1
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Chen J, Larsson L, Swarbrick A, Lundeberg J. Spatial landscapes of cancers: insights and opportunities. Nat Rev Clin Oncol 2024; 21:660-674. [PMID: 39043872 DOI: 10.1038/s41571-024-00926-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2024] [Indexed: 07/25/2024]
Abstract
Solid tumours comprise many different cell types organized in spatially structured arrangements, with substantial intratumour and intertumour heterogeneity. Advances in spatial profiling technologies over the past decade hold promise to capture the complexity of these cellular architectures to build a holistic view of the intricate molecular mechanisms that shape the tumour ecosystem. Some of these mechanisms act at the cellular scale and are controlled by cell-autonomous programmes or communication between nearby cells, whereas other mechanisms result from coordinated efforts between large networks of cells and extracellular molecules organized into tissues and organs. In this Review we provide insights into the application of single-cell and spatial profiling tools, with a focus on spatially resolved transcriptomic tools developed to understand the cellular architecture of the tumour microenvironment and identify opportunities to use them to improve clinical management of cancers.
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Affiliation(s)
- Julia Chen
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Department of Medical Oncology, St George Hospital, Sydney, New South Wales, Australia
| | - Ludvig Larsson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
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2
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Ruan Z, Zhou W, Liu H, Wei J, Pan Y, Yan C, Wei X, Xiang W, Yan C, Chen S, Liu J. Precise detection of cell-type-specific domains in spatial transcriptomics. CELL REPORTS METHODS 2024; 4:100841. [PMID: 39127046 DOI: 10.1016/j.crmeth.2024.100841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/17/2024] [Accepted: 07/17/2024] [Indexed: 08/12/2024]
Abstract
Cell-type-specific domains are the anatomical domains in spatially resolved transcriptome (SRT) tissues where particular cell types are enriched coincidentally. It is challenging to use existing computational methods to detect specific domains with low-proportion cell types, which are partly overlapped with or even inside other cell-type-specific domains. Here, we propose De-spot, which synthesizes segmentation and deconvolution as an ensemble to generate cell-type patterns, detect low-proportion cell-type-specific domains, and display these domains intuitively. Experimental evaluation showed that De-spot enabled us to discover the co-localizations between cancer-associated fibroblasts and immune-related cells that indicate potential tumor microenvironment (TME) domains in given slices, which were obscured by previous computational methods. We further elucidated the identified domains and found that Srgn may be a critical TME marker in SRT slices. By deciphering T cell-specific domains in breast cancer tissues, De-spot also revealed that the proportions of exhausted T cells were significantly increased in invasive vs. ductal carcinoma.
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Affiliation(s)
- Zhihan Ruan
- Centre for Bioinformatics and Intelligent Medicine, College of Computer Science, Nankai University, Tianjin 300350, China
| | - Weijun Zhou
- Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Hong Liu
- The Second Surgical Department of Breast Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China
| | - Jinmao Wei
- Centre for Bioinformatics and Intelligent Medicine, College of Computer Science, Nankai University, Tianjin 300350, China
| | - Yichen Pan
- Centre for Bioinformatics and Intelligent Medicine, College of Computer Science, Nankai University, Tianjin 300350, China
| | - Chaoyang Yan
- Centre for Bioinformatics and Intelligent Medicine, College of Computer Science, Nankai University, Tianjin 300350, China
| | - Xiaoyi Wei
- Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Wenting Xiang
- Centre for Bioinformatics and Intelligent Medicine, College of Computer Science, Nankai University, Tianjin 300350, China
| | - Chengwei Yan
- Centre for Bioinformatics and Intelligent Medicine, College of Computer Science, Nankai University, Tianjin 300350, China
| | - Shengquan Chen
- School of Mathematical Sciences, Nankai University, Tianjin 300350, China
| | - Jian Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Computer Science, Nankai University, Tianjin 300350, China.
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3
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Broomfield BJ, Groom JR. Defining the niche for stem-like CD8 + T cell formation and function. Curr Opin Immunol 2024; 89:102454. [PMID: 39154521 DOI: 10.1016/j.coi.2024.102454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/04/2024] [Accepted: 08/05/2024] [Indexed: 08/20/2024]
Abstract
TCF-1+ CD8+ T cell populations have emerged as critical determinants for long-lived immunological memory. This cell population has stem-like properties and is implicated in improved disease outcomes by driving sustained killing of infected cells and maintaining the immune-cancer equilibrium. During an immune response, several factors, including antigen deposition and affinity, the inflammatory milieu, and T cell priming dynamics, aggregate to skew CD8+ T cell differentiation. Although these mechanisms are altered between acute and chronic disease settings, phenotypically similar stem-like TCF-1+ CD8+ T cell states are formed in each of these settings. Here, we characterize the specialized microenvironments within lymph nodes and the tumor microenvironment, which foster the generation or re-activation of stem-like TCF-1+ CD8+ T cell populations. We highlight the potential for targeting the stem-like CD8+ T cell niche to enhance vaccination and cancer immunotherapy and to track the trajectory of stem-like CD8+ T cells as biomarkers of therapeutic efficacy.
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Affiliation(s)
- Benjamin J Broomfield
- Division of Immunology, Walter and Eliza Hall Institute of Medical Research (WEHI), Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Joanna R Groom
- Division of Immunology, Walter and Eliza Hall Institute of Medical Research (WEHI), Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.
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4
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Fay M, Sievers C, Robbins Y, Yang X, Huynh A, Redman JM, Hodge JW, Schlom J, Gulley JL, Allen CT, Craveiro M. TGF-β neutralization attenuates tumor residency of activated T cells to enhance systemic immunity in mice. iScience 2024; 27:110520. [PMID: 39139402 PMCID: PMC11321305 DOI: 10.1016/j.isci.2024.110520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/27/2024] [Accepted: 07/12/2024] [Indexed: 08/15/2024] Open
Abstract
A tissue resident-like phenotype in tumor infiltrating T cells can limit systemic anti-tumor immunity. Enhanced systemic anti-tumor immunity is observed in head and neck cancer patients after neoadjuvant PD-L1 immune checkpoint blockade (ICB) and transforming growth factor β (TGF-β) neutralization. Using T cell receptor (TCR) sequencing and functional immunity assays in a syngeneic model of oral cancer, we dissect the relative contribution of these treatments to enhanced systemic immunity. The addition of TGF-β neutralization to ICB resulted in the egress of expanded and exhausted CD8+ tumor infiltrating lymphocytes (TILs) into circulation and greater systemic anti-tumor immunity. This enhanced egress associated with reduced expression of Itgae (CD103) and its upstream regulator Znf683. Circulating CD8+ T cells expressed higher Cxcr3 after treatment, an observation also made in samples from patients treated with dual TGF-β neutralization and ICB. These findings provide the scientific rationale for the use of PD-L1 ICB and TGF-β neutralization in newly diagnosed patients with carcinomas prior to definitive treatment of locoregional disease.
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Affiliation(s)
- Magdalena Fay
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cem Sievers
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yvette Robbins
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xinping Yang
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Angel Huynh
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jason M. Redman
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James W. Hodge
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey Schlom
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James L. Gulley
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clint T. Allen
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marco Craveiro
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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5
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Li X, Sharen G, Zhang M, Zhang L, Liu K, Wang Y, Cheng H, Hou M. High expression of PDCD11 in colorectal cancer and its correlation with the prognosis and immune cell infiltration. Heliyon 2024; 10:e35002. [PMID: 39170455 PMCID: PMC11336332 DOI: 10.1016/j.heliyon.2024.e35002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 07/20/2024] [Accepted: 07/21/2024] [Indexed: 08/23/2024] Open
Abstract
Objective To undertake a comprehensive assay of PDCD11 expression in colorectal cancer (CRC) and its association with prognosis and immune cell infiltration (ICIN) utilizing bioinformatics tools. Methods The PDCD11 expression in CRC and pan-cancer was quantified through datasets from TCGA and GEO databases, and the assay was conducted through R software and the GEPIA database. Moreover, mRNA and protein expression data of PDCD11 were attained from the HPA database. It was attempted to establish protein-protein interaction networks of PDCD11 via the STRING and GeneMANIA databases. The association of PDCD11 expression with CRC staging was evaluated through R software, while its association with CRC and pan-cancer prognosis was figured out via the GEPIA database. Furthermore, the relationship of PDCD11 expression with ICIN was assayed using R software and the TIMER database. Additionally, the influences of PDCD11 knockdown on the proliferation, apoptosis, and migration of colon cancer RKO cell lines was evaluated. Results PDCD11 exhibited elevated expression in CRC and various other malignancies, potentially indicating a promotive role in cancer progression. Overexpression of PDCD11 was found to correlate with attenuated overall survival in CRC and other malignancies. Moreover, PDCD11 demonstrated promising predictive capabilities for distinguishing between tumor and non-tumor tissues. The positive association of high PDCD11 expression with the infiltration of neutrophils, dendritic cells, CD8+ T cells, CD4+ T cells, and macrophages, as well as with the expression of immune checkpoint molecules CTLA4 and PD-1 was noteworthy. Lentivirus-mediated PDCD11 knockdown suppressed RKO cell proliferation, colony formation, and migration, while triggered apoptosis in these cells. Conclusion The outcomes unveiled the noticeable function of PDCD11 in CRC and various other malignancies, emphasizing its potential as a prognostic biomarker and therapeutic target.
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Affiliation(s)
- Xiongfeng Li
- Department of Gastrointestinal Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, China
| | - Gaowa Sharen
- Department of Pathology, Affiliated Hospital of Inner Mongolia Medical University & Department of Pathological Anatomy, College of Basic Medicine of Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, China
| | - Minjie Zhang
- Department of Ultrasound, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, China
| | - Lei Zhang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, China
| | - Kejian Liu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, China
| | - Yu Wang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, China
| | - Haidong Cheng
- Department of Gastrointestinal Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, China
| | - Mingxing Hou
- Department of Gastrointestinal Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, China
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6
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Di Nitto C, Ravazza D, Gilardoni E, Look T, Sun M, Prodi E, Moisoiu V, Pellegrino C, Manz MG, Puca E, Weller M, Weiss T, Neri D, De Luca R. An IL-7 fusion protein targeting EDA fibronectin upregulates TCF1 on CD8+ T-cells, preferentially accumulates to neoplastic lesions, and boosts PD-1 blockade. J Immunother Cancer 2024; 12:e008504. [PMID: 39142716 PMCID: PMC11332014 DOI: 10.1136/jitc-2023-008504] [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] [Accepted: 07/27/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Anti-PD-1 antibodies have revolutionized cancer immunotherapy due to their ability to induce long-lasting complete remissions in a proportion of patients. Current research efforts are attempting to identify biomarkers and suitable combination partners to predict or further improve the activity of immune checkpoint inhibitors. Antibody-cytokine fusions are a class of pharmaceuticals that showed the potential to boost the anticancer properties of other immunotherapies. Extradomain A-fibronectin (EDA-FN), which is expressed in most solid and hematological tumors but is virtually undetectable in healthy adult tissues, is an attractive target for the delivery of cytokine at the site of the disease. METHODS In this work, we describe the generation and characterization of a novel interleukin-7-based fusion protein targeting EDA-FN termed F8(scDb)-IL7. The product consists of the F8 antibody specific to the alternatively spliced EDA of FN in the single-chain diabody (scDb) format fused to human IL-7. RESULTS F8(scDb)-IL7 efficiently stimulates human peripheral blood mononuclear cells in vitro. Moreover, the product significantly increases the expression of T Cell Factor 1 (TCF-1) on CD8+T cells compared with an IL2-fusion protein. TCF-1 has emerged as a pivotal transcription factor that influences the durability and potency of immune responses against tumors. In preclinical cancer models, F8(scDb)-IL7 demonstrates potent single-agent activity and eradicates sarcoma lesions when combined with anti-PD-1. CONCLUSIONS Our results provide the rationale to explore the combination of F8(scDb)-IL7 with anti-PD-1 antibodies for the treatment of patients with cancer.
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Affiliation(s)
| | | | | | - Thomas Look
- Department of Neurology and Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
| | - Miaomiao Sun
- Department of Neurology and Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
| | | | - Vlad Moisoiu
- Department of Neurology and Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
| | - Christian Pellegrino
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Markus G. Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | | | - Michael Weller
- Department of Neurology and Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
- University of Zurich, Zurich, Switzerland
| | - Tobias Weiss
- Department of Neurology and Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
- University of Zurich, Zurich, Switzerland
| | - Dario Neri
- Philogen SpA, Siena, Italy
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
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7
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Jackson CM, Pant A, Dinalankara W, Choi J, Jain A, Nitta R, Yazigi E, Saleh L, Zhao L, Nirschl TR, Kochel CM, Hwa-Lin Bergsneider B, Routkevitch D, Patel K, Cho KB, Tzeng S, Neshat SY, Kim YH, Smith BJ, Ramello MC, Sotillo E, Wang X, Green JJ, Bettegowda C, Li G, Brem H, Mackall CL, Pardoll DM, Drake CG, Marchionni L, Lim M. The cytokine Meteorin-like inhibits anti-tumor CD8 + T cell responses by disrupting mitochondrial function. Immunity 2024; 57:1864-1877.e9. [PMID: 39111315 PMCID: PMC11324406 DOI: 10.1016/j.immuni.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 03/08/2024] [Accepted: 07/05/2024] [Indexed: 08/16/2024]
Abstract
Tumor-infiltrating lymphocyte (TIL) hypofunction contributes to the progression of advanced cancers and is a frequent target of immunotherapy. Emerging evidence indicates that metabolic insufficiency drives T cell hypofunction during tonic stimulation, but the signals that initiate metabolic reprogramming in this context are largely unknown. Here, we found that Meteorin-like (METRNL), a metabolically active cytokine secreted by immune cells in the tumor microenvironment (TME), induced bioenergetic failure of CD8+ T cells. METRNL was secreted by CD8+ T cells during repeated stimulation and acted via both autocrine and paracrine signaling. Mechanistically, METRNL increased E2F-peroxisome proliferator-activated receptor delta (PPARδ) activity, causing mitochondrial depolarization and decreased oxidative phosphorylation, which triggered a compensatory bioenergetic shift to glycolysis. Metrnl ablation or downregulation improved the metabolic fitness of CD8+ T cells and enhanced tumor control in several tumor models, demonstrating the translational potential of targeting the METRNL-E2F-PPARδ pathway to support bioenergetic fitness of CD8+ TILs.
