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Sacristán C, Youngblood BA, Lu P, Bally APR, Xu JX, McGary K, Hewitt SL, Boss JM, Skok JA, Ahmed R, Dustin ML. Chronic viral infection alters PD-1 locus subnuclear localization in cytotoxic CD8 + T cells. Cell Rep 2024; 43:114547. [PMID: 39083377 DOI: 10.1016/j.celrep.2024.114547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/15/2024] [Accepted: 07/11/2024] [Indexed: 08/02/2024] Open
Abstract
During chronic infection, virus-specific CD8+ cytotoxic T lymphocytes (CTLs) progressively lose their ability to mount effective antiviral responses. This "exhaustion" is coupled to persistent upregulation of inhibitory receptor programmed death-1 (PD-1) (Pdcd1)-key in suppressing antiviral CTL responses. Here, we investigate allelic Pdcd1 subnuclear localization and transcription during acute and chronic lymphocytic choriomeningitis virus (LCMV) infection in mice. Pdcd1 alleles dissociate from transcriptionally repressive chromatin domains (lamin B) in virus-specific exhausted CTLs but not in naive or effector CTLs. Relative to naive CTLs, nuclear positioning and Pdcd1-lamina dissociation in exhausted CTLs reflect loss of Pdcd1 promoter methylation and greater PD-1 upregulation, although a direct correlation is not observed in effector cells, 8 days post-infection. Genetic deletion of B lymphocyte-induced maturation protein 1 (Blimp-1) enhances Pdcd1-lamina dissociation in effector CTLs, suggesting that Blimp-1 contributes to maintaining Pdcd1 localization to repressive lamina. Our results identify mechanisms governing Pdcd1 subnuclear localization and the broader role of chromatin dynamics in T cell exhaustion.
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Affiliation(s)
- Catarina Sacristán
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Ben A Youngblood
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA; Immunology Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Peiyuan Lu
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Alexander P R Bally
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Jean Xiaojin Xu
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Katelyn McGary
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Susannah L Hewitt
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Jeremy M Boss
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Rafi Ahmed
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Michael L Dustin
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA; The Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
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2
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Hirsch T, Neyens D, Duhamel C, Bayard A, Vanhaver C, Luyckx M, Sala de Oyanguren F, Wildmann C, Dauguet N, Squifflet JL, Montiel V, Deschamps M, van der Bruggen P. IRF4 impedes human CD8 T cell function and promotes cell proliferation and PD-1 expression. Cell Rep 2024; 43:114401. [PMID: 38943641 DOI: 10.1016/j.celrep.2024.114401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/03/2024] [Accepted: 06/11/2024] [Indexed: 07/01/2024] Open
Abstract
Human CD8 tumor-infiltrating lymphocytes (TILs) with impaired effector functions and PD-1 expression are categorized as exhausted. However, the exhaustion-like features reported in TILs might stem from their activation rather than the consequence of T cell exhaustion itself. Using CRISPR-Cas9 and lentiviral overexpression in CD8 T cells from non-cancerous donors, we show that the T cell receptor (TCR)-induced transcription factor interferon regulatory factor 4 (IRF4) promotes cell proliferation and PD-1 expression and hampers effector functions and expression of nuclear factor κB (NF-κB)-regulated genes. While CD8 TILs with impaired interferon γ (IFNγ) production exhibit activation markers IRF4 and CD137 and exhaustion markers thymocyte selection associated high mobility group box (TOX) and PD-1, activated T cells in patients with COVID-19 do not demonstrate elevated levels of TOX and PD-1. These results confirm that IRF4+ TILs are exhausted rather than solely activated. Our study indicates, however, that PD-1 expression, low IFNγ production, and active cycling in TILs are all influenced by IRF4 upregulation after T cell activation.
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Affiliation(s)
- Thibault Hirsch
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium.
| | - Damien Neyens
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Céline Duhamel
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Alexandre Bayard
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | | | - Mathieu Luyckx
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium; Département de Gynécologie, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | | | - Claude Wildmann
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Nicolas Dauguet
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Jean-Luc Squifflet
- Département de Gynécologie, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Virginie Montiel
- Unité de Soins Intensifs, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Mélanie Deschamps
- Unité de Soins Intensifs, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Pierre van der Bruggen
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium; WELBIO Department, WEL Research Institute, Wavre, Belgium
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3
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Arnold F, Kupferschmid L, Weissenborn P, Heldmann L, Hummel JF, Zareba P, Sagar, Rogg M, Schell C, Tanriver Y. Tissue-resident memory T cells break tolerance to renal autoantigens and orchestrate immune-mediated nephritis. Cell Mol Immunol 2024:10.1038/s41423-024-01197-z. [PMID: 38961265 DOI: 10.1038/s41423-024-01197-z] [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: 02/08/2024] [Accepted: 06/13/2024] [Indexed: 07/05/2024] Open
Abstract
Immune-mediated nephritis is a leading cause of acute kidney injury and chronic kidney disease. While the role of B cells and antibodies has been extensively investigated in the past, the advent of immune-checkpoint inhibitors has led to a reappraisal of the role of T cells in renal immunology. However, it remains elusive how T cells with specificity for renal autoantigens are activated and participate in immune-mediated nephritis. Here, we followed the fate and function of pathogen-activated autoreactive CD8 T cells that are specific for a renal autoantigen. We demonstrate that recently activated splenic CD8 T cells developed a hybrid phenotype in the context of renal autoantigen cross-presentation, combining hallmarks of activation and T cell dysfunction. While circulating memory T cells rapidly disappeared, tissue-resident memory T cells emerged and persisted within the kidney, orchestrating immune-mediated nephritis. Notably, T cells infiltrating kidneys of patients with interstitial nephritis also expressed key markers of tissue residency. This study unveils how a tissue-specific immune response can dissociate from its systemic counterpart driving a compartmentalized immune response in the kidneys of mice and man. Consequently, targeting tissue-resident memory T cells emerges as a promising strategy to control immune-mediated kidney disease.
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Affiliation(s)
- Frederic Arnold
- Department of Medicine IV, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Institute of Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Laurence Kupferschmid
- Institute of Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp Weissenborn
- Institute of Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lukas Heldmann
- Institute of Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jonas F Hummel
- Institute of Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Paulina Zareba
- Institute of Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sagar
- Department of Medicine II, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Manuel Rogg
- Institute of Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph Schell
- Institute of Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Yakup Tanriver
- Department of Medicine IV, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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4
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Żyłka K, Kubicki T, Gil L, Dytfeld D. T-cell exhaustion in multiple myeloma. Expert Rev Hematol 2024; 17:295-312. [PMID: 38919090 DOI: 10.1080/17474086.2024.2370552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
INTRODUCTION Chimeric Antigen Receptor (CAR) T-cells and Bispecific Antibodies (BsAb) are the leading platforms for redirecting the immune system against cells expressing the specific antigen, revolutionizing the treatment of hematological malignancies, including multiple myeloma (MM). In MM, drug-resistant relapses are the main therapy-limiting factor and the leading cause of why the disease is still considered incurable. T-cell-engaging therapies hold promise in improving the treatment of MM. However, the effectiveness of these treatments may be hindered by T-cell fitness. T-cell exhaustion is a condition of a gradual decline in effector function, reduced cytokine secretion, and increased expression of inhibitory receptors due to chronic antigen stimulation. AREAS COVERED This review examines findings about T-cell exhaustion in MM in the context of T-cell redirecting BsAbs and CAR-T treatment. EXPERT OPINION The fitness of T-cells has become an important factor in the development of T-cell redirecting therapies. The way T-cell exhaustion relates to these therapies could affect the further development of CAR and BsAbs technologies, as well as the strategies used for clinical use. Therefore, this review aims to explore the current understanding of T-cell exhaustion in MM and its relationship to these therapies.
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Affiliation(s)
- Krzysztof Żyłka
- The Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznań, Poland
| | - Tadeusz Kubicki
- The Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznań, Poland
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL, USA
| | - Lidia Gil
- The Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznań, Poland
| | - Dominik Dytfeld
- The Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznań, Poland
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5
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Broomfield BJ, Tan CW, Qin RZ, Duckworth BC, Alvarado C, Dalit L, Chen J, Mackiewicz L, Muramatsu H, Pellegrini M, Rogers KL, Moon WJ, Nutt SL, Davis MJ, Pardi N, Wimmer VC, Groom JR. Transient inhibition of type I interferon enhances CD8 + T cell stemness and vaccine protection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600763. [PMID: 38979239 PMCID: PMC11230403 DOI: 10.1101/2024.06.26.600763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Developing vaccines that promote CD8 + T cell memory is a challenge for infectious disease and cancer immunotherapy. TCF-1 + stem cell-like memory T (T SCM ) cells are important determinants of long-lived memory. Yet, the developmental requirements for T SCM formation are unclear. Here, we identify the temporal window for type I interferon (IFN-I) receptor (IFNAR) blockade to drive T SCM cell generation. T SCM cells were transcriptionally distinct and emerged from a transitional precursor of exhausted (T PEX ) cellular state concomitant with viral clearance. T SCM differentiation correlated with T cell retention within the lymph node paracortex, due to increased CXCR3 chemokine abundance which disrupted gradient formation. These affects were due a counterintuitive increase in IFNψ, which controlled cell location. Combining IFNAR inhibition with mRNA-LNP vaccination promoted specific T SCM differentiation and enhanced protection against chronic infection. These finding propose a new approach to vaccine design whereby modulation of inflammation promotes memory formation and function. HIGHLIGHTS Early, transient inhibition of the type I interferon (IFN) receptor (IFNAR) during acute viral infection promotes stem cell-like memory T (T SCM ) cell differentiation without establishing chronic infection. T SCM and precursor of exhausted (T PEX ) cellular states are distinguished transcriptionally and by cell surface markers. Developmentally, T SCM cell differentiation occurs via a transition from a T PEX state coinciding with viral clearance. Transient IFNAR blockade increases IFNψ production to modulate the ligands of CXCR3 and couple T SCM differentiation to cell retention within the T cell paracortex of the lymph node. Specific promotion of T SCM cell differentiation with nucleoside-modified mRNA-LNP vaccination elicits enhanced protection against chronic viral challenge.
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6
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Hao J, Li R, Zhao X, Liu X, Chen X, Xie T, Li X, Yao C, Sun Q, Wei K, Gou M, Chi X, Xu W, Ni L, Dong C. NR4A1 transcriptionally regulates the differentiation of stem-like CD8 + T cells in the tumor microenvironment. Cell Rep 2024; 43:114301. [PMID: 38823016 DOI: 10.1016/j.celrep.2024.114301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/11/2024] [Accepted: 05/15/2024] [Indexed: 06/03/2024] Open
Abstract
CD8+ T cells are rendered exhausted in tumor and chronic infection. Among heterogeneous exhausted T cells, a subpopulation of progenitor-like (Tpex) cells have been found important for long-term tumor or pathogen control and are also the main responders in immunotherapy. Using an RFP reporter mouse for the orphan nuclear receptor NR4A1, originally characterized as critical in T cell dysfunction, we discover that the reporter is highly expressed in Tpex cells in tumor and chronic infection. Enforced expression of Nr4a1 promotes Tpex cell accumulation, whereas tumor control is improved after Nr4a1 deletion, associated with increased effector function but decreased long-term maintenance of CD8+ T cells. Integrating chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) analysis, NR4A1 is found to bind and promote the expression of Tpex-related genes, as well as suppress terminal differentiation-associated genes. This study therefore has identified a key role of NR4A1 in Tpex regulation and provides a promising target for immunotherapy.
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Affiliation(s)
- Jing Hao
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China
| | - Ruifeng Li
- Institute for Immunology, Tsinghua University, Beijing, China
| | - Xiaohong Zhao
- Institute for Immunology, Tsinghua University, Beijing, China
| | - Xinwei Liu
- Institute for Immunology, Tsinghua University, Beijing, China
| | - Xiang Chen
- Institute for Immunology, Tsinghua University, Beijing, China
| | - Tian Xie
- Institute for Immunology, Tsinghua University, Beijing, China
| | - Xiaoli Li
- Institute for Immunology, Tsinghua University, Beijing, China
| | - Chenjun Yao
- Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Qinli Sun
- Institute for Immunology, Tsinghua University, Beijing, China
| | - Kun Wei
- Institute for Immunology, Tsinghua University, Beijing, China
| | - Mengting Gou
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China
| | - Xinxin Chi
- Institute for Immunology, Tsinghua University, Beijing, China
| | - Wei Xu
- Institute for Immunology, Tsinghua University, Beijing, China
| | - Ling Ni
- Institute for Immunology, Tsinghua University, Beijing, China
| | - Chen Dong
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China; Westlake University School of Medicine, Hangzhou, Zhejiang, China.
