1
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Lang HP, Osum KC, Friedenberg SG. A review of CD4 + T cell differentiation and diversity in dogs. Vet Immunol Immunopathol 2024; 275:110816. [PMID: 39173398 DOI: 10.1016/j.vetimm.2024.110816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 08/24/2024]
Abstract
CD4+ T cells are an integral component of the adaptive immune response, carrying out many functions to combat a diverse range of pathogenic challenges. These cells exhibit remarkable plasticity, differentiating into specialized subsets such as T helper type 1 (TH1), TH2, TH9, TH17, TH22, regulatory T cells (Tregs), and follicular T helper (TFH) cells. Each subset is capable of addressing a distinct immunological need ranging from pathogen eradication to regulation of immune homeostasis. As the immune response subsides, CD4+ T cells rest down into long-lived memory phenotypes-including central memory (TCM), effector memory (TEM), resident memory (TRM), and terminally differentiated effector memory cells (TEMRA) that are localized to facilitate a swift and potent response upon antigen re-encounter. This capacity for long-term immunological memory and rapid reactivation upon secondary exposure highlights the role CD4+ T cells play in sustaining both adaptive defense mechanisms and maintenance. Decades of mouse, human, and to a lesser extent, pig T cell research has provided the framework for understanding the role of CD4+ T cells in immune responses, but these model systems do not always mimic each other. Although our understanding of pig immunology is not as extensive as mouse or human research, we have gained valuable insight by studying this model. More akin to pigs, our understanding of CD4+ T cells in dogs is much less complete. This disparity exists in part because canine immunologists depend on paradigms from mouse and human studies to characterize CD4+ T cells in dogs, with a fraction of available lineage-defining antibody markers. Despite this, every major CD4+ T cell subset has been described to some extent in dogs. These subsets have been studied in various contexts, including in vitro stimulation, homeostatic conditions, and across a range of disease states. Canine CD4+ T cells have been categorized according to lineage-defining characteristics, trafficking patterns, and what cytokines they produce upon stimulation. This review addresses our current understanding of canine CD4+ T cells from a comparative perspective by highlighting both the similarities and differences from mouse, human, and pig CD4+ T cell biology. We also discuss knowledge gaps in our current understanding of CD4+ T cells in dogs that could provide direction for future studies in the field.
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Affiliation(s)
- Haeree P Lang
- Center for Immunology, University of Minnesota, Minneapolis, MN 55414, USA; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.
| | - Kevin C Osum
- Center for Immunology, University of Minnesota, Minneapolis, MN 55414, USA.
| | - Steven G Friedenberg
- Center for Immunology, University of Minnesota, Minneapolis, MN 55414, USA; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.
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2
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Otsuka S, Dutta D, Wu CJ, Alam MS, Ashwell JD. Calcineurin is an adaptor required for assembly of the TCR signaling complex. Cell Rep 2024; 43:114568. [PMID: 39088318 DOI: 10.1016/j.celrep.2024.114568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/25/2024] [Accepted: 07/17/2024] [Indexed: 08/03/2024] Open
Abstract
The serine/threonine phosphatase calcineurin is a component of the T cell receptor (TCR) signalosome, where it promotes T cell activation by dephosphorylating LckS59. Using small interfering RNA (siRNA)-mediated knockdown and CRISPR-Cas9-targeted genetic disruption of the calcineurin A chain α and β isoforms, we find that calcineurin also functions as an adaptor in TCR-signaled human T cells. Unlike inhibition of its phosphatase activity, in the absence of calcineurin A, TCR signaling results in attenuated actin rearrangement, markedly reduced TCR-Lck microcluster formation and recruitment of the adaptor RhoH, and diminished phosphorylation of critical targets downstream of Lck such as TCRζ and ZAP-70. Reconstitution of deficient T cells with either calcineurin Aα or Aβ restores TCR microcluster formation and signaling, as does reconstitution with a phosphatase-inactive Aα chain. These results assign a non-enzymatic adaptor function to calcineurin in the formation and stabilization of a functional TCR signaling complex.
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Affiliation(s)
- Shizuka Otsuka
- Laboratory of Immune Cell Biology, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Debjani Dutta
- Laboratory of Immune Cell Biology, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chuan-Jin Wu
- Laboratory of Immune Cell Biology, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Muhammad S Alam
- Laboratory of Immune Cell Biology, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan D Ashwell
- Laboratory of Immune Cell Biology, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA.
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3
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Guo M, Liu MYR, Brooks DG. Regulation and impact of tumor-specific CD4 + T cells in cancer and immunotherapy. Trends Immunol 2024; 45:303-313. [PMID: 38508931 DOI: 10.1016/j.it.2024.02.005] [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: 02/20/2024] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/22/2024]
Abstract
CD4+ T cells are crucial in generating and sustaining immune responses. They orchestrate and fine-tune mammalian innate and adaptive immunity through cell-based interactions and the release of cytokines. The role of these cells in contributing to the efficacy of antitumor immunity and immunotherapy has just started to be uncovered. Yet, many aspects of the CD4+ T cell response are still unclear, including the differentiation pathways controlling such cells during cancer progression, the external signals that program them, and how the combination of these factors direct ensuing immune responses or immune-restorative therapies. In this review, we focus on recent advances in understanding CD4+ T cell regulation during cancer progression and the importance of CD4+ T cells in immunotherapies.
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Affiliation(s)
- Mengdi Guo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Melissa Yi Ran Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - David G Brooks
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada.
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4
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Zhang GP, Liao JX, Liu YY, Zhu FQ, Huang HJ, Zhang WJ. Ion channel P2X7 receptor in the progression of cancer. Front Oncol 2024; 13:1297775. [PMID: 38273855 PMCID: PMC10808724 DOI: 10.3389/fonc.2023.1297775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
P2X7 receptor (P2X7) is a non-selective and ATP-sensitive ligand-gated cation channel. Studies have confirmed that it is expressed in a variety of cells and correlates with their function, frequently in immune cells and tumor cells. We found increased expression of this receptor in many tumor cells, and it has a role in tumor survival and progression. In immune cells, upregulation of the receptor has a double effect on tumor suppression as well as tumor promotion. This review describes the structure of P2X7 and its role in the tumor microenvironment and presents possible mechanisms of P2X7 in tumor invasion and metastasis. Understanding the potential of P2X7 for tumor treatment, we also present several therapeutic agents targeting P2X7 and their mechanisms of action. In conclusion, the study of P2X7 is an important guideline for the use of clinical tumor therapy and may be able to provide a new idea for tumor treatment, but considering the complexity of the biological effects of P2X7, the drugs should be used with caution in clinical practice.