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Affiliation(s)
- Christopher M Jackson
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Ayush Pant
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine, and the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wikum Dinalankara
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine, and the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John Choi
- Department of Neurosurgery, Stanford School of Medicine, Palo Alto, CA, USA
| | - Aanchal Jain
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ryan Nitta
- Department of Neurosurgery, Stanford School of Medicine, Palo Alto, CA, USA
| | - Eli Yazigi
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laura Saleh
- Department of Neurosurgery, Stanford School of Medicine, Palo Alto, CA, USA
| | - Liang Zhao
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine, and the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas R Nirschl
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine, and the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christina M Kochel
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine, and the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Denis Routkevitch
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kisha Patel
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kwang Bog Cho
- Department of Neurosurgery, Stanford School of Medicine, Palo Alto, CA, USA
| | - Stephany Tzeng
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD, USA
| | - Sarah Y Neshat
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD, USA
| | - Young-Hoon Kim
- Department of Neurosurgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Barbara J Smith
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Maria Cecilia Ramello
- Center for Cell Therapy, Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Elena Sotillo
- Center for Cell Therapy, Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Xinnan Wang
- Department of Neurosurgery, Stanford School of Medicine, Palo Alto, CA, USA
| | - Jordan J Green
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD, USA
| | - Chetan Bettegowda
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gordon Li
- Department of Neurosurgery, Stanford School of Medicine, Palo Alto, CA, USA
| | - Henry Brem
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Crystal L Mackall
- Center for Cell Therapy, Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA; Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Drew M Pardoll
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine, and the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Charles G Drake
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine, and the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Luigi Marchionni
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine, and the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Lim
- Department of Neurosurgery, Stanford School of Medicine, Palo Alto, CA, USA.
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8
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Gavil NV, Cheng K, Masopust D. Resident memory T cells and cancer. Immunity 2024; 57:1734-1751. [PMID: 39142275 DOI: 10.1016/j.immuni.2024.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/04/2024] [Accepted: 06/28/2024] [Indexed: 08/16/2024]
Abstract
Tissue-resident memory T (TRM) cells positively correlate with cancer survival, but the anti-tumor mechanisms underlying this relationship are not understood. This review reconciles these observations, summarizing concepts of T cell immunosurveillance, fundamental TRM cell biology, and clinical observations on the role of TRM cells in cancer and immunotherapy outcomes. We also discuss emerging strategies that utilize TRM-phenotype cells for patient diagnostics, staging, and therapy. Current challenges are highlighted, including a lack of standardized T cell nomenclature and our limited understanding of relationships between T cell markers and underlying tumor biology. Existing findings are integrated into a summary of the field while emphasizing opportunities for future research.
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Affiliation(s)
- Noah Veis Gavil
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Katarina Cheng
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - David Masopust
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA.
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9
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Chen Y, Shao Z, Hao Z, Xin Z, Chen X, Huang L, Chen D, Lin M, Liu Q, Xu X, Li J, Wu D, Yan J, Chai Y, Wu P. Epithelium/imcDC2 axis facilitates the resistance of neoadjuvant anti-PD-1 in human NSCLC. J Immunother Cancer 2024; 12:e007854. [PMID: 39134346 PMCID: PMC11332012 DOI: 10.1136/jitc-2023-007854] [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] [Accepted: 07/27/2024] [Indexed: 08/21/2024] Open
Abstract
BACKGROUND Therapeutic resistance is a main obstacle to achieve long-term benefits from immune checkpoint inhibitors. The underlying mechanism of neoadjuvant anti-PD-1 resistance remains unclear. METHODS Multi-omics analysis, including mass cytometry, single-cell RNA-seq, bulk RNA-seq, and polychromatic flow cytometry, was conducted using the resected tumor samples in a cohort of non-small cell lung cancer (NSCLC) patients received neoadjuvant anti-PD-1 therapy. Tumor and paired lung samples acquired from treatment-naïve patients were used as a control. In vitro experiments were conducted using primary cells isolated from fresh tissues and lung cancer cell lines. A Lewis-bearing mouse model was used in the in vivo experiment. RESULTS The quantity, differentiation status, and clonal expansion of tissue-resident memory CD8+ T cells (CD8+ TRMs) are positively correlated with therapeutic efficacy of neoadjuvant anti-PD-1 therapy in human NSCLC. In contrast, the quantity of immature CD1c+ classical type 2 dendritic cells (imcDC2) and galectin-9+ cancer cells is negatively correlated with therapeutic efficacy. An epithelium/imDC2 suppressive axis that restrains the antitumor response of CD8+ TRMs via galectin-9/TIM-3 was uncovered. The expression level of CD8+ TRMs and galectin-9+ cancer cell-related genes predict the clinical outcome of anti-PD-1 neoadjuvant therapy in human NSCLC patients. Finally, blockade of TIM-3 and PD-1 could improve the survival of tumor-bearing mouse by promoting the antigen presentation of imcDC2 and CD8+ TRMs-mediated tumor-killing. CONCLUSION Galectin-9 expressing tumor cells sustained the primary resistance of neoadjuvant anti-PD-1 therapy in NSCLC through galectin-9/TIM-3-mediated suppression of imcDC2 and CD8+ TRMs. Supplement of anti-TIM-3 could break the epithelium/imcDC2/CD8+ TRMs suppressive loop to overcome anti-PD-1 resistance. TRIAL REGISTRATION NUMBER NCT03732664.
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Affiliation(s)
- Yongyuan Chen
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zheyu Shao
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhixing Hao
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhongwei Xin
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated of Shandong First Medical University, Jinan, Shandong, China
| | - Xiaoke Chen
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lijian Huang
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Di Chen
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mingjie Lin
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qinyuan Liu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xia Xu
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jinfan Li
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dang Wu
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Yan
- Division of Immunotherapy, The Hiram C. Polk, Jr., Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
| | - Ying Chai
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Pin Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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10
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Wei C, Ma Y, Wang M, Wang S, Yu W, Dong S, Deng W, Bie L, Zhang C, Shen W, Xia Q, Luo S, Li N. Tumor-associated macrophage clusters linked to immunotherapy in a pan-cancer census. NPJ Precis Oncol 2024; 8:176. [PMID: 39117688 PMCID: PMC11310399 DOI: 10.1038/s41698-024-00660-4] [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: 11/24/2023] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
Transcriptional heterogeneity of tumor-associated macrophages (TAMs) has been investigated in individual cancers, but the extent to which these states transcend tumor types and represent a general feature of cancer remains unclear. We performed pan-cancer single-cell RNA sequencing analysis across nine cancer types and identified distinct monocyte/TAM composition patterns. Using spatial analysis from clinical study tissues, we assessed TAM functions in shaping the tumor microenvironment (TME) and influencing immunotherapy. Two specific TAM clusters (pro-inflammatory and pro-tumor) and four TME subtypes showed distinct immunological features, genomic profiles, immunotherapy responses, and cancer prognosis. Pro-inflammatory TAMs resided in immune-enriched niches with exhausted CD8+ T cells, while pro-tumor TAMs were restricted to niches associated with a T-cell-excluded phenotype and hypoxia. We developed a machine learning model to predict immune checkpoint blockade response by integrating TAMs and clinical data. Our study comprehensively characterizes the common features of TAMs and highlights their interaction with the TME.
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Affiliation(s)
- Chen Wei
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Yijie Ma
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Mengyu Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Siyi Wang
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Wenyue Yu
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Shuailei Dong
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Wenying Deng
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Liangyu Bie
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Chi Zhang
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Wei Shen
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Qingxin Xia
- Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
| | - Suxia Luo
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
| | - Ning Li
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
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11
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Kloosterman DJ, Erbani J, Boon M, Farber M, Handgraaf SM, Ando-Kuri M, Sánchez-López E, Fontein B, Mertz M, Nieuwland M, Liu NQ, Forn-Cuni G, van der Wel NN, Grootemaat AE, Reinalda L, van Kasteren SI, de Wit E, Ruffell B, Snaar-Jagalska E, Petrecca K, Brandsma D, Kros A, Giera M, Akkari L. Macrophage-mediated myelin recycling fuels brain cancer malignancy. Cell 2024:S0092-8674(24)00824-9. [PMID: 39137777 DOI: 10.1016/j.cell.2024.07.030] [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: 05/27/2023] [Revised: 04/26/2024] [Accepted: 07/18/2024] [Indexed: 08/15/2024]
Abstract
Tumors growing in metabolically challenged environments, such as glioblastoma in the brain, are particularly reliant on crosstalk with their tumor microenvironment (TME) to satisfy their high energetic needs. To study the intricacies of this metabolic interplay, we interrogated the heterogeneity of the glioblastoma TME using single-cell and multi-omics analyses and identified metabolically rewired tumor-associated macrophage (TAM) subpopulations with pro-tumorigenic properties. These TAM subsets, termed lipid-laden macrophages (LLMs) to reflect their cholesterol accumulation, are epigenetically rewired, display immunosuppressive features, and are enriched in the aggressive mesenchymal glioblastoma subtype. Engulfment of cholesterol-rich myelin debris endows subsets of TAMs to acquire an LLM phenotype. Subsequently, LLMs directly transfer myelin-derived lipids to cancer cells in an LXR/Abca1-dependent manner, thereby fueling the heightened metabolic demands of mesenchymal glioblastoma. Our work provides an in-depth understanding of the immune-metabolic interplay during glioblastoma progression, thereby laying a framework to unveil targetable metabolic vulnerabilities in glioblastoma.
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Affiliation(s)
- Daan J Kloosterman
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Johanna Erbani
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Menno Boon
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Martina Farber
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Shanna M Handgraaf
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Masami Ando-Kuri
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Elena Sánchez-López
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Bauke Fontein
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Marjolijn Mertz
- Bioimaging Facility, Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Marja Nieuwland
- Genomics Core Facility, Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Ning Qing Liu
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Gabriel Forn-Cuni
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Nicole N van der Wel
- Electron Microscopy Centre Amsterdam, Medical Biology, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Anita E Grootemaat
- Electron Microscopy Centre Amsterdam, Medical Biology, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Luuk Reinalda
- The Institute of Chemical Immunology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Sander I van Kasteren
- The Institute of Chemical Immunology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Brian Ruffell
- Department of Immunology, Department of Breast Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Kevin Petrecca
- Montreal Neurological Institute-Hospital, McGill University Health Centre and Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Dieta Brandsma
- Department of Neuro-Oncology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, 1066CX Amsterdam, the Netherlands
| | - Alexander Kros
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Leila Akkari
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands.
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12
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Tran MA, Youssef D, Shroff S, Chowhan D, Beaumont KG, Sebra R, Mehrazin R, Wiklund P, Lin JJ, Horowitz A, Farkas AM, Galsky MD, Sfakianos JP, Bhardwaj N. Urine scRNAseq reveals new insights into the bladder tumor immune microenvironment. J Exp Med 2024; 221:e20240045. [PMID: 38847806 PMCID: PMC11157455 DOI: 10.1084/jem.20240045] [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: 01/07/2024] [Revised: 04/04/2024] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
Due to bladder tumors' contact with urine, urine-derived cells (UDCs) may serve as a surrogate for monitoring the tumor microenvironment (TME) in bladder cancer (BC). However, the composition of UDCs and the extent to which they mirror the tumor remain poorly characterized. We generated the first single-cell RNA-sequencing of BC patient UDCs with matched tumor and peripheral blood mononuclear cells (PBMC). BC urine was more cellular than healthy donor (HD) urine, containing multiple immune populations including myeloid cells, CD4+ and CD8+ T cells, natural killer (NK) cells, B cells, and dendritic cells (DCs) in addition to tumor and stromal cells. Immune UDCs were transcriptionally more similar to tumor than blood. UDCs encompassed cytotoxic and activated CD4+ T cells, exhausted and tissue-resident memory CD8+ T cells, macrophages, germinal-center-like B cells, tissue-resident and adaptive NK cells, and regulatory DCs found in tumor but lacking or absent in blood. Our findings suggest BC UDCs may be surrogates for the TME and serve as therapeutic biomarkers.
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Affiliation(s)
- Michelle A. Tran
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dina Youssef
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sanjana Shroff
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Disha Chowhan
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristin G. Beaumont
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Reza Mehrazin
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Wiklund
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jenny J. Lin
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amir Horowitz
- Department of Immunology and Immunotherapy, The Marc and Jennifer Lipschultz Precision Immunology Institute, 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
| | - Adam M. Farkas
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D. Galsky
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John P. Sfakianos
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nina Bhardwaj
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Extramural Member, Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
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13
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Yang Z, Chu B, Tu Y, Li L, Chen D, Huang S, Huang W, Fan W, Li Q, Zhang C, Yuan Z, Huang J, Leung ELH, Jiang Y. Dual inhibitors of DNMT and HDAC remodels the immune microenvironment of colorectal cancer and enhances the efficacy of anti-PD-L1 therapy. Pharmacol Res 2024; 206:107271. [PMID: 38906202 DOI: 10.1016/j.phrs.2024.107271] [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: 04/25/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 06/23/2024]
Abstract
Colorectal cancer is the second most prevalent and deadly cancer worldwide. The emergence of immune checkpoint therapy has provided a revolutionary strategy for the treatment of solid tumors. However, less than 5 % of colorectal cancer patients respond to immune checkpoint therapy. Thus, it is of great scientific significance to develop "potentiators" for immune checkpoint therapy. In this study, we found that knocking down different DNMT and HDAC isoforms could increase the expression of IFNs in colorectal cancer cells, which can enhance the effectiveness of immune checkpoint therapy. Therefore, the combined inhibition of DNMT and HDAC cloud synergistically enhance the effect of immunotherapy. We found that dual DNMT and HDAC inhibitors C02S could inhibit tumor growth in immunocompetent mice but not in immunocompromised nude mice, which indicates that C02S exerts its antitumor effects through the immune system. Mechanistically, C02S could increase the expression of ERVs, which generated the intracellular levels of dsRNA in tumor cells, and then promotes the expression of IFNs through the RIG-I/MDA5-MAVS signaling pathway. Moreover, C02S increased the immune infiltration of DCs and T cells in microenvironment, and enhanced the efficacy of anti-PD-L1 therapy in MC38 and CT26 mice model. These results confirmed that C02S can activate IFNs through the RIG-I/MDA5-MAVS signaling pathway, remodel the tumor immune microenvironment and enhance the efficacy of immune checkpoint therapy, which provides new evidence and solutions for the development of "potentiator" for colorectal cancer immunotherapy.
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Affiliation(s)
- Zhanbo Yang
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China
| | - Bizhu Chu
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China.
| | - Yao Tu
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China
| | - Lulu Li
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Dawei Chen
- Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518057, China
| | - Shouhui Huang
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China
| | - Wenjun Huang
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China
| | - Weiwen Fan
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China
| | - Qinyuan Li
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Cunlong Zhang
- Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518057, China
| | - Zigao Yuan
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Jumin Huang
- MOE Frontiers Science Center for Precision Oncology, University of Macau, 999078, Macao Special Administrative Region of China; Cancer Center, Faculty of Health Sciences, University of Macau, 999078, Macao Special Administrative Region of China
| | - Elaine Lai-Han Leung
- MOE Frontiers Science Center for Precision Oncology, University of Macau, 999078, Macao Special Administrative Region of China; Cancer Center, Faculty of Health Sciences, University of Macau, 999078, Macao Special Administrative Region of China.
| | - Yuyang Jiang
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China; State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China.