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7
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Ahn T, Bae EA, Seo H. Decoding and overcoming T cell exhaustion: Epigenetic and transcriptional dynamics in CAR-T cells against solid tumors. Mol Ther 2024; 32:1617-1627. [PMID: 38582965 PMCID: PMC11184340 DOI: 10.1016/j.ymthe.2024.04.004] [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: 10/15/2023] [Revised: 02/14/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024] Open
Abstract
T cell exhaustion, which is observed in various chronic infections and malignancies, is characterized by elevated expression of multiple inhibitory receptors, impaired effector functions, decreased proliferation, and reduced cytokine production. Notably, while adoptive T cell therapies, such as chimeric antigen receptor (CAR)-T therapy, have shown promise in treating cancer and other diseases, the efficacy of these therapies is often compromised by T cell exhaustion. It is imperative, therefore, to understand the mechanisms underlying this exhaustion to promote advances in T cell-related therapies. Here, we divided exhausted T cells into three distinct subsets according to their developmental and functional profiles: stem-like progenitor cells, intermediately exhausted cells, and terminally exhausted cells. These subsets are carefully regulated by synergistic mechanisms that involve transcriptional and epigenetic modulators. Key transcription factors, such as TCF1, BACH2, and TOX, are crucial for defining and sustaining exhaustion phenotypes. Concurrently, epigenetic regulators, such as TET2 and DNMT3A, shape the chromatin dynamics that direct T cell fate. The interplay of these molecular drivers has recently been highlighted in CAR-T research, revealing promising therapeutic directions. Thus, a profound understanding of exhausted T cell hierarchies and their molecular complexities may reveal innovative and improved tumor treatment strategies.
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Affiliation(s)
- Taeyoung Ahn
- Laboratory of Cell & Gene Therapy, Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun-Ah Bae
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyungseok Seo
- Laboratory of Cell & Gene Therapy, Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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8
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Lan X, Mi T, Alli S, Guy C, Djekidel MN, Liu X, Boi S, Chowdhury P, He M, Zehn D, Feng Y, Youngblood B. Antitumor progenitor exhausted CD8 + T cells are sustained by TCR engagement. Nat Immunol 2024; 25:1046-1058. [PMID: 38816618 DOI: 10.1038/s41590-024-01843-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 04/16/2024] [Indexed: 06/01/2024]
Abstract
The durability of an antitumor immune response is mediated in part by the persistence of progenitor exhausted CD8+ T cells (Tpex). Tpex serve as a resource for replenishing effector T cells and preserve their quantity through self-renewal. However, it is unknown how T cell receptor (TCR) engagement affects the self-renewal capacity of Tpex in settings of continued antigen exposure. Here we use a Lewis lung carcinoma model that elicits either optimal or attenuated TCR signaling in CD8+ T cells to show that formation of Tpex in tumor-draining lymph nodes and their intratumoral persistence is dependent on optimal TCR engagement. Notably, attenuated TCR stimulation accelerates the terminal differentiation of optimally primed Tpex. This TCR-reinforced Tpex development and self-renewal is coupled to proximal positioning to dendritic cells and epigenetic imprinting involving increased chromatin accessibility at Egr2 and Tcf1 target loci. Collectively, this study highlights the critical function of TCR engagement in sustaining Tpex during tumor progression.
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MESH Headings
- Animals
- CD8-Positive T-Lymphocytes/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/immunology
- Mice
- Carcinoma, Lewis Lung/immunology
- Carcinoma, Lewis Lung/pathology
- Carcinoma, Lewis Lung/metabolism
- Mice, Inbred C57BL
- Hepatocyte Nuclear Factor 1-alpha/metabolism
- Cell Differentiation/immunology
- Dendritic Cells/immunology
- Signal Transduction/immunology
- Mice, Knockout
- Lymphocyte Activation/immunology
- Cell Self Renewal
- Mice, Transgenic
- Early Growth Response Protein 2
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Affiliation(s)
- Xin Lan
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Tian Mi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shanta Alli
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cliff Guy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Xueyan Liu
- Department of Mathematics, University of New Orleans, New Orleans, LA, USA
| | - Shannon Boi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Partha Chowdhury
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Minghong He
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Dietmar Zehn
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Yongqiang Feng
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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9
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Schnell A. Stem-like T cells in cancer and autoimmunity. Immunol Rev 2024. [PMID: 38804499 DOI: 10.1111/imr.13356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Stem-like T cells are characterized by their ability to self-renew, survive long-term, and give rise to a heterogeneous pool of effector and memory T cells. Recent advances in single-cell RNA-sequencing (scRNA-seq) and lineage tracing technologies revealed an important role for stem-like T cells in both autoimmunity and cancer. In cancer, stem-like T cells constitute an important arm of the anti-tumor immune response by giving rise to effector T cells that mediate tumor control. In contrast, in autoimmunity stem-like T cells perform an unfavorable role by forming a reservoir of long-lived autoreactive cells that replenish the pathogenic, effector T-cell pool and thereby driving disease pathology. This review provides background on the discovery of stem-like T cells and their function in cancer and autoimmunity. Moreover, the influence of the microbiota and metabolism on the stem-like T-cell pool is summarized. Lastly, the implications of our knowledge about stem-like T cells for clinical treatment strategies for cancer and autoimmunity will be discussed.
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Affiliation(s)
- Alexandra Schnell
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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10
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Zwick D, Vo MT, Shim YJ, Reijonen H, Do JS. BACH2: The Future of Induced T-Regulatory Cell Therapies. Cells 2024; 13:891. [PMID: 38891024 PMCID: PMC11172166 DOI: 10.3390/cells13110891] [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: 04/16/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/20/2024] Open
Abstract
BACH2 (BTB Domain and CNC Homolog 2) is a transcription factor that serves as a central regulator of immune cell differentiation and function, particularly in T and B lymphocytes. A picture is emerging that BACH2 may function as a master regulator of cell fate that is exquisitely sensitive to cell activation status. In particular, BACH2 plays a key role in stabilizing the phenotype and suppressive function of transforming growth factor-beta (TGF-β)-derived human forkhead box protein P3 (FOXP3)+ inducible regulatory T cells (iTregs), a cell type that holds great clinical potential as a cell therapeutic for diverse inflammatory conditions. As such, BACH2 potentially could be targeted to overcome the instability of the iTreg phenotype and suppressive function that has hampered their clinical application. In this review, we focus on the role of BACH2 in T cell fate and iTreg function and stability. We suggest approaches to modulate BACH2 function that may lead to more stable and efficacious Treg cell therapies.
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Affiliation(s)
- Daniel Zwick
- Frederick National Laboratory, Frederick, MD 21701, USA
| | - Mai Tram Vo
- School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Young Jun Shim
- Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - Helena Reijonen
- Department of Immunology and Theranostics, City of Hope, Duarte, CA 91010, USA;
| | - Jeong-su Do
- Department of Immunology and Theranostics, City of Hope, Duarte, CA 91010, USA;
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11
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Sharma P, Guo A, Poudel S, Boada-Romero E, Verbist KC, Palacios G, Immadisetty K, Chen MJ, Haydar D, Mishra A, Peng J, Madan Babu M, Krenciute G, Glazer ES, Green DR. Rapid metabolic regulation of a novel arginine methylation of KCa3.1 attenuates T cell exhaustion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593421. [PMID: 38798680 PMCID: PMC11118966 DOI: 10.1101/2024.05.09.593421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
T cell exhaustion is linked to persistent antigen exposure and perturbed activation events, correlating with poor disease prognosis. Tumor-mediated T cell exhaustion is well documented; however, how the nutrient-deprived tumor niche affects T cell receptor (TCR) activation is largely unclear. We show that methionine metabolism licenses optimal TCR signaling by regulating the protein arginine methylome, and limiting methionine availability during early TCR signaling promotes subsequent T cell exhaustion. We discovered a novel arginine methylation of a Ca 2+ -activated potassium transporter, KCa3.1, prevention of which results in increased Ca 2+ -mediated NFAT1 activation, NFAT1 promoter occupancy, and T cell exhaustion. Furthermore, methionine supplementation reduces nuclear NFAT1 in tumor-infiltrating T cells and augments their anti-tumor activity. These findings demonstrate metabolic regulation of T cell exhaustion determined during TCR engagement.
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12
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Ojo OA, Shen H, Ingram JT, Bonner JA, Welner RS, Lacaud G, Zajac AJ, Shi LZ. Gfi1 controls the formation of effector CD8 T cells during chronic infection and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.579535. [PMID: 38659890 PMCID: PMC11042319 DOI: 10.1101/2024.04.18.579535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
During chronic infections and tumor progression, CD8 T cells gradually lose their effector functions and become exhausted. These exhausted CD8 T cells are heterogeneous and comprised of different subsets, including self-renewing progenitors that give rise to Ly108 - CX3CR1 + effector-like cells. Generation of these effector-like cells is essential for the control of chronic infections and tumors, albeit limited. However, the precise cues and mechanisms directing the formation and maintenance of exhausted effector-like are incompletely understood. Using genetic mouse models challenged with LCMV Clone 13 or syngeneic tumors, we show that the expression of a transcriptional repressor, growth factor independent 1 (Gfi1) is dynamically regulated in exhausted CD8 T cells, which in turn regulates the formation of exhausted effector-like cells. Gfi1 deletion in T cells dysregulates the chromatin accessibility and transcriptomic programs associated with the differentiation of LCMV Clone 13-specific CD8 T cell exhaustion, preventing the formation of effector-like and terminally exhausted cells while maintaining progenitors and a newly identified Ly108 + CX3CR1 + state. These Ly108 + CX3CR1 + cells have a distinct chromatin profile and may represent an alternative target for therapeutic interventions to combat chronic infections and cancer. In sum, we show that Gfi1 is a critical regulator of the formation of exhausted effector-like cells.
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13
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Minnie SA, Waltner OG, Zhang P, Takahashi S, Nemychenkov NS, Ensbey KS, Schmidt CR, Legg SRW, Comstock M, Boiko JR, Nelson E, Bhise SS, Wilkens AB, Koyama M, Dhodapkar MV, Chesi M, Riddell SR, Green DJ, Spencer A, Furlan SN, Hill GR. TIM-3 + CD8 T cells with a terminally exhausted phenotype retain functional capacity in hematological malignancies. Sci Immunol 2024; 9:eadg1094. [PMID: 38640253 PMCID: PMC11093588 DOI: 10.1126/sciimmunol.adg1094] [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: 12/02/2022] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
Abstract
Chronic antigen stimulation is thought to generate dysfunctional CD8 T cells. Here, we identify a CD8 T cell subset in the bone marrow tumor microenvironment that, despite an apparent terminally exhausted phenotype (TPHEX), expressed granzymes, perforin, and IFN-γ. Concurrent gene expression and DNA accessibility revealed that genes encoding these functional proteins correlated with BATF expression and motif accessibility. IFN-γ+ TPHEX effectively killed myeloma with comparable efficacy to transitory effectors, and disease progression correlated with numerical deficits in IFN-γ+ TPHEX. We also observed IFN-γ+ TPHEX within CD19-targeted chimeric antigen receptor T cells, which killed CD19+ leukemia cells. An IFN-γ+ TPHEX gene signature was recapitulated in TEX cells from human cancers, including myeloma and lymphoma. Here, we characterize a TEX subset in hematological malignancies that paradoxically retains function and is distinct from dysfunctional TEX found in chronic viral infections. Thus, IFN-γ+ TPHEX represent a potential target for immunotherapy of blood cancers.
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Affiliation(s)
- Simone A. Minnie
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Olivia G. Waltner
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Ping Zhang
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Shuichiro Takahashi
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Nicole S. Nemychenkov
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Kathleen S. Ensbey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Christine R. Schmidt
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Samuel RW. Legg
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Melissa Comstock
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Julie R. Boiko
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Department of Pediatrics, University of Washington; WA, UNITED STATES
| | - Ethan Nelson
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Shruti S. Bhise
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Alec B. Wilkens
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Motoko Koyama
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Madhav V. Dhodapkar
- Department of Hematology/Medical Oncology, Atlanta, GA, UNITED STATES
- Winship Cancer Institute, Emory University, Atlanta, GA, UNITED STATES
| | - Marta Chesi
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, AZ, UNITED STATES
| | - Stanley R. Riddell
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Division of Medical Oncology, University of Washington; Seattle, WA, UNITED STATES
| | - Damian J. Green
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Division of Medical Oncology, University of Washington; Seattle, WA, UNITED STATES
| | - Andrew Spencer
- Australian Center for Blood Diseases, Monash University/The Alfred Hospital, Melbourne, VIC, AUSTRALIA
- Malignant Haematology and Stem Cell Transplantation, The Alfred Hospital, Melbourne, VIC, AUSTRALIA
- Department of Clinical Haematology, Monash University, Melbourne, VIC
| | - Scott N. Furlan
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Department of Pediatrics, University of Washington; WA, UNITED STATES
| | - Geoffrey R. Hill
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Division of Medical Oncology, University of Washington; Seattle, WA, UNITED STATES
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14
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Phetsouphanh C, Jacka B, Ballouz S, Jackson KJL, Wilson DB, Manandhar B, Klemm V, Tan HX, Wheatley A, Aggarwal A, Akerman A, Milogiannakis V, Starr M, Cunningham P, Turville SG, Kent SJ, Byrne A, Brew BJ, Darley DR, Dore GJ, Kelleher AD, Matthews GV. Improvement of immune dysregulation in individuals with long COVID at 24-months following SARS-CoV-2 infection. Nat Commun 2024; 15:3315. [PMID: 38632311 PMCID: PMC11024141 DOI: 10.1038/s41467-024-47720-8] [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: 10/09/2023] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
This study investigates the humoral and cellular immune responses and health-related quality of life measures in individuals with mild to moderate long COVID (LC) compared to age and gender matched recovered COVID-19 controls (MC) over 24 months. LC participants show elevated nucleocapsid IgG levels at 3 months, and higher neutralizing capacity up to 8 months post-infection. Increased spike-specific and nucleocapsid-specific CD4+ T cells, PD-1, and TIM-3 expression on CD4+ and CD8+ T cells were observed at 3 and 8 months, but these differences do not persist at 24 months. Some LC participants had detectable IFN-γ and IFN-β, that was attributed to reinfection and antigen re-exposure. Single-cell RNA sequencing at the 24 month timepoint shows similar immune cell proportions and reconstitution of naïve T and B cell subsets in LC and MC. No significant differences in exhaustion scores or antigen-specific T cell clones are observed. These findings suggest resolution of immune activation in LC and return to comparable immune responses between LC and MC over time. Improvement in self-reported health-related quality of life at 24 months was also evident in the majority of LC (62%). PTX3, CRP levels and platelet count are associated with improvements in health-related quality of life.