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Affiliation(s)
- Guang-ping Zhang
- The Second Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
- Department of Critical Medicine, Ganzhou people’s Hospital, Ganzhou, Jiangxi, China
| | - Jun-xiang Liao
- The Second Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Yi-yi Liu
- The Second Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Fu-qi Zhu
- The Second Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Hui-jin Huang
- The Second Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Wen-jun Zhang
- Department of Rehabilitation Medicine, the Second Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
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5
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Weizman OE, Luyten S, Lu P, Song E, Qin K, Mostaghimi D, Ring AM, Iwasaki A. Developing synthetic tools to decipher the tumor-immune interactome. Proc Natl Acad Sci U S A 2023; 120:e2306632120. [PMID: 37871202 PMCID: PMC10622925 DOI: 10.1073/pnas.2306632120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
The ability of immune cells to directly interact with transformed cells is an essential component of immune surveillance and critical for optimal tissue function. The tumor-immune interactome (the collective cellular interactions between oncogenic cells and immune cells) is distinct and varied based on the tissue location and immunogenicity of tumor subtypes. However, comprehensive landscape and the consequences of tumor-interacting immune cells in the tumor microenvironment are not well understood. Current tools are limited in their ability to identify and record interactors in vivo or be utilized for downstream analysis. Here, we describe the development and validation of a technology leveraging synthetic Notch receptors reporting physical tumor cell-immune cell contact in vivo in order to decipher the tumor-immune interactome. We call this approach, Tumor-Immune Interactome Non-biased Discovery Retroviral Reporter or TIINDRR. Using TIINDRR, we identify the tumor-immune interactomes that define immunological refractory and sensitive tumors and how different immunotherapies alter these interactions. Thus, TIINDRR provides a flexible and versatile tool for studying in-vivo tumor-immune cell interactions, aiding in the identification of biologically relevant information needed for the rational design of immune-based therapies.
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Affiliation(s)
- Orr-El Weizman
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Sophia Luyten
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Peiwen Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
- Department of Ophthalmology, Yale University School of Medicine, New Haven, CT06520
| | - Kai Qin
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Darius Mostaghimi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Aaron M. Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT06520
- HHMI, Chevy Chase, MD20815
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Taves MD, Otsuka S, Taylor MA, Donahue KM, Meyer TJ, Cam MC, Ashwell JD. Tumors produce glucocorticoids by metabolite recycling, not synthesis, and activate Tregs to promote growth. J Clin Invest 2023; 133:e164599. [PMID: 37471141 PMCID: PMC10503810 DOI: 10.1172/jci164599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 07/18/2023] [Indexed: 07/22/2023] Open
Abstract
Glucocorticoids are steroid hormones with potent immunosuppressive properties. Their primary source is the adrenals, where they are generated via de novo synthesis from cholesterol. In addition, many tissues have a recycling pathway in which glucocorticoids are regenerated from inactive metabolites by the enzyme 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1, encoded by Hsd11b1). Here, we find that multiple tumor types express Hsd11b1 and produce active glucocorticoids. Genetic ablation of Hsd11b1 in such cells had no effect on in vitro growth, but reduced in vivo tumor progression, which corresponded with increased frequencies of CD8+ tumor-infiltrating lymphocytes (TILs) expressing activation markers and producing effector cytokines. Tumor-derived glucocorticoids were found to promote signatures of Treg activation and suppress signatures of conventional T cell activation in tumor-infiltrating Tregs. Indeed, CD8+ T cell activation was restored and tumor growth reduced in mice with Treg-specific glucocorticoid receptor deficiency. Importantly, pharmacologic inhibition of 11β-HSD1 reduced tumor growth to the same degree as gene knockout and rendered immunotherapy-resistant tumors susceptible to PD-1 blockade. Given that HSD11B1 expression is upregulated in many human tumors and that inhibition of 11β-HSD1 is well tolerated in clinical studies, these data suggest that targeting 11β-HSD1 may be a beneficial adjunct in cancer therapy.
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Affiliation(s)
| | | | | | | | - Thomas J. Meyer
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Margaret C. Cam
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
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7
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Dykema AG, Zhang J, Cheung LS, Connor S, Zhang B, Zeng Z, Cherry CM, Li T, Caushi JX, Nishimoto M, Munoz AJ, Ji Z, Hou W, Zhan W, Singh D, Zhang T, Rashid R, Mitchell-Flack M, Bom S, Tam A, Ionta N, Aye THK, Wang Y, Sawosik CA, Tirado LE, Tomasovic LM, VanDyke D, Spangler JB, Anagnostou V, Yang S, Spicer J, Rayes R, Taube J, Brahmer JR, Forde PM, Yegnasubramanian S, Ji H, Pardoll DM, Smith KN. Lung tumor-infiltrating T reg have divergent transcriptional profiles and function linked to checkpoint blockade response. Sci Immunol 2023; 8:eadg1487. [PMID: 37713507 PMCID: PMC10629528 DOI: 10.1126/sciimmunol.adg1487] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 07/25/2023] [Indexed: 09/17/2023]
Abstract
Regulatory T cells (Treg) are conventionally viewed as suppressors of endogenous and therapy-induced antitumor immunity; however, their role in modulating responses to immune checkpoint blockade (ICB) is unclear. In this study, we integrated single-cell RNA-seq/T cell receptor sequencing (TCRseq) of >73,000 tumor-infiltrating Treg (TIL-Treg) from anti-PD-1-treated and treatment-naive non-small cell lung cancers (NSCLC) with single-cell analysis of tumor-associated antigen (TAA)-specific Treg derived from a murine tumor model. We identified 10 subsets of human TIL-Treg, most of which have high concordance with murine TIL-Treg subsets. Only one subset selectively expresses high levels of TNFRSF4 (OX40) and TNFRSF18 (GITR), whose engangement by cognate ligand mediated proliferative programs and NF-κB activation, as well as multiple genes involved in Treg suppression, including LAG3. Functionally, the OX40hiGITRhi subset is the most highly suppressive ex vivo, and its higher representation among total TIL-Treg correlated with resistance to PD-1 blockade. Unexpectedly, in the murine tumor model, we found that virtually all TIL-Treg-expressing T cell receptors that are specific for TAA fully develop a distinct TH1-like signature over a 2-week period after entry into the tumor, down-regulating FoxP3 and up-regulating expression of TBX21 (Tbet), IFNG, and certain proinflammatory granzymes. Transfer learning of a gene score from the murine TAA-specific TH1-like Treg subset to the human single-cell dataset revealed a highly analogous subcluster that was enriched in anti-PD-1-responding tumors. These findings demonstrate that TIL-Treg partition into multiple distinct transcriptionally defined subsets with potentially opposing effects on ICB-induced antitumor immunity and suggest that TAA-specific TIL-Treg may positively contribute to antitumor responses.
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Affiliation(s)
- Arbor G. Dykema
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jiajia Zhang
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Laurene S. Cheung
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sydney Connor
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Boyang Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Zhen Zeng
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Taibo Li
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Justina X. Caushi
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Marni Nishimoto
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew J. Munoz
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Wenpin Hou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Wentao Zhan
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Dipika Singh
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Tianbei Zhang
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rufiaat Rashid
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Marisa Mitchell-Flack
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sadhana Bom
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ada Tam
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nick Ionta
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thet H. K. Aye
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yi Wang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Camille A. Sawosik
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Lauren E. Tirado
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Luke M. Tomasovic
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Derek VanDyke
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA
| | - Jamie B. Spangler
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Valsamo Anagnostou
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Stephen Yang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Roni Rayes
- Department of Surgery, McGill University, Montreal, Canada
| | - Janis Taube
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Julie R. Brahmer
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Patrick M. Forde
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Srinivasan Yegnasubramanian
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Drew M. Pardoll
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kellie N. Smith
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
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Lin YC, Wu CH, Chen PJ, Huang CH, Yang CK, Dutta A, Huang CT, Lin CY. Murine cytotoxic CD4+ T cells in the tumor microenvironment are at a hyper-maturation stage of Th1 CD4+ T cells sustained by IL-12. Int Immunol 2023; 35:387-400. [PMID: 37202206 DOI: 10.1093/intimm/dxad015] [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: 06/21/2022] [Accepted: 05/16/2023] [Indexed: 05/20/2023] Open
Abstract
The roles of tumor-infiltrating CD4+Foxp3- T cells are not well characterized due to their plasticity of differentiation, and varying levels of activation or exhaustion. To further clarify this issue, we used a model featuring subcutaneous murine colon cancer and analyzed the dynamic changes of phenotype and function of the tumor-associated CD4+ T-cell response. We found that, even at a late stage of tumor growth, the tumor-infiltrating CD4+Foxp3- T cells still expressed effector molecules, inflammatory cytokines and molecules that are expressed at reduced levels in exhausted cells. We used microarrays to examine the gene-expression profiles of different subsets of CD4+ T cells and revealed that the tumor-infiltrating CD4+Foxp3- T cells expressed not only type 1 helper (Th1) cytokines, but also cytolytic granules such as those encoded by Gzmb and Prf1. In contrast to CD4+ regulatory T cells, these cells exclusively co-expressed natural killer receptor markers and cytolytic molecules as shown by flow-cytometry studies. We used an ex vivo killing assay and proved that they could directly suppress CT26 tumor cells through granzyme B and perforin. Finally, we used pathway analysis and ex vivo stimulation to confirm that the CD4+Foxp3- T cells expressed higher levels of IL12rb1 genes and were activated by the IL-12/IL-27 pathway. In conclusion, this work finds that, in late-stage tumors, the tumor-infiltrating lymphocyte population of CD4+ cells harbored a sustained, hyper-maturated Th1 status with cytotoxic function supported by IL-12.
