears perturbed, with decreases in white pulp regions, coinciding with germinal center losses. These disruptions in splenic architecture are associated with diminished Tfh and progenitor CD8 T cell colocalization, providing a potential mechanism for impaired progenitor-to-effector CD8 T cell differentiation during "un-helped" conditions.
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Affiliation(s)
- Paytsar Topchyan
- Blood Research Institute, Versiti Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53213, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, 8701 West Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Ryan Zander
- Blood Research Institute, Versiti Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53213, USA
| | - Moujtaba Y Kasmani
- Blood Research Institute, Versiti Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53213, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, 8701 West Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Christine Nguyen
- Blood Research Institute, Versiti Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53213, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, 8701 West Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Ashley Brown
- Blood Research Institute, Versiti Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53213, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, 8701 West Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Siying Lin
- Blood Research Institute, Versiti Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53213, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, 8701 West Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Robert Burns
- Blood Research Institute, Versiti Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53213, USA
| | - Weiguo Cui
- Blood Research Institute, Versiti Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53213, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, 8701 West Watertown Plank Road, Milwaukee, WI 53226, USA.
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