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Affiliation(s)
| | - Brendan Jacka
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Sara Ballouz
- Garvan Institute for Medical research, Sydney, NSW, Australia
- School of Computer Science and Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, Australia
| | | | - Daniel B Wilson
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Bikash Manandhar
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Vera Klemm
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Victoria, VIC, Australia
| | - Adam Wheatley
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Victoria, VIC, Australia
| | - Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Anouschka Akerman
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | | | - Mitchell Starr
- NSW State Reference Laboratory for HIV, St. Vincent's Centre for Applied Medical Research, Sydney, NSW, Australia
| | - Phillip Cunningham
- NSW State Reference Laboratory for HIV, St. Vincent's Centre for Applied Medical Research, Sydney, NSW, Australia
| | - Stuart G Turville
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Victoria, VIC, Australia
| | - Anthony Byrne
- Heart Lung Clinic, St. Vincent's Hospital Sydney and Faculty of Medicine and Health (UNSW), Sydney, NSW, Australia
| | - Bruce J Brew
- Peter Duncan Neurosciences Unit- St Vincent's Centre for Applied Medical Research, Sydney, NSW, Australia
| | | | - Gregory J Dore
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
- St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Anthony D Kelleher
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia.
- St. Vincent's Hospital, Darlinghurst, NSW, Australia.
| | - Gail V Matthews
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia.
- St. Vincent's Hospital, Darlinghurst, NSW, Australia.
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15
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Zhang Y, Nie Y, Liu X, Wan X, Shi Y, Zhang K, Wu P, He J. Tumor metabolic crosstalk and immunotherapy. Clin Transl Oncol 2024; 26:797-807. [PMID: 37740892 DOI: 10.1007/s12094-023-03304-4] [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: 04/13/2023] [Accepted: 08/08/2023] [Indexed: 09/25/2023]
Abstract
Tumor cells must resist the host's immune system while maintaining growth under harsh conditions of acidity and hypoxia, which indicates that tumors are more robust than normal tissue. Immunotherapeutic agents have little effect on solid tumors, mostly because of the tumor density and the difficulty of penetrating deeply into the tissue to achieve the theoretical therapeutic effect. Various therapeutic strategies targeting the tumor microenvironment (TME) have been developed. Immunometabolic disorders play a dominant role in treatment resistance at both the TME and host levels. Understanding immunometabolic factors and their treatment potential may be a way forward for tumor immunotherapy. Here, we summarize the metabolism of substances that affect tumor progression, the crosstalk between the TME and immunosuppression, and some potential tumor-site targets. We also summarize the progress and challenges of tumor immunotherapy.
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Affiliation(s)
- Yiwen Zhang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Yueli Nie
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xiyu Liu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, 530021, Guangxi, China
- School of Pharmacy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xitian Wan
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Yuanyuan Shi
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Keyong Zhang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Pan Wu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, 530021, Guangxi, China
- School of Pharmacy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jian He
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- School of Pharmacy, Guangxi Medical University, Nanning, 530021, Guangxi, China.
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16
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Yapp C, Nirmal AJ, Zhou F, Maliga Z, Tefft JB, Llopis PM, Murphy GF, Lian CG, Danuser G, Santagata S, Sorger PK. Multiplexed 3D Analysis of Immune States and Niches in Human Tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.10.566670. [PMID: 38014052 PMCID: PMC10680601 DOI: 10.1101/2023.11.10.566670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Tissue homeostasis and the emergence of disease are controlled by changes in the proportions of resident and recruited cells, their organization into cellular neighbourhoods, and their interactions with acellular tissue components. Highly multiplexed tissue profiling (spatial omics)1 makes it possible to study this microenvironment in situ, usually in 4-5 micron thick sections (the standard histopathology format)2. Microscopy-based tissue profiling is commonly performed at a resolution sufficient to determine cell types but not to detect subtle morphological features associated with cytoskeletal reorganisation, juxtracrine signalling, or membrane trafficking3. Here we describe a high-resolution 3D imaging approach able to characterize a wide variety of organelles and structures at sub-micron scale while simultaneously quantifying millimetre-scale spatial features. This approach combines cyclic immunofluorescence (CyCIF) imaging4 of over 50 markers with confocal microscopy of archival human tissue thick enough (30-40 microns) to fully encompass two or more layers of intact cells. 3D imaging of entire cell volumes substantially improves the accuracy of cell phenotyping and allows cell proximity to be scored using plasma membrane apposition, not just nuclear position. In pre-invasive melanoma in situ5, precise phenotyping shows that adjacent melanocytic cells are plastic in state and participate in tightly localised niches of interferon signalling near sites of initial invasion into the underlying dermis. In this and metastatic melanoma, mature and precursor T cells engage in an unexpectedly diverse array of juxtracrine and membrane-membrane interactions as well as looser "neighbourhood" associations6 whose morphologies reveal functional states. These data provide new insight into the transitions occurring during early tumour formation and immunoediting and demonstrate the potential for phenotyping of tissues at a level of detail previously restricted to cultured cells and organoids.
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Affiliation(s)
- Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
| | - Ajit J. Nirmal
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Felix Zhou
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Zoltan Maliga
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Juliann B. Tefft
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
| | - Paula Montero Llopis
- Microscopy Resources on the North Quad (MicRoN), Harvard Medical School, Boston, MA 02115, USA
| | - George F. Murphy
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Christine G. Lian
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Peter K. Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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17
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Weng X, Zheng M, Liu Y, Lou G. The role of Bach2 in regulating CD8 + T cell development and function. Cell Commun Signal 2024; 22:169. [PMID: 38459508 PMCID: PMC10921639 DOI: 10.1186/s12964-024-01551-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/01/2024] [Indexed: 03/10/2024] Open
Abstract
Bach2 was initially discovered in B cells, where it was revealed to control the transcription involved in cell differentiation. Bach2 is intimately connected to CD8 + T lymphocytes in various differentiation states and subsets according to recent findings. Bach2 can regulate primitive T cells, stimulate the development and differentiation of memory CD8 + T cells, inhibit the differentiation of effector CD8 + T cells, and play a significant role in the exhaustion of CD8 + T cells. The appearance and development of diseases are tightly linked to irregular CD8 + T cell differentiation and function. Accordingly, Bach2 offers novel approaches and possible targets for the clinical treatment of associated disorders based on research on these pathways. Here, we summarize the role of Bach2 in the function and differentiation of CD8 + T cells and its potential clinical applications.
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Affiliation(s)
- Xinyu Weng
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79# Qingchun Road, 6A-5, Hangzhou, 310003, China
| | - Min Zheng
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79# Qingchun Road, 6A-5, Hangzhou, 310003, China
| | - Yanning Liu
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79# Qingchun Road, 6A-5, Hangzhou, 310003, China.
| | - Guohua Lou
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79# Qingchun Road, 6A-5, Hangzhou, 310003, China.
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18
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Klysz DD, Fowler C, Malipatlolla M, Stuani L, Freitas KA, Chen Y, Meier S, Daniel B, Sandor K, Xu P, Huang J, Labanieh L, Keerthi V, Leruste A, Bashti M, Mata-Alcazar J, Gkitsas N, Guerrero JA, Fisher C, Patel S, Asano K, Patel S, Davis KL, Satpathy AT, Feldman SA, Sotillo E, Mackall CL. Inosine induces stemness features in CAR-T cells and enhances potency. Cancer Cell 2024; 42:266-282.e8. [PMID: 38278150 PMCID: PMC10923096 DOI: 10.1016/j.ccell.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 10/31/2023] [Accepted: 01/05/2024] [Indexed: 01/28/2024]
Abstract
Adenosine (Ado) mediates immune suppression in the tumor microenvironment and exhausted CD8+ CAR-T cells express CD39 and CD73, which mediate proximal steps in Ado generation. Here, we sought to enhance CAR-T cell potency by knocking out CD39, CD73, or adenosine receptor 2a (A2aR) but observed only modest effects. In contrast, overexpression of Ado deaminase (ADA-OE), which metabolizes Ado to inosine (INO), induced stemness and enhanced CAR-T functionality. Similarly, CAR-T cell exposure to INO augmented function and induced features of stemness. INO induced profound metabolic reprogramming, diminishing glycolysis, increasing mitochondrial and glycolytic capacity, glutaminolysis and polyamine synthesis, and reprogrammed the epigenome toward greater stemness. Clinical scale manufacturing using INO generated enhanced potency CAR-T cell products meeting criteria for clinical dosing. These results identify INO as a potent modulator of CAR-T cell metabolism and epigenetic stemness programming and deliver an enhanced potency platform for cell manufacturing.
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Affiliation(s)
- Dorota D Klysz
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Carley Fowler
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Meena Malipatlolla
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Lucille Stuani
- Department of Pediatrics, Division of Pediatric Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine A Freitas
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Yiyun Chen
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Stefanie Meier
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Bence Daniel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Katalin Sandor
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peng Xu
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jing Huang
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Louai Labanieh
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Vimal Keerthi
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Amaury Leruste
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Malek Bashti
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Janette Mata-Alcazar
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nikolaos Gkitsas
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin A Guerrero
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Chris Fisher
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Sunny Patel
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyle Asano
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Shabnum Patel
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kara L Davis
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Division of Pediatric Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven A Feldman
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Pediatrics, Division of Pediatric Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Medicine, Division of Bone Marrow Transplantation and Cell Therapy, Stanford University School of Medicine, Stanford, CA, USA.
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19
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Hauser AE. Spatial analyses: Focusing on immune-stromal interactions to understand immunity in the tissue context. Semin Arthritis Rheum 2024; 64S:152319. [PMID: 38040516 DOI: 10.1016/j.semarthrit.2023.152319] [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: 08/30/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 12/03/2023]
Abstract
Immune cells perform their tasks in tissues, thus, they are highly dependent on their microenvironment. This means that the tissue context should be considered to fully understand their function. For a long time, it has been difficult to quantify these complex interrelationships in tissues and to spatially map the diversity of cell types involved. In recent years, several methods have become available that allow comprehensive profiling of immune cells and their microenvironment, at both the protein and transcriptional levels. We have used multiplex immunofluorescence histology in combination with machine-learning based cell segmentation and annotation to identify even rare immune cell populations, namely innate lymphoid cells, in various human tissues and found that they preferentially localize in fibrovascular niches. Those niches are located around blood vessels, enriched in stromal cells and extracellular matrix, and represent a location for innate lymphoid cells across various organs. By combining multiplexed histology and spatial transcriptomics on serial sections, we further identified those tissue areas as seed points for COVID-19 induced lung fibrosis and pin-pointed a pro-fibrotic macrophage population as driver of this process, leading to an expansion of the niches. At later disease stages, these areas were populated by lymphocytes, promoting the formation of tertiary lymphoid structures. Whether similar mechanisms apply to other diseases associated with fibrosis, such as autoimmune conditions, awaits further investigation.
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Affiliation(s)
- Anja E Hauser
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany.
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20
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Tyler SR, Lozano-Ojalvo D, Guccione E, Schadt EE. Anti-correlated feature selection prevents false discovery of subpopulations in scRNAseq. Nat Commun 2024; 15:699. [PMID: 38267438 PMCID: PMC10808220 DOI: 10.1038/s41467-023-43406-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 11/07/2023] [Indexed: 01/26/2024] Open
Abstract
While sub-clustering cell-populations has become popular in single cell-omics, negative controls for this process are lacking. Popular feature-selection/clustering algorithms fail the null-dataset problem, allowing erroneous subdivisions of homogenous clusters until nearly each cell is called its own cluster. Using real and synthetic datasets, we find that anti-correlated gene selection reduces or eliminates erroneous subdivisions, increases marker-gene selection efficacy, and efficiently scales to millions of cells.
