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Shannon AE, Teodorescu RN, Soon N, Heil LR, Jacob CC, Remes PM, Rubinstein MP, Searle BC. A workflow for targeted proteomics assay development using a versatile linear ion trap. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596891. [PMID: 38853838 PMCID: PMC11160733 DOI: 10.1101/2024.05.31.596891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Advances in proteomics and mass spectrometry have enabled the study of limited cell populations, such as single-cell proteomics, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive nominal resolution measurements, these instruments are effectively limited to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. We demonstrate a workflow using a newly released, hybrid quadrupole-LIT instrument for developing targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Gas-phase fraction-based DIA enables rapid target library generation in the same background chemical matrix as each quantitative injection. Using a new software tool embedded within EncyclopeDIA for scheduling parallel reaction monitoring assays, we show consistent quantification across three orders of magnitude of input material. Using this approach, we demonstrate measuring peptide quantitative linearity down to 25x dilution in a background of only a 1 ng proteome without requiring stable isotope labeled standards. At 1 ng total protein on column, we found clear consistency between immune cell populations measured using flow cytometry and immune markers measured using LIT-based proteomics. We believe hybrid quadrupole-LIT instruments represent an economic solution to democratizing mass spectrometry in a wide variety of laboratory settings.
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2
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Layug PJ, Vats H, Kannan K, Arsenio J. Sex differences in CD8 + T cell responses during adaptive immunity. WIREs Mech Dis 2024:e1645. [PMID: 38581141 DOI: 10.1002/wsbm.1645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 02/08/2024] [Accepted: 03/14/2024] [Indexed: 04/08/2024]
Abstract
Biological sex is an important variable that influences the immune system's susceptibility to infectious and non-infectious diseases and their outcomes. Sex dimorphic features in innate and adaptive immune cells and their activities may help to explain sex differences in immune responses. T lymphocytes in the adaptive immune system are essential to providing protection against infectious and chronic inflammatory diseases. In this review, T cell responses are discussed with focus on the current knowledge of biological sex differences in CD8+ T cell mediated adaptive immune responses in infectious and chronic inflammatory diseases. Future directions aimed at investigating the molecular and cellular mechanisms underlying sex differences in diverse T cell responses will continue to underscore the significance of understanding sex differences in protective immunity at the cellular level, to induce appropriate T cell-based immune responses in infection, autoimmunity, and cancer. This article is categorized under: Immune System Diseases > Molecular and Cellular Physiology Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Paul Jerard Layug
- Department of Internal Medicine, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, Manitoba, Canada
| | - Harman Vats
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, Manitoba, Canada
- Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kamali Kannan
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, Manitoba, Canada
- Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Janilyn Arsenio
- Department of Internal Medicine, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, Manitoba, Canada
- Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
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3
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Turner L, Van Le TN, Cross E, Queriault C, Knight M, Trihemasava K, Davis J, Schaefer P, Nguyen J, Xu J, Goldspiel B, Hall E, Rome K, Scaglione M, Eggert J, Au-Yeung B, Wallace DC, Mesaros C, Baur JA, Bailis W. Single-cell NAD(H) levels predict clonal lymphocyte expansion dynamics. Sci Immunol 2024; 9:eadj7238. [PMID: 38489349 PMCID: PMC11064129 DOI: 10.1126/sciimmunol.adj7238] [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: 07/12/2023] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
Adaptive immunity requires the expansion of high-affinity lymphocytes from a heterogeneous pool. Whereas current models explain this through signal transduction, we hypothesized that antigen affinity tunes discrete metabolic pathways to license clonal lymphocyte dynamics. Here, we identify nicotinamide adenine dinucleotide (NAD) biosynthesis as a biochemical hub for the T cell receptor affinity-dependent metabolome. Through this central anabolic role, we found that NAD biosynthesis governs a quiescence exit checkpoint, thereby pacing proliferation. Normalizing cellular NAD(H) likewise normalizes proliferation across affinities, and enhancing NAD biosynthesis permits the expansion of lower affinity clones. Furthermore, single-cell differences in NAD(H) could predict division potential for both T and B cells, before the first division, unmixing proliferative heterogeneity. We believe that this supports a broader paradigm in which complex signaling networks converge on metabolic pathways to control single-cell behavior.
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Affiliation(s)
- Lucien Turner
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Tran Ngoc Van Le
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Eric Cross
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104
| | - Clemence Queriault
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Montana Knight
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Krittin Trihemasava
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - James Davis
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104
| | - Patrick Schaefer
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Janet Nguyen
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Jimmy Xu
- Center of Excellence in Environmental Toxicology & Department of Systems Pharmacology & Translational Therapeutics, University of Pennsylvania; Philadelphia, PA 19104
| | - Brian Goldspiel
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Elise Hall
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Kelly Rome
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Michael Scaglione
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
| | - Joel Eggert
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University; Atlanta, GA 30322
| | - Byron Au-Yeung
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University; Atlanta, GA 30322
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
- Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104
| | - Clementina Mesaros
- Center of Excellence in Environmental Toxicology & Department of Systems Pharmacology & Translational Therapeutics, University of Pennsylvania; Philadelphia, PA 19104
| | - Joseph A Baur
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104
| | - Will Bailis
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104
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4
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Kaminskiy Y, Ganeeva I, Chasov V, Kudriaeva A, Bulatov E. Asymmetric T-cell division: insights from cutting-edge experimental techniques and implications for immunotherapy. Front Immunol 2024; 15:1301378. [PMID: 38495874 PMCID: PMC10940324 DOI: 10.3389/fimmu.2024.1301378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/02/2024] [Indexed: 03/19/2024] Open
Abstract
Asymmetric cell division is a fundamental process conserved throughout evolution, employed by both prokaryotic and eukaryotic organisms. Its significance lies in its ability to govern cell fate and facilitate the generation of diverse cell types. Therefore, attaining a detailed mechanistic understanding of asymmetric cell division becomes essential for unraveling the complexities of cell fate determination in both healthy and pathological conditions. However, the role of asymmetric division in T-cell biology has only recently been unveiled. Here, we provide an overview of the T-cell asymmetric division field with the particular emphasis on experimental methods and models with the aim to guide the researchers in the selection of appropriate in vitro/in vivo models to study asymmetric division in T cells. We present a comprehensive investigation into the mechanisms governing the asymmetric division in various T-cell subsets underscoring the importance of the asymmetry in fate-determining factor segregation and transcriptional and epigenetic regulation. Furthermore, the intricate interplay of T-cell receptor signaling and the asymmetric division geometry are explored, shedding light on the spatial organization and the impact on cellular fate.
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Affiliation(s)
- Yaroslav Kaminskiy
- Department of Oncology and Pathology, Karolinska Institutet, SciLifeLab, Solna, Sweden
| | - Irina Ganeeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Vitaly Chasov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Anna Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Emil Bulatov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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5
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Abadie K, Clark EC, Valanparambil RM, Ukogu O, Yang W, Daza RM, Ng KKH, Fathima J, Wang AL, Lee J, Nasti TH, Bhandoola A, Nourmohammad A, Ahmed R, Shendure J, Cao J, Kueh HY. Reversible, tunable epigenetic silencing of TCF1 generates flexibility in the T cell memory decision. Immunity 2024; 57:271-286.e13. [PMID: 38301652 PMCID: PMC10922671 DOI: 10.1016/j.immuni.2023.12.006] [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: 03/09/2023] [Revised: 10/09/2023] [Accepted: 12/07/2023] [Indexed: 02/03/2024]
Abstract
The immune system encodes information about the severity of a pathogenic threat in the quantity and type of memory cells it forms. This encoding emerges from lymphocyte decisions to maintain or lose self-renewal and memory potential during a challenge. By tracking CD8+ T cells at the single-cell and clonal lineage level using time-resolved transcriptomics, quantitative live imaging, and an acute infection model, we find that T cells will maintain or lose memory potential early after antigen recognition. However, following pathogen clearance, T cells may regain memory potential if initially lost. Mechanistically, this flexibility is implemented by a stochastic cis-epigenetic switch that tunably and reversibly silences the memory regulator, TCF1, in response to stimulation. Mathematical modeling shows how this flexibility allows memory T cell numbers to scale robustly with pathogen virulence and immune response magnitudes. We propose that flexibility and stochasticity in cellular decisions ensure optimal immune responses against diverse threats.
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Affiliation(s)
- Kathleen Abadie
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Elisa C Clark
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Rajesh M Valanparambil
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Obinna Ukogu
- Department of Applied Mathematics, University of Washington, Seattle, WA 98105, USA
| | - Wei Yang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kenneth K H Ng
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Jumana Fathima
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Allan L Wang
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Judong Lee
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Tahseen H Nasti
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Avinash Bhandoola
- T-Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Armita Nourmohammad
- Department of Applied Mathematics, University of Washington, Seattle, WA 98105, USA; Department of Physics, University of Washington, Seattle, WA 98105, USA; Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rafi Ahmed
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA.
| | - Junyue Cao
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Laboratory of Single-Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY 10065, USA.
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA.
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6
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Bulliard Y, Andersson BS, Baysal MA, Damiano J, Tsimberidou AM. Reprogramming T cell differentiation and exhaustion in CAR-T cell therapy. J Hematol Oncol 2023; 16:108. [PMID: 37880715 PMCID: PMC10601191 DOI: 10.1186/s13045-023-01504-7] [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: 08/24/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
T cell differentiation is a highly regulated, multi-step process necessary for the progressive establishment of effector functions, immunological memory, and long-term control of pathogens. In response to strong stimulation, as seen in severe or chronic infections or cancer, T cells acquire a state of hypo-responsiveness known as exhaustion, limiting their effector function. Recent advances in autologous chimeric antigen receptor (CAR)-T cell therapies have revolutionized the treatment of hematologic malignancies by taking advantage of the basic principles of T cell biology to engineer products that promote long-lasting T cell response. However, many patients' malignancies remain unresponsive to treatment or are prone to recur. Discoveries in T cell biology, including the identification of key regulators of differentiation and exhaustion, offer novel opportunities to have a durable impact on the fate of CAR-T cells after infusion. Such next-generation CAR-T cell therapies and their clinical implementation may result in the next leap forward in cancer treatment for selected patients. In this context, this review summarizes the foundational principles of T cell differentiation and exhaustion and describes how they can be utilized and targeted to further improve the design and efficacy of CAR-T cell therapies.
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Affiliation(s)
| | - Borje S Andersson
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Mehmet A Baysal
- Unit 455, Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Jason Damiano
- Appia Bio, 6160 Bristol Pkwy, Culver City, CA, 90230, USA
| | - Apostolia M Tsimberidou
- Unit 455, Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA.
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7
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Vick LV, Canter RJ, Monjazeb AM, Murphy WJ. Multifaceted effects of obesity on cancer immunotherapies: Bridging preclinical models and clinical data. Semin Cancer Biol 2023; 95:88-102. [PMID: 37499846 PMCID: PMC10836337 DOI: 10.1016/j.semcancer.2023.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/04/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
Obesity, defined by excessive body fat, is a highly complex condition affecting numerous physiological processes, such as metabolism, proliferation, and cellular homeostasis. These multifaceted effects impact cells and tissues throughout the host, including immune cells as well as cancer biology. Because of the multifaceted nature of obesity, common parameters used to define it (such as body mass index in humans) can be problematic, and more nuanced methods are needed to characterize the pleiotropic metabolic effects of obesity. Obesity is well-accepted as an overall negative prognostic factor for cancer incidence, progression, and outcome. This is in part due to the meta-inflammatory and immunosuppressive effects of obesity. Immunotherapy is increasingly used in cancer therapy, and there are many different types of immunotherapy approaches. The effects of obesity on immunotherapy have only recently been studied with the demonstration of an "obesity paradox", in which some immune therapies have been demonstrated to result in greater efficacy in obese subjects despite the direct adverse effects of obesity and excess body fat acting on the cancer itself. The multifactorial characteristics that influence the effects of obesity (age, sex, lean muscle mass, underlying metabolic conditions and drugs) further confound interpretation of clinical data and necessitate the use of more relevant preclinical models mirroring these variables in the human scenario. Such models will allow for more nuanced mechanistic assessment of how obesity can impact, both positively and negatively, cancer biology, host metabolism, immune regulation, and how these intersecting processes impact the delivery and outcome of cancer immunotherapy.