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Affiliation(s)
- Yung-Chang Lin
- Division of Medical Oncology/Hematology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333423, Taiwan
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333323, Taiwan
| | - Cheng-Heng Wu
- Division of Hepatogastroenterology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Branch, No. 5, Fushin Street, Kweishan, Taoyuan 333423, Taiwan
| | - Pin-Jung Chen
- Division of Hepatogastroenterology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Branch, No. 5, Fushin Street, Kweishan, Taoyuan 333423, Taiwan
| | - Chien-Hao Huang
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333323, Taiwan
- Division of Hepatogastroenterology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Branch, No. 5, Fushin Street, Kweishan, Taoyuan 333423, Taiwan
| | - Chan-Keng Yang
- Division of Medical Oncology/Hematology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333423, Taiwan
| | - Avijit Dutta
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333323, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan 333323, Taiwan
| | - Ching-Tai Huang
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333323, Taiwan
- Division of Infectious Diseases, Department of Medicine, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333423, Taiwan
| | - Chun-Yen Lin
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333323, Taiwan
- Division of Hepatogastroenterology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Branch, No. 5, Fushin Street, Kweishan, Taoyuan 333423, Taiwan
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9
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Aybey B, Zhao S, Brors B, Staub E. Immune cell type signature discovery and random forest classification for analysis of single cell gene expression datasets. Front Immunol 2023; 14:1194745. [PMID: 37609075 PMCID: PMC10441575 DOI: 10.3389/fimmu.2023.1194745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/14/2023] [Indexed: 08/24/2023] Open
Abstract
Background Robust immune cell gene expression signatures are central to the analysis of single cell studies. Nearly all known sets of immune cell signatures have been derived by making use of only single gene expression datasets. Utilizing the power of multiple integrated datasets could lead to high-quality immune cell signatures which could be used as superior inputs to machine learning-based cell type classification approaches. Results We established a novel workflow for the discovery of immune cell type signatures based primarily on gene-versus-gene expression similarity. It leverages multiple datasets, here seven single cell expression datasets from six different cancer types and resulted in eleven immune cell type-specific gene expression signatures. We used these to train random forest classifiers for immune cell type assignment for single-cell RNA-seq datasets. We obtained similar or better prediction results compared to commonly used methods for cell type assignment in independent benchmarking datasets. Our gene signature set yields higher prediction scores than other published immune cell type gene sets in random forest-based cell type classification. We further demonstrate how our approach helps to avoid bias in downstream statistical analyses by re-analysis of a published IFN stimulation experiment. Discussion and conclusion We demonstrated the quality of our immune cell signatures and their strong performance in a random forest-based cell typing approach. We argue that classifying cells based on our comparably slim sets of genes accompanied by a random forest-based approach not only matches or outperforms widely used published approaches. It also facilitates unbiased downstream statistical analyses of differential gene expression between cell types for significantly more genes compared to previous cell classification algorithms.
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Affiliation(s)
- Bogac Aybey
- Oncology Data Science, Merck Healthcare KGaA, Darmstadt, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sheng Zhao
- Oncology Data Science, Merck Healthcare KGaA, Darmstadt, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Eike Staub
- Oncology Data Science, Merck Healthcare KGaA, Darmstadt, Germany
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10
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Vienot A, Jacquin M, Rebucci-Peixoto M, Pureur D, Ghiringhelli F, Assenat E, Hammel P, Rosmorduc O, Stouvenot M, Allaire M, Bouattour M, Regnault H, Fratte S, Raymond E, Soularue E, Husson-Wetzel S, Di Martino V, Muller A, Clairet AL, Fagnoni-Legat C, Adotevi O, Meurisse A, Vernerey D, Borg C. Evaluation of the interest to combine a CD4 Th1-inducer cancer vaccine derived from telomerase and atezolizumab plus bevacizumab in unresectable hepatocellular carcinoma: a randomized non-comparative phase II study (TERTIO - PRODIGE 82). BMC Cancer 2023; 23:710. [PMID: 37516867 PMCID: PMC10387199 DOI: 10.1186/s12885-023-11065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/13/2023] [Indexed: 07/31/2023] Open
Abstract
BACKGROUND Several cancer immunotherapies that target the PD-L1/PD-1 pathway show promising clinical activity in patients with hepatocellular carcinoma (HCC). However, the standard of care in first-line treatment with atezolizumab (anti-PD-L1 therapy) in combination with bevacizumab is associated with a limited objective response rate. Telomerase reverse transcriptase (TERT) activation meets the criteria of oncogenic addiction in HCC and could be actionable therapeutic target and a relevant tumor antigen. Therefore we hypothesized that combining anti-PD-1/PD-L1 therapy with an anti-telomerase vaccine might be an attractive therapy in HCC. UCPVax is a therapeutic cancer vaccine composed of two separate peptides derived from telomerase (human TERT). UCPVax has been evaluated in a multicenter phase I/II study in non-small cell lung cancers and has demonstrated to be safe and immunogenic, and is under evaluation in combination with atezolizumab in a phase II clinical trial in tumors where telomerase reactivation contributes to an oncogene addiction (HPV+ cancers). The aim of the TERTIO study is to determine the clinical interest and immunological efficacy of a treatment combining the CD4 helper T-inducer cancer anti-telomerase vaccine (UCPVax) with atezolizumab and bevacizumab in unresectable HCC in a multicenter randomized phase II study. METHODS Patients with locally advanced, metastatic or unresectable HCC who have not previously received systemic anti-cancer treatment are eligible. The primary end point is the objective response rate at 6 months. Patients will be allocated to a treatment arm with a randomization 2:1. In both arms, patients will receive atezolizumab at fixed dose of 1200 mg IV infusion and bevacizumab at fixed dose of 15 mg/kg IV infusion, every 3 weeks, according to the standard of care. In the experimental arm, these treatments will be combined with the UCPVax vaccine at 0.5 mg subcutaneously. DISCUSSION Combining anti-PD-1/PD-L1 therapy with an anti-telomerase vaccine gains serious consideration in HCC, in order to extend the clinical efficacy of anti-PD-1/PD-L1. Indeed, anti-cancer vaccines can induce tumor-specific T cell expansion and activation and therefore restore the cancer-immunity cycle in patients lacking pre-existing anti-tumor responses. Thus, there is a strong rational to combine immune checkpoint blockade therapy and anticancer vaccine (UCPVax) in order to activate antitumor T cell immunity and bypass the immunosuppression in the tumor microenvironment in HCC. This pivotal proof of concept study will evaluate the efficacy and safety of the combination of a CD4 Th1-inducer cancer vaccine derived from telomerase (UCPVax) and atezolizumab plus bevacizumab in unresectable HCC, as well as confirming their synergic mechanism, and settling the basis for a new combination for future clinical trials. TRIAL REGISTRATION NCT05528952.