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14
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Wang Y, Yang S, Han B, Du X, Sun H, Du Y, Liu Y, Lu P, Di J, Luu LDW, Lv X, Hu S, Wang L, Jiang R. Single-cell landscape revealed immune characteristics associated with disease phases in brucellosis patients. IMETA 2024; 3:e226. [PMID: 39135683 PMCID: PMC11316929 DOI: 10.1002/imt2.226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 08/15/2024]
Abstract
A comprehensive immune landscape for Brucella infection is crucial for developing new treatments for brucellosis. Here, we utilized single-cell RNA sequencing (scRNA-seq) of 290,369 cells from 35 individuals, including 29 brucellosis patients from acute (n = 10), sub-acute (n = 9), and chronic (n = 10) phases as well as six healthy donors. Enzyme-linked immunosorbent assays were applied for validation within this cohort. Brucella infection caused a significant change in the composition of peripheral immune cells and inflammation was a key feature of brucellosis. Acute patients are characterized by potential cytokine storms resulting from systemic upregulation of S100A8/A9, primarily due to classical monocytes. Cytokine storm may be mediated by activating S100A8/A9-TLR4-MyD88 signaling pathway. Moreover, monocytic myeloid-derived suppressor cells were the probable contributors to immune paralysis in acute patients. Chronic patients are characterized by a dysregulated Th1 response, marked by reduced expression of IFN-γ and Th1 signatures as well as a high exhausted state. Additionally, Brucella infection can suppress apoptosis in myeloid cells (e.g., mDCs, classical monocytes), inhibit antigen presentation in professional antigen-presenting cells (APCs; e.g., mDC) and nonprofessional APCs (e.g., monocytes), and induce exhaustion in CD8+ T/NK cells, potentially resulting in the establishment of chronic infection. Overall, our study systemically deciphered the coordinated immune responses of Brucella at different phases of the infection, which facilitated a full understanding of the immunopathogenesis of brucellosis and may aid the development of new effective therapeutic strategies, especially for those with chronic infection.
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Affiliation(s)
- Yi Wang
- Experimental Research Center, Capital Institute of PediatricsBeijingChina
| | - Siyuan Yang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
- Beijing Institute of Infectious DiseasesBeijingChina
- National Center for Infectious Diseases, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious DiseasesBeijingChina
| | - Bing Han
- Clinical and Research Center of Infectious Diseases, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
- Beijing Quality Control and Improvement Center of Infectious DiseaseBeijingChina
| | - Xiufang Du
- The Department of Infectious DiseasesThe Third People's Hospital of Linfen CityLinfenShanxiChina
| | - Huali Sun
- Department of Infectious DiseasesThe Affiliated Hospital of Qingdao UniversityQingdaoShandongChina
| | - Yufeng Du
- The Department of Infectious DiseasesThe Third People's Hospital of Linfen CityLinfenShanxiChina
| | - Yinli Liu
- The Department of Infectious DiseasesThe Third People's Hospital of Linfen CityLinfenShanxiChina
| | - Panpan Lu
- The Department of Infectious DiseasesThe Third People's Hospital of Linfen CityLinfenShanxiChina
| | - Jinyu Di
- Department of Clinical LaboratoryThe Third People's Hospital of Lifen CityLinfenShanxiChina
| | | | - Xiao Lv
- Department of Clinical LaboratoryThe Third People's Hospital of Lifen CityLinfenShanxiChina
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Linghang Wang
- National Center for Infectious Diseases, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Rongmeng Jiang
- National Center for Infectious Diseases, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
- Beijing Quality Control and Improvement Center of Infectious DiseaseBeijingChina
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15
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Zebley CC, Zehn D, Gottschalk S, Chi H. T cell dysfunction and therapeutic intervention in cancer. Nat Immunol 2024; 25:1344-1354. [PMID: 39025962 DOI: 10.1038/s41590-024-01896-9] [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: 04/12/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024]
Abstract
Recent advances in immunotherapy have affirmed the curative potential of T cell-based approaches for treating relapsed and refractory cancers. However, the therapeutic efficacy is limited in part owing to the ability of cancers to evade immunosurveillance and adapt to immunological pressure. In this Review, we provide a brief overview of cancer-mediated immunosuppressive mechanisms with a specific focus on the repression of the surveillance and effector function of T cells. We discuss CD8+ T cell exhaustion and functional heterogeneity and describe strategies for targeting the molecular checkpoints that restrict T cell differentiation and effector function to bolster immunotherapeutic effects. We also delineate the emerging contributions of the tumor microenvironment to T cell metabolism and conclude by highlighting discovery-based approaches for developing future cellular therapies. Continued exploration of T cell biology and engineering hold great promise for advancing therapeutic interventions for cancer.
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Affiliation(s)
- Caitlin C Zebley
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA.
- 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 and Center for Infection Prevention (ZIP), Technical University of Munich, Freising, Germany
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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16
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Sultan H, Takeuchi Y, Ward JP, Sharma N, Liu TT, Sukhov V, Firulyova M, Song Y, Ameh S, Brioschi S, Khantakova D, Arthur CD, White JM, Kohlmiller H, Salazar AM, Burns R, Costa HA, Moynihan KD, Yeung YA, Djuretic I, Schumacher TN, Sheehan KCF, Colonna M, Allison JP, Murphy KM, Artyomov MN, Schreiber RD. Neoantigen-specific cytotoxic Tr1 CD4 T cells suppress cancer immunotherapy. Nature 2024; 632:182-191. [PMID: 39048822 PMCID: PMC11291290 DOI: 10.1038/s41586-024-07752-y] [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: 10/28/2022] [Accepted: 06/25/2024] [Indexed: 07/27/2024]
Abstract
CD4+ T cells can either enhance or inhibit tumour immunity. Although regulatory T cells have long been known to impede antitumour responses1-5, other CD4+ T cells have recently been implicated in inhibiting this response6,7. Yet, the nature and function of the latter remain unclear. Here, using vaccines containing MHC class I (MHC-I) neoantigens (neoAgs) and different doses of tumour-derived MHC-II neoAgs, we discovered that whereas the inclusion of vaccines with low doses of MHC-II-restricted peptides (LDVax) promoted tumour rejection, vaccines containing high doses of the same MHC-II neoAgs (HDVax) inhibited rejection. Characterization of the inhibitory cells induced by HDVax identified them as type 1 regulatory T (Tr1) cells expressing IL-10, granzyme B, perforin, CCL5 and LILRB4. Tumour-specific Tr1 cells suppressed tumour rejection induced by anti-PD1, LDVax or adoptively transferred tumour-specific effector T cells. Mechanistically, HDVax-induced Tr1 cells selectively killed MHC-II tumour antigen-presenting type 1 conventional dendritic cells (cDC1s), leading to low numbers of cDC1s in tumours. We then documented modalities to overcome this inhibition, specifically via anti-LILRB4 blockade, using a CD8-directed IL-2 mutein, or targeted loss of cDC2/monocytes. Collectively, these data show that cytotoxic Tr1 cells, which maintain peripheral tolerance, also inhibit antitumour responses and thereby function to impede immune control of cancer.
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Affiliation(s)
- Hussein Sultan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Yoshiko Takeuchi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Jeffrey P Ward
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Naveen Sharma
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tian-Tian Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Vladimir Sukhov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maria Firulyova
- Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Yuang Song
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Samuel Ameh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Simone Brioschi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Darya Khantakova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Cora D Arthur
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - J Michael White
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Heather Kohlmiller
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | | | | | | | - Ton N Schumacher
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, Leiden University, Leiden, Netherlands
| | - Kathleen C F Sheehan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - James P Allison
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert D Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
- The Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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17
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Zhao B, Zhang M, Tang J, Zou D, Liu F, Shi Q, Gao T, Li C, Zhu G. Efficacy and safety of PD-1 monoclonal antibody combined with interferon-alpha 1b and anlotinib hydrochloride as the second-line therapy in patients with unresectable advanced melanoma: A retrospective study. Cancer Med 2024; 13:e70087. [PMID: 39166495 PMCID: PMC11337113 DOI: 10.1002/cam4.70087] [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: 02/08/2024] [Revised: 06/24/2024] [Accepted: 07/28/2024] [Indexed: 08/23/2024] Open
Abstract
BACKGROUND Immune-checkpoint inhibitors are now used more commonly in combination than monotherapy as the first-line choice in patients with unresectable advanced melanoma. Nevertheless, for cases that progressed after the initial combination therapy, the subsequent regimen option can be very difficult. Herein, we reported the efficacy and safety of a triple combination regimen in Chinese unresectable advanced melanoma patients who had poor responses to the first-line immune therapy. METHODS We reviewed the clinical profiles of patients diagnosed with stage IIIC-IV melanoma between June 1, 2020, and September 30, 2023. The patients who failed the prior immune therapies and received anti-PD-1 mono antibody plus interferon(IFN)-alpha 1b and anlotinib hydrochloride as the second-line therapy were enrolled in the retrospective analysis. Additionally, we examined the exhaustion of T-cells using mIHC staining in available tumor samples. RESULTS Fifty-five patients were included in this study. The median follow-up period was 13.6 months. The objective response rate evaluated by the investigators was 9.1%(1CR, 4PR). The disease control rate was 47.3%. The median overall survival was 17.6 months, and the median progression-free survival was 2.8 months. The adverse events rate of any grade was 100%. Grade 3 or 4 irAEs were observed in 29.1% of cases. Multiplex immunohistochemical staining revealed an increased trend of TIM3 expression on tumor-infiltrating T cells in patients without objective response. CONCLUSION PD-1 monoclonal antibody plus interferon-alpha 1b plus anlotinib showed acceptable tolerability and anticancer benefits in Chinese metastatic melanoma patients as a second-line therapy.
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Affiliation(s)
- Bolun Zhao
- Department of Dermatology, Xijing HospitalFourth Military Medical UniversityXi'anChina
| | - Mengyu Zhang
- Department of Dermatology, Xijing HospitalFourth Military Medical UniversityXi'anChina
| | - Jingyi Tang
- Department of Dermatology, Xijing HospitalFourth Military Medical UniversityXi'anChina
| | - Daopei Zou
- Department of Dermatology, Xijing HospitalFourth Military Medical UniversityXi'anChina
| | - Fang Liu
- Department of Dermatology, Xijing HospitalFourth Military Medical UniversityXi'anChina
| | - Qiong Shi
- Department of Dermatology, Xijing HospitalFourth Military Medical UniversityXi'anChina
| | - Tianwen Gao
- Department of Dermatology, Xijing HospitalFourth Military Medical UniversityXi'anChina
| | - Chunying Li
- Department of Dermatology, Xijing HospitalFourth Military Medical UniversityXi'anChina
| | - Guannan Zhu
- Department of Dermatology, Xijing HospitalFourth Military Medical UniversityXi'anChina
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18
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Liu C, Li K, Sui X, Zhao T, Zhang T, Chen Z, Wu H, Li C, Li H, Yang F, Liu Z, Lu Y, Wang J, Chen X, Liu P. Patient-Derived Tumor Organoids Combined with Function-Associated ScRNA-Seq for Dissecting the Local Immune Response of Lung Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400185. [PMID: 38896792 PMCID: PMC11336893 DOI: 10.1002/advs.202400185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 06/03/2024] [Indexed: 06/21/2024]
Abstract
In vitro models coupled with multimodal approaches are needed to dissect the dynamic response of local tumor immune microenvironment (TIME) to immunotherapy. Here the patient-derived primary lung cancer organoids (pLCOs) are generated by isolating tumor cell clusters, including the infiltrated immune cells. A function-associated single-cell RNA sequencing (FascRNA-seq) platform allowing both phenotypic evaluation and scRNA-seq at single-organoid level is developed to dissect the TIME of individual pLCOs. The analysis of 171 individual pLCOs derived from seven patients reveals that pLCOs retain the TIME heterogeneity in the parenchyma of parental tumor tissues, providing models with identical genetic background but various TIME. Linking the scRNA-seq data of individual pLCOs with their responses to anti-PD-1 (αPD-1) immune checkpoint blockade (ICB) allows to confirm the central role of CD8+ T cells in anti-tumor immunity, to identify potential tumor-reactive T cells with a set of 10 genes, and to unravel the factors regulating T cell activity, including CD99 gene. In summary, the study constructs a joint phenotypic and transcriptomic FascRNA-seq platform to dissect the dynamic response of local TIME under ICB treatment, providing a promising approach to evaluate novel immunotherapies and to understand the underlying molecular mechanisms.
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Affiliation(s)
- Chang Liu
- School of Biomedical EngineeringTsinghua UniversityBeijing100084China
| | - Kaiyi Li
- School of Biomedical EngineeringTsinghua UniversityBeijing100084China
| | - Xizhao Sui
- Department of Thoracic SurgeryPeople's HospitalPeking UniversityBeijing100034China
| | - Tian Zhao
- School of Biomedical EngineeringTsinghua UniversityBeijing100084China
| | - Ting Zhang
- Beijing Advanced Innovation Centre for Biomedical EngineeringKey Laboratory for Biomechanics and Mechanobiology of Ministry of EducationSchool of Biological Science and Medical EngineeringBeihang UniversityBeijing100083China
| | - Zhongyao Chen
- School of Biomedical EngineeringTsinghua UniversityBeijing100084China
| | - Hainan Wu
- Beijing Advanced Innovation Centre for Biomedical EngineeringKey Laboratory for Biomechanics and Mechanobiology of Ministry of EducationSchool of Biological Science and Medical EngineeringBeihang UniversityBeijing100083China
| | - Chao Li
- Department of Thoracic SurgeryPeople's HospitalPeking UniversityBeijing100034China
| | - Hao Li
- Department of Thoracic SurgeryPeople's HospitalPeking UniversityBeijing100034China
| | - Fan Yang
- Department of Thoracic SurgeryPeople's HospitalPeking UniversityBeijing100034China
| | - Zhidong Liu
- Beijing Chest HospitalCapital Medical University & Beijing Tuberculosis and Thoracic Tumor Research InstituteBeijing101125China
| | - You‐Yong Lu
- Laboratory of Molecular OncologyKey Laboratory of Carcinogenesis and Translational Research (Ministry of Education)School of OncologyBeijing Cancer Hospital and InstitutePeking UniversityBeijing100142China
| | - Jun Wang
- Department of Thoracic SurgeryPeople's HospitalPeking UniversityBeijing100034China
| | - Xiaofang Chen
- Beijing Advanced Innovation Centre for Biomedical EngineeringKey Laboratory for Biomechanics and Mechanobiology of Ministry of EducationSchool of Biological Science and Medical EngineeringBeihang UniversityBeijing100083China
| | - Peng Liu
- School of Biomedical EngineeringTsinghua UniversityBeijing100084China
- Changping LaboratoryBeijing102299China
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19
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Russell J, Chen L, Liu A, Wang J, Ghosh S, Zhong X, Shi H, Beutler B, Nair-Gill E. Lrp10 suppresses IL7R limiting CD8 T cell homeostatic expansion and anti-tumor immunity. EMBO Rep 2024; 25:3601-3626. [PMID: 38956225 PMCID: PMC11315911 DOI: 10.1038/s44319-024-00191-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: 12/14/2023] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
Signals emanating from the T-cell receptor (TCR), co-stimulatory receptors, and cytokine receptors each influence CD8 T-cell fate. Understanding how these signals respond to homeostatic and microenvironmental cues can reveal new ways to therapeutically direct T-cell function. Through forward genetic screening in mice, we discover that loss-of-function mutations in LDL receptor-related protein 10 (Lrp10) cause naive and central memory CD8 T cells to accumulate in peripheral lymphoid organs. Lrp10 encodes a conserved cell surface protein of unknown immunological function. T-cell activation induces Lrp10 expression, which post-translationally suppresses IL7 receptor (IL7R) levels. Accordingly, Lrp10 deletion enhances T-cell homeostatic expansion through IL7R signaling. Lrp10-deficient mice are also intrinsically resistant to syngeneic tumors. This phenotype depends on dense tumor infiltration of CD8 T cells, which display increased memory cell characteristics, reduced terminal exhaustion, and augmented responses to immune checkpoint inhibition. Here, we present Lrp10 as a new negative regulator of CD8 T-cell homeostasis and a host factor that controls tumor resistance with implications for immunotherapy.