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Affiliation(s)
- Logan V Vick
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Robert J Canter
- Department of Surgery, Division of Surgical Oncology, University of California Davis Comprehensive Cancer Center, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Arta M Monjazeb
- Department of Radiation Oncology, University of California Davis Comprehensive Cancer Center, University of California School of Medicine, Sacramento, CA, USA
| | - William J Murphy
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, CA, USA; Department of Internal Medicine, Division of Malignant Hematology, Cellular Therapy and Transplantation, University of California Davis School of Medicine, Sacramento, CA, USA.
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8
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Terrabuio E, Zenaro E, Constantin G. The role of the CD8+ T cell compartment in ageing and neurodegenerative disorders. Front Immunol 2023; 14:1233870. [PMID: 37575227 PMCID: PMC10416633 DOI: 10.3389/fimmu.2023.1233870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 08/15/2023] Open
Abstract
CD8+ lymphocytes are adaptive immunity cells with the particular function to directly kill the target cell following antigen recognition in the context of MHC class I. In addition, CD8+ T cells may release pro-inflammatory cytokines, such as tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ), and a plethora of other cytokines and chemoattractants modulating immune and inflammatory responses. A role for CD8+ T cells has been suggested in aging and several diseases of the central nervous system (CNS), including Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, limbic encephalitis-induced temporal lobe epilepsy and Susac syndrome. Here we discuss the phenotypic and functional alterations of CD8+ T cell compartment during these conditions, highlighting similarities and differences between CNS disorders. Particularly, we describe the pathological changes in CD8+ T cell memory phenotypes emphasizing the role of senescence and exhaustion in promoting neuroinflammation and neurodegeneration. We also discuss the relevance of trafficking molecules such as selectins, mucins and integrins controlling the extravasation of CD8+ T cells into the CNS and promoting disease development. Finally, we discuss how CD8+ T cells may induce CNS tissue damage leading to neurodegeneration and suggest that targeting detrimental CD8+ T cells functions may have therapeutic effect in CNS disorders.
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Affiliation(s)
- Eleonora Terrabuio
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
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9
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Nizharadze T, Becker NB, Höfer T. Quantitating CD8 + T cell memory development. Trends Immunol 2023; 44:519-529. [PMID: 37277233 DOI: 10.1016/j.it.2023.05.004] [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: 04/17/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023]
Abstract
In acute immune responses to infection, memory T cells develop that can spawn recall responses. This process has not been observable directly in vivo. Here we highlight the utility of mathematical inference to derive quantitatively testable models of mammalian CD8+ T cell memory development from complex experimental data. Previous inference studies suggested that precursors of memory T cells arise early during the immune response. Recent work has both validated a crucial prediction of this T cell diversification model and refined the model. While multiple developmental routes to distinct memory subsets might exist, a branch point occurs early in proliferating T cell blasts, from which separate differentiation pathways emerge for slowly dividing precursors of re-expandable memory cells and rapidly dividing effectors.
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Affiliation(s)
- Tamar Nizharadze
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Nils B Becker
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany.
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10
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Azulay M, Shahar M, Shany E, Elbaz E, Lifshits S, Törngren M, Friedmann A, Kramer R, Hedlund G. Tumor-targeted superantigens produce curative tumor immunity with induction of memory and demonstrated antigen spreading. J Transl Med 2023; 21:222. [PMID: 36967382 PMCID: PMC10041807 DOI: 10.1186/s12967-023-04064-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Despite remarkable progress, the immunotherapies currently used in the clinic, such as immune checkpoint blockade (ICB) therapy, still have limited efficacy against many types of solid tumors. One major barrier to effective treatment is the lack of a durable long-term response. Tumor-targeted superantigen (TTS) therapy may overcome this barrier to enhance therapeutic efficacy. TTS proteins, such as the clinical-stage molecule naptumomab estafenatox (NAP), increase tumor recognition and killing by both coating tumor cells with bacterial-derived superantigens (SAgs) and selectively expanding T-cell lineages that can recognize them. The present study investigated the efficacy and mechanism of action of repeated TTS (C215Fab-SEA) treatments leading to a long-term antitumor immune response as monotherapy or in combination with PD-1/PD-L1 inhibitors in murine tumor models. METHODS We used syngeneic murine tumor models expressing the human EpCAM target (C215 antigen) to assess the efficacy and mechanism of action of repeated treatment with TTS C215Fab-SEA alone or with anti-PD-1/PD-L1 monoclonal antibodies. Tumor draining lymph nodes (TDLNs) and tumor tissues were processed and analyzed by immunophenotyping and immunohistochemistry. Isolated RNA from tumors was used to analyze gene expression and the TCR repertoire. Tumor rechallenge and T-cell transfer studies were conducted to test the long-term antitumor memory response. RESULTS TTS therapy inhibited tumor growth and achieved complete tumor rejection, leading to a T-cell-dependent long-term memory response against the tumor. The antitumor effect was derived from inflammatory responses converting the immunosuppressive TME into a proinflammatory state with an increase in T-cell infiltration, activation and high T-cell diversity. The combination of TTS with ICB therapy was significantly more effective than the monotherapies and resulted in higher tumor-free rates. CONCLUSIONS These new results indicate that TTSs not only can turn a "cold" tumor into a "hot" tumor but also can enable epitope spreading and memory response, which makes TTSs ideal candidates for combination with ICB agents and other anticancer agents.
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Affiliation(s)
| | | | | | - Eti Elbaz
- NeoTX Therapeutics LTD, Rehovot, Israel
| | | | | | - Adam Friedmann
- NeoTX Therapeutics LTD, Rehovot, Israel
- Department of Genetics, The Hebrew University, Jerusalem, Israel
| | | | - Gunnar Hedlund
- NeoTX Therapeutics LTD, Rehovot, Israel
- ImmunoPoint Consulting AB, Lund, Sweden
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11
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Quezada LK, Jin W, Liu YC, Kim ES, He Z, Indralingam CS, Tysl T, Labarta-Bajo L, Wehrens EJ, Jo Y, Kazane KR, Hattori C, Zuniga EI, Yeo GW, Chang JT. Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection. PLoS Biol 2023; 21:e3001983. [PMID: 36716323 PMCID: PMC9886247 DOI: 10.1371/journal.pbio.3001983] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/03/2023] [Indexed: 02/01/2023] Open
Abstract
During a microbial infection, responding CD8+ T cells give rise to effector cells that provide acute host defense and memory cells that provide sustained protection. An alternative outcome is exhaustion, a state of T cell dysfunction that occurs in the context of chronic infections and cancer. Although it is evident that exhausted CD8+ T (TEX) cells are phenotypically and molecularly distinct from effector and memory CD8+ T cells, the factors regulating the earliest events in the differentiation process of TEX cells remain incompletely understood. Here, we performed single-cell RNA-sequencing and single-cell ATAC-sequencing of CD8+ T cells responding to LCMV-Armstrong (LCMV-Arm) or LCMV-Clone 13 (LCMV-Cl13), which result in acute or chronic infections, respectively. Compared to CD8+ T cells that had undergone their first division in response to LCMV-Arm (Div1ARM) cells, CD8+ T cells that had undergone their first division in response to LCMV-Cl13 (Div1CL13) expressed higher levels of genes encoding transcription factors previously associated with exhaustion, along with higher levels of Ezh2, the catalytic component of the Polycomb Repressive Complex 2 (PRC2) complex, which mediates epigenetic silencing. Modulation of Ezh2 resulted in altered expression of exhaustion-associated molecules by CD8+ T cells responding to LCMV-Cl13, though the specific cellular and infectious contexts, rather than simply the level of Ezh2 expression, likely determine the eventual outcome. Taken together, these findings suggest that the differentiation paths of CD8+ T cells responding to acute versus chronic infections may diverge earlier than previously appreciated.
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Affiliation(s)
- Lauren K. Quezada
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Yi Chia Liu
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Eleanor S. Kim
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Cynthia S. Indralingam
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Tiffani Tysl
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Lara Labarta-Bajo
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ellen J. Wehrens
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Yeara Jo
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Katelynn R. Kazane
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Christopher Hattori
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Elina I. Zuniga
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, United States of America
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, California, United States of America
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12
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Nüssing S, Sutton VR, Trapani JA, Parish IA. Beyond target cell death - Granzyme serine proteases in health and disease. Mol Aspects Med 2022; 88:101152. [PMID: 36368281 DOI: 10.1016/j.mam.2022.101152] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 10/06/2022] [Accepted: 10/22/2022] [Indexed: 11/09/2022]
Abstract
Granzymes are a family of small (∼32 kDa) serine proteases with a range of substrate specificities that are stored in, and released from, the cytoplasmic secretory vesicles ('granules') of cytotoxic T lymphocytes and natural killer cells. Granzymes are not digestive proteases but finely tuned processing enzymes that target their substrates in specific ways to activate various signalling pathways, or to inactivate viral proteins and other targets. Great emphasis has been placed on studying the pro-apoptotic functions of granzymes, which largely depend on their synergy with the pore-forming protein perforin, on which they rely for penetration into the target cell cytosol to access their substrates. While a critical role for granzyme B in target cell apoptosis is undisputed, both it and the remaining granzymes also influence a variety of other biological processes (including important immunoregulatory functions), which are discussed in this review. This includes the targeting of many extracellular as well as intracellular substrates, and can also lead to deleterious outcomes for the host if granzyme expression or function are dysregulated or abrogated. A final important consideration is that granzyme repertoire, biochemistry and function vary considerably across species, probably resulting from the pressures applied by viruses and other pathogens across evolutionary time. This has implications for the interpretation of granzyme function in preclinical models of disease.
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Affiliation(s)
- Simone Nüssing
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Vivien R Sutton
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Joseph A Trapani
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3052, Australia.
| | - Ian A Parish
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3052, Australia; John Curtin School of Medical Research, ANU, ACT, Australia.
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13
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Huang J, Leary S, Xiang J. Distinct strengths of mTORC1 control T-cell memory via transcriptional FOXO1 and metabolic AMPKα1 pathways in linear cell differentiation and asymmetric cell division models. Cell Mol Immunol 2022; 19:1073-1076. [PMID: 35589987 PMCID: PMC9508075 DOI: 10.1038/s41423-022-00879-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 01/26/2023] Open
Affiliation(s)
- Junqiong Huang
- Cancer Research Cluster, Saskatchewan Cancer Agency, Saskatoon, SK, Canada
- Department of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Blood Transfusion, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Scot Leary
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jim Xiang
- Cancer Research Cluster, Saskatchewan Cancer Agency, Saskatoon, SK, Canada.