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Affiliation(s)
- Scott R Tyler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Daniel Lozano-Ojalvo
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ernesto Guccione
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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21
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Wang Y, He S, Calendo G, Bui T, Tian Y, Lee CY, Zhou Y, Zhao X, Abraham C, Mo W, Chen M, Sanders-Braggs R, Madzo J, Issa JP, Hexner EO, Wiest DL, Reshef R, Xue HH, Zhang Y. Tissue-infiltrating alloreactive T cells require Id3 to deflect PD-1-mediated immune suppression during GVHD. Blood 2024; 143:166-177. [PMID: 37871574 PMCID: PMC10797551 DOI: 10.1182/blood.2023021126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/25/2023] Open
Abstract
ABSTRACT Persisting alloreactive donor T cells in target tissues are a determinant of graft-versus-host disease (GVHD), but the transcriptional regulators that control the persistence and function of tissue-infiltrating T cells remain elusive. We demonstrate here that Id3, a DNA-binding inhibitor, is critical for sustaining T-cell responses in GVHD target tissues in mice, including the liver and intestine. Id3 loss results in aberrantly expressed PD-1 in polyfunctional T helper 1 (Th1) cells, decreased tissue-infiltrating PD-1+ polyfunctional Th1 cell numbers, impaired maintenance of liver TCF-1+ progenitor-like T cells, and inhibition of GVHD. PD-1 blockade restores the capacity of Id3-ablated donor T cells to mediate GVHD. Single-cell RNA-sequencing analysis revealed that Id3 loss leads to significantly decreased CD28- and PI3K/AKT-signaling activity in tissue-infiltrating polyfunctional Th1 cells, an indicator of active PD-1/PD-L1 effects. Id3 is also required for protecting CD8+ T cells from the PD-1 pathway-mediated suppression during GVHD. Genome-wide RNA-sequencing analysis reveals that Id3 represses transcription factors (e.g., Nfatc2, Fos, Jun, Ets1, and Prdm1) that are critical for PD-1 transcription, exuberant effector differentiation, and interferon responses and dysfunction of activated T cells. Id3 achieves these effects by restraining the chromatin accessibility for these transcription factors. Id3 ablation in donor T cells preserved their graft vs tumor effects in mice undergoing allogeneic hematopoietic stem cell transplantation. Furthermore, CRISPR/Cas9 knockout of ID3 in human CD19-directed chimeric antigen receptor T cells retained their antitumor activity in NOD/SCID/IL2Rg-/- mice early after administration. These findings identify that ID3 is an important target to reduce GVHD, and the gene-editing program of ID3 may have broad implications in T-cell-based immunotherapy.
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Affiliation(s)
- Ying Wang
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Shan He
- Fels Institute and Department of Cancer Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | | | - Tien Bui
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Yuanyuan Tian
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Che Young Lee
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Yan Zhou
- Fox Chase Cancer Center, Temple University, Philadelphia, PA
| | - Xin Zhao
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Ciril Abraham
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
- Fels Institute and Department of Cancer Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Wenbin Mo
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Mimi Chen
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | | | - Jozef Madzo
- Coriell Institute for Medical Research, Camden, NJ
| | | | - Elizabeth O. Hexner
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David L. Wiest
- Fox Chase Cancer Center, Temple University, Philadelphia, PA
| | - Ran Reshef
- Blood and Marrow Transplantation and Cell Therapy Program, Columbia University Irving Medical Center, New York, NY
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Yi Zhang
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
- Fels Institute and Department of Cancer Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
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22
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Beltra JC, Abdel-Hakeem MS, Manne S, Zhang Z, Huang H, Kurachi M, Su L, Picton L, Ngiow SF, Muroyama Y, Casella V, Huang YJ, Giles JR, Mathew D, Belman J, Klapholz M, Decaluwe H, Huang AC, Berger SL, Garcia KC, Wherry EJ. Stat5 opposes the transcription factor Tox and rewires exhausted CD8 + T cells toward durable effector-like states during chronic antigen exposure. Immunity 2023; 56:2699-2718.e11. [PMID: 38091951 PMCID: PMC10752292 DOI: 10.1016/j.immuni.2023.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 08/23/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
Rewiring exhausted CD8+ T (Tex) cells toward functional states remains a therapeutic challenge. Tex cells are epigenetically programmed by the transcription factor Tox. However, epigenetic remodeling occurs as Tex cells transition from progenitor (Texprog) to intermediate (Texint) and terminal (Texterm) subsets, suggesting development flexibility. We examined epigenetic transitions between Tex cell subsets and revealed a reciprocally antagonistic circuit between Stat5a and Tox. Stat5 directed Texint cell formation and re-instigated partial effector biology during this Texprog-to-Texint cell transition. Constitutive Stat5a activity antagonized Tox and rewired CD8+ T cells from exhaustion to a durable effector and/or natural killer (NK)-like state with superior anti-tumor potential. Temporal induction of Stat5 activity in Tex cells using an orthogonal IL-2:IL2Rβ-pair fostered Texint cell accumulation, particularly upon PD-L1 blockade. Re-engaging Stat5 also partially reprogrammed the epigenetic landscape of exhaustion and restored polyfunctionality. These data highlight therapeutic opportunities of manipulating the IL-2-Stat5 axis to rewire Tex cells toward more durably protective states.
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Affiliation(s)
- Jean-Christophe Beltra
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - Mohamed S Abdel-Hakeem
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini, Cairo 11562, Egypt
| | - Sasikanth Manne
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhen Zhang
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hua Huang
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Makoto Kurachi
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa 920-8640, Japan
| | - Leon Su
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lora Picton
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shin Foong Ngiow
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuki Muroyama
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Valentina Casella
- Infection Biology Laboratory, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Yinghui J Huang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - Divij Mathew
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan Belman
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Max Klapholz
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hélène Decaluwe
- Cytokines and Adaptive Immunity Laboratory, Sainte-Justine University Hospital Research Center, Montreal, QC, Canada; Department of Microbiology and Immunology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada; Immunology and Rheumatology Division, Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Alexander C Huang
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - K Christopher Garcia
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Parker Institute for Cancer Immunotherapy, 1 Letterman Drive, Suite D3500, San Francisco, CA 94129, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA.
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23
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Schenkel JM, Pauken KE. Localization, tissue biology and T cell state - implications for cancer immunotherapy. Nat Rev Immunol 2023; 23:807-823. [PMID: 37253877 DOI: 10.1038/s41577-023-00884-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Tissue localization is a critical determinant of T cell immunity. CD8+ T cells are contact-dependent killers, which requires them to physically be within the tissue of interest to kill peptide-MHC class I-bearing target cells. Following their migration and extravasation into tissues, T cells receive many extrinsic cues from the local microenvironment, and these signals shape T cell differentiation, fate and function. Because major organ systems are variable in their functions and compositions, they apply disparate pressures on T cells to adapt to the local microenvironment. Additional complexity arises in the context of malignant lesions (either primary or metastatic), and this has made understanding the factors that dictate T cell function and longevity in tumours challenging. Moreover, T cell differentiation state influences how cues from the microenvironment are interpreted by tissue-infiltrating T cells, highlighting the importance of T cell state in the context of tissue biology. Here, we review the intertwined nature of T cell differentiation state, location, survival and function, and explain how dysfunctional T cell populations can adopt features of tissue-resident memory T cells to persist in tumours. Finally, we discuss how these factors have shaped responses to cancer immunotherapy.
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Affiliation(s)
- Jason M Schenkel
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Kristen E Pauken
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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24
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Louie RHY, Cai C, Samir J, Singh M, Deveson IW, Ferguson JM, Amos TG, McGuire HM, Gowrishankar K, Adikari T, Balderas R, Bonomi M, Ruella M, Bishop D, Gottlieb D, Blyth E, Micklethwaite K, Luciani F. CAR + and CAR - T cells share a differentiation trajectory into an NK-like subset after CD19 CAR T cell infusion in patients with B cell malignancies. Nat Commun 2023; 14:7767. [PMID: 38012187 PMCID: PMC10682404 DOI: 10.1038/s41467-023-43656-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy is effective in treating B cell malignancies, but factors influencing the persistence of functional CAR+ T cells, such as product composition, patients' lymphodepletion, and immune reconstitution, are not well understood. To shed light on this issue, here we conduct a single-cell multi-omics analysis of transcriptional, clonal, and phenotypic profiles from pre- to 1-month post-infusion of CAR+ and CAR- T cells from patients from a CARTELL study (ACTRN12617001579381) who received a donor-derived 4-1BB CAR product targeting CD19. Following infusion, CAR+ T cells and CAR- T cells shows similar differentiation profiles with clonally expanded populations across heterogeneous phenotypes, demonstrating clonal lineages and phenotypic plasticity. We validate these findings in 31 patients with large B cell lymphoma treated with CD19 CAR T therapy. For these patients, we identify using longitudinal mass-cytometry data an association between NK-like subsets and clinical outcomes at 6 months with both CAR+ and CAR- T cells. These results suggest that non-CAR-derived signals can provide information about patients' immune recovery and be used as correlate of clinically relevant parameters.
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Affiliation(s)
- Raymond Hall Yip Louie
- School of Computer Science and Engineering, UNSW Sydney, Sydney, NSW, Australia
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Curtis Cai
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Jerome Samir
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Mandeep Singh
- Garvan Institute for Medical Research, Sydney, NSW, Australia
| | - Ira W Deveson
- Garvan Institute for Medical Research, Sydney, NSW, Australia
| | | | - Timothy G Amos
- Garvan Institute for Medical Research, Sydney, NSW, Australia
| | - Helen Marie McGuire
- Ramaciotti Facility for Human Systems Biology, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Infection, Immunity and Inflammation Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Kavitha Gowrishankar
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Thiruni Adikari
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | | | - Martina Bonomi
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- Department of Physics, University of Bologna, Bologna, Italy
| | - Marco Ruella
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - David Bishop
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - David Gottlieb
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Emily Blyth
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Kenneth Micklethwaite
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
- NSW Health Pathology Blood Transplant and Cell Therapies Laboratory - ICPMR Westmead, Sydney, NSW, Australia
| | - Fabio Luciani
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia.
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia.
- Garvan Institute for Medical Research, Sydney, NSW, Australia.
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25
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Liu Z, Zhang Y, Ma N, Yang Y, Ma Y, Wang F, Wang Y, Wei J, Chen H, Tartarone A, Velotta JB, Dayyani F, Gabriel E, Wakefield CJ, Kidane B, Carbonelli C, Long L, Liu Z, Su J, Li Z. Progenitor-like exhausted SPRY1 +CD8 + T cells potentiate responsiveness to neoadjuvant PD-1 blockade in esophageal squamous cell carcinoma. Cancer Cell 2023; 41:1852-1870.e9. [PMID: 37832554 DOI: 10.1016/j.ccell.2023.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 08/15/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023]
Abstract
Neoadjuvant immune checkpoint blockade (ICB) demonstrates promise in operable esophageal squamous cell carcinoma (ESCC), but lacks available efficacy biomarkers. Here, we perform single-cell RNA-sequencing of tumors from patients with ESCC undergoing neoadjuvant ICB, revealing a subset of exhausted CD8+ T cells expressing SPRY1 (CD8+ Tex-SPRY1) that displays a progenitor exhausted T cell (Tpex) phenotype and correlates with complete response to ICB. We validate CD8+ Tex-SPRY1 cells as an ICB-specific predictor of improved response and survival using independent ICB-/non-ICB cohorts and demonstrate that expression of SPRY1 in CD8+ T cells enforces Tpex phenotype and enhances ICB efficacy. Additionally, CD8+ Tex-SPRY1 cells contribute to proinflammatory phenotype of macrophages and functional state of B cells, which thereby promotes antitumor immunity by enhancing CD8+ T cell effector functions. Overall, our findings unravel progenitor-like CD8+ Tex-SPRY1 cells' role in effective responses to ICB for ESCC and inform mechanistic biomarkers for future individualized immunotherapy.
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Affiliation(s)
- Zhichao Liu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Institute of Thoracic Oncology, Shanghai 200030, China
| | - Yaru Zhang
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
| | - Ning Ma
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Institute of Thoracic Oncology, Shanghai 200030, China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Institute of Thoracic Oncology, Shanghai 200030, China
| | - Yunlong Ma
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Feng Wang
- State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Yan Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Jinzhi Wei
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Hongyan Chen
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Alfredo Tartarone
- Division of Medical Oncology, Department of Onco-Hematology, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture (PZ) 85028, Italy
| | - Jeffrey B Velotta
- Department of Thoracic Surgery, Kaiser Permanente Oakland Medical Center, Kaiser Permanente Northern California, Oakland, CA 94611, USA
| | - Farshid Dayyani
- Chao Comprehensive Cancer Center, University of California Irvine, Orange, CA 92868, USA
| | - Emmanuel Gabriel
- Department of Surgery, Division of Surgical Oncology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Connor J Wakefield
- Department of Internal Medicine, Brooke Army Medical Center, Fort Sam Houston, TX 78234, USA
| | - Biniam Kidane
- Section of Thoracic Surgery, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Cristiano Carbonelli
- Pneumology Unit, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo 71013, Italy
| | - Lingyun Long
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Jianzhong Su
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China.
| | - Zhigang Li
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Institute of Thoracic Oncology, Shanghai 200030, China.
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26
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Abstract
T cells can acquire a broad spectrum of differentiation states following activation. At the extreme ends of this continuum are short-lived cells equipped with effector machinery and more quiescent, long-lived cells with heightened proliferative potential and stem cell-like developmental plasticity. The latter encompass stem-like exhausted T cells and memory T cells, both of which have recently emerged as key determinants of cancer immunity and response to immunotherapy. Here, we discuss key similarities and differences in the regulation and function of stem-like exhausted CD8+ T cells and memory CD8+ T cells, and consider their context-specific contributions to protective immunity in diverse outcomes of cancer, including tumour escape, long-term control and eradication. Finally, we emphasize how recent advances in the understanding of the molecular regulation of stem-like exhausted T cells and memory T cells are being explored for clinical benefit in cancer immunotherapies such as checkpoint inhibition, adoptive cell therapy and vaccination.
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Affiliation(s)
- Thomas Gebhardt
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Simone L Park
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.