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Affiliation(s)
- Angélique Vienot
- Department of Medical Oncology, University Hospital of Besançon, 25000, Besançon, France.
- Clinical Investigational Center, CIC-1431, Besançon, France.
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire Et Génique, Besançon, France.
- Groupe Coopérateur Multidisciplinaire en Oncologie (GERCOR) Oncology Multidisciplinary Group, Paris, France.
| | - Marion Jacquin
- Department of Medical Oncology, University Hospital of Besançon, 25000, Besançon, France
- Clinical Investigational Center, CIC-1431, Besançon, France
| | - Magali Rebucci-Peixoto
- Department of Medical Oncology, University Hospital of Besançon, 25000, Besançon, France
- Clinical Investigational Center, CIC-1431, Besançon, France
| | - Dimitri Pureur
- Department of Medical Oncology, University Hospital of Besançon, 25000, Besançon, France
- Department of Hepatology, University Hospital of Besançon, Besançon, France
| | - François Ghiringhelli
- Department of Medical Oncology, Georges François Leclerc Cancer Center-UNICANCER, Dijon, France
| | - Eric Assenat
- Department of Medical Oncology, Saint Eloi Hospital, University Hospital, Montpellier of Montpellier, France
| | - Pascal Hammel
- Department of Digestive and Medical Oncology, Paul-Brousse Hospital, Villejuif, France
| | - Olivier Rosmorduc
- Department of Hepato-Biliary, Paul-Brousse Hospital, Villejuif, France
| | - Morgane Stouvenot
- Department of Medical Oncology, University Hospital of Besançon, 25000, Besançon, France
- Department of Gastroenterology, University Hospital of Besançon, Besançon, France
| | - Manon Allaire
- Department of Hepatogastroenterology, Pitié Salpêtrière Hospital, Paris, France
| | | | - Hélène Regnault
- Department of Gastroenterology and Hepatology, Henri Mondor Hospital, Creteil, France
| | - Serge Fratte
- Department of Gastroenterology, Nord Franche Comté Hospital, Montbéliard, France
| | - Eric Raymond
- Department of Medical Oncology, Paris Saint-Joseph Hospital, Paris, France
| | - Emilie Soularue
- Department of Medical Oncology, Institute Mutualiste Montsouris, Paris, France
| | - Stéphanie Husson-Wetzel
- Department of Gastroenterology, Groupe Hospitalier de La Région Mulhouse Sud Alsace, Mulhouse, France
| | - Vincent Di Martino
- Department of Hepatology, University Hospital of Besançon, Besançon, France
| | - Allison Muller
- Department of Clinical Research and Innovation, Vigilance Unit, University Hospital of Besançon, Besançon, France
| | - Anne-Laure Clairet
- Department of Pharmacy, University Hospital of Besançon, Besançon, France
| | | | - Olivier Adotevi
- Department of Medical Oncology, University Hospital of Besançon, 25000, Besançon, France
- Clinical Investigational Center, CIC-1431, Besançon, France
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire Et Génique, Besançon, France
| | - Aurélia Meurisse
- Department of Medical Oncology, University Hospital of Besançon, 25000, Besançon, France
- Methodology and Quality of Life in Oncology Unit, University Hospital of Besançon, Besançon, France
| | - Dewi Vernerey
- Department of Medical Oncology, University Hospital of Besançon, 25000, Besançon, France
- Methodology and Quality of Life in Oncology Unit, University Hospital of Besançon, Besançon, France
| | - Christophe Borg
- Department of Medical Oncology, University Hospital of Besançon, 25000, Besançon, France
- Clinical Investigational Center, CIC-1431, Besançon, France
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire Et Génique, Besançon, France
- Groupe Coopérateur Multidisciplinaire en Oncologie (GERCOR) Oncology Multidisciplinary Group, Paris, France
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11
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Lim J, Kang I, La J, Ku KB, Kang BH, Kim Y, Park WH, Lee HK. Harnessing type I interferon-mediated immunity to target malignant brain tumors. Front Immunol 2023; 14:1203929. [PMID: 37304294 PMCID: PMC10247981 DOI: 10.3389/fimmu.2023.1203929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/15/2023] [Indexed: 06/13/2023] Open
Abstract
Type I interferons have long been appreciated as a cytokine family that regulates antiviral immunity. Recently, their role in eliciting antitumor immune responses has gained increasing attention. Within the immunosuppressive tumor microenvironment (TME), interferons stimulate tumor-infiltrating lymphocytes to promote immune clearance and essentially reshape a "cold" TME into an immune-activating "hot" TME. In this review, we focus on gliomas, with an emphasis on malignant glioblastoma, as these brain tumors possess a highly invasive and heterogenous brain TME. We address how type I interferons regulate antitumor immune responses against malignant gliomas and reshape the overall immune landscape of the brain TME. Furthermore, we discuss how these findings can translate into future immunotherapies targeting brain tumors in general.
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Affiliation(s)
- Juhee Lim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - In Kang
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jeongwoo La
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Keun Bon Ku
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Department of Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Byeong Hoon Kang
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Yumin Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Won Hyung Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Heung Kyu Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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12
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Khan SM, Desai R, Coxon A, Livingstone A, Dunn GP, Petti A, Johanns TM. Impact of CD4 T cells on intratumoral CD8 T-cell exhaustion and responsiveness to PD-1 blockade therapy in mouse brain tumors. J Immunother Cancer 2022; 10:jitc-2022-005293. [PMID: 36543376 PMCID: PMC9772691 DOI: 10.1136/jitc-2022-005293] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Glioblastoma is a fatal disease despite aggressive multimodal therapy. PD-1 blockade, a therapy that reinvigorates hypofunctional exhausted CD8 T cells (Tex) in many malignancies, has not shown efficacy in glioblastoma. Loss of CD4 T cells can lead to an exhausted CD8 T-cell phenotype, and terminally exhausted CD8 T cells (Tex term) do not respond to PD-1 blockade. GL261 and CT2A are complementary orthotopic models of glioblastoma. GL261 has a functional CD4 T-cell compartment and is responsive to PD-1 blockade; notably, CD4 depletion abrogates this survival benefit. CT2A is composed of dysfunctional CD4 T cells and is PD-1 blockade unresponsive. We leverage these models to understand the impact of CD4 T cells on CD8 T-cell exhaustion and PD-1 blockade sensitivity in glioblastoma. METHODS Single-cell RNA sequencing was performed on flow sorted tumor-infiltrating lymphocytes from female C57/BL6 mice implanted with each model, with and without PD-1 blockade therapy. CD8+ and CD4+ T cells were identified and separately analyzed. Survival analyses were performed comparing PD-1 blockade therapy, CD40 agonist or combinatorial therapy. RESULTS The CD8 T-cell compartment of the models is composed of heterogenous CD8 Tex subsets, including progenitor exhausted CD8 T cells (Tex prog), intermediate Tex, proliferating Tex, and Tex term. GL261 is enriched with the PD-1 responsive Tex prog subset relative to the CT2A and CD4-depleted GL261 models, which are composed predominantly of the PD-1 blockade refractory Tex term subset. Analysis of the CD4 T-cell compartments revealed that the CT2A microenvironment is enriched with a suppressive Treg subset and an effector CD4 T-cell subset that expresses an inhibitory interferon-stimulated (Isc) signature. Finally, we demonstrate that addition of CD40 agonist to PD-1 blockade therapy improves survival in CT2A tumor-bearing mice. CONCLUSIONS Here, we describe that dysfunctional CD4 T cells are associated with terminal CD8 T-cell exhaustion, suggesting CD4 T cells impact PD-1 blockade efficacy by controlling the severity of exhaustion. Given that CD4 lymphopenia is frequently observed in patients with glioblastoma, this may represent a basis for resistance to PD-1 blockade. We demonstrate that CD40 agonism may circumvent a dysfunctional CD4 compartment to improve PD-1 blockade responsiveness, supporting a novel synergistic immunotherapeutic approach.