- Department of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
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14
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Todorov H, Prieux M, Laubreton D, Bouvier M, Wang S, de Bernard S, Arpin C, Cannoodt R, Saelens W, Bonnaffoux A, Gandrillon O, Crauste F, Saeys Y, Marvel J. CD8 memory precursor cell generation is a continuous process. iScience 2022; 25:104927. [PMID: 36065187 PMCID: PMC9440290 DOI: 10.1016/j.isci.2022.104927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/21/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022] Open
Abstract
In this work, we studied the generation of memory precursor cells following an acute infection by analyzing single-cell RNA-seq data that contained CD8 T cells collected during the postinfection expansion phase. We used different tools to reconstruct the developmental trajectory that CD8 T cells followed after activation. Cells that exhibited a memory precursor signature were identified and positioned on this trajectory. We found that these memory precursors are generated continuously with increasing numbers arising over time. Similarly, expression of genes associated with effector functions was also found to be raised in memory precursors at later time points. The ability of cells to enter quiescence and differentiate into memory cells was confirmed by BrdU pulse-chase experiment in vivo. Analysis of cell counts indicates that the vast majority of memory cells are generated at later time points from cells that have extensively divided. Trajectory inference tools reconstruct the timing of memory precursors generation The trajectory is defined by both cell cycle and effector functions encoding genes Memory precursors numbers in lymphoid organs increase with time after priming In vivo BrdU labeling validate the in silico data
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Affiliation(s)
- Helena Todorov
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | - Margaux Prieux
- Centre International de recherche en Infectiologie, Université de Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Superieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Laboratoire de Biologie et de Modélisation de la cellule, Université de Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Daphne Laubreton
- Centre International de recherche en Infectiologie, Université de Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Superieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Matteo Bouvier
- Laboratoire de Biologie et de Modélisation de la cellule, Université de Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Lyon, France
- Vidium, Lyon, France
| | - Shaoying Wang
- Centre International de recherche en Infectiologie, Université de Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Superieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Christophe Arpin
- Centre International de recherche en Infectiologie, Université de Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Superieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Robrecht Cannoodt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Data Intuitive, Lebbeke, Belgium
| | - Wouter Saelens
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | | | - Olivier Gandrillon
- Laboratoire de Biologie et de Modélisation de la cellule, Université de Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Lyon, France
- Inria, Villeurbanne, France
| | - Fabien Crauste
- Laboratoire MAP5 (UMR CNRS 8145), Université de Paris, Paris, France
| | - Yvan Saeys
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | - Jacqueline Marvel
- Centre International de recherche en Infectiologie, Université de Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Superieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Corresponding author
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15
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Estrada LD, Ağaç Çobanoğlu D, Wise A, Maples RW, Çobanoğlu MC, Farrar JD. Adrenergic signaling controls early transcriptional programs during CD8+ T cell responses to viral infection. PLoS One 2022; 17:e0272017. [PMID: 35944008 PMCID: PMC9362915 DOI: 10.1371/journal.pone.0272017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/11/2022] [Indexed: 11/27/2022] Open
Abstract
Norepinephrine is a key sympathetic neurotransmitter, which acts to suppress CD8 + T cell cytokine secretion and lytic activity by signaling through the β2-adrenergic receptor (ADRB2). Although ADRB2 signaling is considered generally immunosuppressive, its role in regulating the differentiation of effector T cells in response to infection has not been investigated. Using an adoptive transfer approach, we compared the expansion and differentiation of wild type (WT) to Adrb2-/- CD8 + T cells throughout the primary response to vesicular stomatitis virus (VSV) infection in vivo. We measured the dynamic changes in transcriptome profiles of antigen-specific CD8 + T cells as they responded to VSV. Within the first 7 days of infection, WT cells out-paced the expansion of Adrb2-/- cells, which correlated with reduced expression of IL-2 and the IL-2Rα in the absence of ADRB2. RNASeq analysis identified over 300 differentially expressed genes that were both temporally regulated following infection and selectively regulated in WT vs Adrb2-/- cells. These genes contributed to major transcriptional pathways including cytokine receptor activation, signaling in cancer, immune deficiency, and neurotransmitter pathways. By parsing genes within groups that were either induced or repressed over time in response to infection, we identified three main branches of genes that were differentially regulated by the ADRB2. These gene sets were predicted to be regulated by specific transcription factors involved in effector T cell development, such as Tbx21 and Eomes. Collectively, these data demonstrate a significant role for ADRB2 signaling in regulating key transcriptional pathways during CD8 + T cells responses to infection that may dramatically impact their functional capabilities and downstream memory cell development.
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Affiliation(s)
- Leonardo D. Estrada
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Didem Ağaç Çobanoğlu
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Aaron Wise
- Encodia Inc., San Diego, CA, United States of America
| | - Robert W. Maples
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Murat Can Çobanoğlu
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - J. David Farrar
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, United States of America
- * E-mail:
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16
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Cheong A, Nagel ZD. Human Variation in DNA Repair, Immune Function, and Cancer Risk. Front Immunol 2022; 13:899574. [PMID: 35935942 PMCID: PMC9354717 DOI: 10.3389/fimmu.2022.899574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
DNA damage constantly threatens genome integrity, and DNA repair deficiency is associated with increased cancer risk. An intuitive and widely accepted explanation for this relationship is that unrepaired DNA damage leads to carcinogenesis due to the accumulation of mutations in somatic cells. But DNA repair also plays key roles in the function of immune cells, and immunodeficiency is an important risk factor for many cancers. Thus, it is possible that emerging links between inter-individual variation in DNA repair capacity and cancer risk are driven, at least in part, by variation in immune function, but this idea is underexplored. In this review we present an overview of the current understanding of the links between cancer risk and both inter-individual variation in DNA repair capacity and inter-individual variation in immune function. We discuss factors that play a role in both types of variability, including age, lifestyle, and environmental exposures. In conclusion, we propose a research paradigm that incorporates functional studies of both genome integrity and the immune system to predict cancer risk and lay the groundwork for personalized prevention.
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17
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Richard AC. Divide and Conquer: Phenotypic and Temporal Heterogeneity Within CD8+ T Cell Responses. Front Immunol 2022; 13:949423. [PMID: 35911755 PMCID: PMC9334874 DOI: 10.3389/fimmu.2022.949423] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/22/2022] [Indexed: 11/23/2022] Open
Abstract
The advent of technologies that can characterize the phenotypes, functions and fates of individual cells has revealed extensive and often unexpected levels of diversity between cells that are nominally of the same subset. CD8+ T cells, also known as cytotoxic T lymphocytes (CTLs), are no exception. Investigations of individual CD8+ T cells both in vitro and in vivo have highlighted the heterogeneity of cellular responses at the levels of activation, differentiation and function. This review takes a broad perspective on the topic of heterogeneity, outlining different forms of variation that arise during a CD8+ T cell response. Specific attention is paid to the impact of T cell receptor (TCR) stimulation strength on heterogeneity. In particular, this review endeavors to highlight connections between variation at different cellular stages, presenting known mechanisms and key open questions about how variation between cells can arise and propagate.
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18
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Ying T, Alexander H. Quantifying information of intracellular signaling: progress with machine learning. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:10.1088/1361-6633/ac7a4a. [PMID: 35724636 PMCID: PMC9507437 DOI: 10.1088/1361-6633/ac7a4a] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Cells convey information about their extracellular environment to their core functional machineries. Studying the capacity of intracellular signaling pathways to transmit information addresses fundamental questions about living systems. Here, we review how information-theoretic approaches have been used to quantify information transmission by signaling pathways that are functionally pleiotropic and subject to molecular stochasticity. We describe how recent advances in machine learning have been leveraged to address the challenges of complex temporal trajectory datasets and how these have contributed to our understanding of how cells employ temporal coding to appropriately adapt to environmental perturbations.
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Affiliation(s)
- Tang Ying
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- International Academic Center of Complex Systems, Beijing Normal University, Zhuhai 519087, China
| | - Hoffmann Alexander
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
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19
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Li Y, Li X, Geng X, Zhao H. The IL-2A receptor pathway and its role in lymphocyte differentiation and function. Cytokine Growth Factor Rev 2022; 67:66-79. [DOI: 10.1016/j.cytogfr.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/03/2022]
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20
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Vardam-Kaur T, van Dijk S, Peng C, Wanhainen KM, Jameson SC, Borges da Silva H. The Extracellular ATP Receptor P2RX7 Imprints a Promemory Transcriptional Signature in Effector CD8 + T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1686-1699. [PMID: 35264459 PMCID: PMC8976739 DOI: 10.4049/jimmunol.2100555] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
Development of CD8+ central memory T (Tcm) and resident memory T (Trm) cells, which promote immunity in the circulation and in barrier tissues, respectively, is not completely understood. Tcm and Trm cells may arise from common precursors; however, their fate-inducing signals are elusive. We found that virus-specific effector CD8+ T cells display heterogeneous expression of the extracellular ATP sensor P2RX7. P2RX7-high expression is confined, at peak effector phase, to CD62L+ memory precursors, which preferentially form Tcm cells. Among early effector CD8+ T cells, asymmetrical P2RX7 distribution correlated with distinct transcriptional signatures, with P2RX7-high cells enriched for memory and tissue residency sets. P2RX7-high early effectors preferentially form both Tcm and Trm cells. Defective Tcm and Trm cell formation in P2RX7 deficiency is significantly reverted when the transcriptional repressor Zeb2 is ablated. Mechanistically, P2RX7 negatively regulates Zeb2 expression, at least partially through TGF-β sensing in early effector CD8+ T cells. Our study indicates that unequal P2RX7 upregulation in effector CD8+ T cells is a foundational element of the early Tcm/Trm fate.
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Affiliation(s)
| | - Sarah van Dijk
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, AZ; and
| | - Changwei Peng
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Kelsey M Wanhainen
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Stephen C Jameson
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
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21
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STAT3 Role in T-Cell Memory Formation. Int J Mol Sci 2022; 23:ijms23052878. [PMID: 35270020 PMCID: PMC8910982 DOI: 10.3390/ijms23052878] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 12/12/2022] Open
Abstract
Along with the clinical success of immuno-oncology drugs and cellular therapies, T-cell biology has attracted considerable attention in the immunology community. Long-term immunity, traditionally analyzed in the context of infection, is increasingly studied in cancer. Many signaling pathways, transcription factors, and metabolic regulators have been shown to participate in the formation of memory T cells. There is increasing evidence that the signal transducer and activator of transcription-3 (STAT3) signaling pathway is crucial for the formation of long-term T-cell immunity capable of efficient recall responses. In this review, we summarize what is currently known about STAT3 role in the context of memory T-cell formation and antitumor immunity.
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22
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Heritable changes in division speed accompany the diversification of single T cell fate. Proc Natl Acad Sci U S A 2022; 119:2116260119. [PMID: 35217611 PMCID: PMC8892279 DOI: 10.1073/pnas.2116260119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 11/18/2022] Open
Abstract
Rapid clonal expansion of antigen-specific T cells is a fundamental feature of adaptive immune responses. Here, we utilize continuous live-cell imaging in vitro to track the division speed and genealogical connections of all descendants derived from a single naive CD8+ T cell throughout up to ten divisions of activation-induced proliferation. Bayesian inference of tree-structured data reveals that clonal expansion is divided into a homogenously fast burst phase encompassing two to three divisions and a subsequent diversification phase during which T cells segregate into quickly dividing effector T cells and more slowly cycling memory precursors. Our work highlights cell cycle speed as a major heritable property that is regulated in parallel to key lineage decisions of activated T cells. Rapid clonal expansion of antigen-specific T cells is a fundamental feature of adaptive immune responses. It enables the outgrowth of an individual T cell into thousands of clonal descendants that diversify into short-lived effectors and long-lived memory cells. Clonal expansion is thought to be programmed upon priming of a single naive T cell and then executed by homogenously fast divisions of all of its descendants. However, the actual speed of cell divisions in such an emerging “T cell family” has never been measured with single-cell resolution. Here, we utilize continuous live-cell imaging in vitro to track the division speed and genealogical connections of all descendants derived from a single naive CD8+ T cell throughout up to ten divisions of activation-induced proliferation. This comprehensive mapping of T cell family trees identifies a short burst phase, in which division speed is homogenously fast and maintained independent of external cytokine availability or continued T cell receptor stimulation. Thereafter, however, division speed diversifies, and model-based computational analysis using a Bayesian inference framework for tree-structured data reveals a segregation into heritably fast- and slow-dividing branches. This diversification of division speed is preceded already during the burst phase by variable expression of the interleukin-2 receptor alpha chain. Later it is accompanied by selective expression of memory marker CD62L in slower dividing branches. Taken together, these data demonstrate that T cell clonal expansion is structured into subsequent burst and diversification phases, the latter of which coincides with specification of memory versus effector fate.