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27
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Smith AJ, Thurman RE, Zeng W, Grogan B, Lucas S, Gutierrez G, Heiser RA, Wo SW, Blackmarr A, Peterson S, Gardai SJ. Nonfucosylation of an anti-TIGIT antibody enhances FcγR engagement, driving innate immune activation and antitumor activity. Front Immunol 2023; 14:1280986. [PMID: 38022590 PMCID: PMC10654636 DOI: 10.3389/fimmu.2023.1280986] [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: 08/21/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
Abstract
TIGIT is an immune checkpoint receptor expressed on activated and memory T cells, immunosuppressive T regulatory cells, and natural killer (NK) cells. TIGIT has emerged as an attractive target for antitumor therapies, due to its proposed immunosuppressive effects on lymphocyte function and T cell activation. We generated an anti-TIGIT monoclonal antibody (mAb) that binds with high affinity to human, non-human primate, and murine TIGIT and through multiple experimental methodologies demonstrated that checkpoint blockade alone is insufficient for antitumor activity. Generating anti-TIGIT mAbs with various Fc backbones we show that muting the Fc-Fcγ receptor (FcγR) interaction failed to drive antitumor activity, while mAbs with Fc functional backbones demonstrate substantial antitumor activity, mediated through activation of antigen-presenting cells (APCs), T cell priming, and NK-mediated depletion of suppressive Tregs and exhausted T cells. Further, nonfucosylation of the Fc backbone resulted in enhanced immune responses and antitumor activity relative to the intact IgG1 backbone. The improved activity correlated with the biased FcγR interaction profile of the nonfucosylated anti-TIGIT mAb, which supports that FcγRIIIa binding with decreased FcγRIIb binding favorably activates APCs and enhances tumor-specific CD8+ T cell responses. The anti-TIGIT mAbs with intact FcγR interacting backbones also demonstrated synergistic enhancement of other standard antitumor treatments, including anti-PD-1 treatment and a model monomethyl auristatin E antibody-drug conjugate. These findings highlight the importance of the anti-TIGIT mAb's Fc backbone to its antitumor activity and the extent to which this activity can be enhanced through nonfucosylation of the backbone.
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Russ BE, Barugahare A, Dakle P, Tsyganov K, Quon S, Yu B, Li J, Lee JKC, Olshansky M, He Z, Harrison PF, See M, Nussing S, Morey AE, Udupa VA, Bennett TJ, Kallies A, Murre C, Collas P, Powell D, Goldrath AW, Turner SJ. Active maintenance of CD8 + T cell naivety through regulation of global genome architecture. Cell Rep 2023; 42:113301. [PMID: 37858463 PMCID: PMC10679840 DOI: 10.1016/j.celrep.2023.113301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/07/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
The differentiation of naive CD8+ T lymphocytes into cytotoxic effector and memory CTL results in large-scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organization underpin these transcriptional programs. We use Hi-C to map changes in the spatial organization of long-range genome contacts within naive, effector, and memory virus-specific CD8+ T cells. We observe that the architecture of the naive CD8+ T cell genome is distinct from effector and memory genome configurations, with extensive changes within discrete functional chromatin domains associated with effector/memory differentiation. Deletion of BACH2, or to a lesser extent, reducing SATB1 DNA binding, within naive CD8+ T cells results in a chromatin architecture more reminiscent of effector/memory states. This suggests that key transcription factors within naive CD8+ T cells act to restrain T cell differentiation by actively enforcing a unique naive chromatin state.
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Affiliation(s)
- Brendan E Russ
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Adele Barugahare
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pushkar Dakle
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Kirril Tsyganov
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Sara Quon
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Bingfei Yu
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Jasmine Li
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Jason K C Lee
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Moshe Olshansky
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Zhaohren He
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Paul F Harrison
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Michael See
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Simone Nussing
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Alison E Morey
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Vibha A Udupa
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Taylah J Bennett
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Phillipe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - David Powell
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ananda W Goldrath
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Stephen J Turner
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
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29
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Li F, Chen D, Zeng Q, Du Y. Possible Mechanisms of Lymphopenia in Severe Tuberculosis. Microorganisms 2023; 11:2640. [PMID: 38004652 PMCID: PMC10672989 DOI: 10.3390/microorganisms11112640] [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: 09/14/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis). In lymphopenia, T cells are typically characterized by progressive loss and a decrease in their count results. Lymphopenia can hinder immune responses and lead to systemic immunosuppression, which is strongly associated with mortality. Lymphopenia is a significant immunological abnormality in the majority of patients with severe and advanced TB, and its severity is linked to disease outcomes. However, the underlying mechanism remains unclear. Currently, the research on the pathogenesis of lymphopenia during M. tuberculosis infection mainly focuses on how it affects lymphocyte production, survival, or tissue redistribution. This includes impairing hematopoiesis, inhibiting T-cell proliferation, and inducing lymphocyte apoptosis. In this study, we have compiled the latest research on the possible mechanisms that may cause lymphopenia during M. tuberculosis infection. Lymphopenia may have serious consequences in severe TB patients. Additionally, we discuss in detail potential intervention strategies to prevent lymphopenia, which could help understand TB immunopathogenesis and achieve the goal of preventing and treating severe TB.
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Affiliation(s)
- Fei Li
- Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China; (D.C.); (Q.Z.); (Y.D.)
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30
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Wu H, Zhao X, Hochrein SM, Eckstein M, Gubert GF, Knöpper K, Mansilla AM, Öner A, Doucet-Ladevèze R, Schmitz W, Ghesquière B, Theurich S, Dudek J, Gasteiger G, Zernecke A, Kobold S, Kastenmüller W, Vaeth M. Mitochondrial dysfunction promotes the transition of precursor to terminally exhausted T cells through HIF-1α-mediated glycolytic reprogramming. Nat Commun 2023; 14:6858. [PMID: 37891230 PMCID: PMC10611730 DOI: 10.1038/s41467-023-42634-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
T cell exhaustion is a hallmark of cancer and persistent infections, marked by inhibitory receptor upregulation, diminished cytokine secretion, and impaired cytolytic activity. Terminally exhausted T cells are steadily replenished by a precursor population (Tpex), but the metabolic principles governing Tpex maintenance and the regulatory circuits that control their exhaustion remain incompletely understood. Using a combination of gene-deficient mice, single-cell transcriptomics, and metabolomic analyses, we show that mitochondrial insufficiency is a cell-intrinsic trigger that initiates the functional exhaustion of T cells. At the molecular level, we find that mitochondrial dysfunction causes redox stress, which inhibits the proteasomal degradation of hypoxia-inducible factor 1α (HIF-1α) and promotes the transcriptional and metabolic reprogramming of Tpex cells into terminally exhausted T cells. Our findings also bear clinical significance, as metabolic engineering of chimeric antigen receptor (CAR) T cells is a promising strategy to enhance the stemness and functionality of Tpex cells for cancer immunotherapy.
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Affiliation(s)
- Hao Wu
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Xiufeng Zhao
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Sophia M Hochrein
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Miriam Eckstein
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Gabriela F Gubert
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Konrad Knöpper
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Ana Maria Mansilla
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Arman Öner
- Division of Clinical Pharmacology, Department of Medicine IV, Ludwig Maximilians University (LMU) Munich, University Hospital, Munich, Germany
| | - Remi Doucet-Ladevèze
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Werner Schmitz
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Bart Ghesquière
- Laboratory of Applied Mass Spectrometry, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium and Metabolomics Core Facility Leuven, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Sebastian Theurich
- Ludwig Maximilians University (LMU) Munich, University Hospital, Department of Medicine III, Munich, Germany and LMU Gene Center, Cancer and Immunometabolism Research Group, Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, a partnership between the DKFZ Heidelberg and the University Hospital of the LMU, Munich, Germany
| | - Jan Dudek
- Comprehensive Heart Failure Center (CHFC), University Hospital, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Georg Gasteiger
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Alma Zernecke
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Sebastian Kobold
- Division of Clinical Pharmacology, Department of Medicine IV, Ludwig Maximilians University (LMU) Munich, University Hospital, Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, a partnership between the DKFZ Heidelberg and the University Hospital of the LMU, Munich, Germany
| | - Wolfgang Kastenmüller
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Martin Vaeth
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians University of Würzburg, Würzburg, Germany.
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31
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Giles JR, Globig AM, Kaech SM, Wherry EJ. CD8 + T cells in the cancer-immunity cycle. Immunity 2023; 56:2231-2253. [PMID: 37820583 PMCID: PMC11237652 DOI: 10.1016/j.immuni.2023.09.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023]
Abstract
CD8+ T cells are end effectors of cancer immunity. Most forms of effective cancer immunotherapy involve CD8+ T cell effector function. Here, we review the current understanding of T cell function in cancer, focusing on key CD8+ T cell subtypes and states. We discuss factors that influence CD8+ T cell differentiation and function in cancer through a framework that incorporates the classic three-signal model and a fourth signal-metabolism-and also consider the impact of the tumor microenvironment from a T cell perspective. We argue for the notion of immunotherapies as "pro-drugs" that act to augment or modulate T cells, which ultimately serve as the drug in vivo, and for the importance of overall immune health in cancer treatment and prevention. The progress in understanding T cell function in cancer has and will continue to improve harnessing of the immune system across broader tumor types to benefit more patients.
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Affiliation(s)
- Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anna-Maria Globig
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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32
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Horton BL, D’Souza AD, Zagorulya M, McCreery CV, Abhiraman GC, Picton L, Sheen A, Agarwal Y, Momin N, Wittrup KD, White FM, Garcia KC, Spranger S. Overcoming lung cancer immunotherapy resistance by combining nontoxic variants of IL-12 and IL-2. JCI Insight 2023; 8:e172728. [PMID: 37669107 PMCID: PMC10619440 DOI: 10.1172/jci.insight.172728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/31/2023] [Indexed: 09/07/2023] Open
Abstract
Engineered cytokine-based approaches for immunotherapy of cancer are poised to enter the clinic, with IL-12 being at the forefront. However, little is known about potential mechanisms of resistance to cytokine therapies. We found that orthotopic murine lung tumors were resistant to systemically delivered IL-12 fused to murine serum albumin (MSA, IL12-MSA) because of low IL-12 receptor (IL-12R) expression on tumor-reactive CD8+ T cells. IL2-MSA increased binding of IL12-MSA by tumor-reactive CD8+ T cells, and combined administration of IL12-MSA and IL2-MSA led to enhanced tumor-reactive CD8+ T cell effector differentiation, decreased numbers of tumor-infiltrating CD4+ regulatory T cells, and increased survival of lung tumor-bearing mice. Predictably, the combination of IL-2 and IL-12 at therapeutic doses led to significant dose-limiting toxicity. Administering IL-12 and IL-2 analogs with preferential binding to cells expressing Il12rb1 and CD25, respectively, led to a significant extension of survival in mice with lung tumors while abrogating dose-limiting toxicity. These findings suggest that IL-12 and IL-2 represent a rational approach to combination cytokine therapy whose dose-limiting toxicity can be overcome with engineered cytokine variants.
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Affiliation(s)
- Brendan L. Horton
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
| | - Alicia D. D’Souza
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
- MIT-Harvard Health Sciences and Technology, Cambridge, Massachusetts, USA
| | - Maria Zagorulya
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
- Department of Biology, MIT, Cambridge, Massachusetts, USA
| | | | - Gita C. Abhiraman
- Program in Immunology
- Department of Molecular and Cellular Physiology, and
| | - Lora Picton
- Department of Molecular and Cellular Physiology, and
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Allison Sheen
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
- Department of Biological Engineering and
| | - Yash Agarwal
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
- Department of Biological Engineering and
| | - Noor Momin
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
- Department of Biological Engineering and
| | - K. Dane Wittrup
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
- Department of Biological Engineering and
- Department of Chemical Engineering, MIT, Cambridge, Massachusetts, USA
| | - Forest M. White
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
- Department of Biological Engineering and
| | - K. Christopher Garcia
- Department of Molecular and Cellular Physiology, and
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Stefani Spranger
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
- Department of Biology, MIT, Cambridge, Massachusetts, USA
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33
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Elliot TAE, Lecky DAJ, Bending D. T-cell response to checkpoint blockade immunotherapies: from fundamental mechanisms to treatment signatures. Essays Biochem 2023; 67:967-977. [PMID: 37386922 PMCID: PMC10539945 DOI: 10.1042/ebc20220247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 07/01/2023]
Abstract
Immune checkpoint immunotherapies act to block inhibitory receptors on the surface of T cells and other cells of the immune system. This can increase activation of immune cells and promote tumour clearance. Whilst this is very effective in some types of cancer, significant proportions of patients do not respond to single-agent immunotherapy. To improve patient outcomes, we must first mechanistically understand what drives therapy resistance. Many studies have utilised genetic, transcriptional, and histological signatures to find correlates of effective responses to treatment. It is key that we understand pretreatment predictors of response, but also to understand how the immune system becomes treatment resistant during therapy. Here, we review our understanding of the T-cell signatures that are critical for response, how these immune signatures change during treatment, and how this information can be used to rationally design therapeutic strategies. We highlight how chronic antigen recognition drives heterogeneous T-cell exhaustion and the role of T-cell receptor (TCR) signal strength in exhausted T-cell differentiation and molecular response to therapy. We explore how dynamic changes in negative feedback pathways can promote resistance to single-agent therapy. We speculate that this resistance may be circumvented in the future through identifying the most effective combinations of immunotherapies to promote sustained and durable antitumour responses.