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Affiliation(s)
- Saad M Khan
- Department of Neurosurgery, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Rupen Desai
- Department of Neurosurgery, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Andrew Coxon
- Department of Neurosurgery, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Alexandra Livingstone
- Department of Medicine, Division of Medical Oncology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Gavin P Dunn
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Allegra Petti
- Department of Neurosurgery, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Tanner M Johanns
- Department of Medicine, Division of Medical Oncology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
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13
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Horzum U, Yanik H, Taskiran EZ, Esendagli G. Effector Th1 cells under PD-1 and CTLA-4 checkpoint blockade abrogate the upregulation of multiple inhibitory receptors and by-pass exhaustion. Immunology 2022; 167:640-650. [PMID: 36053975 DOI: 10.1111/imm.13560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023] Open
Abstract
Immune checkpoint inhibitor (ICI) immunotherapy relies on the restoration of T-cell functions. The ICI receptors are not only found on exhausted T cells but also upregulated upon activation and reach high levels on effector T cells. In an ex vivo model, this study explored the consequences of PD-1 and cytotoxic T-lymphocyte antigen (CTLA-4) blockade applied during specific time frames of T-cell stimulation that coincide with distinct functional phases in type 1 helper T (Th1) cells. When applied at an early stimulation stage, the checkpoint blockade interfered with the upregulation of multiple inhibitory receptors such as PD-1, LAG3, TIM-3 and CTLA-4. Moreover, extension of the blockade period restricted the hyporesponsiveness in T cells. Alternatively, a short-term ICI treatment was advantageous when applied at late time frames of Th1 cell stimulation. Here, a transition phase from effector to exhausted state, which coincided with the late time frames of Th1 stimulation, was clearly determined together with the transcriptomics data demonstrating the initiation of significant alterations in metabolic pathways, genetic information processes, effector and exhaustion specific pathways. Applied in this transition phase, PD-1 and/or CTLA-4 blockade downregulated the inhibitory receptors which were already present on the effector Th1 cells, potentially through endocytic pathways. Therefore, the efficacy of ICI therapy was modulated by the functional status of T cells and can be improved by modifying the timing and duration of PD-1 and CTLA-4 blockade. In conclusion, the ICI therapy not only supports the reactivation of T cells but can also constrain de novo exhaustion.
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Affiliation(s)
- Utku Horzum
- Department of Basic Oncology, Hacettepe University Cancer Institute, Ankara, Turkey
- Division of Molecular Pathophysiology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Hamdullah Yanik
- Department of Basic Oncology, Hacettepe University Cancer Institute, Ankara, Turkey
| | - Ekim Z Taskiran
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Gunes Esendagli
- Department of Basic Oncology, Hacettepe University Cancer Institute, Ankara, Turkey
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14
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Rajasekaran K, Guan X, Tafazzol A, Hamidi H, Darwish M, Yadav M. Tetramer-aided sorting and single-cell RNA sequencing facilitate transcriptional profiling of antigen-specific CD8+ T cells. Transl Oncol 2022; 27:101559. [PMID: 36279715 PMCID: PMC9594627 DOI: 10.1016/j.tranon.2022.101559] [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: 07/28/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent advances in single-cell technologies and an improved understanding of tumor antigens have empowered researchers to investigate tumor antigen-specific CD8+ T cells at the single-cell level. Peptide-MHC I tetramers are often utilized to enrich antigen-specific CD8+ T cells, which however, introduces the undesired risk of altering their clonal distribution or their transcriptional state. This study addresses the feasibility of utilizing tetramers to enrich antigen-specific CD8+ T cells for single-cell analysis. METHODS HLA-A*02:01-restricted human cytomegalovirus (CMV) pp65 peptide-specific CD8+ T cells were used as a model for analyzing antigen-specific CD8+ T cells. Single-cell RNA sequencing and TCR sequencing were performed to compare the frequency and gene expression profile of pp65-specific TCR clones between tetramer-sorted, unstimulated- and tetramer-stimulated total CD8+ T cells. RESULTS The relative frequency of pp65-specific TCR clones and their transcriptional profile remained largely unchanged following tetramer-based sorting. In contrast, tetramer-mediated stimulation of CD8+ T cells resulted in significant gene expression changes in pp65-specific CD8+ T cells. An Antigen-Specific Response (ASR) gene signature was derived from tetramer-stimulated pp65-specific CD8+ T cells. The ASR signature had a predictive value and was significantly associated with progression free survival in lung cancer patients treated with anti-PD-L1, anti-VEGF, chemotherapy combination (NCT02366143). The predictive power of the ASR signature was independent of the conventional CD8 effector signature. CONCLUSIONS Our findings validate the approach of enriching antigen-specific CD8+ T cells through tetramer-aided Fluorescence-Activated Cell Sorting (FACS) sorting for single-cell analysis and also identifies an ASR gene signature that has value in predicting response to cancer immunotherapy.