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Affiliation(s)
- Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Luming Chen
- Medical Scientist Training Program, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Aijie Liu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Subarna Ghosh
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Hexin Shi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Evan Nair-Gill
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA.
- Department of Internal Medicine, Division of Rheumatic Diseases, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA.
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20
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Ni L. Potential mechanisms of cancer stem-like progenitor T-cell bio-behaviours. Clin Transl Med 2024; 14:e1817. [PMID: 39169517 DOI: 10.1002/ctm2.1817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024] Open
Abstract
In situations involving continuous exposure to antigens, such as chronic infections or cancer, antigen-specific CD8+ T cells can become dysfunctional or exhausted. This change is marked by increased expression levels of inhibitory receptors (PD-1 and Tim-3). Stem-like progenitor exhausted (Tpex) cells, a subset of exhausted cells that express TCF-1 and are mainly found in the lymph nodes, demonstrate the ability to self-renew and exhibit a high rate of proliferation. Tpex cells can further differentiate into transitional intermediate exhausted (Tex-int) cells and terminally exhausted (Tex-term) cells. Alternatively, they can directly differentiate into Tex-term cells. Tpex cells are the predominant subset that respond to immune checkpoint inhibitors (ICI), making them a prime candidate for improving the efficacy of ICI therapy. This review article aimed to present the latest developments in the field of Tpex formation, expansion, and differentiation in the context of cancer, as well as their responses to ICIs in cancer immunotherapy. Consequently, it may be possible to develop novel treatments that exclusively target Tpex cells, thus improving overall treatment outcomes. KEY POINTS: Tpex cells are located in lymph nodes and TLS. Several pathways control the differentiation trajectories of Tpex cells, including epigenetic factors, transcription factors, cytokines, age, sex, etc.
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Affiliation(s)
- Ling Ni
- Institute for Immunology and School of Basic Medicine, Tsinghua University, Beijing, China
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21
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Choi WS, Kwon H, Yi E, Lee H, Kim JM, Park HJ, Choi EJ, Choi ME, Sung YH, Won CH, Sung CO, Kim HS. HPK1 Dysregulation-Associated NK Cell Dysfunction and Defective Expansion Promotes Metastatic Melanoma Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400920. [PMID: 38828677 PMCID: PMC11304315 DOI: 10.1002/advs.202400920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/10/2024] [Indexed: 06/05/2024]
Abstract
Distant metastasis, the leading cause of cancer death, is efficiently kept in check by immune surveillance. Studies have uncovered peripheral natural killer (NK) cells as key antimetastatic effectors and their dysregulation during metastasis. However, the molecular mechanism governing NK cell dysfunction links to metastasis remains elusive. Herein, MAP4K1 encoding HPK1 is aberrantly overexpressed in dysfunctional NK cells in the periphery and the metastatic site. Conditional HPK1 overexpression in NK cells suffices to exacerbate melanoma lung metastasis but not primary tumor growth. Conversely, MAP4K1-deficient mice are resistant to metastasis and further protected by combined immune-checkpoint inhibitors. Mechanistically, HPK1 restrains NK cell cytotoxicity and expansion via activating receptors. Likewise, HPK1 limits human NK cell activation and associates with melanoma NK cell dysfunction couples to TGF-β1 and patient response to immune checkpoint therapy. Thus, HPK1 is an intracellular checkpoint controlling NK-target cell responses, which is dysregulated and hijacked by tumors during metastatic progression.
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Affiliation(s)
- Woo Seon Choi
- Department of MicrobiologyStem Cell Immunomodulation Research CenterAsan Medical CenterUniversity of Ulsan College of MedicineSeoul05505Republic of Korea
| | - Hyung‐Joon Kwon
- Department of MicrobiologyStem Cell Immunomodulation Research CenterAsan Medical CenterUniversity of Ulsan College of MedicineSeoul05505Republic of Korea
| | - Eunbi Yi
- Department of MicrobiologyStem Cell Immunomodulation Research CenterAsan Medical CenterUniversity of Ulsan College of MedicineSeoul05505Republic of Korea
| | - Haeun Lee
- Department of MicrobiologyStem Cell Immunomodulation Research CenterAsan Medical CenterUniversity of Ulsan College of MedicineSeoul05505Republic of Korea
| | - Jung Min Kim
- Department of MicrobiologyStem Cell Immunomodulation Research CenterAsan Medical CenterUniversity of Ulsan College of MedicineSeoul05505Republic of Korea
| | - Hyo Jin Park
- Department of MicrobiologyStem Cell Immunomodulation Research CenterAsan Medical CenterUniversity of Ulsan College of MedicineSeoul05505Republic of Korea
| | - Eun Ji Choi
- Department of DermatologyAsan Institute for Life SciencesAsan Medical CenterUniversity of Ulsan College of MedicineSeoul05505Republic of Korea
| | - Myoung Eun Choi
- Department of DermatologyAsan Institute for Life SciencesAsan Medical CenterUniversity of Ulsan College of MedicineSeoul05505Republic of Korea
| | - Young Hoon Sung
- Department of Cell and Genetic EngineeringAsan Medical CenterUniversity of Ulsan College of MedicineSeoul05505Republic of Korea
| | - Chong Hyun Won
- Department of DermatologyAsan Institute for Life SciencesAsan Medical CenterUniversity of Ulsan College of MedicineSeoul05505Republic of Korea
| | - Chang Ohk Sung
- Department of PathologyAsan Medical Institute of Convergence Science and TechnologyAsan Medical CenterUniversity of Ulsan College of MedicineSeoul05505Republic of Korea
| | - Hun Sik Kim
- Department of MicrobiologyStem Cell Immunomodulation Research CenterAsan Medical CenterUniversity of Ulsan College of MedicineSeoul05505Republic of Korea
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22
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Schnell A. Stem-like T cells in cancer and autoimmunity. Immunol Rev 2024; 325:9-22. [PMID: 38804499 DOI: 10.1111/imr.13356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 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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23
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Ligon JA, Cupit-Link MC, Yu C, Levine J, Foley T, Rotz S, Sharma A, Gomez-Lobo V, Shah NN. Pediatric Cancer Immunotherapy and Potential for Impact on Fertility: A Need for Evidence-Based Guidance. Transplant Cell Ther 2024; 30:737-749. [PMID: 38866240 DOI: 10.1016/j.jtct.2024.06.006] [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: 02/27/2024] [Revised: 05/28/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024]
Abstract
The use of immunotherapies for the treatment of cancer in children, adolescents, and young adults has become common. As the use of immunotherapy has expanded, including in earlier lines of therapy, it has become evident that several aspects of how these immunotherapies impact longer-term outcomes among survivors are understudied. Traditional cancer therapies like alkylating and platin agents carry the greatest risk of infertility, but little is known about the impact of novel immunotherapies on fertility. This topic is of great interest to patients, patient advocates, and clinicians. In this article, we review immunotherapeutic agents used to treat childhood and young adult cancers and discuss potential mechanisms by which they may impact fertility based on the known interplay between the immune system and reproductive organs. We highlight the relative paucity of high-quality literature examining these late effects. We discuss interventions to optimize fertility preservation (FP) for our patients. Conducting longitudinal, collaborative, and prospective research on the fertility outcomes of pediatric and young adult patients with cancer who receive immunotherapy is critical to learn how to effectively counsel our patients on long-term fertility outcomes and indications for FP procedures. Collection of patient-level data will be necessary to draft evidence-based guidelines on which providers can make therapy recommendations.
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Affiliation(s)
- John A Ligon
- Department of Pediatrics, Division of Hematology Oncology, University of Florida, Gainesville, Florida; University of Florida Health Cancer Center, Gainesville, Florida.
| | | | - Christine Yu
- Department of Pediatric Medicine, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Jennifer Levine
- Center for Cancer and Blood Disorders, Division of Oncology, Children's National Hospital, Washington District of Columbia
| | - Toni Foley
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Seth Rotz
- Division of Pediatric Hematology and Oncology and Blood and Marrow Transplantation, Cleveland Clinic, Cleveland, Ohio
| | - Akshay Sharma
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Veronica Gomez-Lobo
- Pediatric and Adolescent Gynecology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland; Pediatric and Adolescent Gynecology, Children's National Hospital, Washington, District of Columbia
| | - Nirali N Shah
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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24
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Rodriguez BL, Huang J, Gibson L, Fradette JJ, Chen HIH, Koyano K, Cortez C, Li B, Ho C, Ashique AM, Lin VY, Crawley S, Roda JM, Chen P, Fan B, Kim J, Sissons J, Sitrin J, Kaplan DD, Gibbons DL, Rivera LB. Antitumor Activity of a Novel LAIR1 Antagonist in Combination with Anti-PD1 to Treat Collagen-Rich Solid Tumors. Mol Cancer Ther 2024; 23:1144-1158. [PMID: 38648067 PMCID: PMC11293989 DOI: 10.1158/1535-7163.mct-23-0866] [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: 12/06/2023] [Revised: 03/05/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024]
Abstract
We recently reported that resistance to PD-1 blockade in a refractory lung cancer-derived model involved increased collagen deposition and the collagen-binding inhibitory receptor leukocyte-associated immunoglobulin-like receptor 1 (LAIR1). Thus, we hypothesized that LAIR1 and collagen cooperated to suppress therapeutic response. In this study, we report that LAIR1 is associated with tumor stroma and is highly expressed by intratumoral myeloid cells in both human tumors and mouse models of cancer. Stroma-associated myeloid cells exhibit a suppressive phenotype and correlate with LAIR1 expression in human cancer. NGM438, a novel humanized LAIR1 antagonist mAb, elicits myeloid inflammation and allogeneic T-cell responses by binding to LAIR1 and blocking collagen engagement. Furthermore, a mouse-reactive NGM438 surrogate antibody sensitized refractory KP mouse lung tumors to anti-PD-1 therapy and resulted in increased intratumoral CD8+ T-cell content and inflammatory gene expression. These data place LAIR1 at the intersection of stroma and suppressive myeloid cells and support the notion that blockade of the LAIR1/collagen axis can potentially address resistance to checkpoint inhibitor therapy in the clinic.
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Affiliation(s)
- B. Leticia Rodriguez
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiawei Huang
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Laura Gibson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared J. Fradette
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hung-I H. Chen
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Kikuye Koyano
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Czrina Cortez
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Betty Li
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Carmence Ho
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | | | - Vicky Y. Lin
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | | | - Julie M. Roda
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Peirong Chen
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Bin Fan
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Jeong Kim
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - James Sissons
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | | | | | - Don L. Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lee B. Rivera
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
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25
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Ye J, Wei B, Zhou G, Xu Y, He Y, Hu X, Chen X, Zhang G, Liu H. Multi-dimensional characterization of apoptosis in the tumor microenvironment and therapeutic relevance in melanoma. Cell Oncol (Dordr) 2024; 47:1333-1353. [PMID: 38502270 PMCID: PMC11322377 DOI: 10.1007/s13402-024-00930-0] [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] [Accepted: 02/23/2024] [Indexed: 03/21/2024] Open
Abstract
PURPOSE Melanoma is widely utilized as a prominent model for the development of immunotherapy, thought an inadequate immune response can occur. Moreover, the development of apoptosis-related therapies and combinations with other therapeutic strategies is impeded by the limited understanding of apoptosis's role within diverse tumor immune microenvironments (TMEs). METHODS Here, we constructed an apoptosis-related tumor microenvironment signature (ATM) and employ multi-dimensional analysis to understand the roles of apoptosis in tumor microenvironment. We further assessed the clinical applications of ATM in nine independent cohorts, and anticipated the impact of ATM on cellular drug response in cultured cells. RESULTS Our ATM model exhibits robust performance in survival prediction in multiple melanoma cohorts. Different ATM groups exhibited distinct molecular signatures and biological processes. The low ATM group exhibited significant enrichment in B cell activation-related pathways. What's more, plasma cells showed the lowest ATM score, highlighting their role as pivotal contributors in the ATM model. Mechanistically, the analysis of the interplay between plasma cells and other immune cells elucidated their crucial role in orchestrating an effective anti-tumor immune response. Significantly, the ATM signature exhibited associations with therapeutic efficacy of immune checkpoint blockade and the drug sensitivity of various agents, including FDA-approved and clinically utilized drugs targeting the VEGF signaling pathway. Finally, ATM was associated with tertiary lymphoid structures (TLS), exhibiting stronger patient stratification ability compared to classical "hot tumors". CONCLUSION Our findings indicate that ATM is a prognostic factor and is associated with the immune response and drug sensitivity in melanoma.
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Affiliation(s)
- Jing Ye
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China
| | - Benliang Wei
- Big Data Institute, Central South University, Changsha, Hunan, 410008, China
| | - Guowei Zhou
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China
| | - Yantao Xu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China
| | - Yi He
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China
| | - Xiheng Hu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China.
- Furong Laboratory, Changsha, Hunan, China.
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China.
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China.
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China.
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China.
- Furong Laboratory, Changsha, Hunan, China.
| | - Guanxiong Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China.
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China.
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China.
| | - Hong Liu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China.
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China.
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China.
- Big Data Institute, Central South University, Changsha, Hunan, 410008, China.
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26
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Li F, Wang J, Li M, Zhang X, Tang Y, Song X, Zhang Y, Pei L, Liu J, Zhang C, Li X, Xu Y, Zhang Y. Identifying cell type-specific transcription factor-mediated activity immune modules reveal implications for immunotherapy and molecular classification of pan-cancer. Brief Bioinform 2024; 25:bbae368. [PMID: 39082649 PMCID: PMC11289680 DOI: 10.1093/bib/bbae368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 06/11/2024] [Accepted: 07/15/2024] [Indexed: 08/03/2024] Open
Abstract
Systematic investigation of tumor-infiltrating immune (TII) cells is important to the development of immunotherapies, and the clinical response prediction in cancers. There exists complex transcriptional regulation within TII cells, and different immune cell types display specific regulation patterns. To dissect transcriptional regulation in TII cells, we first integrated the gene expression profiles from single-cell datasets, and proposed a computational pipeline to identify TII cell type-specific transcription factor (TF) mediated activity immune modules (TF-AIMs). Our analysis revealed key TFs, such as BACH2 and NFKB1 play important roles in B and NK cells, respectively. We also found some of these TF-AIMs may contribute to tumor pathogenesis. Based on TII cell type-specific TF-AIMs, we identified eight CD8+ T cell subtypes. In particular, we found the PD1 + CD8+ T cell subset and its specific TF-AIMs associated with immunotherapy response. Furthermore, the TII cell type-specific TF-AIMs displayed the potential to be used as predictive markers for immunotherapy response of cancer patients. At the pan-cancer level, we also identified and characterized six molecular subtypes across 9680 samples based on the activation status of TII cell type-specific TF-AIMs. Finally, we constructed a user-friendly web interface CellTF-AIMs (http://bio-bigdata.hrbmu.edu.cn/CellTF-AIMs/) for exploring transcriptional regulatory pattern in various TII cell types. Our study provides valuable implications and a rich resource for understanding the mechanisms involved in cancer microenvironment and immunotherapy.