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Affiliation(s)
- Thomas A E Elliot
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - David A J Lecky
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - David Bending
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
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34
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Lee S, Lee K, Bae H, Lee K, Lee J, Ma J, Lee YJ, Lee BR, Park WY, Im SJ. Defining a TCF1-expressing progenitor allogeneic CD8 + T cell subset in acute graft-versus-host disease. Nat Commun 2023; 14:5869. [PMID: 37737221 PMCID: PMC10516895 DOI: 10.1038/s41467-023-41357-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 09/01/2023] [Indexed: 09/23/2023] Open
Abstract
Graft-versus-host disease (GvHD) is a severe complication of hematopoietic stem cell transplantation driven by activated allogeneic T cells. Here, we identify a distinct subset of T cell factor-1 (TCF1)+ CD8+ T cells in mouse allogeneic and xenogeneic transplant models of acute GvHD. These TCF1+ cells exhibit distinct characteristics compared to TCF1- cells, including lower expression of inhibitory receptors and higher expression of costimulatory molecules. Notably, the TCF1+ subset displays exclusive proliferative potential and could differentiate into TCF1- effector cells upon antigenic stimulation. Pathway analyses support the role of TCF1+ and TCF1- subsets as resource cells and effector cells, respectively. Furthermore, the TCF1+ CD8+ T cell subset is primarily present in the spleen and exhibits a resident phenotype. These findings provide insight into the differentiation of allogeneic and xenogeneic CD8+ T cells and have implications for the development of immunotherapeutic strategies targeting acute GvHD.
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Affiliation(s)
- Solhwi Lee
- Department of Immunology, Graduate School of Basic Medical Science, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kunhee Lee
- Department of Immunology, Graduate School of Basic Medical Science, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Hyeonjin Bae
- Department of Immunology, Graduate School of Basic Medical Science, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyungmin Lee
- Department of Immunology, Graduate School of Basic Medical Science, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Junghwa Lee
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Junhui Ma
- Department of Immunology, Graduate School of Basic Medical Science, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Ye Ji Lee
- GENINUS Inc., Seoul, Republic of Korea
| | | | - Woong-Yang Park
- GENINUS Inc., Seoul, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Se Jin Im
- Department of Immunology, Graduate School of Basic Medical Science, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea.
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35
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Li WS, Zhang QQ, Li Q, Liu SY, Yuan GQ, Pan YW. Innate immune response restarts adaptive immune response in tumors. Front Immunol 2023; 14:1260705. [PMID: 37781382 PMCID: PMC10538570 DOI: 10.3389/fimmu.2023.1260705] [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: 07/20/2023] [Accepted: 08/25/2023] [Indexed: 10/03/2023] Open
Abstract
The imbalance of immune response plays a crucial role in the development of diseases, including glioblastoma. It is essential to comprehend how the innate immune system detects tumors and pathogens. Endosomal and cytoplasmic sensors can identify diverse cancer cell antigens, triggering the production of type I interferon and pro-inflammatory cytokines. This, in turn, stimulates interferon stimulating genes, enhancing the presentation of cancer antigens, and promoting T cell recognition and destruction of cancer cells. While RNA and DNA sensing of tumors and pathogens typically involve different receptors and adapters, their interaction can activate adaptive immune response mechanisms. This review highlights the similarity in RNA and DNA sensing mechanisms in the innate immunity of both tumors and pathogens. The aim is to enhance the anti-tumor innate immune response, identify regions of the tumor that are not responsive to treatment, and explore new targets to improve the response to conventional tumor therapy and immunotherapy.
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Affiliation(s)
- Wen-shan Li
- The Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Neurology of Gansu Province, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
- Department of Neurosurgery, Qinghai Provincial People’s Hospital, Xining, Qinghai, China
| | - Qing-qing Zhang
- Department of Respiratory and Critical Care Medicine, Qinghai University Affiliated Hospital, Xining, Qinghai, China
| | - Qiao Li
- The Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Neurology of Gansu Province, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Shang-yu Liu
- The Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Neurology of Gansu Province, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Guo-qiang Yuan
- The Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Neurology of Gansu Province, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Ya-wen Pan
- The Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Neurology of Gansu Province, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
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36
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Neubert EN, DeRogatis JM, Lewis SA, Viramontes KM, Ortega P, Henriquez ML, Buisson R, Messaoudi I, Tinoco R. HMGB2 regulates the differentiation and stemness of exhausted CD8 + T cells during chronic viral infection and cancer. Nat Commun 2023; 14:5631. [PMID: 37704621 PMCID: PMC10499904 DOI: 10.1038/s41467-023-41352-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Chronic infections and cancers evade the host immune system through mechanisms that induce T cell exhaustion. The heterogeneity within the exhausted CD8+ T cell pool has revealed the importance of stem-like progenitor (Tpex) and terminal (Tex) exhausted T cells, although the mechanisms underlying their development are not fully known. Here we report High Mobility Group Box 2 (HMGB2) protein expression is upregulated and sustained in exhausted CD8+ T cells, and HMGB2 expression is critical for their differentiation. Through epigenetic and transcriptional programming, we identify HMGB2 as a cell-intrinsic regulator of the differentiation and maintenance of Tpex cells during chronic viral infection and in tumors. Despite Hmgb2-/- CD8+ T cells expressing TCF-1 and TOX, these master regulators were unable to sustain Tpex differentiation and long-term survival during persistent antigen. Furthermore, HMGB2 also had a cell-intrinsic function in the differentiation and function of memory CD8+ T cells after acute viral infection. Our findings show that HMGB2 is a key regulator of CD8+ T cells and may be an important molecular target for future T cell-based immunotherapies.
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Affiliation(s)
- Emily N Neubert
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
- Center for Virus Research, University of California Irvine, Irvine, CA, 92697, USA
| | - Julia M DeRogatis
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Sloan A Lewis
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
- La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Karla M Viramontes
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Pedro Ortega
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, 92697, USA
| | - Monique L Henriquez
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Rémi Buisson
- Center for Virus Research, University of California Irvine, Irvine, CA, 92697, USA
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, 92697, USA
| | - Ilhem Messaoudi
- Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY, 40536, USA
| | - Roberto Tinoco
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA.
- Center for Virus Research, University of California Irvine, Irvine, CA, 92697, USA.
- Institute for Immunology, University of California, Irvine, Irvine, CA, 92697, USA.
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA.
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37
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Lan X, Zebley CC, Youngblood B. Cellular and molecular waypoints along the path of T cell exhaustion. Sci Immunol 2023; 8:eadg3868. [PMID: 37656775 PMCID: PMC10618911 DOI: 10.1126/sciimmunol.adg3868] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/09/2023] [Indexed: 09/03/2023]
Abstract
Thirty years of foundational research investigating molecular and cellular mechanisms promoting T cell exhaustion are now enabling rational design of T cell-based therapies for the treatment of chronic infections and cancer. Once described as a static cell fate, it is now well appreciated that the developmental path toward exhaustion is composed of a heterogeneous pool of cells with varying degrees of effector potential that ultimately converge on a terminally differentiated state. Recent description of the developmental stages along the differentiation trajectory of T cell exhaustion has provided insight into past immunotherapeutic success and future opportunities. Here, we discuss the hallmarks of distinct developmental stages occurring along the path to T cell dysfunction and the impact of these discrete CD8+ T cell fates on cancer immunotherapy.
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Affiliation(s)
- Xin Lan
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Caitlin C. Zebley
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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38
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Rudloff MW, Zumbo P, Favret NR, Roetman JJ, Detrés Román CR, Erwin MM, Murray KA, Jonnakuti ST, Dündar F, Betel D, Philip M. Hallmarks of CD8 + T cell dysfunction are established within hours of tumor antigen encounter before cell division. Nat Immunol 2023; 24:1527-1539. [PMID: 37537361 PMCID: PMC10878719 DOI: 10.1038/s41590-023-01578-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/07/2023] [Indexed: 08/05/2023]
Abstract
Tumor-specific CD8+ T cells (TST) in patients with cancer are dysfunctional and unable to halt cancer progression. TST dysfunction, also known as exhaustion, is thought to be driven by chronic T cell antigen receptor (TCR) stimulation over days to weeks. However, we know little about the interplay between CD8+ T cell function, cell division and epigenetic remodeling within hours of activation. Here, we assessed early CD8+ T cell differentiation, cell division, chromatin accessibility and transcription in tumor-bearing mice and acutely infected mice. Surprisingly, despite robust activation and proliferation, TST had near complete effector function impairment even before undergoing cell division and had acquired hallmark chromatin accessibility features previously associated with later dysfunction/exhaustion. Moreover, continued tumor/antigen exposure drove progressive epigenetic remodeling, 'imprinting' the dysfunctional state. Our study reveals the rapid divergence of T cell fate choice before cell division in the context of tumors versus infection.
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Affiliation(s)
- Michael W Rudloff
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Natalie R Favret
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Jessica J Roetman
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Carlos R Detrés Román
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Megan M Erwin
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Kristen A Murray
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Sriya T Jonnakuti
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Friederike Dündar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mary Philip
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA.
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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39
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Pachmayr LO, Muehlbauer A, Flommersfeld S, Graml F, Hoenninger J, von Baumgarten L, Buchholz VR, Grassmann S. Unbiased chemokine receptor screening reveals similar efficacy of lymph node- and tumor-targeted T cell immunotherapy. Cancer Immunol Immunother 2023; 72:3111-3124. [PMID: 37301772 PMCID: PMC10412482 DOI: 10.1007/s00262-023-03472-w] [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: 03/13/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023]
Abstract
Localization is a crucial prerequisite for immune cell function and solid tumors evade immune control by modulating immune cell infiltration into the tumor stroma. Immunosuppressive cells like regulatory T cells are attracted, while cytotoxic CD8+ T cells are excluded. Engineering CD8+ T cells with chemokine receptors is a potent strategy to turn this mechanism of directed immune cell recruitment against the tumor. Here, we utilized fluorescent tagging to track the migratory behavior of tumor-specific T cells engineered with a library of all murine chemokine receptors in vivo. We then asked whether chemokine receptor-mediated redirection of antigen-specific T cells into tumors or tumor-draining lymph nodes showed superior anti-tumoral activity. We found that both targeting approaches showed higher therapeutic efficacy than control T cells. However, multiple receptors conveying the same homing pattern did not augment infiltration. Instead, in the MC38 colon carcinoma model, anti-tumoral efficacy as well as lymph node vs. tumor-homing patterns were mostly driven by CCR4 and CCR6, respectively. Overall, our data, based on fluorescent receptor tagging, identify the tumor-draining lymph node and the tumor itself as viable targets for chemokine receptor-mediated enhancement of adoptive T cell therapy.
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Affiliation(s)
- Ludwig O Pachmayr
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Anton Muehlbauer
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Sophie Flommersfeld
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Franziska Graml
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Julian Hoenninger
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | | | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany.
| | - Simon Grassmann
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany.
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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40
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Sun L, Kienzler JC, Reynoso JG, Lee A, Shiuan E, Li S, Kim J, Ding L, Monteleone AJ, Owens GC, Phillips JJ, Everson RG, Nathanson D, Cloughesy TF, Li G, Liau LM, Hugo W, Kim W, Prins RM. Immune checkpoint blockade induces distinct alterations in the microenvironments of primary and metastatic brain tumors. J Clin Invest 2023; 133:e169314. [PMID: 37655659 PMCID: PMC10471177 DOI: 10.1172/jci169314] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/12/2023] [Indexed: 09/02/2023] Open
Abstract
In comparison with responses in recurrent glioblastoma (rGBM), the intracranial response of brain metastases (BrM) to immune checkpoint blockade (ICB) is less well studied. Here, we present an integrated single-cell RNA-Seq (scRNA-Seq) study of 19 ICB-naive and 9 ICB-treated BrM samples from our own and published data sets. We compared them with our previously published scRNA-Seq data from rGBM and found that ICB led to more prominent T cell infiltration into BrM than rGBM. These BrM-infiltrating T cells exhibited a tumor-specific phenotype and displayed greater activated/exhausted features. We also used multiplex immunofluorescence and spatial transcriptomics to reveal that ICB reduced a distinct CD206+ macrophage population in the perivascular space, which may modulate T cell entry into BrM. Furthermore, we identified a subset of progenitor exhausted T cells that correlated with longer overall survival in BrM patients. Our study provides a comprehensive immune cellular landscape of ICB's effect on metastatic brain tumors and offers insights into potential strategies for improving ICB efficacy for brain tumor patients.
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Affiliation(s)
- Lu Sun
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
| | - Jenny C. Kienzler
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Inflammation Research Group, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | | | - Alexander Lee
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
| | | | | | | | - Lizhong Ding
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Department of Medicine/Dermatology, UCLA, Los Angeles, California, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
| | | | | | - Joanna J. Phillips
- Helen Diller Family Comprehensive Cancer Center and
- Department of Neurological Surgery, UCSF, San Francisco, California, USA
| | - Richard G. Everson
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - David Nathanson
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - Timothy F. Cloughesy
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Department of Neurology/Neuro-Oncology, UCLA, Los Angeles, California, USA
| | | | - Linda M. Liau
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - Willy Hugo
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Department of Medicine/Dermatology, UCLA, Los Angeles, California, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
| | - Won Kim
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - Robert M. Prins
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
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41
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Zawidzka EM, Biavati L, Thomas A, Zanettini C, Marchionni L, Leone R, Borrello I. Tumor-Specific CD8 + T Cells from the Bone Marrow Resist Exhaustion and Exhibit Increased Persistence in Tumor-Bearing Hosts as Compared to Tumor Infiltrating Lymphocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555119. [PMID: 37693379 PMCID: PMC10491133 DOI: 10.1101/2023.08.28.555119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Immunotherapy is now an integral aspect of cancer therapy. Strategies employing adoptive cell therapy (ACT) have seen the establishment of chimeric antigen receptor (CAR)-T cells using peripheral blood lymphocytes as well as tumor infiltrating lymphocytes (TILs) with significant clinical results. Despite these successes, the limitations of the current strategies are also emerging and novel approaches are needed. The bone marrow (BM) is an immunological niche that houses T cells with specificity for previously encountered antigens, including tumor-associated antigens from certain solid cancers. This study sought to improve our understanding of tumor-specific BM T cells in the context of solid tumors by comparing them with TILs, and to assess whether there is a rationale for using the BM as a source of T cells for ACT against solid malignancies. Herein, we demonstrate that T cells from the BM appear superior to TILs as a source of cells for cellular therapy. Specifically, they possess a memory-enriched phenotype and exhibit improved effector function, greater persistence within a tumor-bearing host, and the capacity for increased tumor infiltration. Taken together, these data provide a foundation for further exploring the BM as a source of tumor-specific T cells for ACT in solid malignancies.