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15
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Borchmann S, Selenz C, Lohmann M, Ludwig H, Gassa A, Brägelmann J, Lohneis P, Meder L, Mattlener J, Breid S, Nill M, Fassunke J, Wisdom AJ, Compes A, Gathof B, Alakus H, Kirsch D, Hekmat K, Büttner R, Reinhardt HC, Hallek M, Ullrich RT. Tripartite antigen-agnostic combination immunotherapy cures established poorly immunogenic tumors. J Immunother Cancer 2022; 10:e004781. [PMID: 36223955 PMCID: PMC9562723 DOI: 10.1136/jitc-2022-004781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Single-agent immunotherapy has shown remarkable efficacy in selected cancer entities and individual patients. However, most patients fail to respond. This is likely due to diverse immunosuppressive mechanisms acting in a concerted way to suppress the host anti-tumor immune response. Combination immunotherapy approaches that are effective in such poorly immunogenic tumors mostly rely on precise knowledge of antigenic determinants on tumor cells. Creating an antigen-agnostic combination immunotherapy that is effective in poorly immunogenic tumors for which an antigenic determinant is not known is a major challenge. METHODS We use multiple cell line and poorly immunogenic syngeneic, autochthonous, and autologous mouse models to evaluate the efficacy of a novel combination immunotherapy named tripartite immunotherapy (TRI-IT). To elucidate TRI-ITs mechanism of action we use immune cell depletions and comprehensive tumor and immune infiltrate characterization by flow cytometry, RNA sequencing and diverse functional assays. RESULTS We show that combined adoptive cellular therapy (ACT) with lymphokine-activated killer cells, cytokine-induced killer cells, Vγ9Vδ2-T-cells (γδ-T-cells) and T-cells enriched for tumor recognition (CTLs) display synergistic antitumor effects, which are further enhanced by cotreatment with anti-PD1 antibodies. Most strikingly, the full TRI-IT protocol, a combination of this ACT with anti-PD1 antibodies, local immunotherapy of agonists against toll-like receptor 3, 7 and 9 and pre-ACT lymphodepletion, eradicates and induces durable anti-tumor immunity in a variety of poorly immunogenic syngeneic, autochthonous, as well as autologous humanized patient-derived models. Mechanistically, we show that TRI-IT coactivates adaptive cellular and humoral, as well as innate antitumor immune responses to mediate its antitumor effect without inducing off-target toxicity. CONCLUSIONS Overall, TRI-IT is a novel, highly effective, antigen-agnostic, non-toxic combination immunotherapy. In this study, comprehensive insights into its preclinical efficacy, even in poorly immunogenic tumors, and mode of action are given, so that translation into clinical trials is the next step.
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Affiliation(s)
- Sven Borchmann
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Carolin Selenz
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Mia Lohmann
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
| | - Hanna Ludwig
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Asmae Gassa
- Department of Cardiothoracic Surgery, University of Cologne, Cologne, Germany
| | - Johannes Brägelmann
- Mildred Scheel School of Oncology, University Hospital Cologne, Medical Faculty, Cologne, Germany
| | - Philipp Lohneis
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Lydia Meder
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Julia Mattlener
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
| | - Sara Breid
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Marieke Nill
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Jana Fassunke
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Amy J Wisdom
- Department of Radiation Oncology and Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Anik Compes
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Birgit Gathof
- Institute of Transfusion Medicine, University of Cologne, Cologne, Germany
| | - Hakan Alakus
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - David Kirsch
- Department of Radiation Oncology and Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Khosro Hekmat
- Department of Cardiothoracic Surgery, University of Cologne, Cologne, Germany
| | | | - H Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen,University Duisburg-Essen, German Cancer Consortium (DKTK partner site Essen), Essen, Germany
| | - Michael Hallek
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
| | - Roland T Ullrich
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
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Andreatta M, Tjitropranoto A, Sherman Z, Kelly MC, Ciucci T, Carmona SJ. A CD4 + T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections. eLife 2022; 11:e76339. [PMID: 35829695 PMCID: PMC9323004 DOI: 10.7554/elife.76339] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
CD4+ T cells are critical orchestrators of immune responses against a large variety of pathogens, including viruses. While multiple CD4+ T cell subtypes and their key transcriptional regulators have been identified, there is a lack of consistent definition for CD4+ T cell transcriptional states. In addition, the progressive changes affecting CD4+ T cell subtypes during and after immune responses remain poorly defined. Using single-cell transcriptomics, we characterized the diversity of CD4+ T cells responding to self-resolving and chronic viral infections in mice. We built a comprehensive map of virus-specific CD4+ T cells and their evolution over time, and identified six major cell states consistently observed in acute and chronic infections. During the course of acute infections, T cell composition progressively changed from effector to memory states, with subtype-specific gene modules and kinetics. Conversely, in persistent infections T cells acquired distinct, chronicity-associated programs. By single-cell T cell receptor (TCR) analysis, we characterized the clonal structure of virus-specific CD4+ T cells across individuals. Virus-specific CD4+ T cell responses were essentially private across individuals and most T cells differentiated into both Tfh and Th1 subtypes irrespective of their TCR. Finally, we showed that our CD4+ T cell map can be used as a reference to accurately interpret cell states in external single-cell datasets across tissues and disease models. Overall, this study describes a previously unappreciated level of adaptation of the transcriptional states of CD4+ T cells responding to viruses and provides a new computational resource for CD4+ T cell analysis.
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Affiliation(s)
- Massimo Andreatta
- Department of Oncology, UNIL CHUV and Ludwig Institute for Cancer Research Lausanne, University of LausanneLausanneSwitzerland
- Agora Cancer Research CenterLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Ariel Tjitropranoto
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of RochesterRochesterUnited States
| | - Zachary Sherman
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of RochesterRochesterUnited States
| | - Michael C Kelly
- Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research IncFrederickUnited States
| | - Thomas Ciucci
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of RochesterRochesterUnited States
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Santiago J Carmona
- Department of Oncology, UNIL CHUV and Ludwig Institute for Cancer Research Lausanne, University of LausanneLausanneSwitzerland
- Agora Cancer Research CenterLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
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17
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Liu Q, Wang L, Lin H, Wang Z, Wu J, Guo J, Wen S, Ran L, Yue Z, Su X, Wu Q, Tang J, Li Z, Hu L, Xu L, Ye L, Huang Q. Tumor-Specific CD4+ T Cells Restrain Established Metastatic Melanoma by Developing Into Cytotoxic CD4– T Cells. Front Immunol 2022; 13:875718. [PMID: 35784297 PMCID: PMC9243303 DOI: 10.3389/fimmu.2022.875718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Cytotoxic CD8+ T cells are the main focus of efforts to understand anti-tumor immunity and immunotherapy. The adoptive transfer of tumor-reactive cytotoxic CD8+ T lymphocytes expanded and differentiated in vitro has long been considered the primary strategy in adaptive anti-tumor immunity, however, the majority of the transferred tumor antigen-specific CD8+ T cells differentiated into CD39+CD69+ exhausted progenies, limiting its effects in repressing tumor growth. Contrarily, less attention has been addressed to the role of CD4+ T cells during tumorigenesis. Using a mouse model of metastatic melanoma, we found that transferring tumor-specific CD4+ T cells into recipients induces substantial regression of the established metastatic tumors. Notably, in vitro activated CD4+ T cells developed into cytotoxic CD4- T cells in vivo and get exhausted gradually. The blockade of PD-L1 signaling resulted in an expansion of tumor specific CD4+ T cells, which could better control the established metastatic melanoma. Moreover, the tumor-specific memory CD4+ T cell can prevent mice from tumor metastasis, and the tumor-specific effector CD4+ T cells can also mitigate the established metastatic tumor. Overall, our findings suggest a novel mechanism of CD4+ T cells in curtailing tumor metastasis and confirm their therapeutic role in combination with PD-L1 blockade in cancer immunotherapy. Hence, a better understanding of cytotoxic CD4- T cell-mediated tumor regression could provide an alternative choice for patients exhibiting suboptimal or no response to CD8+ T cell-based immunotherapies.