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Affiliation(s)
- Feng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Jingwen Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Mengyue Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Xiaomeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Yongjuan Tang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Xinyu Song
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Yifang Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Liying Pei
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Jiaqi Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
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27
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Li W, Pan L, Hong W, Ginhoux F, Zhang X, Xiao C, Li X. A single-cell pan-cancer analysis to show the variability of tumor-infiltrating myeloid cells in immune checkpoint blockade. Nat Commun 2024; 15:6142. [PMID: 39034339 PMCID: PMC11271490 DOI: 10.1038/s41467-024-50478-8] [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: 12/03/2023] [Accepted: 07/12/2024] [Indexed: 07/23/2024] Open
Abstract
Myeloid cells are vital components of the immune system and have pivotal functions in orchestrating immune responses. Understanding their functions within the tumor microenvironment and their interactions with tumor-infiltrating lymphocytes presents formidable challenges across diverse cancer types, particularly with regards to cancer immunotherapies. Here, we explore tumor-infiltrating myeloid cells (TIMs) by conducting a pan-cancer analysis using single-cell transcriptomics across eight distinct cancer types, encompassing a total of 192 tumor samples from 129 patients. By examining gene expression patterns and transcriptional activities of TIMs in different cancer types, we discern notable alterations in abundance of TIMs and kinetic behaviors prior to and following immunotherapy. We also identify specific cell-cell interaction targets in immunotherapy; unique and shared regulatory profiles critical for treatment response; and TIMs associated with survival outcomes. Overall, our study illuminates the heterogeneity of TIMs and improves our understanding of tissue-specific and cancer-specific myeloid subsets within the context of tumor immunotherapies.
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Affiliation(s)
- Weiyuan Li
- School of Medicine, Yunnan University, Kunming, Yunnan, 650091, China
- Department of Reproductive Medicine, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, 650031, China
| | - Lu Pan
- Institute of Environmental Medicine, Karolinska Institutet, Solna, 171 65, Sweden
| | - Weifeng Hong
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, 310005, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310005, China
- Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, 310005, China
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
- Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800, Villejuif, France
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xuan Zhang
- Department of Colorectal Surgery, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Chunjie Xiao
- School of Medicine, Yunnan University, Kunming, Yunnan, 650091, China.
| | - Xuexin Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning, China.
- Institute of Health Sciences, China Medical University, Shenyang, 110122, Liaoning, China.
- Department of Physiology and Pharmacology, Karolinska Institute, Solna, 171 65, Sweden.
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28
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Vanmeerbeek I, Naulaerts S, Sprooten J, Laureano RS, Govaerts J, Trotta R, Pretto S, Zhao S, Cafarello ST, Verelst J, Jacquemyn M, Pociupany M, Boon L, Schlenner SM, Tejpar S, Daelemans D, Mazzone M, Garg AD. Targeting conserved TIM3 +VISTA + tumor-associated macrophages overcomes resistance to cancer immunotherapy. SCIENCE ADVANCES 2024; 10:eadm8660. [PMID: 39028818 PMCID: PMC11259173 DOI: 10.1126/sciadv.adm8660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 06/14/2024] [Indexed: 07/21/2024]
Abstract
Despite the success of immunotherapy, overcoming immunoresistance in cancer remains challenging. We identified a unique niche of tumor-associated macrophages (TAMs), coexpressing T cell immunoglobulin and mucin domain-containing 3 (TIM3) and V-domain immunoglobulin suppressor of T cell activation (VISTA), that dominated human and mouse tumors resistant to most of the currently used immunotherapies. TIM3+VISTA+ TAMs were sustained by IL-4-enriching tumors with low (neo)antigenic and T cell-depleted features. TIM3+VISTA+ TAMs showed an anti-inflammatory and protumorigenic phenotype coupled with inability to sense type I interferon (IFN). This was established with cancer cells succumbing to immunogenic cell death (ICD). Dying cancer cells not only triggered autocrine type I IFNs but also exposed HMGB1/VISTA that engaged TIM3/VISTA on TAMs to suppress paracrine IFN-responses. Accordingly, TIM3/VISTA blockade synergized with paclitaxel, an ICD-inducing chemotherapy, to repolarize TIM3+VISTA+ TAMs to proinflammatory TAMs that killed cancer cells via tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) signaling. We propose targeting TIM3+VISTA+ TAMs to overcome immunoresistant tumors.
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Affiliation(s)
- Isaure Vanmeerbeek
- Laboratory of Cell Stress and Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Stefan Naulaerts
- Laboratory of Cell Stress and Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jenny Sprooten
- Laboratory of Cell Stress and Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Raquel S. Laureano
- Laboratory of Cell Stress and Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jannes Govaerts
- Laboratory of Cell Stress and Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Rosa Trotta
- Laboratory of Tumour Inflammation and Angiogenesis, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory of Tumour Inflammation and Angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Samantha Pretto
- Laboratory of Tumour Inflammation and Angiogenesis, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory of Tumour Inflammation and Angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Shikang Zhao
- Laboratory of Tumour Inflammation and Angiogenesis, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory of Tumour Inflammation and Angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sarah Trusso Cafarello
- Laboratory of Tumour Inflammation and Angiogenesis, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory of Tumour Inflammation and Angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Joren Verelst
- Laboratory of Tumour Inflammation and Angiogenesis, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory of Tumour Inflammation and Angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Maarten Jacquemyn
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Leuven, Belgium
| | - Martyna Pociupany
- Laboratory of Cell Stress and Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | | | - Susan M. Schlenner
- Laboratory of Adaptive Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Sabine Tejpar
- Laboratory for Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Dirk Daelemans
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Leuven, Belgium
| | - Massimiliano Mazzone
- Laboratory of Tumour Inflammation and Angiogenesis, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory of Tumour Inflammation and Angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Abhishek D. Garg
- Laboratory of Cell Stress and Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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Tooley K, Jerby L, Escobar G, Krovi SH, Mangani D, Dandekar G, Cheng H, Madi A, Goldschmidt E, Lambden C, Krishnan RK, Rozenblatt-Rosen O, Regev A, Anderson AC. Pan-cancer mapping of single CD8 + T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity. Cell Rep Med 2024; 5:101640. [PMID: 38959885 PMCID: PMC11293343 DOI: 10.1016/j.xcrm.2024.101640] [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: 05/31/2023] [Revised: 01/05/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024]
Abstract
CD8+ T cells must persist and function in diverse tumor microenvironments to exert their effects. Thus, understanding common underlying expression programs could better inform the next generation of immunotherapies. We apply a generalizable matrix factorization algorithm that recovers both shared and context-specific expression programs from diverse datasets to a single-cell RNA sequencing (scRNA-seq) compendium of 33,161 CD8+ T cells from 132 patients with seven human cancers. Our meta-single-cell analyses uncover a pan-cancer T cell dysfunction program that predicts clinical non-response to checkpoint blockade in melanoma and highlights CXCR6 as a pan-cancer marker of chronically activated T cells. Cxcr6 is trans-activated by AP-1 and repressed by TCF1. Using mouse models, we show that Cxcr6 deletion in CD8+ T cells increases apoptosis of PD1+TIM3+ cells, dampens CD28 signaling, and compromises tumor growth control. Our study uncovers a TCF1:CXCR6 axis that counterbalances PD1-mediated suppression of CD8+ cell responses and is essential for effective anti-tumor immunity.
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Affiliation(s)
- Katherine Tooley
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Livnat Jerby
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Giulia Escobar
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - S Harsha Krovi
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Davide Mangani
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gitanjali Dandekar
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hanning Cheng
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Asaf Madi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ella Goldschmidt
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Conner Lambden
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Rajesh K Krishnan
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Ana C Anderson
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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30
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Yamaguchi H, Hsu JM, Sun L, Wang SC, Hung MC. Advances and prospects of biomarkers for immune checkpoint inhibitors. Cell Rep Med 2024; 5:101621. [PMID: 38906149 PMCID: PMC11293349 DOI: 10.1016/j.xcrm.2024.101621] [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: 01/11/2024] [Revised: 04/22/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Immune checkpoint inhibitors (ICIs) activate anti-cancer immunity by blocking T cell checkpoint molecules such as programmed death 1 (PD-1) and cytotoxic T lymphocyte-associated protein 4 (CTLA-4). Although ICIs induce some durable responses in various cancer patients, they also have disadvantages, including low response rates, the potential for severe side effects, and high treatment costs. Therefore, selection of patients who can benefit from ICI treatment is critical, and identification of biomarkers is essential to improve the efficiency of ICIs. In this review, we provide updated information on established predictive biomarkers (tumor programmed death-ligand 1 [PD-L1] expression, DNA mismatch repair deficiency, microsatellite instability high, and tumor mutational burden) and potential biomarkers currently under investigation such as tumor-infiltrated and peripheral lymphocytes, gut microbiome, and signaling pathways related to DNA damage and antigen presentation. In particular, this review aims to summarize the current knowledge of biomarkers, discuss issues, and further explore future biomarkers.
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Affiliation(s)
- Hirohito Yamaguchi
- Graduate Institute of Cell Biology, China Medical University, Taichung City 406040, Taiwan; Graduate Institute of Biomedical Sciences and Institute of Biochemistry and Molecular Biology, China Medical University, Taichung City 406040, Taiwan; Cancer Biology and Precision Therapeutics Center and Research Center for Cancer Biology, China Medical University, Taichung City 40402, Taiwan
| | - Jung-Mao Hsu
- Graduate Institute of Biomedical Sciences and Institute of Biochemistry and Molecular Biology, China Medical University, Taichung City 406040, Taiwan; Cancer Biology and Precision Therapeutics Center and Research Center for Cancer Biology, China Medical University, Taichung City 40402, Taiwan
| | - Linlin Sun
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| | - Shao-Chun Wang
- Graduate Institute of Biomedical Sciences and Institute of Biochemistry and Molecular Biology, China Medical University, Taichung City 406040, Taiwan; Cancer Biology and Precision Therapeutics Center and Research Center for Cancer Biology, China Medical University, Taichung City 40402, Taiwan; Center for Molecular Medicine, China Medical University Hospital, Taichung City 40402, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences and Institute of Biochemistry and Molecular Biology, China Medical University, Taichung City 406040, Taiwan; Cancer Biology and Precision Therapeutics Center and Research Center for Cancer Biology, China Medical University, Taichung City 40402, Taiwan; Center for Molecular Medicine, China Medical University Hospital, Taichung City 40402, Taiwan.
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31
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Schlenker R, Schwalie PC, Dettling S, Huesser T, Irmisch A, Mariani M, Martínez Gómez JM, Ribeiro A, Limani F, Herter S, Yángüez E, Hoves S, Somandin J, Siebourg-Polster J, Kam-Thong T, de Matos IG, Umana P, Dummer R, Levesque MP, Bacac M. Myeloid-T cell interplay and cell state transitions associated with checkpoint inhibitor response in melanoma. MED 2024; 5:759-779.e7. [PMID: 38593812 DOI: 10.1016/j.medj.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/23/2023] [Accepted: 03/17/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND The treatment of melanoma, the deadliest form of skin cancer, has greatly benefited from immunotherapy. However, many patients do not show a durable response, which is only partially explained by known resistance mechanisms. METHODS We performed single-cell RNA sequencing of tumor immune infiltrates and matched peripheral blood mononuclear cells of 22 checkpoint inhibitor (CPI)-naive stage III-IV metastatic melanoma patients. After sample collection, the same patients received CPI treatment, and their response was assessed. FINDINGS CPI responders showed high levels of classical monocytes in peripheral blood, which preferentially transitioned toward CXCL9-expressing macrophages in tumors. Trajectories of tumor-infiltrating CD8+ T cells diverged at the level of effector memory/stem-like T cells, with non-responder cells progressing into a state characterized by cellular stress and apoptosis-related gene expression. Consistently, predicted non-responder-enriched myeloid-T/natural killer cell interactions were primarily immunosuppressive, while responder-enriched interactions were supportive of T cell priming and effector function. CONCLUSIONS Our study illustrates that the tumor immune microenvironment prior to CPI treatment can be indicative of response. In perspective, modulating the myeloid and/or effector cell compartment by altering the described cell interactions and transitions could improve immunotherapy response. FUNDING This research was funded by Roche Pharma Research and Early Development.
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Affiliation(s)
- Ramona Schlenker
- Roche Innovation Center Munich, Roche Pharma Research and Early Development (pRED), Penzberg, Germany.
| | | | - Steffen Dettling
- Roche Innovation Center Munich, Roche Pharma Research and Early Development (pRED), Penzberg, Germany
| | - Tamara Huesser
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Anja Irmisch
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marisa Mariani
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Julia M Martínez Gómez
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alison Ribeiro
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Florian Limani
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Sylvia Herter
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Emilio Yángüez
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Sabine Hoves
- Roche Innovation Center Munich, Roche Pharma Research and Early Development (pRED), Penzberg, Germany
| | - Jitka Somandin
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | | | | | | | - Pablo Umana
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marina Bacac
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
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32
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Parkhurst M, Goff SL, Lowery FJ, Beyer RK, Halas H, Robbins PF, Prickett TD, Gartner JJ, Sindiri S, Krishna S, Zacharakis N, Ngo L, Ray S, Bera A, Shepherd R, Levin N, Kim SP, Copeland A, Nah S, Levi S, Parikh N, Kwong MLM, Klemen ND, Yang JC, Rosenberg SA. Adoptive transfer of personalized neoantigen-reactive TCR-transduced T cells in metastatic colorectal cancer: phase 2 trial interim results. Nat Med 2024:10.1038/s41591-024-03109-0. [PMID: 38992129 DOI: 10.1038/s41591-024-03109-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/04/2024] [Indexed: 07/13/2024]
Abstract
Adoptive cell transfer (ACT) with neoantigen-reactive T lymphocytes can mediate cancer regression. Here we isolated unique, personalized, neoantigen-reactive T cell receptors (TCRs) from tumor-infiltrating lymphocytes of patients with metastatic gastrointestinal cancers and incorporated the TCR α and β chains into gamma retroviral vectors. We transduced autologous peripheral blood lymphocytes and adoptively transferred these cells into patients after lymphodepleting chemotherapy. In a phase 2 single-arm study, we treated seven patients with metastatic, mismatch repair-proficient colorectal cancers who had progressive disease following multiple previous therapies. The primary end point of the study was the objective response rate as measured using RECIST 1.1, and the secondary end points were safety and tolerability. There was no prespecified interim analysis defined in this study. Three patients had objective clinical responses by RECIST criteria including regressions of metastases to the liver, lungs and lymph nodes lasting 4 to 7 months. All patients received T cell populations containing ≥50% TCR-transduced cells, and all T cell populations were polyfunctional in that they secreted IFNγ, GM-CSF, IL-2 and granzyme B specifically in response to mutant peptides compared with wild-type counterparts. TCR-transduced cells were detected in the peripheral blood of five patients, including the three responders, at levels ≥10% of CD3+ cells 1 month post-ACT. In one patient who responded to therapy, ~20% of CD3+ peripheral blood lymphocytes expressed transduced TCRs more than 2 years after treatment. This study provides early results suggesting that ACT with T cells genetically modified to express personalized neoantigen-reactive TCRs can be tolerated and can mediate tumor regression in patients with metastatic colorectal cancers. ClinicalTrials.gov registration: NCT03412877 .