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23
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Argenty J, Rouquié N, Bories C, Mélique S, Duplan-Eche V, Saoudi A, Fazilleau N, Lesourne R. A selective LIS1 requirement for mitotic spindle assembly discriminates distinct T-cell division mechanisms within the T-cell lineage. eLife 2022; 11:80277. [PMID: 36519536 PMCID: PMC9797186 DOI: 10.7554/elife.80277] [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: 05/13/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
The ability to proliferate is a common feature of most T-cell populations. However, proliferation follows different cell-cycle dynamics and is coupled to different functional outcomes according to T-cell subsets. Whether the mitotic machineries supporting these qualitatively distinct proliferative responses are identical remains unknown. Here, we show that disruption of the microtubule-associated protein LIS1 in mouse models leads to proliferative defects associated with a blockade of T-cell development after β-selection and of peripheral CD4+ T-cell expansion after antigen priming. In contrast, cell divisions in CD8+ T cells occurred independently of LIS1 following T-cell antigen receptor stimulation, although LIS1 was required for proliferation elicited by pharmacological activation. In thymocytes and CD4+ T cells, LIS1 deficiency did not affect signaling events leading to activation but led to an interruption of proliferation after the initial round of division and to p53-induced cell death. Proliferative defects resulted from a mitotic failure, characterized by the presence of extra-centrosomes and the formation of multipolar spindles, causing abnormal chromosomes congression during metaphase and separation during telophase. LIS1 was required to stabilize dynein/dynactin complexes, which promote chromosome attachment to mitotic spindles and ensure centrosome integrity. Together, these results suggest that proliferative responses are supported by distinct mitotic machineries across T-cell subsets.
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Affiliation(s)
- Jérémy Argenty
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Nelly Rouquié
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Cyrielle Bories
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Suzanne Mélique
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Valérie Duplan-Eche
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Abdelhadi Saoudi
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Nicolas Fazilleau
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Renaud Lesourne
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
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24
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Meldgaard TS, Blengio F, Maffione D, Sammicheli C, Tavarini S, Nuti S, Kratzer R, Medini D, Siena E, Bertholet S. Single-Cell Analysis of Antigen-Specific CD8+ T-Cell Transcripts Reveals Profiles Specific to mRNA or Adjuvanted Protein Vaccines. Front Immunol 2021; 12:757151. [PMID: 34777370 PMCID: PMC8586650 DOI: 10.3389/fimmu.2021.757151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/05/2021] [Indexed: 12/29/2022] Open
Abstract
CD8+ T cells play a key role in mediating protective immunity after immune challenges such as infection or vaccination. Several subsets of differentiated CD8+ T cells have been identified, however, a deeper understanding of the molecular mechanism that underlies T-cell differentiation is lacking. Conventional approaches to the study of immune responses are typically limited to the analysis of bulk groups of cells that mask the cells' heterogeneity (RNA-seq, microarray) and to the assessment of a relatively limited number of biomarkers that can be evaluated simultaneously at the population level (flow and mass cytometry). Single-cell analysis, on the other hand, represents a possible alternative that enables a deeper characterization of the underlying cellular heterogeneity. In this study, a murine model was used to characterize immunodominant hemagglutinin (HA533-541)-specific CD8+ T-cell responses to nucleic- and protein-based influenza vaccine candidates, using single-cell sorting followed by transcriptomic analysis. Investigation of single-cell gene expression profiles enabled the discovery of unique subsets of CD8+ T cells that co-expressed cytotoxic genes after vaccination. Moreover, this method enabled the characterization of antigen specific CD8+ T cells that were previously undetected. Single-cell transcriptome profiling has the potential to allow for qualitative discrimination of cells, which could lead to novel insights on biological pathways involved in cellular responses. This approach could be further validated and allow for more informed decision making in preclinical and clinical settings.
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Affiliation(s)
- Trine Sundebo Meldgaard
- Research & Development, GSK, Siena, Italy
- Biochemistry & Molecular Biology, University of Siena, Siena, Italy
| | - Fabiola Blengio
- Chemical & Biological Sciences, University of Torino, Torino, Italy
| | - Denise Maffione
- Chemical & Biological Sciences, University of Torino, Torino, Italy
| | | | | | - Sandra Nuti
- Research & Development, GSK, Siena, Italy
- Research & Development, GSK, Rockville, MD, United States
| | | | | | | | - Sylvie Bertholet
- Research & Development, GSK, Siena, Italy
- Research & Development, GSK, Rockville, MD, United States
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25
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Heckler M, Ali LR, Clancy-Thompson E, Qiang L, Ventre KS, Lenehan P, Roehle K, Luoma A, Boelaars K, Peters V, McCreary J, Boschert T, Wang ES, Suo S, Marangoni F, Mempel TR, Long HW, Wucherpfennig KW, Dougan M, Gray NS, Yuan GC, Goel S, Tolaney SM, Dougan SK. Inhibition of CDK4/6 Promotes CD8 T-cell Memory Formation. Cancer Discov 2021; 11:2564-2581. [PMID: 33941591 PMCID: PMC8487897 DOI: 10.1158/2159-8290.cd-20-1540] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/25/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022]
Abstract
CDK4/6 inhibitors are approved to treat breast cancer and are in trials for other malignancies. We examined CDK4/6 inhibition in mouse and human CD8+ T cells during early stages of activation. Mice receiving tumor-specific CD8+ T cells treated with CDK4/6 inhibitors displayed increased T-cell persistence and immunologic memory. CDK4/6 inhibition upregulated MXD4, a negative regulator of MYC, in both mouse and human CD8+ T cells. Silencing of Mxd4 or Myc in mouse CD8+ T cells demonstrated the importance of this axis for memory formation. We used single-cell transcriptional profiling and T-cell receptor clonotype tracking to evaluate recently activated human CD8+ T cells in patients with breast cancer before and during treatment with either palbociclib or abemaciclib. CDK4/6 inhibitor therapy in humans increases the frequency of CD8+ memory precursors and downregulates their expression of MYC target genes, suggesting that CDK4/6 inhibitors in patients with cancer may augment long-term protective immunity. SIGNIFICANCE: CDK4/6 inhibition skews newly activated CD8+ T cells toward a memory phenotype in mice and humans with breast cancer. CDK4/6 inhibitors may have broad utility outside breast cancer, particularly in the neoadjuvant setting to augment CD8+ T-cell priming to tumor antigens prior to dosing with checkpoint blockade.This article is highlighted in the In This Issue feature, p. 2355.
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Affiliation(s)
- Max Heckler
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Lestat R Ali
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Eleanor Clancy-Thompson
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Li Qiang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Katherine S Ventre
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Patrick Lenehan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Kevin Roehle
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Adrienne Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Kelly Boelaars
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Vera Peters
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Julia McCreary
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Program in Chemical Biology, Harvard Medical School, Boston, Massachusetts
| | - Tamara Boschert
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eric S Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shengbao Suo
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Francesco Marangoni
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, Massachusetts
| | - Thorsten R Mempel
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, Massachusetts
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Michael Dougan
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Guo-Cheng Yuan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Shom Goel
- Peter MacCallum Cancer Centre, Melbourne, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Sara M Tolaney
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stephanie K Dougan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
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Xu T, Pereira RM, Martinez GJ. An Updated Model for the Epigenetic Regulation of Effector and Memory CD8 + T Cell Differentiation. THE JOURNAL OF IMMUNOLOGY 2021; 207:1497-1505. [PMID: 34493604 DOI: 10.4049/jimmunol.2100633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/22/2021] [Indexed: 11/19/2022]
Abstract
Naive CD8+ T cells, upon encountering their cognate Ag in vivo, clonally expand and differentiate into distinct cell fates, regulated by transcription factors and epigenetic modulators. Several models have been proposed to explain the differentiation of CTLs, although none fully recapitulate the experimental evidence. In this review article, we will summarize the latest research on the epigenetic regulation of CTL differentiation as well as provide a combined model that contemplates them.
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Affiliation(s)
- Tianhao Xu
- Discipline of Microbiology and Immunology, Center for Cancer Cell Biology, Immunology and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL; and
| | - Renata M Pereira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Gustavo J Martinez
- Discipline of Microbiology and Immunology, Center for Cancer Cell Biology, Immunology and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL; and
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27
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Bamodu OA, Wang YH, Yeh CT, Ho CH, Chiang YT, Kao WT, Liu CH, Wu CC. Concomitant High Apoptosis Inhibitor of Macrophage (AIM) and Low Prostate-Specific Antigen (PSA) Indicates Activated T Cell-Mediated Anticancer Immunity, Enhance Sensitivity to Pembrolizumab, and Elicit Good Prognosis in Prostate Cancer. Biomedicines 2021; 9:biomedicines9091225. [PMID: 34572412 PMCID: PMC8469063 DOI: 10.3390/biomedicines9091225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Despite its widespread use, the use of prostate-specific antigen (PSA) alone as a screening biomarker for prostate cancer (PCa) leads often to unwarranted prostate biopsy, over-diagnosis, and consequently, over-treatment, because of its limited specificity. There are reports that the apoptosis inhibitor of macrophage (AIM), secreted mainly by macrophages and epithelial cells, is upregulated during inflammation and facilitates immune recognition of cancerous cells by blocking human regulator of complement activation. OBJECTIVE These controversies around the PSA utility necessitate a reexamination of its use as a screening tool. More so, despite the suggested implication of AIM in anticancer immunosurveillance, there is a dearth of information on its role in therapy response, disease progression, and clinical outcomes of patients with PCa. These inform the present study to probe the nature and role of AIM/PSA signaling in anticancer immunity and prognosis in PCa. METHODS A combination of bioinformatics-aided statistical analyses, gene function annotation, and immune infiltrate analyses, coupled with tissue staining, and function assays, namely migration, invasion, and clonogenicity assays, we employed. RESULTS We demonstrated that AIM and PSA expression levels are inversely correlated in PCa clinical samples and cell lines, with AIMlowPSAhigh defining PCa, compared to AIMhighPSAlow in normal samples. Concomitant aberrant PSA and significantly suppressed AIM expression levels positively correlated with high-grade disease and characterized by advanced stage prostate cancer, regardless of mutation status. We found that a high PSA/AIM ratio is associated with disease recurrence in patients with prostate cancer but is equivocal for overall survival. In addition, PSA-associated AIM suppression is implicated in the enhanced 'metastability' of PCa and a high AIM/PSA ratio is associated with strong castration-induced regression. CRISPR-mediated AIM knockout was associated with higher PSA expression while ectopic expression of AIM significantly attenuated the migration and invasive capability of PC3 and DU145 cells. Interestingly, compared to normal samples, we observed that AIM, biomarkers of T-cell activation and M1 phenotype markers are co-suppressed in PCa samples. CONCLUSION Herein, we demonstrate that AIM/CD5L binds to PSA and that a high PSA/AIM ratio defines advanced stage PCa (regardless of mutation status), is implicated in enhanced metastability, and associated with disease recurrence, while a high AIM/PSA ratio is associated with strong castration-induced regression. More so, the ectopic expression of AIM significantly enhances the anticancer effect of Pembrolizumab and elicits an increased CD8+ T-cell count in AIMhiPSAloPDL1+ PCa cases that are respondent to Pembrolizumab treatment.