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Affiliation(s)
- Elizabeth M. Zawidzka
- Johns Hopkins University School of Medicine, Bloomberg Kimmel Institute for Cancer Immunotherapy
| | - Luca Biavati
- Johns Hopkins University School of Medicine, Bloomberg Kimmel Institute for Cancer Immunotherapy
| | - Amy Thomas
- Johns Hopkins University School of Medicine, Bloomberg Kimmel Institute for Cancer Immunotherapy
| | | | | | - Robert Leone
- Johns Hopkins University School of Medicine, Bloomberg Kimmel Institute for Cancer Immunotherapy
| | - Ivan Borrello
- Johns Hopkins University School of Medicine, Bloomberg Kimmel Institute for Cancer Immunotherapy
- Current Address: Tampa General Hospital Cancer Institute
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42
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Pichler AC, Carrié N, Cuisinier M, Ghazali S, Voisin A, Axisa PP, Tosolini M, Mazzotti C, Golec DP, Maheo S, do Souto L, Ekren R, Blanquart E, Lemaitre L, Feliu V, Joubert MV, Cannons JL, Guillerey C, Avet-Loiseau H, Watts TH, Salomon BL, Joffre O, Grinberg-Bleyer Y, Schwartzberg PL, Lucca LE, Martinet L. TCR-independent CD137 (4-1BB) signaling promotes CD8 +-exhausted T cell proliferation and terminal differentiation. Immunity 2023; 56:1631-1648.e10. [PMID: 37392737 PMCID: PMC10649891 DOI: 10.1016/j.immuni.2023.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 03/29/2023] [Accepted: 06/08/2023] [Indexed: 07/03/2023]
Abstract
CD137 (4-1BB)-activating receptor represents a promising cancer immunotherapeutic target. Yet, the cellular program driven by CD137 and its role in cancer immune surveillance remain unresolved. Using T cell-specific deletion and agonist antibodies, we found that CD137 modulates tumor infiltration of CD8+-exhausted T (Tex) cells expressing PD1, Lag-3, and Tim-3 inhibitory receptors. T cell-intrinsic, TCR-independent CD137 signaling stimulated the proliferation and the terminal differentiation of Tex precursor cells through a mechanism involving the RelA and cRel canonical NF-κB subunits and Tox-dependent chromatin remodeling. While Tex cell accumulation induced by prophylactic CD137 agonists favored tumor growth, anti-PD1 efficacy was improved with subsequent CD137 stimulation in pre-clinical mouse models. Better understanding of T cell exhaustion has crucial implications for the treatment of cancer and infectious diseases. Our results identify CD137 as a critical regulator of Tex cell expansion and differentiation that holds potential for broad therapeutic applications.
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Affiliation(s)
- Andrea C Pichler
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France; Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nadège Carrié
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France
| | - Marine Cuisinier
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France; Institut Universitaire du Cancer, CHU Toulouse, Toulouse, France
| | - Samira Ghazali
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), UPS, INSERM, CNRS, Toulouse, France
| | - Allison Voisin
- Centre de Recherche en Cancérologie de Lyon, Labex DEVweCAN, INSERM, CNRS, Université Claude Bernard Lyon 1, Centre Léon Bérard, Lyon, France
| | - Pierre-Paul Axisa
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France
| | - Marie Tosolini
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France
| | - Céline Mazzotti
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France; Institut Universitaire du Cancer, CHU Toulouse, Toulouse, France
| | - Dominic P Golec
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sabrina Maheo
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France; Institut Universitaire du Cancer, CHU Toulouse, Toulouse, France
| | - Laura do Souto
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France; Institut Universitaire du Cancer, CHU Toulouse, Toulouse, France
| | - Rüçhan Ekren
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France
| | - Eve Blanquart
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France
| | - Lea Lemaitre
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France
| | - Virginie Feliu
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France
| | - Marie-Véronique Joubert
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France; Institut Universitaire du Cancer, CHU Toulouse, Toulouse, France
| | - Jennifer L Cannons
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Camille Guillerey
- Cancer Immunotherapies Group, The University of Queensland, Brisbane, QLD, Australia
| | - Hervé Avet-Loiseau
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France; Institut Universitaire du Cancer, CHU Toulouse, Toulouse, France
| | - Tania H Watts
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Benoit L Salomon
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), UPS, INSERM, CNRS, Toulouse, France; Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Olivier Joffre
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), UPS, INSERM, CNRS, Toulouse, France
| | - Yenkel Grinberg-Bleyer
- Centre de Recherche en Cancérologie de Lyon, Labex DEVweCAN, INSERM, CNRS, Université Claude Bernard Lyon 1, Centre Léon Bérard, Lyon, France
| | - Pamela L Schwartzberg
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Liliana E Lucca
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France.
| | - Ludovic Martinet
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier (UPS), Toulouse, France; Institut Universitaire du Cancer, CHU Toulouse, Toulouse, France.
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43
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Hackstein CP, Spitzer J, Symeonidis K, Horvatic H, Bedke T, Steglich B, Klein S, Assmus LM, Odainic A, Szlapa J, Kessler N, Beyer M, Schmithausen R, Latz E, Flavell RA, Garbi N, Kurts C, Kümmerer BM, Trebicka J, Roers A, Huber S, Schmidt SV, Knolle PA, Abdullah Z. Interferon-induced IL-10 drives systemic T-cell dysfunction during chronic liver injury. J Hepatol 2023; 79:150-166. [PMID: 36870611 DOI: 10.1016/j.jhep.2023.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 03/06/2023]
Abstract
BACKGROUND & AIMS Patients with chronic liver disease (CLD), including cirrhosis, are at increased risk of intractable viral infections and are hyporesponsive to vaccination. Hallmarks of CLD and cirrhosis include microbial translocation and elevated levels of type I interferon (IFN-I). We aimed to investigate the relevance of microbiota-induced IFN-I in the impaired adaptive immune responses observed in CLD. METHODS We combined bile duct ligation (BDL) and carbon tetrachloride (CCl4) models of liver injury with vaccination or lymphocytic choriomeningitis virus infection in transgenic mice lacking IFN-I in myeloid cells (LysM-Cre IFNARflox/flox), IFNAR-induced IL-10 (MX1-Cre IL10flox/flox) or IL-10R in T cells (CD4-DN IL-10R). Key pathways were blocked in vivo with specific antibodies (anti-IFNAR and anti-IL10R). We assessed T-cell responses and antibody titers after HBV and SARS-CoV-2 vaccinations in patients with CLD and healthy individuals in a proof-of-concept clinical study. RESULTS We demonstrate that BDL- and CCL4-induced prolonged liver injury leads to impaired T-cell responses to vaccination and viral infection in mice, subsequently leading to persistent infection. We observed a similarly defective T-cell response to vaccination in patients with cirrhosis. Innate sensing of translocated gut microbiota induced IFN-I signaling in hepatic myeloid cells that triggered excessive IL-10 production upon viral infection. IL-10R signaling in antigen-specific T cells rendered them dysfunctional. Antibiotic treatment and inhibition of IFNAR or IL-10Ra restored antiviral immunity without detectable immune pathology in mice. Notably, IL-10Ra blockade restored the functional phenotype of T cells from vaccinated patients with cirrhosis. CONCLUSION Innate sensing of translocated microbiota induces IFN-/IL-10 expression, which drives the loss of systemic T-cell immunity during prolonged liver injury. IMPACT AND IMPLICATIONS Chronic liver injury and cirrhosis are associated with enhanced susceptibility to viral infections and vaccine hyporesponsiveness. Using different preclinical animal models and patient samples, we identified that impaired T-cell immunity in BDL- and CCL4-induced prolonged liver injury is driven by sequential events involving microbial translocation, IFN signaling leading to myeloid cell-induced IL-10 expression, and IL-10 signaling in antigen-specific T cells. Given the absence of immune pathology after interference with IL-10R, our study highlights a potential novel target to reconstitute T-cell immunity in patients with CLD that can be explored in future clinical studies.
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Affiliation(s)
- Carl-Philipp Hackstein
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Germany; Current address: Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, UK
| | - Jasper Spitzer
- Institute of Innate Immunity, University Hospital Bonn, Germany
| | - Konstantinos Symeonidis
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Germany
| | - Helena Horvatic
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Germany
| | - Tanja Bedke
- Medizinische Klinik und Poliklinik, Hamburg Center for Translational Immunology (HCTI), Universitätsklinikum Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Babett Steglich
- Medizinische Klinik und Poliklinik, Hamburg Center for Translational Immunology (HCTI), Universitätsklinikum Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sabine Klein
- Medizinische Klinik 1, Universitätsklinikum Frankfurt, Goethe Universität I, Medizinische Klinik und Poliklinik, Germany
| | - Lisa M Assmus
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Germany
| | | | - Jennifer Szlapa
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Germany
| | - Nina Kessler
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Germany
| | - Marc Beyer
- Molecular Immunology in Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, Germany
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Natalio Garbi
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Germany
| | - Christian Kurts
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Germany
| | - Beate M Kümmerer
- Institute of Virology, University Hospital Bonn, Germany; German Center for Infection Research, Bonn-Cologne Site, Germany
| | - Jonel Trebicka
- Medizinische Klinik 1, Universitätsklinikum Frankfurt, Goethe Universität I, Medizinische Klinik und Poliklinik, Germany
| | - Axel Roers
- Institute of Immunology, University of Heidelberg, Germany
| | - Samuel Huber
- Medizinische Klinik und Poliklinik, Hamburg Center for Translational Immunology (HCTI), Universitätsklinikum Hamburg-Eppendorf, 20246 Hamburg, Germany
| | | | - Percy A Knolle
- Institute of Molecular Immunology and Experimental Oncology, Technical University of Munich, Germany; German Center for Infection Research, Munich Site, Germany
| | - Zeinab Abdullah
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Germany.
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44
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Anderson ND, Birch J, Accogli T, Criado I, Khabirova E, Parks C, Wood Y, Young MD, Porter T, Richardson R, Albon SJ, Popova B, Lopes A, Wynn R, Hough R, Gohil SH, Pule M, Amrolia PJ, Behjati S, Ghorashian S. Transcriptional signatures associated with persisting CD19 CAR-T cells in children with leukemia. Nat Med 2023; 29:1700-1709. [PMID: 37407840 PMCID: PMC10353931 DOI: 10.1038/s41591-023-02415-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/23/2023] [Indexed: 07/07/2023]
Abstract
In the context of relapsed and refractory childhood pre-B cell acute lymphoblastic leukemia (R/R B-ALL), CD19-targeting chimeric antigen receptor (CAR)-T cells often induce durable remissions, which requires the persistence of CAR-T cells. In this study, we systematically analyzed CD19 CAR-T cells of 10 children with R/R B-ALL enrolled in the CARPALL trial via high-throughput single-cell gene expression and T cell receptor sequencing of infusion products and serial blood and bone marrow samples up to 5 years after infusion. We show that long-lived CAR-T cells developed a CD4/CD8 double-negative phenotype with an exhausted-like memory state and distinct transcriptional signature. This persistence signature was dominant among circulating CAR-T cells in all children with a long-lived treatment response for which sequencing data were sufficient (4/4, 100%). The signature was also present across T cell subsets and clonotypes, indicating that persisting CAR-T cells converge transcriptionally. This persistence signature was also detected in two adult patients with chronic lymphocytic leukemia with decade-long remissions who received a different CD19 CAR-T cell product. Examination of single T cell transcriptomes from a wide range of healthy and diseased tissues across children and adults indicated that the persistence signature may be specific to long-lived CAR-T cells. These findings raise the possibility that a universal transcriptional signature of clinically effective, persistent CD19 CAR-T cells exists.
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Affiliation(s)
| | - Jack Birch
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Theo Accogli
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Ignacio Criado
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
| | | | | | | | | | | | - Rachel Richardson
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sarah J Albon
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Bilyana Popova
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Andre Lopes
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Robert Wynn
- Department of Bone Marrow Transplantation, Royal Manchester Children's Hospital, Manchester, UK
| | - Rachael Hough
- Children and Young People's Cancer Service, University College London Hospitals NHS Foundation Trust, London, UK
| | - Satyen H Gohil
- Department of Haematology, University College London Hospitals NHS Foundation Trust, London, UK
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Martin Pule
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Persis J Amrolia
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Bone Marrow Transplantation, Great Ormond Street Hospital for Children, London, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
| | - Sara Ghorashian
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK.
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK.