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Lien Ngo
- Surgery Branch, NCI, NIH, Bethesda, MD, USA
| | | | | | | | - Noam Levin
- Surgery Branch, NCI, NIH, Bethesda, MD, USA
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Liu M, Zhao Z, Wang C, Sang S, Cui Y, Lv C, Yang X, Zhang N, Xiong K, Chen B, Dong Q, Liu K, Gu Y. Harnessing genetic interactions for prediction of immune checkpoint inhibitors response signature in cancer cells. Cancer Lett 2024; 594:216991. [PMID: 38797232 DOI: 10.1016/j.canlet.2024.216991] [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: 01/10/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Genetic interactions (GIs) refer to two altered genes having a combined effect that is not seen individually. They play a crucial role in influencing drug efficacy. We utilized CGIdb 2.0 (http://www.medsysbio.org/CGIdb2/), an updated database of comprehensively published GIs information, encompassing synthetic lethality (SL), synthetic viability (SV), and chemical-genetic interactions. CGIdb 2.0 elucidates GIs relationships between or within protein complex models by integrating protein-protein physical interactions. Additionally, we introduced GENIUS (GENetic Interactions mediated drUg Signature) to leverage GIs for identifying the response signature of immune checkpoint inhibitors (ICIs). GENIUS identified high MAP4K4 expression as a resistant signature and high HERC4 expression as a sensitive signature for ICIs treatment. Melanoma patients with high expression of MAP4K4 were associated with decreased efficacy and poorer survival following ICIs treatment. Conversely, overexpression of HERC4 in melanoma patients correlated with a positive response to ICIs. Notably, HERC4 enhances sensitivity to immunotherapy by facilitating antigen presentation. Analyses of immune cell infiltration and single-cell data revealed that B cells expressing MAP4K4 may contribute to resistance to ICIs in melanoma. Overall, CGIdb 2.0, provides integrated GIs data, thus serving as a crucial tool for exploring drug effects.
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Affiliation(s)
- Mingyue Liu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhangxiang Zhao
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC), Chongqing University Three Gorges Hospital, Chongqing University, Wanzhou, Chongqing, China
| | - Chengyu Wang
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Shaocong Sang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yanrui Cui
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chen Lv
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiuqi Yang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Nan Zhang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kai Xiong
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Bo Chen
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qi Dong
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Kaidong Liu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yunyan Gu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
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De León-Rodríguez SG, Aguilar-Flores C, Gajón JA, Juárez-Flores Á, Mantilla A, Gerson-Cwilich R, Martínez-Herrera JF, Villegas-Osorno DA, Gutiérrez-Quiroz CT, Buenaventura-Cisneros S, Sánchez-Prieto MA, Castelán-Maldonado E, Rivera Rivera S, Fuentes-Pananá EM, Bonifaz LC. TCF1-positive and TCF1-negative TRM CD8 T cell subsets and cDC1s orchestrate melanoma protection and immunotherapy response. J Immunother Cancer 2024; 12:e008739. [PMID: 38969523 PMCID: PMC11227852 DOI: 10.1136/jitc-2023-008739] [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] [Accepted: 06/10/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND Melanoma, the most lethal form of skin cancer, has undergone a transformative treatment shift with the advent of checkpoint blockade immunotherapy (CBI). Understanding the intricate network of immune cells infiltrating the tumor and orchestrating the control of melanoma cells and the response to CBI is currently of utmost importance. There is evidence underscoring the significance of tissue-resident memory (TRM) CD8 T cells and classic dendritic cell type 1 (cDC1) in cancer protection. Transcriptomic studies also support the existence of a TCF7+ (encoding TCF1) T cell as the most important for immunotherapy response, although uncertainty exists about whether there is a TCF1+TRM T cell due to evidence indicating TCF1 downregulation for tissue residency activation. METHODS We used multiplexed immunofluorescence and spectral flow cytometry to evaluate TRM CD8 T cells and cDC1 in two melanoma patient cohorts: one immunotherapy-naive and the other receiving immunotherapy. The first cohort was divided between patients free of disease or with metastasis 2 years postdiagnosis while the second between CBI responders and non-responders. RESULTS Our study identifies two CD8+TRM subsets, TCF1+ and TCF1-, correlating with melanoma protection. TCF1+TRM cells show heightened expression of IFN-γ and Ki67 while TCF1- TRM cells exhibit increased expression of cytotoxic molecules. In metastatic patients, TRM subsets undergo a shift in marker expression, with the TCF1- subset displaying increased expression of exhaustion markers. We observed a close spatial correlation between cDC1s and TRMs, with TCF1+TRM/cDC1 pairs enriched in the stroma and TCF1- TRM/cDC1 pairs in tumor areas. Notably, these TCF1- TRMs express cytotoxic molecules and are associated with apoptotic melanoma cells. Both TCF1+ and TCF1- TRM subsets, alongside cDC1, prove relevant to CBI response. CONCLUSIONS Our study supports the importance of TRM CD8 T cells and cDC1 in melanoma protection while also highlighting the existence of functionally distinctive TCF1+ and TCF1- TRM subsets, both crucial for melanoma control and CBI response.
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Affiliation(s)
- Saraí G De León-Rodríguez
- Posgrado en Ciencias Biológicas, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Unidad de Investigación Médica en Inmunoquímica, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Cristina Aguilar-Flores
- Unidad de Investigación Médica en Inmunología, UMAE Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Julián A Gajón
- Unidad de Investigación Médica en Inmunoquímica, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
- Posgrado en Ciencias Bioquímicas, Facultad de Química, Universad Nacional Autónoma de México, Mexico City, Mexico
| | - Ángel Juárez-Flores
- Unidad de Investigación Médica en Inmunoquímica, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
- Unidad de Investigación en Virología y Cáncer, Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico
| | - Alejandra Mantilla
- Servicio de Patología, Hospital de Oncología Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | | | - José Fabián Martínez-Herrera
- Medical Center American British Cowdray, Mexico City, Mexico
- Latin American Network for Cancer Research (LAN-CANCER), Lima, Peru
| | | | - Claudia T Gutiérrez-Quiroz
- UMAE Hospital de Especialidades, Centro Médico Nacional General Manuel Avila Camacho, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | | | - Mario Alberto Sánchez-Prieto
- Unidad Médica de Alta Especialidad No.25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo Leon, Mexico
- División de Atención Oncológica en Adultos. Coordinación de Atención Oncológica, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Edmundo Castelán-Maldonado
- Unidad Médica de Alta Especialidad No.25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo Leon, Mexico
| | - Samuel Rivera Rivera
- Medical Center American British Cowdray, Mexico City, Mexico
- División de Atención Oncológica en Adultos. Coordinación de Atención Oncológica, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Ezequiel M Fuentes-Pananá
- Unidad de Investigación en Virología y Cáncer, Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico
| | - Laura C Bonifaz
- Unidad de Investigación Médica en Inmunoquímica, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
- Coordinación de investigación en salud, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
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Alteber Z, Cojocaru G, Granit RZ, Barbiro I, Wool A, Frenkel M, Novik A, Shuchami A, Liang Y, Carmi VD, Sabath N, Foreman R, Petrenko N, He J, Kliger Y, Levy-Barda A, Eitan R, Raban O, Sadot E, Sulimani O, Nathan AA, Adewoye H, Ferre P, Levine Z, Ophir E. PVRIG is Expressed on Stem-Like T Cells in Dendritic Cell-Rich Niches in Tumors and Its Blockade May Induce Immune Infiltration in Non-Inflamed Tumors. Cancer Immunol Res 2024; 12:876-890. [PMID: 38752503 DOI: 10.1158/2326-6066.cir-23-0752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/29/2024] [Accepted: 05/10/2024] [Indexed: 07/03/2024]
Abstract
Cancers that are poorly immune infiltrated pose a substantial challenge, with current immunotherapies yielding limited clinical success. Stem-like memory T cells (TSCM) have been identified as a subgroup of T cells that possess strong proliferative capacity and that can expand and differentiate following interactions with dendritic cells (DCs). In this study, we explored the pattern of expression of a recently discovered inhibitory receptor poliovirus receptor-related immunoglobulin domain protein (PVRIG) and its ligand, poliovirus receptor-related ligand 2 (PVRL2), in the human tumor microenvironment. Using spatial and single-cell RNA transcriptomics data across diverse cancer indications, we found that among the T-cell checkpoints, PVRIG is uniquely expressed on TSCM and PVRL2 is expressed on DCs in immune aggregate niches in tumors. PVRIG blockade could therefore enhance TSCM-DC interactions and efficiently drive T-cell infiltration to tumors. Consistent with these data, following PVRIG blockade in patients with poorly infiltrated tumors, we observed immune modulation including increased tumor T-cell infiltration, T-cell receptor (TCR) clonality, and intratumoral T-cell expansion, all of which were associated with clinical benefit. These data suggest PVRIG blockade as a promising strategy to induce potent antitumor T-cell responses, providing a novel approach to overcome resistance to immunotherapy in immune-excluded tumors.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jiang He
- Vizgen Inc., Cambridge, Massachusetts
| | | | - Adva Levy-Barda
- Biobank, Department of Pathology, Rabin Medical Center, Petah Tikva, Israel
| | - Ram Eitan
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
- Gynecologic Oncology Division, Helen Schneider Hospital for Women, Rabin Medical Center, Petah Tikva, Israel
| | - Oded Raban
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
- Gynecologic Oncology Division, Helen Schneider Hospital for Women, Rabin Medical Center, Petah Tikva, Israel
| | - Eran Sadot
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
- Department of Surgery, Rabin Medical Center, Petach Tikva, Israel
| | - Omri Sulimani
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
- Department of Surgery, Rabin Medical Center, Petach Tikva, Israel
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36
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Zemek RM, Anagnostou V, Pires da Silva I, Long GV, Lesterhuis WJ. Exploiting temporal aspects of cancer immunotherapy. Nat Rev Cancer 2024; 24:480-497. [PMID: 38886574 DOI: 10.1038/s41568-024-00699-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/25/2024] [Indexed: 06/20/2024]
Abstract
Many mechanisms underlying an effective immunotherapy-induced antitumour response are transient and critically time dependent. This is equally true for several immunological events in the tumour microenvironment induced by other cancer treatments. Immune checkpoint therapy (ICT) has proven to be very effective in the treatment of some cancers, but unfortunately, with many cancer types, most patients do not experience a benefit. To improve outcomes, a multitude of clinical trials are testing combinations of ICT with various other treatment modalities. Ideally, those combination treatments should take time-dependent immunological events into account. Recent studies have started to map the dynamic cellular and molecular changes that occur during treatment with ICT, in the tumour and systemically. Here, we overlay the dynamic ICT response with the therapeutic response following surgery, radiotherapy, chemotherapy and targeted therapies. We propose that by combining treatments in a time-conscious manner, we may optimally exploit the interactions between the individual therapies.
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Affiliation(s)
- Rachael M Zemek
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Inês Pires da Silva
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Crown Princess Mary Cancer Centre Westmead, Blacktown Hospital, Sydney, New South Wales, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Royal North Shore and Mater Hospitals, Sydney, New South Wales, Australia
| | - Willem Joost Lesterhuis
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia.
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37
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Choi JE, Qiao Y, Kryczek I, Yu J, Gurkan J, Bao Y, Gondal M, Tien JCY, Maj T, Yazdani S, Parolia A, Xia H, Zhou J, Wei S, Grove S, Vatan L, Lin H, Li G, Zheng Y, Zhang Y, Cao X, Su F, Wang R, He T, Cieslik M, Green MD, Zou W, Chinnaiyan AM. PIKfyve controls dendritic cell function and tumor immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582543. [PMID: 38464258 PMCID: PMC10925294 DOI: 10.1101/2024.02.28.582543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The modern armamentarium for cancer treatment includes immunotherapy and targeted therapy, such as protein kinase inhibitors. However, the mechanisms that allow cancer-targeting drugs to effectively mobilize dendritic cells (DCs) and affect immunotherapy are poorly understood. Here, we report that among shared gene targets of clinically relevant protein kinase inhibitors, high PIKFYVE expression was least predictive of complete response in patients who received immune checkpoint blockade (ICB). In immune cells, high PIKFYVE expression in DCs was associated with worse response to ICB. Genetic and pharmacological studies demonstrated that PIKfyve ablation enhanced DC function via selectively altering the alternate/non-canonical NF-κB pathway. Both loss of Pikfyve in DCs and treatment with apilimod, a potent and specific PIKfyve inhibitor, restrained tumor growth, enhanced DC-dependent T cell immunity, and potentiated ICB efficacy in tumor-bearing mouse models. Furthermore, the combination of a vaccine adjuvant and apilimod reduced tumor progression in vivo. Thus, PIKfyve negatively controls DCs, and PIKfyve inhibition has promise for cancer immunotherapy and vaccine treatment strategies.
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Affiliation(s)
- Jae Eun Choi
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yuanyuan Qiao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Ilona Kryczek
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Jiali Yu
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Gurkan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi Bao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Mahnoor Gondal
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jean Ching-Yi Tien
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Tomasz Maj
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Sahr Yazdani
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Abhijit Parolia
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Houjun Xia
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - JiaJia Zhou
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Shuang Wei
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Sara Grove
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Linda Vatan
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Heng Lin
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Gaopeng Li
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zheng
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xuhong Cao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rui Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Tongchen He
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Michael D. Green
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Weiping Zou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Arul M. Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
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Ishigaki H, Yamauchi T, Long MD, Hoki T, Yamamoto Y, Oba T, Ito F. Generation, Transcriptomic States, and Clinical Relevance of CX3CR1+ CD8 T Cells in Melanoma. CANCER RESEARCH COMMUNICATIONS 2024; 4:1802-1814. [PMID: 38881188 PMCID: PMC11267618 DOI: 10.1158/2767-9764.crc-24-0199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/28/2024] [Accepted: 06/12/2024] [Indexed: 06/18/2024]
Abstract
Recent progress in single-cell profiling technologies has revealed significant phenotypic and transcriptional heterogeneity in tumor-infiltrating CD8+ T cells. However, the transition between the different states of intratumoral antigen-specific CD8+ T cells remains elusive. Here, we sought to examine the generation, transcriptomic states, and the clinical relevance of melanoma-infiltrating CD8+ T cells expressing a chemokine receptor and T-cell differentiation marker, CX3C chemokine receptor 1 (CX3CR1). Analysis of single-cell datasets revealed distinct human melanoma-infiltrating CD8+ T-cell clusters expressing genes associated with effector T-cell function but with distinguishing expression of CX3CR1 or PDCD1. No obvious impact of CX3CR1 expression in melanoma on the response to immune checkpoint inhibitor therapy was observed while increased pretreatment and on-treatment frequency of a CD8+ T-cell cluster expressing high levels of exhaustion markers was associated with poor response to the treatment. Adoptively transferred antigen-specific CX3CR1- CD8+ T cells differentiated into the CX3CR1+ subset in mice treated with FTY720, which inhibits lymphocyte egress from secondary lymphoid tissues, suggesting the intratumoral generation of CX3CR1+ CD8+ T cells rather than their trafficking from secondary lymphoid organs. Furthermore, analysis of adoptively transferred antigen-specific CD8+ T cells, in which the Cx3cr1 gene was replaced with a marker gene confirmed that CX3CR1+ CD8+ T cells could directly differentiate from the intratumoral CX3CR1- subset. These findings highlight that tumor antigen-specific CX3CR1- CD8+ T cells can fully differentiate outside the secondary lymphoid organs and generate CX3CR1+ CD8+ T cells in the tumor microenvironment, which are distinct from CD8+ T cells that express markers of exhaustion. SIGNIFICANCE Intratumoral T cells are composed of heterogeneous subpopulations with various phenotypic and transcriptional states. This study illustrates the intratumoral generation of antigen-specific CX3CR1+ CD8+ T cells that exhibit distinct transcriptomic signatures and clinical relevance from CD8+ T cells expressing markers of exhaustion.