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Affiliation(s)
- Oluwaseun Adebayo Bamodu
- Department of Urology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (Y.-T.C.); (W.-T.K.); (C.-H.L.)
- Department of Medical Research, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (Y.-H.W.); (C.-T.Y.)
- Cancer Center, Department of Hematology and Oncology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan
| | - Yuan-Hung Wang
- Department of Medical Research, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (Y.-H.W.); (C.-T.Y.)
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- TMU Research Center of Urology and Kidney (TMU-RCUK), Taipei Medical University, Taipei 110, Taiwan
| | - Chi-Tai Yeh
- Department of Medical Research, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (Y.-H.W.); (C.-T.Y.)
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu City 300, Taiwan
| | - Chen-Hsun Ho
- Division of Urology, Department of Surgery, Shin Kong Wu Ho-Su Memorial Hospital, Taipei 111, Taiwan;
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
| | - Yi-Te Chiang
- Department of Urology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (Y.-T.C.); (W.-T.K.); (C.-H.L.)
- TMU Research Center of Urology and Kidney (TMU-RCUK), Taipei Medical University, Taipei 110, Taiwan
- Department of Urology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Wei-Tang Kao
- Department of Urology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (Y.-T.C.); (W.-T.K.); (C.-H.L.)
- TMU Research Center of Urology and Kidney (TMU-RCUK), Taipei Medical University, Taipei 110, Taiwan
| | - Chia-Hung Liu
- Department of Urology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (Y.-T.C.); (W.-T.K.); (C.-H.L.)
- TMU Research Center of Urology and Kidney (TMU-RCUK), Taipei Medical University, Taipei 110, Taiwan
- Department of Urology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Chia-Chang Wu
- Department of Urology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (Y.-T.C.); (W.-T.K.); (C.-H.L.)
- TMU Research Center of Urology and Kidney (TMU-RCUK), Taipei Medical University, Taipei 110, Taiwan
- Department of Urology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Correspondence: ; Tel.: +886-02-224-900-88 (ext. 8111); Fax: +886-02-22490088
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28
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Jenkins MM, Bachus H, Botta D, Schultz MD, Rosenberg AF, León B, Ballesteros-Tato A. Lung dendritic cells migrate to the spleen to prime long-lived TCF1 hi memory CD8 + T cell precursors after influenza infection. Sci Immunol 2021; 6:eabg6895. [PMID: 34516781 DOI: 10.1126/sciimmunol.abg6895] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Meagan M Jenkins
- Division of Clinical Immunology and Rheumatology Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Holly Bachus
- Division of Clinical Immunology and Rheumatology Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Davide Botta
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael D Schultz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alexander F Rosenberg
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA.,Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Beatriz León
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - André Ballesteros-Tato
- Division of Clinical Immunology and Rheumatology Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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29
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Dijkgraaf FE, Kok L, Schumacher TNM. Formation of Tissue-Resident CD8 + T-Cell Memory. Cold Spring Harb Perspect Biol 2021; 13:cshperspect.a038117. [PMID: 33685935 PMCID: PMC8327830 DOI: 10.1101/cshperspect.a038117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Resident memory CD8+ T (Trm) cells permanently reside in nonlymphoid tissues where they act as a first line of defense against recurrent pathogens. How and when antigen-inexperienced CD8+ T cells differentiate into Trm has been a topic of major interest, as knowledge on how to steer this process may be exploited in the development of vaccines and anticancer therapies. Here, we first review the current understanding of the early signals that CD8+ T cells receive before they have entered the tissue and that govern their capacity to develop into tissue-resident memory T cells. Subsequently, we discuss the tissue-derived factors that promote Trm maturation in situ. Combined, these data sketch a model in which a subset of responding T cells develops a heightened capacity to respond to local cues present in the tissue microenvironment, which thereby imprints their ability to contribute to the tissue-resident memory CD8+ T-cell pool that provide local control against pathogens.
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Affiliation(s)
- Feline E Dijkgraaf
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, 1066 Amsterdam, the Netherlands
| | - Lianne Kok
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, 1066 Amsterdam, the Netherlands
| | - Ton N M Schumacher
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, 1066 Amsterdam, the Netherlands
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30
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Hagen SH, Hennesen J, Altfeld M. Assessment of escape from X chromosome inactivation and gene expression in single human immune cells. STAR Protoc 2021; 2:100641. [PMID: 34355200 PMCID: PMC8319808 DOI: 10.1016/j.xpro.2021.100641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
X-chromosomal genes escaping from X chromosome inactivation (XCI) in immune cells can contribute to sex-specific differences in immune responses. This protocol describes the specific steps to determine escape from XCI and to simultaneously quantify mRNA expression of multiple genes at the single immune cell level using a single-nucleotide polymorphism approach. The protocol furthermore allows the analysis of allele-specific expression of X-chromosomal genes. For complete details on the use and execution of this protocol, please refer to Hagen et al. (2020). Approach to investigate escape from XCI and gene expression in single cells Simultaneous gene expression measurement of over 100 genes in one cell Assessment of allele-specific expression of genes with monoallelic expression pattern
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Affiliation(s)
- Sven Hendrik Hagen
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, Hamburg 20251, Germany
| | - Jana Hennesen
- Technology Platform Flow Cytometry / FACS, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, Hamburg 20251, Germany
| | - Marcus Altfeld
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, Hamburg 20251, Germany
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31
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Frith K, Munier CML, Hastings L, Mowat D, Wilson M, Seddiki N, Macintosh R, Kelleher AD, Gray P, Zaunders JJ. The Role of ZEB2 in Human CD8 T Lymphocytes: Clinical and Cellular Immune Profiling in Mowat-Wilson Syndrome. Int J Mol Sci 2021; 22:ijms22105324. [PMID: 34070208 PMCID: PMC8158478 DOI: 10.3390/ijms22105324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
The Zeb2 gene encodes a transcription factor (ZEB2) that acts as an important immune mediator in mice, where it is expressed in early-activated effector CD8 T cells, and limits effector differentiation. Zeb2 homozygous knockout mice have deficits in CD8 T cells and NK cells. Mowat–Wilson syndrome (MWS) is a rare genetic disease resulting from heterozygous mutations in ZEB2 causing disease by haploinsufficiency. Whether ZEB2 exhibits similar expression patterns in human CD8 T cells is unknown, and MWS patients have not been comprehensively studied to identify changes in CD8 lymphocytes and NK cells, or manifestations of immunodeficiency. By using transcriptomic assessment, we demonstrated that ZEB2 is expressed in early-activated effector CD8 T cells of healthy human volunteers following vaccinia inoculation and found evidence of a role for TGFß-1/SMAD signaling in these cells. A broad immunological assessment of six genetically diagnosed MWS patients identified two patients with a history of recurrent sinopulmonary infections, one of whom had recurrent oral candidiasis, one with lymphopenia, two with thrombocytopenia and three with detectable anti-nuclear antibodies. Immunoglobulin levels, including functional antibody responses to protein and polysaccharide vaccination, were normal. The MWS patients had a significantly lower CD8 T cell subset as % of lymphocytes, compared to healthy controls (median 16.4% vs. 25%, p = 0.0048), and resulting increased CD4:CD8 ratio (2.6 vs. 1.8; p = 0.038). CD8 T cells responded normally to mitogen stimulation in vitro and memory CD8 T cells exhibited normal proportions of subsets with important tissue-specific homing markers and cytotoxic effector molecules. There was a trend towards a decrease in the CD8 T effector memory subset (3.3% vs. 5.9%; p = 0.19). NK cell subsets were normal. This is the first evidence that ZEB2 is expressed in early-activated human effector CD8 T cells, and that haploinsufficiency of ZEB2 in MWS patients had a slight effect on immune function, skewing T cells away from CD8 differentiation. To date there is insufficient evidence to support an immunodeficiency occurring in MWS patients.
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Affiliation(s)
- Katie Frith
- Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.H.); (D.M.); (R.M.); (P.G.)
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Correspondence: (K.F.); (C.M.L.M.); (J.J.Z.)
| | - C. Mee Ling Munier
- The Kirby Institute for Infection and Immunity in Society, UNSW Sydney, Sydney, NSW 2052, Australia;
- Correspondence: (K.F.); (C.M.L.M.); (J.J.Z.)
| | - Lucy Hastings
- Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.H.); (D.M.); (R.M.); (P.G.)
| | - David Mowat
- Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.H.); (D.M.); (R.M.); (P.G.)
| | - Meredith Wilson
- Department of Clinical Genetics, Children’s Hospital at Westmead, Sydney, NSW 2145, Australia;
| | - Nabila Seddiki
- INSERM U955 Eq16, Vaccine Research Institute and Université Paris Est Créteil, F-94010 Créteil, France;
| | - Rebecca Macintosh
- Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.H.); (D.M.); (R.M.); (P.G.)
| | - Anthony D. Kelleher
- The Kirby Institute for Infection and Immunity in Society, UNSW Sydney, Sydney, NSW 2052, Australia;
- Centre for Applied Medical Research, St Vincent’s Hospital, Darlinghurst, NSW 2010, Australia
| | - Paul Gray
- Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.H.); (D.M.); (R.M.); (P.G.)
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW 2052, Australia
| | - John James Zaunders
- The Kirby Institute for Infection and Immunity in Society, UNSW Sydney, Sydney, NSW 2052, Australia;
- Centre for Applied Medical Research, St Vincent’s Hospital, Darlinghurst, NSW 2010, Australia
- Correspondence: (K.F.); (C.M.L.M.); (J.J.Z.)
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32
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E2A-regulated epigenetic landscape promotes memory CD8 T cell differentiation. Proc Natl Acad Sci U S A 2021; 118:2013452118. [PMID: 33859041 DOI: 10.1073/pnas.2013452118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
During an acute viral infection, CD8 T cells encounter a myriad of antigenic and inflammatory signals of variable strength, which sets off individual T cells on their own differentiation trajectories. However, the developmental path for each of these cells will ultimately lead to one of only two potential outcomes after clearance of the infection-death or survival and development into memory CD8 T cells. How this cell fate decision is made remains incompletely understood. In this study, we explore the transcriptional changes during effector and memory CD8 T cell differentiation at the single-cell level. Using single-cell, transcriptome-derived gene regulatory network analysis, we identified two main groups of regulons that govern this differentiation process. These regulons function in concert with changes in the enhancer landscape to confer the establishment of the regulatory modules underlying the cell fate decision of CD8 T cells. Furthermore, we found that memory precursor effector cells maintain chromatin accessibility at enhancers for key memory-related genes and that these enhancers are highly enriched for E2A binding sites. Finally, we show that E2A directly regulates accessibility of enhancers of many memory-related genes and that its overexpression increases the frequency of memory precursor effector cells and accelerates memory cell formation while decreasing the frequency of short-lived effector cells. Overall, our results suggest that effector and memory CD8 T cell differentiation is largely regulated by two transcriptional circuits, with E2A serving as an important epigenetic regulator of the memory circuit.