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45
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Lee MH, Theodoropoulos J, Huuhtanen J, Bhattacharya D, Järvinen P, Tornberg S, Nísen H, Mirtti T, Uski I, Kumari A, Peltonen K, Draghi A, Donia M, Kreutzman A, Mustjoki S. Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:1260-1276. [PMID: 37484198 PMCID: PMC10361538 DOI: 10.1158/2767-9764.crc-22-0514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/27/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023]
Abstract
The successful use of expanded tumor-infiltrating lymphocytes (TIL) in adoptive TIL therapies has been reported, but the effects of the TIL expansion, immunophenotype, function, and T cell receptor (TCR) repertoire of the infused products relative to the tumor microenvironment (TME) are not well understood. In this study, we analyzed the tumor samples (n = 58) from treatment-naïve patients with renal cell carcinoma (RCC), "pre-rapidly expanded" TILs (pre-REP TIL, n = 15) and "rapidly expanded" TILs (REP TIL, n = 25) according to a clinical-grade TIL production protocol, with single-cell RNA (scRNA)+TCRαβ-seq (TCRαβ sequencing), TCRβ-sequencing (TCRβ-seq), and flow cytometry. REP TILs encompassed a greater abundance of CD4+ than CD8+ T cells, with increased LAG-3 and low PD-1 expressions in both CD4+ and CD8+ T cell compartments compared with the pre-REP TIL and tumor T cells. The REP protocol preferentially expanded small clones of the CD4+ phenotype (CD4, IL7R, KLRB1) in the TME, indicating that the largest exhausted T cell clones in the tumor do not expand during the expansion protocol. In addition, by generating a catalog of RCC-associated TCR motifs from >1,000 scRNA+TCRαβ-seq and TCRβ-seq RCC, healthy and other cancer sample cohorts, we quantified the RCC-associated TCRs from the expansion protocol. Unlike the low-remaining amount of anti-viral TCRs throughout the expansion, the quantity of the RCC-associated TCRs was high in the tumors and pre-REP TILs but decreased in the REP TILs. Our results provide an in-depth understanding of the origin, phenotype, and TCR specificity of RCC TIL products, paving the way for a more rationalized production of TILs. Significance TILs are a heterogenous group of immune cells that recognize and attack the tumor, thus are utilized in various clinical trials. In our study, we explored the TILs in patients with kidney cancer by expanding the TILs using a clinical-grade protocol, as well as observed their characteristics and ability to recognize the tumor using in-depth experimental and computational tools.
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Affiliation(s)
- Moon Hee Lee
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Jason Theodoropoulos
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Jani Huuhtanen
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Dipabarna Bhattacharya
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Petrus Järvinen
- Abdominal Center, Urology, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Sara Tornberg
- Abdominal Center, Urology, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Harry Nísen
- Abdominal Center, Urology, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Tuomas Mirtti
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biomedical Engineering, School of Medicine, Emory University, Atlanta, Georgia
| | - Ilona Uski
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Anita Kumari
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Karita Peltonen
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Arianna Draghi
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Marco Donia
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Anna Kreutzman
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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46
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Zheng P, Dou Y, Wang Q. Immune response and treatment targets of chronic hepatitis B virus infection: innate and adaptive immunity. Front Cell Infect Microbiol 2023; 13:1206720. [PMID: 37424786 PMCID: PMC10324618 DOI: 10.3389/fcimb.2023.1206720] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection is a major global public health risk that threatens human life and health, although the number of vaccinated people has increased. The clinical outcome of HBV infection depends on the complex interplay between viral replication and the host immune response. Innate immunity plays an important role in the early stages of the disease but retains no long-term immune memory. However, HBV evades detection by the host innate immune system through stealth. Therefore, adaptive immunity involving T and B cells is crucial for controlling and clearing HBV infections that lead to liver inflammation and damage. The persistence of HBV leads to immune tolerance owing to immune cell dysfunction, T cell exhaustion, and an increase in suppressor cells and cytokines. Although significant progress has been made in HBV treatment in recent years, the balance between immune tolerance, immune activation, inflammation, and fibrosis in chronic hepatitis B remains unknown, making a functional cure difficult to achieve. Therefore, this review focuses on the important cells involved in the innate and adaptive immunity of chronic hepatitis B that target the host immune system and identifies treatment strategies.
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Affiliation(s)
- Peiyu Zheng
- Department of Infectious Diseases, The First Hospital of Shanxi Medical University, Taiyuan, China
- Graduate School of Shanxi Medical University, Taiyuan, China
| | - Yongqing Dou
- Department of Infectious Diseases, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Qinying Wang
- Department of Infectious Diseases, The First Hospital of Shanxi Medical University, Taiyuan, China
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47
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Jung IY, Noguera-Ortega E, Bartoszek R, Collins SM, Williams E, Davis M, Jadlowsky JK, Plesa G, Siegel DL, Chew A, Levine BL, Berger SL, Moon EK, Albelda SM, Fraietta JA. Tissue-resident memory CAR T cells with stem-like characteristics display enhanced efficacy against solid and liquid tumors. Cell Rep Med 2023; 4:101053. [PMID: 37224816 PMCID: PMC10313923 DOI: 10.1016/j.xcrm.2023.101053] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/21/2023] [Accepted: 04/27/2023] [Indexed: 05/26/2023]
Abstract
Chimeric antigen receptor (CAR) T cells demonstrate remarkable success in treating hematological malignancies, but their effectiveness in non-hematopoietic cancers remains limited. This study proposes enhancing CAR T cell function and localization in solid tumors by modifying the epigenome governing tissue-residency adaptation and early memory differentiation. We identify that a key factor in human tissue-resident memory CAR T cell (CAR-TRM) formation is activation in the presence of the pleotropic cytokine, transforming growth factor β (TGF-β), which enforces a core program of both "stemness" and sustained tissue residency by mediating chromatin remodeling and concurrent transcriptional changes. This approach leads to a practical and clinically actionable in vitro production method for engineering peripheral blood T cells into a large number of "stem-like" CAR-TRM cells resistant to tumor-associated dysfunction, possessing an enhanced ability to accumulate in situ and rapidly eliminate cancer cells for more effective immunotherapy.
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Affiliation(s)
- In-Young Jung
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Estela Noguera-Ortega
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert Bartoszek
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sierra M Collins
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erik Williams
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Megan Davis
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julie K Jadlowsky
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gabriela Plesa
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Donald L Siegel
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anne Chew
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bruce L Levine
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Edmund K Moon
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven M Albelda
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph A Fraietta
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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48
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Baxter AE, Huang H, Giles JR, Chen Z, Wu JE, Drury S, Dalton K, Park SL, Torres L, Simone BW, Klapholz M, Ngiow SF, Freilich E, Manne S, Alcalde V, Ekshyyan V, Berger SL, Shi J, Jordan MS, Wherry EJ. The SWI/SNF chromatin remodeling complexes BAF and PBAF differentially regulate epigenetic transitions in exhausted CD8 + T cells. Immunity 2023; 56:1320-1340.e10. [PMID: 37315535 DOI: 10.1016/j.immuni.2023.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/28/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023]
Abstract
CD8+ T cell exhaustion (Tex) limits disease control during chronic viral infections and cancer. Here, we investigated the epigenetic factors mediating major chromatin-remodeling events in Tex-cell development. A protein-domain-focused in vivo CRISPR screen identified distinct functions for two versions of the SWI/SNF chromatin-remodeling complex in Tex-cell differentiation. Depletion of the canonical SWI/SNF form, BAF, impaired initial CD8+ T cell responses in acute and chronic infection. In contrast, disruption of PBAF enhanced Tex-cell proliferation and survival. Mechanistically, PBAF regulated the epigenetic and transcriptional transition from TCF-1+ progenitor Tex cells to more differentiated TCF-1- Tex subsets. Whereas PBAF acted to preserve Tex progenitor biology, BAF was required to generate effector-like Tex cells, suggesting that the balance of these factors coordinates Tex-cell subset differentiation. Targeting PBAF improved tumor control both alone and in combination with anti-PD-L1 immunotherapy. Thus, PBAF may present a therapeutic target in cancer immunotherapy.
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Affiliation(s)
- Amy E Baxter
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hua Huang
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Josephine R Giles
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zeyu Chen
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jennifer E Wu
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sydney Drury
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Katherine Dalton
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Simone L Park
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Leonel Torres
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Brandon W Simone
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Max Klapholz
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Radiation Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shin Foong Ngiow
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Elizabeth Freilich
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sasikanth Manne
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Victor Alcalde
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Viktoriya Ekshyyan
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Junwei Shi
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Martha S Jordan
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - E John Wherry
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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49
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Romine KA, Bottomly D, Yashar W, Long N, Viehdorfer M, McWeeney SK, Tyner JW. Immune cell proportions correlate with clinicogenomic features and ex vivo drug responses in acute myeloid leukemia. Front Oncol 2023; 13:1192829. [PMID: 37361575 PMCID: PMC10285384 DOI: 10.3389/fonc.2023.1192829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction The implementation of small-molecule and immunotherapies in acute myeloid leukemia (AML) has been challenging due to genetic and epigenetic variability amongst patients. There are many potential mechanisms by which immune cells could influence small-molecule or immunotherapy responses, yet, this area remains understudied. Methods Here we performed cell type enrichment analysis from over 560 AML patient bone marrow and peripheral blood samples from the Beat AML dataset to describe the functional immune landscape of AML. Results We identify multiple cell types that significantly correlate with AML clinical and genetic features, and we also observe significant correlations of immune cell proportions with ex vivo small-molecule and immunotherapy responses. Additionally, we generated a signature of terminally exhausted T cells (Tex) and identified AML with high monocytic proportions as strongly correlating with increased proportions of these immunosuppressive T cells. Discussion Our work, which is accessible through a new "Cell Type" module in our visualization platform (Vizome; http://vizome.org/), can be leveraged to investigate potential contributions of different immune cells on many facets of the biology of AML.
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Affiliation(s)
- Kyle A. Romine
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
| | - Daniel Bottomly
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
| | - William Yashar
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Nicola Long
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Matthew Viehdorfer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
| | - Shannon K. McWeeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
| | - Jeffrey W. Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, United States
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50
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Hao Y, Miraghazadeh B, Chand R, Davies AR, Cardinez C, Kwong K, Downes MB, Sweet RA, Cañete PF, D'Orsogna LJ, Fulcher DA, Choo S, Yip D, Peters G, Yip S, Witney MJ, Nekrasov M, Feng ZP, Tscharke DC, Vinuesa CG, Cook MC. CTLA4 protects against maladaptive cytotoxicity during the differentiation of effector and follicular CD4 + T cells. Cell Mol Immunol 2023:10.1038/s41423-023-01027-8. [PMID: 37161048 PMCID: PMC10166697 DOI: 10.1038/s41423-023-01027-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/11/2023] [Indexed: 05/11/2023] Open
Abstract
As chronic antigenic stimulation from infection and autoimmunity is a feature of primary antibody deficiency (PAD), analysis of affected patients could yield insights into T-cell differentiation and explain how environmental exposures modify clinical phenotypes conferred by single-gene defects. CD57 marks dysfunctional T cells that have differentiated after antigenic stimulation. Indeed, while circulating CD57+ CD4+ T cells are normally rare, we found that they are increased in patients with PAD and markedly increased with CTLA4 haploinsufficiency or blockade. We performed single-cell RNA-seq analysis of matched CD57+ CD4+ T cells from blood and tonsil samples. Circulating CD57+ CD4+ T cells (CD4cyt) exhibited a cytotoxic transcriptome similar to that of CD8+ effector cells, could kill B cells, and inhibited B-cell responses. CTLA4 restrained the formation of CD4cyt. While CD57 also marked an abundant subset of follicular helper T cells, which is consistent with their antigen-driven differentiation, this subset had a pre-exhaustion transcriptomic signature marked by TCF7, TOX, and ID3 expression and constitutive expression of CTLA4 and did not become cytotoxic even after CTLA4 inhibition. Thus, CD57+ CD4+ T-cell cytotoxicity and exhaustion phenotypes are compartmentalised between blood and germinal centers. CTLA4 is a key modifier of CD4+ T-cell cytotoxicity, and the pathological CD4cyt phenotype is accentuated by infection.
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Affiliation(s)
- Yuwei Hao
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Bahar Miraghazadeh
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Rochna Chand
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Ainsley R Davies
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Chelisa Cardinez
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Kristy Kwong
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Morgan B Downes
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Rebecca A Sweet
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Pablo F Cañete
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Lloyd J D'Orsogna
- Department of Immunology, Fiona Stanley Hospital, Perth, WA, Australia
| | - David A Fulcher
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Sharon Choo
- Department of Immunology, The Royal Children's Hospital, Melbourne, VIC, Australia
| | - Desmond Yip
- Department of Medical Oncology, The Canberra Hospital, Canberra, ACT, Australia
- ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Geoffrey Peters
- Department of Medical Oncology, The Canberra Hospital, Canberra, ACT, Australia
- ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Sonia Yip
- NHMRC Clinical Trials Unit, The University of Sydney, Sydney, NSW, Australia
| | - Matthew J Witney
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Maxim Nekrasov
- The ACRF Biomolecular Resource Facility, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Zhi-Ping Feng
- ANU Bioinformatics Consultancy, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - David C Tscharke
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Carola G Vinuesa
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Matthew C Cook
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia.
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
- ANU Medical School, The Australian National University, Canberra, ACT, Australia.
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom.
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