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Affiliation(s)
- Hirohito Ishigaki
- Department of Surgery, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, California.
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan.
| | - Takayoshi Yamauchi
- Department of Surgery, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, California.
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York.
| | - Mark D. Long
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York.
| | - Toshifumi Hoki
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York.
- Oncology Science Unit, MSD Japan, Tokyo, Japan.
| | - Yuta Yamamoto
- Department of Surgery, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, California.
- Department of Surgery, Shinshu University School of Medicine, Matsumoto, Japan.
| | - Takaaki Oba
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York.
- Department of Surgery, Shinshu University School of Medicine, Matsumoto, Japan.
| | - Fumito Ito
- Department of Surgery, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, California.
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York.
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39
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Holder AM, Dedeilia A, Sierra-Davidson K, Cohen S, Liu D, Parikh A, Boland GM. Defining clinically useful biomarkers of immune checkpoint inhibitors in solid tumours. Nat Rev Cancer 2024; 24:498-512. [PMID: 38867074 DOI: 10.1038/s41568-024-00705-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 06/14/2024]
Abstract
Although more than a decade has passed since the approval of immune checkpoint inhibitors (ICIs) for the treatment of melanoma and non-small-cell lung, breast and gastrointestinal cancers, many patients still show limited response. US Food and Drug Administration (FDA)-approved biomarkers include programmed cell death 1 ligand 1 (PDL1) expression, microsatellite status (that is, microsatellite instability-high (MSI-H)) and tumour mutational burden (TMB), but these have limited utility and/or lack standardized testing approaches for pan-cancer applications. Tissue-based analytes (such as tumour gene signatures, tumour antigen presentation or tumour microenvironment profiles) show a correlation with immune response, but equally, these demonstrate limited efficacy, as they represent a single time point and a single spatial assessment. Patient heterogeneity as well as inter- and intra-tumoural differences across different tissue sites and time points represent substantial challenges for static biomarkers. However, dynamic biomarkers such as longitudinal biopsies or novel, less-invasive markers such as blood-based biomarkers, radiomics and the gut microbiome show increasing potential for the dynamic identification of ICI response, and patient-tailored predictors identified through neoadjuvant trials or novel ex vivo tumour models can help to personalize treatment. In this Perspective, we critically assess the multiple new static, dynamic and patient-specific biomarkers, highlight the newest consortia and trial efforts, and provide recommendations for future clinical trials to make meaningful steps forwards in the field.
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Affiliation(s)
- Ashley M Holder
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Sonia Cohen
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - David Liu
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Aparna Parikh
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Genevieve M Boland
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
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40
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Moynihan KD, Kumar MP, Sultan H, Pappas DC, Park T, Chin SM, Bessette P, Lan RY, Nguyen HC, Mathewson ND, Ni I, Chen W, Lee Y, Liao-Chan S, Chen J, Schumacher TN, Schreiber RD, Yeung YA, Djuretic IM. IL2 Targeted to CD8+ T Cells Promotes Robust Effector T-cell Responses and Potent Antitumor Immunity. Cancer Discov 2024; 14:1206-1225. [PMID: 38563906 PMCID: PMC11215410 DOI: 10.1158/2159-8290.cd-23-1266] [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: 10/25/2023] [Revised: 02/05/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
IL2 signals pleiotropically on diverse cell types, some of which contribute to therapeutic activity against tumors, whereas others drive undesired activity, such as immunosuppression or toxicity. We explored the theory that targeting of IL2 to CD8+ T cells, which are key antitumor effectors, could enhance its therapeutic index. To this aim, we developed AB248, a CD8 cis-targeted IL2 that demonstrates over 500-fold preference for CD8+ T cells over natural killer and regulatory T cells (Tregs), which may contribute to toxicity and immunosuppression, respectively. AB248 recapitulated IL2's effects on CD8+ T cells in vitro and induced selective expansion of CD8+T cells in primates. In mice, an AB248 surrogate demonstrated superior antitumor activity and enhanced tolerability as compared with an untargeted IL2Rβγ agonist. Efficacy was associated with the expansion and phenotypic enhancement of tumor-infiltrating CD8+ T cells, including the emergence of a "better effector" population. These data support the potential utility of AB248 in clinical settings. Significance: The full potential of IL2 therapy remains to be unlocked. We demonstrate that toxicity can be decoupled from antitumor activity in preclinical models by limiting IL2 signaling to CD8+ T cells, supporting the development of CD8+ T cell-selective IL2 for the treatment of cancer. See related article by Kaptein et al. p. 1226.
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Affiliation(s)
| | - Manu P. Kumar
- Asher Biotherapeutics, Inc., South San Francisco, California.
| | - Hussein Sultan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
| | | | - Terrence Park
- Asher Biotherapeutics, Inc., South San Francisco, California.
| | - S. Michael Chin
- Asher Biotherapeutics, Inc., South San Francisco, California.
| | - Paul Bessette
- Asher Biotherapeutics, Inc., South San Francisco, California.
| | - Ruth Y. Lan
- Asher Biotherapeutics, Inc., South San Francisco, California.
| | - Henry C. Nguyen
- Asher Biotherapeutics, Inc., South San Francisco, California.
| | | | - Irene Ni
- Asher Biotherapeutics, Inc., South San Francisco, California.
| | - Wei Chen
- Asher Biotherapeutics, Inc., South San Francisco, California.
| | - Yonghee Lee
- Asher Biotherapeutics, Inc., South San Francisco, California.
| | - Sindy Liao-Chan
- Asher Biotherapeutics, Inc., South San Francisco, California.
| | - Jessie Chen
- Asher Biotherapeutics, Inc., South San Francisco, California.
| | - Ton N.M. Schumacher
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam; Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Robert D. Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
| | - Yik A. Yeung
- Asher Biotherapeutics, Inc., South San Francisco, California.
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Wang Z, Zhao Y, Wo Y, Peng Y, Hu W, Wu Z, Liu P, Shang Y, Liu C, Chen X, Huang K, Chen Y, Hong H, Li F, Sun Y. The single cell immunogenomic landscape after neoadjuvant immunotherapy combined chemotherapy in esophageal squamous cell carcinoma. Cancer Lett 2024; 593:216951. [PMID: 38734159 DOI: 10.1016/j.canlet.2024.216951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Neoadjuvant immunotherapy represents promising strategy in the treatment of esophageal squamous cell carcinoma (ESCC). However, the mechanisms underlying its impact on treatment sensitivity or resistance remain a subject of controversy. In this study, we conducted single-cell RNA and T/B cell receptor (scTCR/scBCR) sequencing of CD45+ immune cells on samples from 10 patients who received neoadjuvant immunotherapy and chemotherapy. We also validated our findings using multiplexed immunofluorescence and analyzed bulk RNA-seq from other cohorts in public database. By integrating analysis of 87357 CD45+ cells, we found GZMK + effector memory T cells (Tem) were relatively enriched and CXCL13+ exhausted T cells (Tex) and regulator T cells (Treg) decreased among responders, indicating a persistent anti-tumor memory process. Additionally, the enhanced presence of BCR expansion and somatic hypermutation process within TNFRSF13B + memory B cells (Bmem) suggested their roles in antigen presentation. This was further corroborated by the evidence of the T-B co-stimulation pattern and CXCL13-CXCR5 axis. The complexity of myeloid cell heterogeneity was also particularly pronounced. The elevated expression of S100A7 in ESCC, as detected by bulk RNA-seq, was associated with an exhausted and immunosuppressive tumor microenvironment. In summary, this study has unveiled a potential regulatory network among immune cells and the clonal dynamics of their functions, and the mechanisms of exhaustion and memory conversion between GZMK + Tem and TNFRSF13B + Bmem from antigen presentation and co-stimulation perspectives during neoadjuvant PD-1 blockade treatment in ESCC.
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MESH Headings
- Humans
- Neoadjuvant Therapy/methods
- Esophageal Squamous Cell Carcinoma/immunology
- Esophageal Squamous Cell Carcinoma/genetics
- Esophageal Squamous Cell Carcinoma/therapy
- Esophageal Squamous Cell Carcinoma/drug therapy
- Esophageal Squamous Cell Carcinoma/pathology
- Esophageal Neoplasms/immunology
- Esophageal Neoplasms/genetics
- Esophageal Neoplasms/therapy
- Esophageal Neoplasms/drug therapy
- Esophageal Neoplasms/pathology
- Immunotherapy/methods
- Single-Cell Analysis/methods
- Female
- Male
- Tumor Microenvironment/immunology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Chemokine CXCL13/genetics
- Chemokine CXCL13/metabolism
- Middle Aged
- Aged
- Memory T Cells/immunology
- Memory T Cells/metabolism
- Leukocyte Common Antigens/metabolism
- Leukocyte Common Antigens/genetics
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/drug effects
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Receptors, Antigen, B-Cell/immunology
- Receptors, CXCR5/metabolism
- Receptors, CXCR5/genetics
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Affiliation(s)
- Zheyi Wang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue Zhao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Wo
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yizhou Peng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weilei Hu
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China; State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Zhigang Wu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pengcheng Liu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan Shang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chunnan Liu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kan Huang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuting Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hui Hong
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fei Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Yihua Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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42
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Strongin Z, Raymond Marchand L, Deleage C, Pampena MB, Cardenas MA, Beusch CM, Hoang TN, Urban EA, Gourves M, Nguyen K, Tharp GK, Lapp S, Rahmberg AR, Harper J, Del Rio Estrada PM, Gonzalez-Navarro M, Torres-Ruiz F, Luna-Villalobos YA, Avila-Rios S, Reyes-Teran G, Sekaly R, Silvestri G, Kulpa DA, Saez-Cirion A, Brenchley JM, Bosinger SE, Gordon DE, Betts MR, Kissick HT, Paiardini M. Distinct SIV-specific CD8 + T cells in the lymph node exhibit simultaneous effector and stem-like profiles and are associated with limited SIV persistence. Nat Immunol 2024; 25:1245-1256. [PMID: 38886592 DOI: 10.1038/s41590-024-01875-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 05/14/2024] [Indexed: 06/20/2024]
Abstract
Human immunodeficiency virus (HIV) cure efforts are increasingly focused on harnessing CD8+ T cell functions, which requires a deeper understanding of CD8+ T cells promoting HIV control. Here we identifiy an antigen-responsive TOXhiTCF1+CD39+CD8+ T cell population with high expression of inhibitory receptors and low expression of canonical cytolytic molecules. Transcriptional analysis of simian immunodeficiency virus (SIV)-specific CD8+ T cells and proteomic analysis of purified CD8+ T cell subsets identified TOXhiTCF1+CD39+CD8+ T cells as intermediate effectors that retained stem-like features with a lineage relationship with terminal effector T cells. TOXhiTCF1+CD39+CD8+ T cells were found at higher frequency than TCF1-CD39+CD8+ T cells in follicular microenvironments and were preferentially located in proximity of SIV-RNA+ cells. Their frequency was associated with reduced plasma viremia and lower SIV reservoir size. Highly similar TOXhiTCF1+CD39+CD8+ T cells were detected in lymph nodes from antiretroviral therapy-naive and antiretroviral therapy-suppressed people living with HIV, suggesting this population of CD8+ T cells contributes to limiting SIV and HIV persistence.
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Affiliation(s)
- Zachary Strongin
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Laurence Raymond Marchand
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - M Betina Pampena
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Christian Michel Beusch
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Timothy N Hoang
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Elizabeth A Urban
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Mael Gourves
- Institut Pasteur, Université Paris Cité, Viral Reservoirs and Immune Control Unit, Paris, France
- Institut Pasteur, Université Paris Cité, HIV Inflammation and Persistence Unit, Paris, France
| | - Kevin Nguyen
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gregory K Tharp
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Stacey Lapp
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Andrew R Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAIDNIH, Bethesda, MD, USA
| | - Justin Harper
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Perla M Del Rio Estrada
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Mauricio Gonzalez-Navarro
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Fernanda Torres-Ruiz
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Yara Andrea Luna-Villalobos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Santiago Avila-Rios
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Comision Coordinadora de los Institutos Nacionales de Salud y Hospitales de Alta Especialidad, Mexico City, Mexico
| | - Rafick Sekaly
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Deanna A Kulpa
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Asier Saez-Cirion
- Institut Pasteur, Université Paris Cité, Viral Reservoirs and Immune Control Unit, Paris, France
- Institut Pasteur, Université Paris Cité, HIV Inflammation and Persistence Unit, Paris, France
| | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAIDNIH, Bethesda, MD, USA
| | - Steven E Bosinger
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - David Ezra Gordon
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haydn T Kissick
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Vaccine Center, Emory University, Atlanta, GA, USA.
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43
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Lee J, Whitney JB. Immune checkpoint inhibition as a therapeutic strategy for HIV eradication: current insights and future directions. Curr Opin HIV AIDS 2024; 19:179-186. [PMID: 38747727 DOI: 10.1097/coh.0000000000000863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
PURPOSE OF REVIEW HIV-1 infection contributes substantially to global morbidity and mortality, with no immediate promise of an effective prophylactic vaccine. Combination antiretroviral therapy (ART) suppresses HIV replication, but latent viral reservoirs allow the virus to persist and reignite active replication if ART is discontinued. Moreover, inflammation and immune disfunction persist despite ART-mediated suppression of HIV. Immune checkpoint molecules facilitate immune dysregulation and viral persistence. However, their therapeutic modulation may offer an avenue to enhance viral immune control for patients living with HIV-1 (PLWH). RECENT FINDINGS The success of immune checkpoint inhibitor (ICI) therapy in oncology suggests that targeting these same immune pathways might be an effective therapeutic approach for treating PLWH. Several ICIs have been evaluated for their ability to reinvigorate exhausted T cells, and possibly reverse HIV latency, in both preclinical and clinical HIV-1 studies. SUMMARY Although there are very encouraging findings showing enhanced CD8 + T-cell function with ICI therapy in HIV infection, it remains uncertain whether ICIs alone could demonstrably impact the HIV reservoir. Moreover, safety concerns and significant clinical adverse events present a hurdle to the development of ICI approaches. This review provides an update on the current knowledge regarding the development of ICIs for the remission of HIV-1 in PWH. We detail recent findings from simian immunodeficiency virus (SIV)-infected rhesus macaque models, clinical trials in PLWH, and the role of soluble immune checkpoint molecules in HIV pathogenesis.