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33
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Karolak A, Branciamore S, McCune JS, Lee PP, Rodin AS, Rockne RC. Concepts and Applications of Information Theory to Immuno-Oncology. Trends Cancer 2021; 7:335-346. [PMID: 33618998 PMCID: PMC8156485 DOI: 10.1016/j.trecan.2020.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 01/27/2023]
Abstract
Recent successes of immune-modulating therapies for cancer have stimulated research on information flow within the immune system and, in turn, clinical applications of concepts from information theory. Through information theory, one can describe and formalize, in a mathematically rigorous fashion, the function of interconnected components of the immune system in health and disease. Specifically, using concepts including entropy, mutual information, and channel capacity, one can quantify the storage, transmission, encoding, and flow of information within and between cellular components of the immune system on multiple temporal and spatial scales. To understand, at the quantitative level, immune signaling function and dysfunction in cancer, we present a methodology-oriented review of information-theoretic treatment of biochemical signal transduction and transmission coupled with mathematical modeling.
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Affiliation(s)
- Aleksandra Karolak
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute of City of Hope, Duarte, CA, USA; Division of Mathematical Oncology, Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA.
| | - Sergio Branciamore
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jeannine S McCune
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Peter P Lee
- Department of Immuno-Oncology, Beckman Research Institute of City of Hope, CA, USA
| | - Andrei S Rodin
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Russell C Rockne
- Division of Mathematical Oncology, Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
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34
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Chung HK, McDonald B, Kaech SM. The architectural design of CD8+ T cell responses in acute and chronic infection: Parallel structures with divergent fates. J Exp Med 2021; 218:211912. [PMID: 33755719 PMCID: PMC7992501 DOI: 10.1084/jem.20201730] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/19/2022] Open
Abstract
In response to infection, T cells adopt a range of differentiation states, creating numerous heterogeneous subsets that exhibit different phenotypes, functions, and migration patterns. This T cell heterogeneity is a universal feature of T cell immunity, needed to effectively control pathogens in a context-dependent manner and generate long-lived immunity to those pathogens. Here, we review new insights into differentiation state dynamics and population heterogeneity of CD8+ T cells in acute and chronic viral infections and cancer and highlight the parallels and distinctions between acute and chronic antigen stimulation settings. We focus on transcriptional and epigenetic networks that modulate the plasticity and terminal differentiation of antigen-specific CD8+ T cells and generate functionally diverse T cell subsets with different roles to combat infection and cancer.
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Affiliation(s)
- H Kay Chung
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA
| | - Bryan McDonald
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA.,Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA
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35
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Kok L, Dijkgraaf FE, Urbanus J, Bresser K, Vredevoogd DW, Cardoso RF, Perié L, Beltman JB, Schumacher TN. A committed tissue-resident memory T cell precursor within the circulating CD8+ effector T cell pool. J Exp Med 2021; 217:151985. [PMID: 32728699 PMCID: PMC7537386 DOI: 10.1084/jem.20191711] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 05/01/2020] [Accepted: 06/16/2020] [Indexed: 11/29/2022] Open
Abstract
An increasing body of evidence emphasizes the role of tissue-resident memory T cells (TRM) in the defense against recurring pathogens and malignant neoplasms. However, little is known with regard to the origin of these cells and their kinship to other CD8+ T cell compartments. To address this issue, we followed the antigen-specific progeny of individual naive CD8+ T cells to the T effector (TEFF), T circulating memory (TCIRCM), and TRM pools by lineage-tracing and single-cell transcriptome analysis. We demonstrate that a subset of T cell clones possesses a heightened capacity to form TRM, and that enriched expression of TRM–fate-associated genes is already apparent in the circulating TEFF offspring of such clones. In addition, we demonstrate that the capacity to generate TRM is permanently imprinted at the clonal level, before skin entry. Collectively, these data provide compelling evidence for early stage TRM fate decisions and the existence of committed TRM precursor cells in the circulatory TEFF compartment.
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Affiliation(s)
- Lianne Kok
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Feline E Dijkgraaf
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Jos Urbanus
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Kaspar Bresser
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - David W Vredevoogd
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Rebeca F Cardoso
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Leïla Perié
- Institut Curie, Université Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique UMR168, Paris, France
| | - Joost B Beltman
- Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
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36
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Pipkin ME. Runx proteins and transcriptional mechanisms that govern memory CD8 T cell development. Immunol Rev 2021; 300:100-124. [PMID: 33682165 DOI: 10.1111/imr.12954] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
Adaptive immunity to intracellular pathogens and tumors is mediated by antigen-experienced CD8 T cells. Individual naive CD8 T cells have the potential to differentiate into a diverse array of antigen-experienced subsets that exhibit distinct effector functions, life spans, anatomic positioning, and potential for regenerating an entirely new immune response during iterative pathogenic exposures. The developmental process by which activated naive cells undergo diversification involves regulation of chromatin structure and transcription but is not entirely understood. This review examines how alterations in chromatin structure, transcription factor binding, extracellular signals, and single-cell gene expression explain the differential development of distinct effector (TEFF ) and memory (TMEM ) CD8 T cell subsets. Special emphasis is placed on how Runx proteins function with additional transcription factors to pioneer changes in chromatin accessibility and drive transcriptional programs that establish the core attributes of cytotoxic T lymphocytes, subdivide circulating and non-circulating TMEM cell subsets, and govern terminal differentiation. The discussion integrates the roles of specific cytokine signals, transcriptional circuits and how regulation of individual nucleosomes and RNA polymerase II activity can contribute to the process of differentiation. A model that integrates many of these features is discussed to conceptualize how activated CD8 T cells arrive at their fates.
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Affiliation(s)
- Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute - FL, Jupiter, FL, USA
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37
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Lafouresse F, Jugele R, Müller S, Doineau M, Duplan-Eche V, Espinosa E, Puisségur MP, Gadat S, Valitutti S. Stochastic asymmetric repartition of lytic machinery in dividing CD8 + T cells generates heterogeneous killing behavior. eLife 2021; 10:62691. [PMID: 33427199 PMCID: PMC7867409 DOI: 10.7554/elife.62691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/08/2021] [Indexed: 12/27/2022] Open
Abstract
Cytotoxic immune cells are endowed with a high degree of heterogeneity in their lytic function, but how this heterogeneity is generated is still an open question. We therefore investigated if human CD8+ T cells could segregate their lytic components during telophase, using imaging flow cytometry, confocal microscopy, and live-cell imaging. We show that CD107a+-intracellular vesicles, perforin, and granzyme B unevenly segregate in a constant fraction of telophasic cells during each division round. Mathematical modeling posits that unequal lytic molecule inheritance by daughter cells results from the random distribution of lytic granules on the two sides of the cleavage furrow. Finally, we establish that the level of lytic compartment in individual cytotoxic T lymphocyte (CTL) dictates CTL killing capacity.
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Affiliation(s)
- Fanny Lafouresse
- INSERM U1037, Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse III-Paul Sabatier, Toulouse, France
| | - Romain Jugele
- INSERM U1037, Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse III-Paul Sabatier, Toulouse, France
| | - Sabina Müller
- INSERM U1037, Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse III-Paul Sabatier, Toulouse, France
| | - Marine Doineau
- Toulouse School of Economics, CNRS UMR 5314, Université Toulouse 1 Capitole, France and Institut Universitaire de France, Toulouse, France
| | - Valérie Duplan-Eche
- INSERM, UMR1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France
| | - Eric Espinosa
- INSERM U1037, Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse III-Paul Sabatier, Toulouse, France
| | - Marie-Pierre Puisségur
- INSERM U1037, Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse III-Paul Sabatier, Toulouse, France
| | - Sébastien Gadat
- Toulouse School of Economics, CNRS UMR 5314, Université Toulouse 1 Capitole, France and Institut Universitaire de France, Toulouse, France
| | - Salvatore Valitutti
- INSERM U1037, Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse III-Paul Sabatier, Toulouse, France.,Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
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38
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Hagen SH, Henseling F, Hennesen J, Savel H, Delahaye S, Richert L, Ziegler SM, Altfeld M. Heterogeneous Escape from X Chromosome Inactivation Results in Sex Differences in Type I IFN Responses at the Single Human pDC Level. Cell Rep 2020; 33:108485. [PMID: 33296655 PMCID: PMC7833293 DOI: 10.1016/j.celrep.2020.108485] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 09/11/2020] [Accepted: 11/12/2020] [Indexed: 12/28/2022] Open
Abstract
Immune responses differ between women and men, and type I interferon (IFN) responses following Toll-like receptor 7 (TLR7) stimulation are higher in women. The precise mechanisms driving these sex differences in immunity are unknown. To investigate possible genetic factors, we quantify escape from X chromosome inactivation (XCI) for TLR7 and four other genes (RPS6KA3, CYBB, BTK, and IL13RA1) at the single plasmacytoid dendritic cell (pDC) level. We observe escape from XCI for all investigated genes, leading to biallelic expression patterns. pDCs with biallelic gene expression have significantly higher mRNA levels of the respective genes. Unstimulated pDCs with biallelic TLR7 expression exhibit significantly higher IFNα/β mRNA levels, and IFNα exposure results in significantly increased IFNα/β protein production by pDCs. These results identify unanticipated heterogeneity in escape from XCI of several genes in pDCs and highlight the important contribution of X chromosome factors to sex differences in type I IFN responses, which might explain observed sex differences in human diseases.
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Affiliation(s)
- Sven Hendrik Hagen
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, Hamburg 20251, Germany
| | - Florian Henseling
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, Hamburg 20251, Germany
| | - Jana Hennesen
- Technology Platform Flow Cytometry/FACS, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, Hamburg 20251, Germany
| | - Hélène Savel
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR1219 and Inria, team SISTM, Bordeaux, France
| | - Solenne Delahaye
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR1219 and Inria, team SISTM, Bordeaux, France
| | - Laura Richert
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR1219 and Inria, team SISTM, Bordeaux, France
| | - Susanne Maria Ziegler
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, Hamburg 20251, Germany
| | - Marcus Altfeld
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, Hamburg 20251, Germany.
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39
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Parga-Vidal L, van Gisbergen KPJM. Area under Immunosurveillance: Dedicated Roles of Memory CD8 T-Cell Subsets. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a037796. [PMID: 32839203 DOI: 10.1101/cshperspect.a037796] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Immunological memory, defined as the ability to respond in an enhanced manner upon secondary encounter with the same pathogen, can provide substantial protection against infectious disease. The improved protection is mediated in part by different populations of memory CD8 T cells that are retained after primary infection. Memory cells persist in the absence of pathogen-derived antigens and enable secondary CD8 T-cell responses with accelerated kinetics and of larger magnitude after reencounter with the same pathogen. At least three subsets of memory T cells have been defined that are referred to as central memory CD8 T cells (Tcm), effector memory CD8 T cells (Tem), and tissue-resident memory CD8 T cells (Trm). Tcm and Tem are circulating memory T cells that mediate bodywide immune surveillance in search of invading pathogens. In contrast, Trm permanently reside in peripheral barrier tissues, where they form a stationary defensive line of sentinels that alert the immune system upon pathogen reencounter. The characterization of these different subsets has been instrumental in our understanding of the strategies that memory T cells employ to counter invading pathogens. It is clear that memory T cells not only have a numerical advantage over naive T cells resulting in improved protection in secondary responses, but also acquire distinct sets of competencies that assist in pathogen clearance. Nevertheless, inherent challenges are associated with the allocation of memory T cells to a limited number of subsets. The classification of memory T cells into Tcm, Tem, and Trm may not take into account the full extent of the heterogeneity that is observed in the memory population. Therefore, in this review, we will revisit the current classification of memory subsets, elaborate on functional and migratory properties attributed to Tcm, Tem, and Trm, and discuss how potential heterogeneity within these populations arises and persists.