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Affiliation(s)
- Qiao Liu
- Institute of Immunology, Third Military Medical University, Chongqing, China
- *Correspondence: Qiao Liu, ; Lilin Ye, ; ; Qizhao Huang,
| | - Lisha Wang
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Huayu Lin
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Zhiming Wang
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Jialin Wu
- Department of Respiratory Disease, General Hospital of Xinjiang Military Command, Urumqi, China
| | - Junyi Guo
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shuqiong Wen
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ling Ran
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Zhengliang Yue
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Xingxing Su
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Qing Wu
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Jianfang Tang
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Zhirong Li
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Li Hu
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Lifan Xu
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Lilin Ye
- Institute of Immunology, Third Military Medical University, Chongqing, China
- *Correspondence: Qiao Liu, ; Lilin Ye, ; ; Qizhao Huang,
| | - Qizhao Huang
- Institute of Immunology, Third Military Medical University, Chongqing, China
- Guangdong Provincial Key Laboratory of Immune Regulation and Immunotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- *Correspondence: Qiao Liu, ; Lilin Ye, ; ; Qizhao Huang,
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18
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Brown M. Engaging Pattern Recognition Receptors in Solid Tumors to Generate Systemic Antitumor Immunity. Cancer Treat Res 2022; 183:91-129. [PMID: 35551657 DOI: 10.1007/978-3-030-96376-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Malignant tumors frequently exploit innate immunity to evade immune surveillance. The priming, function, and polarization of antitumor immunity fundamentally depends upon context provided by the innate immune system, particularly antigen presenting cells. Such context is determined in large part by sensing of pathogen specific and damage associated features by pathogen recognition receptors (PRRs). PRR activation induces the delivery of T cell priming cues (e.g. chemokines, co-stimulatory ligands, and cytokines) from antigen presenting cells, playing a decisive role in the cancer immunity cycle. Indeed, endogenous PRR activation within the tumor microenvironment (TME) has been shown to generate spontaneous antitumor T cell immunity, e.g., cGAS-STING mediated activation of antigen presenting cells after release of DNA from dying tumor cells. Thus, instigating intratumor PRR activation, particularly with the goal of generating Th1-promoting inflammation that stokes endogenous priming of antitumor CD8+ T cells, is a growing area of clinical investigation. This approach is analogous to in situ vaccination, ultimately providing a personalized antitumor response against relevant tumor associated antigens. Here I discuss clinical stage intratumor modalities that function via activation of PRRs. These approaches are being tested in various solid tumor contexts including melanoma, colorectal cancer, glioblastoma, head and neck squamous cell carcinoma, bladder cancer, and pancreatic cancer. Their mechanism (s) of action relative to other immunotherapy approaches (e.g., antigen-defined cancer vaccines, CAR T cells, dendritic cell vaccines, and immune checkpoint blockade), as well as their potential to complement these approaches are also discussed. Examples to be reviewed include TLR agonists, STING agonists, RIG-I agonists, and attenuated or engineered viruses and bacterium. I also review common key requirements for effective in situ immune activation, discuss differences between various strategies inclusive of mechanisms that may ultimately limit or preclude antitumor efficacy, and provide a summary of relevant clinical data.
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Affiliation(s)
- Michael Brown
- Department of Neurosurgery, Duke University, Durham, NC, USA.
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19
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Vithanage GVRK, Wei HC, Jang SRJ. Bistability in a model of tumor-immune system interactions with an oncolytic viral therapy. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:1559-1587. [PMID: 35135217 DOI: 10.3934/mbe.2022072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A mathematical model of tumor-immune system interactions with an oncolytic virus therapy for which the immune system plays a twofold role against cancer cells is derived. The immune cells can kill cancer cells but can also eliminate viruses from the therapy. In addition, immune cells can either be stimulated to proliferate or be impaired to reduce their growth by tumor cells. It is shown that if the tumor killing rate by immune cells is above a critical value, the tumor can be eradicated for all sizes, where the critical killing rate depends on whether the immune system is immunosuppressive or proliferative. For a reduced tumor killing rate with an immunosuppressive immune system, that bistability exists in a large parameter space follows from our numerical bifurcation study. Depending on the tumor size, the tumor can either be eradicated or be reduced to a size less than its carrying capacity. However, reducing the viral killing rate by immune cells always increases the effectiveness of the viral therapy. This reduction may be achieved by manipulating certain genes of viruses via genetic engineering or by chemical modification of viral coat proteins to avoid detection by the immune cells.
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Affiliation(s)
- G V R K Vithanage
- Department of Mathematics and Statistics, Texas Tech University, Texas 79409, USA
| | - Hsiu-Chuan Wei
- Department of Applied Mathematics, Feng Chia University, Taichung 40724, Taiwan
| | - Sophia R-J Jang
- Department of Mathematics and Statistics, Texas Tech University, Texas 79409, USA
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20
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Cui C, Wang J, Fagerberg E, Chen PM, Connolly KA, Damo M, Cheung JF, Mao T, Askari AS, Chen S, Fitzgerald B, Foster GG, Eisenbarth SC, Zhao H, Craft J, Joshi NS. Neoantigen-driven B cell and CD4 T follicular helper cell collaboration promotes anti-tumor CD8 T cell responses. Cell 2021; 184:6101-6118.e13. [PMID: 34852236 PMCID: PMC8671355 DOI: 10.1016/j.cell.2021.11.007] [Citation(s) in RCA: 207] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 07/21/2021] [Accepted: 11/05/2021] [Indexed: 12/31/2022]
Abstract
CD4 T follicular helper (TFH) cells support B cells, which are critical for germinal center (GC) formation, but the importance of TFH-B cell interactions in cancer is unclear. We found enrichment of TFH cell transcriptional signature correlates with GC B cell signature and with prolonged survival in individuals with lung adenocarcinoma (LUAD). We further developed a murine LUAD model in which tumor cells express B cell- and T cell-recognized neoantigens. Interactions between tumor-specific TFH and GC B cells, as well as interleukin (IL)-21 primarily produced by TFH cells, are necessary for tumor control and effector CD8 T cell function. Development of TFH cells requires B cells and B cell-recognized neoantigens. Thus, tumor neoantigens can regulate the fate of tumor-specific CD4 T cells by facilitating their interactions with tumor-specific B cells, which in turn promote anti-tumor immunity by enhancing CD8 T cell effector functions.
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Affiliation(s)
- Can Cui
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jiawei Wang
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06510, USA
| | - Eric Fagerberg
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ping-Min Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Kelli A Connolly
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Martina Damo
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Julie F Cheung
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Adnan S Askari
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shuting Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Brittany Fitzgerald
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Gena G Foster
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Stephanie C Eisenbarth
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Internal Medicine (Rheumatology, Allergy and Immunology), Yale University School of Medicine, New Haven, CT 06520, USA; Department of Lab Medicine, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - Joseph Craft
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Internal Medicine (Rheumatology, Allergy and Immunology), Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Nikhil S Joshi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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21
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Julé AM, Hoyt KJ, Wei K, Gutierrez-Arcelus M, Taylor ML, Ng J, Lederer JA, Case SM, Chang MH, Cohen EM, Dedeoglu F, Hazen MM, Hausmann JS, Halyabar O, Janssen E, Lo J, Lo MS, Meidan E, Roberts JE, Son MBF, Sundel RP, Lee PY, Chatila T, Nigrovic PA, Henderson LA. Th1 polarization defines the synovial fluid T cell compartment in oligoarticular juvenile idiopathic arthritis. JCI Insight 2021; 6:e149185. [PMID: 34403374 PMCID: PMC8492302 DOI: 10.1172/jci.insight.149185] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022] Open
Abstract
Oligoarticular juvenile idiopathic arthritis (oligo JIA) is the most common form of chronic inflammatory arthritis in children, yet the cause of this disease remains unknown. To understand immune responses in oligo JIA, we immunophenotyped synovial fluid T cells with flow cytometry, bulk RNA-Seq, single-cell RNA-Seq (scRNA-Seq), DNA methylation studies, and Treg suppression assays. In synovial fluid, CD4+, CD8+, and γδ T cells expressed Th1-related markers, whereas Th17 cells were not enriched. Th1 skewing was prominent in CD4+ T cells, including Tregs, and was associated with severe disease. Transcriptomic studies confirmed a Th1 signature in CD4+ T cells from synovial fluid. The regulatory gene expression signature was preserved in Tregs, even those exhibiting Th1 polarization. These Th1-like Tregs maintained Treg-specific methylation patterns and suppressive function, supporting the stability of this Treg population in the joint. Although synovial fluid CD4+ T cells displayed an overall Th1 phenotype, scRNA-Seq uncovered heterogeneous effector and regulatory subpopulations, including IFN-induced Tregs, peripheral helper T cells, and cytotoxic CD4+ T cells. In conclusion, oligo JIA is characterized by Th1 polarization that encompasses Tregs but does not compromise their regulatory identity. Targeting Th1-driven inflammation and augmenting Treg function may represent important therapeutic approaches in oligo JIA.