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Affiliation(s)
- Jina Lee
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA
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44
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Zhang D, Jiang D, Jiang L, Ma J, Wang X, Xu X, Chen Z, Jiang M, Ye W, Wang J, Meng W, Qiu W, Hou Y, Huang J, Jiao Y, Liu Y, Liu Z. HLA-A + tertiary lymphoid structures with reactivated tumor infiltrating lymphocytes are associated with a positive immunotherapy response in esophageal squamous cell carcinoma. Br J Cancer 2024; 131:184-195. [PMID: 38762674 PMCID: PMC11231239 DOI: 10.1038/s41416-024-02712-9] [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: 01/06/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND Immune checkpoint blockade (ICB) therapy provides remarkable clinical benefits for multiple cancer types. However, the overall response rate to ICB therapy remains low in esophageal squamous cell carcinoma (ESCC). This study aimed to identify biomarkers of ICB therapy for ESCC and interrogate its potential clinical relevance. METHODS We investigated gene expression in 42 treatment-naïve ESCC tumor tissues and identified differentially expressed genes, tumor-infiltrating lymphocytes and immune-related genes signatures associated with differential immunotherapy responses. We systematically assessed the tumor microenvironment using the NanoString GeoMx digital spatial profiler, single-cell RNA-seq and multiplex immunohistochemistry in ESCC. Finally, we evaluated the associations between HLA-A-positive tertiary lymphoid structures (TLSs) and patients' responses to ICB in 60 ESCC patients. RESULTS Tumor infiltrating B lymphocytes and several immune-related gene signatures, such as the antigen presenting machinery (APM) signature, are significantly elevated in ICB treatment responders. Multiplex immunohistochemistry identified the presence of HLA-A+ TLSs and showed that TLS-resident cells increasingly express HLA-A as TLSs mature. Most TLS-resident HLA-A+ cells are tumor-infiltrating T (TIL-T) or tumor-infiltrating B (TIL-B) lymphocytes. Digital spatial profiling of spatially distinct TIL-T lymphocytes and single-cell RNA-seq data from 60 ESCC tumor tissues revealed that CXCL13-expressing exhausted TIL-Ts inside TLSs are reactivated with elevated expression of the APM signature as TLSs mature. Finally, we demonstrated that HLA-A+ TLSs and their major cellular components, TIL-Ts and TIL-Bs, are associated with a clinical benefit from ICB treatment for ESCC. CONCLUSIONS HLA-A+ TLSs are present in ESCC tumor tissues. TLS-resident TIL-Ts with elevated expression of the APM signature may be reactivated. HLA-A+ TLSs and their major cellular components, TIL-Ts and TIL-Bs, may serve as biomarkers for ICB-treated ESCC patients.
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Affiliation(s)
- Dandan Zhang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Dongxian Jiang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Liping Jiang
- 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, 100021, Beijing, China
| | - Jiakang Ma
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Xiaobing Wang
- 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, 100021, Beijing, China
| | - Xingyu Xu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Ziqiang Chen
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Mengping Jiang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Wenjing Ye
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jie Wang
- Departments of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Weida Meng
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Wenqing Qiu
- Shanghai Xuhui Central Hospital, Shanghai, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jing Huang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuchen Jiao
- 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, 100021, Beijing, China.
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 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, 100021, Beijing, China.
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45
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Choi JE, Qiao Y, Kryczek I, Yu J, Gurkan J, Bao Y, Gondal M, Tien JCY, Maj T, Yazdani S, Parolia A, Xia H, Zhou J, Wei S, Grove S, Vatan L, Lin H, Li G, Zheng Y, Zhang Y, Cao X, Su F, Wang R, He T, Cieslik M, Green MD, Zou W, Chinnaiyan AM. PIKfyve, expressed by CD11c-positive cells, controls tumor immunity. Nat Commun 2024; 15:5487. [PMID: 38942798 PMCID: PMC11213953 DOI: 10.1038/s41467-024-48931-9] [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: 08/17/2023] [Accepted: 05/15/2024] [Indexed: 06/30/2024] Open
Abstract
Cancer treatment continues to shift from utilizing traditional therapies to targeted ones, such as protein kinase inhibitors and immunotherapy. Mobilizing dendritic cells (DC) and other myeloid cells with antigen presenting and cancer cell killing capacities is an attractive but not fully exploited approach. Here, we show that PIKFYVE is a shared gene target of clinically relevant protein kinase inhibitors and high expression of this gene in DCs is associated with poor patient response to immune checkpoint blockade (ICB) therapy. Genetic and pharmacological studies demonstrate that PIKfyve ablation enhances the function of CD11c+ cells (predominantly dendritic cells) via selectively altering the non-canonical NF-κB pathway. Both loss of Pikfyve in CD11c+ cells and treatment with apilimod, a potent and specific PIKfyve inhibitor, restrained tumor growth, enhanced DC-dependent T cell immunity, and potentiated ICB efficacy in tumor-bearing mouse models. Furthermore, the combination of a vaccine adjuvant and apilimod reduced tumor progression in vivo. Thus, PIKfyve negatively regulates the function of CD11c+ cells, and PIKfyve inhibition has promise for cancer immunotherapy and vaccine treatment strategies.
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Affiliation(s)
- Jae Eun Choi
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Yuanyuan Qiao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Ilona Kryczek
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Jiali Yu
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Gurkan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yi Bao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Mahnoor Gondal
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jean Ching-Yi Tien
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Tomasz Maj
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Sahr Yazdani
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Abhijit Parolia
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Houjun Xia
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - JiaJia Zhou
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Shuang Wei
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Sara Grove
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Linda Vatan
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Heng Lin
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Gaopeng Li
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zheng
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xuhong Cao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rui Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Tongchen He
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Michael D Green
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Weiping Zou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA.
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA.
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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46
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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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47
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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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48
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Talvard-Balland N, Braun LM, Dixon KO, Zwick M, Engel H, Hartmann A, Duquesne S, Penter L, Andrieux G, Rindlisbacher L, Acerbis A, Ehmann J, Köllerer C, Ansuinelli M, Rettig A, Moschallski K, Apostolova P, Brummer T, Illert AL, Schramm MA, Cheng Y, Köttgen A, Duyster J, Menssen HD, Ritz J, Blazar BR, Boerries M, Schmitt-Gräff A, Sariipek N, Van Galen P, Buescher JM, Cabezas-Wallscheid N, Pahl HL, Pearce EL, Soiffer RJ, Wu CJ, Vago L, Becher B, Köhler N, Wertheimer T, Kuchroo VK, Zeiser R. Oncogene-induced TIM-3 ligand expression dictates susceptibility to anti-TIM-3 therapy in mice. J Clin Invest 2024; 134:e177460. [PMID: 38916965 PMCID: PMC11324309 DOI: 10.1172/jci177460] [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: 11/08/2023] [Accepted: 06/20/2024] [Indexed: 06/27/2024] Open
Abstract
Leukemia relapse is a major cause of death after allogeneic hematopoietic cell transplantation (allo-HCT). We tested the potential of targeting T cell (Tc) immunoglobulin and mucin-containing molecule 3 (TIM-3) for improving graft-versus-leukemia (GVL) effects. We observed differential expression of TIM-3 ligands when hematopoietic stem cells overexpressed certain oncogenic-driver mutations. Anti-TIM-3 Ab treatment improved survival of mice bearing leukemia with oncogene-induced TIM-3 ligand expression. Conversely, leukemia cells with low ligand expression were anti-TIM-3 treatment resistant. In vitro, TIM-3 blockade or genetic deletion in CD8+ Tc enhanced Tc activation, proliferation, and IFN-γ production while enhancing GVL effects, preventing Tc exhaustion, and improving Tc cytotoxicity and glycolysis in vivo. Conversely, TIM-3 deletion in myeloid cells did not affect allogeneic Tc proliferation and activation in vitro, suggesting that anti-TIM-3 treatment-mediated GVL effects are Tc induced. In contrast to anti-programmed cell death protein 1 (anti-PD-1) and anti-cytotoxic T lymphocyte-associated protein 4 (anti-CTLA-4) treatment, anti-TIM-3-treatment did not enhance acute graft-versus-host disease (aGVHD). TIM-3 and its ligands were frequently expressed in acute myeloid leukemia (AML) cells of patients with post-allo-HCT relapse. We decipher the connections between oncogenic mutations found in AML and TIM-3 ligand expression and identify anti-TIM-3 treatment as a strategy for enhancing GVL effects via metabolic and transcriptional Tc reprogramming without exacerbation of aGVHD. Our findings support clinical testing of anti-TIM-3 Ab in patients with AML relapse after allo-HCT.
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MESH Headings
- Animals
- Hepatitis A Virus Cellular Receptor 2/genetics
- Hepatitis A Virus Cellular Receptor 2/metabolism
- Mice
- Hematopoietic Stem Cell Transplantation
- Graft vs Leukemia Effect/immunology
- Graft vs Leukemia Effect/genetics
- Humans
- Allografts
- Ligands
- Oncogenes
- CD8-Positive T-Lymphocytes/immunology
- Mice, Knockout
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/pathology
- CTLA-4 Antigen/genetics
- CTLA-4 Antigen/immunology
- CTLA-4 Antigen/metabolism
- CTLA-4 Antigen/antagonists & inhibitors
- Gene Expression Regulation, Leukemic
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Affiliation(s)
- Nana Talvard-Balland
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
- CIBSS–Centre for Integrative Biological Signalling Studies, and
| | - Lukas M. Braun
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Karen O. Dixon
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts, USA
- Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Melissa Zwick
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Helena Engel
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
| | - Alina Hartmann
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
| | - Sandra Duquesne
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
| | - Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, Massachusetts, USA
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité–Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lukas Rindlisbacher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Andrea Acerbis
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
| | - Jule Ehmann
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
| | - Christoph Köllerer
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
| | - Michela Ansuinelli
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, Massachusetts, USA
- Hematology, Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Andres Rettig
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
| | - Kevin Moschallski
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
| | - Petya Apostolova
- German Cancer Consortium (DKTK) Partner Site Freiburg, a partnership between German Cancer Research Center (DKFZ) and Medical Center, University of Freiburg, Freiburg, Germany
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tilman Brummer
- German Cancer Consortium (DKTK) Partner Site Freiburg, a partnership between German Cancer Research Center (DKFZ) and Medical Center, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS–Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Institute of Molecular Medicine and Cell Research (IMMZ), Freiburg, Germany
| | - Anna L. Illert
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
- German Cancer Consortium (DKTK) Partner Site Freiburg, a partnership between German Cancer Research Center (DKFZ) and Medical Center, University of Freiburg, Freiburg, Germany
- Department of Internal Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | | | - Yurong Cheng
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center–University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center–University of Freiburg, Freiburg, Germany
| | - Justus Duyster
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
| | | | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, Massachusetts, USA
| | - Bruce R. Blazar
- University of Minnesota, Department of Pediatrics, Division of Blood and Marrow Transplant & Cellular Therapy, Minneapolis, Minnesota, USA
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, a partnership between German Cancer Research Center (DKFZ) and Medical Center, University of Freiburg, Freiburg, Germany
| | | | - Nurefsan Sariipek
- Division of Hematology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Peter Van Galen
- Division of Hematology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Joerg M. Buescher
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Heike L. Pahl
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
| | - Erika L. Pearce
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert J. Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, Massachusetts, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, Massachusetts, USA
| | - Luca Vago
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Natalie Köhler
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
- CIBSS–Centre for Integrative Biological Signalling Studies, and
| | - Tobias Wertheimer
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Vijay K. Kuchroo
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts, USA
| | - Robert Zeiser
- Department of Internal Medicine I, Faculty of Medicine and Medical Center
- German Cancer Consortium (DKTK) Partner Site Freiburg, a partnership between German Cancer Research Center (DKFZ) and Medical Center, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS–Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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49
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He S, Gubin MM, Rafei H, Basar R, Dede M, Jiang X, Liang Q, Tan Y, Kim K, Gillison ML, Rezvani K, Peng W, Haymaker C, Hernandez S, Solis LM, Mohanty V, Chen K. Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles. iScience 2024; 27:110096. [PMID: 38957791 PMCID: PMC11217617 DOI: 10.1016/j.isci.2024.110096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/03/2024] [Accepted: 05/21/2024] [Indexed: 07/04/2024] Open
Abstract
Recent developments in immunotherapy, including immune checkpoint blockade (ICB) and adoptive cell therapy (ACT), have encountered challenges such as immune-related adverse events and resistance, especially in solid tumors. To advance the field, a deeper understanding of the molecular mechanisms behind treatment responses and resistance is essential. However, the lack of functionally characterized immune-related gene sets has limited data-driven immunological research. To address this gap, we adopted non-negative matrix factorization on 83 human bulk RNA sequencing (RNA-seq) datasets and constructed 28 immune-specific gene sets. After rigorous immunologist-led manual annotations and orthogonal validations across immunological contexts and functional omics data, we demonstrated that these gene sets can be applied to refine pan-cancer immune subtypes, improve ICB response prediction and functionally annotate spatial transcriptomic data. These functional gene sets, informing diverse immune states, will advance our understanding of immunology and cancer research.
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Affiliation(s)
- Shan He
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew M. Gubin
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hind Rafei
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rafet Basar
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Merve Dede
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xianli Jiang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qingnan Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yukun Tan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kunhee Kim
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maura L. Gillison
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Weiyi Peng
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharia Hernandez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luisa M. Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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50
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Wang B, Wang K, Wu D, Sahni S, Jiang P, Ruppin E. Decoupling the correlation between cytotoxic and exhausted T lymphocyte states enhances melanoma immunotherapy response prediction. iScience 2024; 27:109926. [PMID: 38832027 PMCID: PMC11145333 DOI: 10.1016/j.isci.2024.109926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/24/2024] [Accepted: 05/03/2024] [Indexed: 06/05/2024] Open
Abstract
Cytotoxic T lymphocyte (CTL) and terminal exhausted T lymphocyte (ETL) activities crucially influence immune checkpoint inhibitor (ICI) response. Despite this, the efficacy of ETL and CTL transcriptomic signatures for response prediction remains limited. Investigating this across the TCGA and publicly available single-cell cohorts, we find a strong positive correlation between ETL and CTL expression signatures in most cancers. We hence posited that their limited predictability arises due to their mutually canceling effects on ICI response. Thus, we developed DETACH, a computational method to identify a gene set whose expression pinpoints to a subset of melanoma patients where the CTL and ETL correlation is low. DETACH enhances CTL's prediction accuracy, outperforming existing signatures. DETACH signature genes activity also demonstrates a positive correlation with lymphocyte infiltration and the prevalence of reactive T cells in the tumor microenvironment (TME), advancing our understanding of the CTL cell state within the TME.
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Affiliation(s)
- Binbin Wang
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Kun Wang
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Di Wu
- Laboratory of Pathology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Sahil Sahni
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Peng Jiang
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
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