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Affiliation(s)
- Loreto Parga-Vidal
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066CX Amsterdam, The Netherlands
| | - Klaas P J M van Gisbergen
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066CX Amsterdam, The Netherlands
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40
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Eomes cannot replace its paralog T-bet during expansion and differentiation of CD8 effector T cells. PLoS Pathog 2020; 16:e1008870. [PMID: 32991634 PMCID: PMC7546498 DOI: 10.1371/journal.ppat.1008870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/09/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022] Open
Abstract
The two T-box transcription factors T-bet and Eomesodermin (Eomes) are important regulators of cytotoxic lymphocytes (CTLs), such as activated CD8 T cells, which are essential in the fight against intracellular pathogens and tumors. Both transcription factors share a great degree of homology based on sequence analysis and as a result exert partial functional redundancy during viral infection. However, the actual degree of redundancy between T-bet and Eomes remains a matter of debate and is further confounded by their distinct spatiotemporal expression pattern in activated CD8 T cells. To directly investigate the functional overlap of these transcription factors, we generated a new mouse model in which Eomes expression is under the transcriptional control of the endogenous Tbx21 (encoding for T-bet) locus. Applying this model, we demonstrate that the induction of Eomes in lieu of T-bet cannot rescue T-bet deficiency in CD8 T cells during acute lymphocytic choriomeningitis virus (LCMV) infection. We found that the expression of Eomes instead of T-bet was not sufficient for early cell expansion or effector cell differentiation. Finally, we show that imposed expression of Eomes after acute viral infection promotes some features of exhaustion but must act in concert with other factors during chronic viral infection to establish all hallmarks of exhaustion. In summary, our results clearly underline the importance of T-bet in guiding canonical CTL development during acute viral infections. According to the World Health Organization infectious diseases kill over 17 million people per year. At the same time highly infectious viral diseases, such as Ebola and COVID-19 that are lacking specific treatments, are emerging to pose additional threats. It is therefore pivotal to precisely understand how our immune system responds towards pathogens to develop new treatment options. Here we have investigated the role of two related molecules, named T-bet and Eomes, that guide the development and function of lymphocytes in their fight against intracellular pathogens. We specifically focused on cytotoxic lymphocytes as these cells dominate the early phase of viral containment. We show that T-bet is essential for the expansion of cytotoxic lymphocytes and equip lymphocytes with the ability to efficiently eliminate virus-infected cells. Hence, our study provides new insights into the importance and specific actions of T-bet during acute viral infections and how this might be harnessed for future therapeutic interventions.
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41
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Early programming of CD8 + T cell response by the orphan nuclear receptor NR4A3. Proc Natl Acad Sci U S A 2020; 117:24392-24402. [PMID: 32913051 DOI: 10.1073/pnas.2007224117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Enhancing long-term persistence while simultaneously potentiating the effector response of CD8+ T cells has been a long-standing goal in immunology to produce better vaccines and adoptive cell therapy products. NR4A3 is a transcription factor of the orphan nuclear receptor family. While it is rapidly and transiently expressed following T cell activation, its role in the early stages of T cell response is unknown. We show that NR4A3-deficient murine CD8+ T cells differentiate preferentially into memory precursor and central memory cells, but also produce more cytokines. This is explained by an early influence of NR4A3 deficiency on the memory transcriptional program and on accessibility of chromatin regions with motifs for bZIP transcription factors, which impacts the transcription of Fos/Jun target genes. Our results reveal a unique and early role for NR4A3 in programming CD8+ T cell differentiation and function. Manipulating NR4A3 activity may represent a promising strategy to improve vaccination and T cell therapy.
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42
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Boland BS, He Z, Tsai MS, Olvera JG, Omilusik KD, Duong HG, Kim ES, Limary AE, Jin W, Milner JJ, Yu B, Patel SA, Louis TL, Tysl T, Kurd NS, Bortnick A, Quezada LK, Kanbar JN, Miralles A, Huylebroeck D, Valasek MA, Dulai PS, Singh S, Lu LF, Bui JD, Murre C, Sandborn WJ, Goldrath AW, Yeo GW, Chang JT. Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses. Sci Immunol 2020; 5:5/50/eabb4432. [PMID: 32826341 PMCID: PMC7733868 DOI: 10.1126/sciimmunol.abb4432] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/24/2020] [Indexed: 12/19/2022]
Abstract
Inflammatory bowel disease (IBD) encompasses a spectrum of gastrointestinal disorders driven by dysregulated immune responses against gut microbiota. We integrated single-cell RNA and antigen receptor sequencing to elucidate key components, cellular states, and clonal relationships of the peripheral and gastrointestinal mucosal immune systems in health and ulcerative colitis (UC). UC was associated with an increase in IgG1+ plasma cells in colonic tissue, increased colonic regulatory T cells characterized by elevated expression of the transcription factor ZEB2, and an enrichment of a γδ T cell subset in the peripheral blood. Moreover, we observed heterogeneity in CD8+ tissue-resident memory T (TRM) cells in colonic tissue, with four transcriptionally distinct states of differentiation observed across health and disease. In the setting of UC, there was a marked shift of clonally related CD8+ TRM cells toward an inflammatory state, mediated, in part, by increased expression of the T-box transcription factor Eomesodermin. Together, these results provide a detailed atlas of transcriptional changes occurring in adaptive immune cells in the context of UC and suggest a role for CD8+ TRM cells in IBD.
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Affiliation(s)
- Brigid S Boland
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Matthew S Tsai
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jocelyn G Olvera
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kyla D Omilusik
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Han G Duong
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Eleanor S Kim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Abigail E Limary
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - J Justin Milner
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Bingfei Yu
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shefali A Patel
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tiani L Louis
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tiffani Tysl
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nadia S Kurd
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Alexandra Bortnick
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Lauren K Quezada
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jad N Kanbar
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ara Miralles
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Danny Huylebroeck
- Department of Development and Regeneration, University of Leuven, Leuven, Belgium.,Department of Cell Biology, Erasmus University Medical Center Rotterdam, 3015 CN Rotterdam, Netherlands
| | - Mark A Valasek
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Parambir S Dulai
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Siddharth Singh
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Li-Fan Lu
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jack D Bui
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Cornelis Murre
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - William J Sandborn
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ananda W Goldrath
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. .,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - John T Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA. .,Division of Gastroenterology, VA San Diego Healthcare System, San Diego, CA, USA
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43
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Kelly B, Pearce EL. Amino Assets: How Amino Acids Support Immunity. Cell Metab 2020; 32:154-175. [PMID: 32649859 DOI: 10.1016/j.cmet.2020.06.010] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/06/2020] [Accepted: 06/15/2020] [Indexed: 12/18/2022]
Abstract
Amino acids are fundamental building blocks supporting life. Their role in protein synthesis is well defined, but they contribute to a host of other intracellular metabolic pathways, including ATP generation, nucleotide synthesis, and redox balance, to support cellular and organismal function. Immune cells critically depend on such pathways to acquire energy and biomass and to reprogram their metabolism upon activation to support growth, proliferation, and effector functions. Amino acid metabolism plays a key role in this metabolic rewiring, and it supports various immune cell functions beyond increased protein synthesis. Here, we review the mechanisms by which amino acid metabolism promotes immune cell function, and how these processes could be targeted to improve immunity in pathological conditions.
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Affiliation(s)
- Beth Kelly
- Max Planck Institute for Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Erika L Pearce
- Max Planck Institute for Immunobiology and Epigenetics, Freiburg 79108, Germany.
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44
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Zamora AE, Crawford JC, Allen EK, Guo XZJ, Bakke J, Carter RA, Abdelsamed HA, Moustaki A, Li Y, Chang TC, Awad W, Dallas MH, Mullighan CG, Downing JR, Geiger TL, Chen T, Green DR, Youngblood BA, Zhang J, Thomas PG. Pediatric patients with acute lymphoblastic leukemia generate abundant and functional neoantigen-specific CD8 + T cell responses. Sci Transl Med 2020; 11:11/498/eaat8549. [PMID: 31243155 DOI: 10.1126/scitranslmed.aat8549] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 11/16/2018] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
Abstract
Cancer arises from the accumulation of genetic alterations, which can lead to the production of mutant proteins not expressed by normal cells. These mutant proteins can be processed and presented on the cell surface by major histocompatibility complex molecules as neoepitopes, allowing CD8+ T cells to mount responses against them. For solid tumors, only an average 2% of neoepitopes predicted by algorithms have detectable endogenous antitumor T cell responses. This suggests that low mutation burden tumors, which include many pediatric tumors, are poorly immunogenic. Here, we report that pediatric patients with acute lymphoblastic leukemia (ALL) have tumor-associated neoepitope-specific CD8+ T cells, responding to 86% of tested neoantigens and recognizing 68% of the tested neoepitopes. These responses include a public neoantigen from the ETV6-RUNX1 fusion that is targeted in seven of nine tested patients. We characterized phenotypic and transcriptional profiles of CD8+ tumor-infiltrating lymphocytes (TILs) at the single-cell level and found a heterogeneous population that included highly functional effectors. Moreover, we observed immunodominance hierarchies among the CD8+ TILs restricted to one or two putative neoepitopes. Our results indicate that robust antitumor immune responses are induced in pediatric ALL despite their low mutation burdens and emphasize the importance of immunodominance in shaping cellular immune responses. Furthermore, these data suggest that pediatric cancers may be amenable to immunotherapies aimed at enhancing immune recognition of tumor-specific neoantigens.
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Affiliation(s)
- Anthony E Zamora
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xi-Zhi J Guo
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jesse Bakke
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Department of Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, MI 48858, USA
| | - Robert A Carter
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hossam A Abdelsamed
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ardiana Moustaki
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yongjin Li
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ti-Cheng Chang
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Walid Awad
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mari H Dallas
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Terrence L Geiger
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Benjamin A Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA. .,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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45
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Renkema KR, Huggins MA, Borges da Silva H, Knutson TP, Henzler CM, Hamilton SE. KLRG1 + Memory CD8 T Cells Combine Properties of Short-Lived Effectors and Long-Lived Memory. THE JOURNAL OF IMMUNOLOGY 2020; 205:1059-1069. [PMID: 32611727 DOI: 10.4049/jimmunol.1901512] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/04/2020] [Indexed: 12/13/2022]
Abstract
CD8 effector T cells with a CD127hi KLRG1- phenotype are considered precursors to the long-lived memory pool, whereas KLRG1+CD127low cells are viewed as short-lived effectors. Nevertheless, we and others have shown that a KLRG1+CD127low population persists into the memory phase and that these T cells (termed long-lived effector cells [LLEC]) display robust protective function during acute rechallenge with bacteria or viruses. Whether these T cells represent a true memory population or are instead a remnant effector cell population that failed to undergo initial contraction has remained unclear. In this study, we show that LLEC from mice express a distinct phenotypic and transcriptional signature that shares characteristics of both early effectors and long-lived memory cells. We also find that in contrast to KLRG1+ effector cells, LLEC undergo homeostatic proliferation and are not critically dependent on IL-15 for their maintenance. Furthermore, we find that LLEC are predominantly derived from KLRG1+ effector cells when isolated at day 12 of the response. Our work challenges the concept that the KLRG1+CD127low population is dominated by short-lived cells and shows that KLRG1 downregulation is not a prerequisite to become a long-lived protective memory T cell.
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Affiliation(s)
- Kristin R Renkema
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455; and
| | - Matthew A Huggins
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455; and
| | - Henrique Borges da Silva
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455; and
| | - Todd P Knutson
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN 55455
| | - Christy M Henzler
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN 55455
| | - Sara E Hamilton
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455; .,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455; and
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46
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Morris SE, Farber DL, Yates AJ. Tissue-Resident Memory T Cells in Mice and Humans: Towards a Quantitative Ecology. THE JOURNAL OF IMMUNOLOGY 2020; 203:2561-2569. [PMID: 31685700 DOI: 10.4049/jimmunol.1900767] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022]
Abstract
In recent years, tissue-resident memory T cells (TRM) have emerged as essential components of immunological memory. Following antigenic challenge, TRM remain in nonlymphoid tissues and defend against re-exposure. Although accumulating evidence suggests important roles for TRM in mediating protective immunity, fundamental aspects of the population biology of TRM remain poorly understood. In this article, we discuss how results from different systems shed light on the ecological dynamics of TRM in mice and humans. We highlight the importance of dissecting processes contributing to TRM maintenance, and how these might vary across phenotypically and spatially heterogeneous subsets. We also discuss how the diversity of TRM communities within specific tissues may evolve under competition and in response to antigenic perturbation. Throughout, we illustrate how mathematical models can clarify inferences obtained from experimental data and help elucidate the homeostatic mechanisms underpinning the ecology of TRM populations.
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Affiliation(s)
- Sinead E Morris
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032
| | - Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032.,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032; and.,Department of Surgery, Columbia University Medical Center, New York, NY 10032
| | - Andrew J Yates
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032;
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47
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Milner JJ, Toma C, He Z, Kurd NS, Nguyen QP, McDonald B, Quezada L, Widjaja CE, Witherden DA, Crowl JT, Shaw LA, Yeo GW, Chang JT, Omilusik KD, Goldrath AW. Heterogenous Populations of Tissue-Resident CD8 + T Cells Are Generated in Response to Infection and Malignancy. Immunity 2020; 52:808-824.e7. [PMID: 32433949 PMCID: PMC7784612 DOI: 10.1016/j.immuni.2020.04.007] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 01/21/2020] [Accepted: 04/17/2020] [Indexed: 11/23/2022]
Abstract
Tissue-resident memory CD8+ T cells (Trm) provide host protection through continuous surveillance of non-lymphoid tissues. Using single-cell RNA-sequencing (scRNA-seq) and genetic reporter mice, we identified discrete lineages of intestinal antigen-specific CD8+ T cells, including a Blimp1hiId3lo tissue-resident effector cell population most prominent in the early phase of acute viral and bacterial infections and a molecularly distinct Blimp1loId3hi tissue-resident memory population that subsequently accumulated at later infection time points. These Trm populations exhibited distinct cytokine production, secondary memory potential, and transcriptional programs including differential roles for transcriptional regulators Blimp1, T-bet, Id2, and Id3 in supporting and maintaining intestinal Trm. Extending our analysis to malignant tissue, we also identified discrete populations of effector-like and memory-like CD8+ T cell populations with tissue-resident gene-expression signatures that shared features of terminally exhausted and progenitor-exhausted T cells, respectively. Our findings provide insight into the development and functional heterogeneity of Trm cells, which has implications for enhancing vaccination and immunotherapy approaches.
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Affiliation(s)
- J Justin Milner
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Clara Toma
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nadia S Kurd
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Quynh P Nguyen
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Bryan McDonald
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Lauren Quezada
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Deborah A Witherden
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - John T Crowl
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Laura A Shaw
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - John T Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kyla D Omilusik
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
| | - Ananda W Goldrath
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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48
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Kurd NS, He Z, Louis TL, Milner JJ, Omilusik KD, Jin W, Tsai MS, Widjaja CE, Kanbar JN, Olvera JG, Tysl T, Quezada LK, Boland BS, Huang WJ, Murre C, Goldrath AW, Yeo GW, Chang JT. Early precursors and molecular determinants of tissue-resident memory CD8 + T lymphocytes revealed by single-cell RNA sequencing. Sci Immunol 2020; 5:eaaz6894. [PMID: 32414833 PMCID: PMC7341730 DOI: 10.1126/sciimmunol.aaz6894] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/16/2020] [Indexed: 01/06/2023]
Abstract
During an immune response to microbial infection, CD8+ T cells give rise to distinct classes of cellular progeny that coordinately mediate clearance of the pathogen and provide long-lasting protection against reinfection, including a subset of noncirculating tissue-resident memory (TRM) cells that mediate potent protection within nonlymphoid tissues. Here, we used single-cell RNA sequencing to examine the gene expression patterns of individual CD8+ T cells in the spleen and small intestine intraepithelial lymphocyte (siIEL) compartment throughout the course of their differentiation in response to viral infection. These analyses revealed previously unknown transcriptional heterogeneity within the siIEL CD8+ T cell population at several stages of differentiation, representing functionally distinct TRM cell subsets and a subset of TRM cell precursors within the tissue early in infection. Together, these findings may inform strategies to optimize CD8+ T cell responses to protect against microbial infection and cancer.
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Affiliation(s)
- Nadia S Kurd
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tiani L Louis
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - J Justin Milner
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kyla D Omilusik
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Matthew S Tsai
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Jad N Kanbar
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jocelyn G Olvera
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tiffani Tysl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lauren K Quezada
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Wendy J Huang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Cornelis Murre
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ananda W Goldrath
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - John T Chang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Division of Gastroenterology, VA San Diego Healthcare System, San Diego, CA, USA
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49
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Jaeger-Ruckstuhl CA, Hinterbrandner M, Höpner S, Correnti CE, Lüthi U, Friedli O, Freigang S, Al Sayed MF, Bührer ED, Amrein MA, Schürch CM, Radpour R, Riether C, Ochsenbein AF. TNIK signaling imprints CD8 + T cell memory formation early after priming. Nat Commun 2020; 11:1632. [PMID: 32242021 PMCID: PMC7118140 DOI: 10.1038/s41467-020-15413-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/04/2020] [Indexed: 01/15/2023] Open
Abstract
Co-stimulatory signals, cytokines and transcription factors regulate the balance between effector and memory cell differentiation during T cell activation. Here, we analyse the role of the TRAF2-/NCK-interacting kinase (TNIK), a signaling molecule downstream of the tumor necrosis factor superfamily receptors such as CD27, in the regulation of CD8+ T cell fate during acute infection with lymphocytic choriomeningitis virus. Priming of CD8+ T cells induces a TNIK-dependent nuclear translocation of β-catenin with consecutive Wnt pathway activation. TNIK-deficiency during T cell activation results in enhanced differentiation towards effector cells, glycolysis and apoptosis. TNIK signaling enriches for memory precursors by favouring symmetric over asymmetric cell division. This enlarges the pool of memory CD8+ T cells and increases their capacity to expand after re-infection in serial re-transplantation experiments. These findings reveal that TNIK is an important regulator of effector and memory T cell differentiation and induces a population of stem cell-like memory T cells. Coordinate expression of multiple factors play critical roles in the regulation between effector and memory CD8+ T cell differentiation. Here the authors show upon acute viral infection TNIK is critically required as a regulator of effector and memory T cell differentiation.
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Affiliation(s)
- Carla A Jaeger-Ruckstuhl
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, 3010, Switzerland.,Department of BioMedical Research (DBMR), University of Bern, Bern, 3008, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, 3012, Switzerland.,Program in Immunology, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, 98109, USA
| | - Magdalena Hinterbrandner
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, 3010, Switzerland.,Department of BioMedical Research (DBMR), University of Bern, Bern, 3008, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, 3012, Switzerland
| | - Sabine Höpner
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, 3010, Switzerland.,Department of BioMedical Research (DBMR), University of Bern, Bern, 3008, Switzerland
| | - Colin E Correnti
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, 98109, USA
| | - Ursina Lüthi
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, 3010, Switzerland.,Department of BioMedical Research (DBMR), University of Bern, Bern, 3008, Switzerland
| | - Olivier Friedli
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, 3012, Switzerland.,Institute of Pathology, University of Bern, Bern, 3008, Switzerland
| | - Stefan Freigang
- Institute of Pathology, University of Bern, Bern, 3008, Switzerland
| | - Mohamad F Al Sayed
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, 3010, Switzerland.,Department of BioMedical Research (DBMR), University of Bern, Bern, 3008, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, 3012, Switzerland
| | - Elias D Bührer
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, 3010, Switzerland.,Department of BioMedical Research (DBMR), University of Bern, Bern, 3008, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, 3012, Switzerland
| | - Michael A Amrein
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, 3010, Switzerland.,Department of BioMedical Research (DBMR), University of Bern, Bern, 3008, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, 3012, Switzerland
| | - Christian M Schürch
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, 3010, Switzerland.,Department of BioMedical Research (DBMR), University of Bern, Bern, 3008, Switzerland.,Institute of Pathology, University of Bern, Bern, 3008, Switzerland
| | - Ramin Radpour
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, 3010, Switzerland.,Department of BioMedical Research (DBMR), University of Bern, Bern, 3008, Switzerland
| | - Carsten Riether
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, 3010, Switzerland.,Department of BioMedical Research (DBMR), University of Bern, Bern, 3008, Switzerland
| | - Adrian F Ochsenbein
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, 3010, Switzerland. .,Department of BioMedical Research (DBMR), University of Bern, Bern, 3008, Switzerland.
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50
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Borsa M, Barnstorf I, Baumann NS, Pallmer K, Yermanos A, Gräbnitz F, Barandun N, Hausmann A, Sandu I, Barral Y, Oxenius A. Modulation of asymmetric cell division as a mechanism to boost CD8 + T cell memory. Sci Immunol 2020; 4:4/34/eaav1730. [PMID: 30979796 DOI: 10.1126/sciimmunol.aav1730] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/19/2019] [Indexed: 12/29/2022]
Abstract
Asymmetric partitioning of fate determinants is a mechanism that contributes to T cell differentiation. However, it remains unclear whether the ability of T cells to divide asymmetrically is influenced by their differentiation state, as well as whether enforcing asymmetric cell division (ACD) rates would have an impact on T cell differentiation and memory formation. Using the murine LCMV infection model, we established a correlation between cell stemness and the ability of CD8+ T cells to undergo ACD. Transient mTOR inhibition was proven to increase ACD rates in naïve and memory cells and to install this ability in exhausted CD8+ T cells. Functionally, enforced ACD correlated with increased memory potential, leading to more efficient recall response and viral control upon acute or chronic LCMV infection. Moreover, transient mTOR inhibition also increased ACD rates in human CD8+ T cells. Transcriptional profiling revealed that progenies emerging from enforced ACD exhibited more pronounced early memory signatures, which functionally endowed these cells with better survival in the absence of antigen exposure and more robust homing to secondary lymphoid organs, providing critical access to survival niches. Our data provide important insights into how ACD can improve long-term survival and function of T cells and open new perspectives for vaccination and adoptive T cell transfer therapies.
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Affiliation(s)
- Mariana Borsa
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Isabel Barnstorf
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Nicolas S Baumann
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Katharina Pallmer
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Alexander Yermanos
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Fabienne Gräbnitz
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Niculò Barandun
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Annika Hausmann
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Ioana Sandu
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Yves Barral
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Annette Oxenius
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.
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