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Affiliation(s)
- Amélie M. Julé
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kacie J. Hoyt
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Maria Gutierrez-Arcelus
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Maria L. Taylor
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Julie Ng
- Division of Pulmonary and Critical Care Medicine, and
| | - James A. Lederer
- Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Siobhan M. Case
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Margaret H. Chang
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ezra M. Cohen
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Fatma Dedeoglu
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Melissa M. Hazen
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan S. Hausmann
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Olha Halyabar
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Erin Janssen
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey Lo
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mindy S. Lo
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Esra Meidan
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jordan E. Roberts
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mary Beth F. Son
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Robert P. Sundel
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pui Y. Lee
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Talal Chatila
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Peter A. Nigrovic
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lauren A. Henderson
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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22
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Madhok A, Bhat SA, Philip CS, Sureshbabu SK, Chiplunkar S, Galande S. Transcriptome Signature of Vγ9Vδ2 T Cells Treated With Phosphoantigens and Notch Inhibitor Reveals Interplay Between TCR and Notch Signaling Pathways. Front Immunol 2021; 12:660361. [PMID: 34526984 PMCID: PMC8435775 DOI: 10.3389/fimmu.2021.660361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
Gamma delta (γδ) T cells, especially the Vγ9Vδ2 subtype, have been implicated in cancer therapy and thus have earned the spotlight in the past decade. Although one of the most important properties of γδ T cells is their activation by phosphoantigens, which are intermediates of the Mevalonate and Rohmer pathway of isoprenoid biosynthesis, such as IPP and HDMAPP, respectively, the global effects of such treatments on Vγ9Vδ2 T cells remain elusive. Here, we used the high-throughput transcriptomics approach to elucidate the transcriptional changes in human Vγ9Vδ2 T cells upon HDMAPP, IPP, and anti-CD3 treatments in combination with interleukin 2 (IL2) cytokine stimulation. These activation treatments exhibited a dramatic surge in transcription with distinctly enriched pathways. We further assessed the transcriptional dynamics upon inhibition of Notch signaling coupled with activation treatments. We observed that the metabolic processes are most affected upon Notch inhibition via GSI-X. The key effector genes involved in gamma-delta cytotoxic function were downregulated upon Notch blockade even in combination with activation treatment, suggesting a transcriptional crosstalk between T-cell receptor (TCR) signaling and Notch signaling in Vγ9Vδ2 T cells. Collectively, we demonstrate the effect of the activation of TCR signaling by phosphoantigens or anti-CD3 on the transcriptional status of Vγ9Vδ2 T cells along with IL2 stimulation. We further show that the blockade of Notch signaling antagonistically affects this activation.
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Affiliation(s)
- Ayush Madhok
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science and Education and Research (IISER), Pune, India
| | - Sajad Ahmad Bhat
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Chinna Susan Philip
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Shalini Kashipathi Sureshbabu
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Shubhada Chiplunkar
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Sanjeev Galande
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science and Education and Research (IISER), Pune, India.,Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
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23
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Methods for Characterization of Senescent Circulating and Tumor-Infiltrating T-Cells: An Overview from Multicolor Flow Cytometry to Single-Cell RNA Sequencing. Methods Mol Biol 2021; 2325:79-95. [PMID: 34053052 DOI: 10.1007/978-1-0716-1507-2_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Immunosenescence is the general term used to describe the aging-associated decline of immunological function that explains the higher susceptibility to infectious diseases and cancer, increased autoimmunity, or the reduced effectiveness of vaccinations. Senescence of CD8+ T-cells has been described in all these conditions.The most important classical markers of T senescent cells are the cell cycle inhibitors p16ink4a, p21, and p53, together with positivity for SA-βgal expression and the acquirement of a peculiar IFNγ -based secretory phenotype commonly defined SASP (Senescence Associated Secretory Phenotype). Other surface markers are the CD28 and CD27 loss together with gain of expression of CD45RA, CD57, TIGIT, and/or KLRG1. However, this characterization could not be sufficient to distinguish from truly senescent cells and exhausted T-cells. Furthermore, more complexity is added by the wide heterogeneity of T-cells subset in aged individuals or in the tumor microenvironment. A combined analysis by multicolor flow cytometry for surface and intracellular markers integrated with gene-expression arrays and single-cell RNA sequencing is required to develop effective interventions for therapeutic modulation of specific T-cell subsets. The RNASeq offers the great possibility to reveal at single-cell resolution the exact molecular hallmarks of senescent CD8+ T-cells without the limitations of bulk analysis. Furthermore, the comprehensive integration of multidimensional approaches (genomics, epigenomics, proteomics, metabolomics) will increase our global understanding of how immunosenescence of T-cells is interlinked to human aging.
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24
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Ma J, Tibbitt CA, Georén SK, Christian M, Murrell B, Cardell LO, Bachert C, Coquet JM. Single-cell analysis pinpoints distinct populations of cytotoxic CD4 + T cells and an IL-10 +CD109 + T H2 cell population in nasal polyps. Sci Immunol 2021; 6:6/62/eabg6356. [PMID: 34389612 DOI: 10.1126/sciimmunol.abg6356] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/02/2021] [Indexed: 12/27/2022]
Abstract
Chronic rhinosinusitis with nasal polyps (CRSwNP) is characterized by a chronic inflammatory process often associated with comorbid asthma. In this study, we analyzed the transcriptomes of single T helper (TH) cells from nasal polyps of patients with CRSwNP and validated these findings using multiparameter flow cytometry. Polyp tissue contained suppressive T regulatory (Treg) cells, TH2 cells, type 2 innate lymphoid cells, and three transcriptionally distinct subsets of cytotoxic CD4+ T cells (CD4+ CTL). GATA3 expression was a feature of polyp Treg cells, whereas TH2 cells highly expressed TCN1, CD200R, and HPGDS and were enriched for genes involved in lipid metabolism. Only a portion of polyp TH2 cells expressed the prostaglandin D2 receptor CRTH2, whereas a subpopulation of CD109+CRTH2- TH2 cells expressed mRNA for common inhibitor receptors including LAG3 and TIM3 and produced IL-10. Together, we resolved the complexity of TH cells in patients with CRSwNP, identifying several distinct clusters of CD4+ CTL and a population of CD109+CRTH2- TH2 cells with putative regulatory potential.
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Affiliation(s)
- Junjie Ma
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Christopher A Tibbitt
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Susanna Kumlien Georén
- Division of ENT Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.,Department of Otorhinolaryngology, Karolinska University Hospital, Stockholm, Sweden
| | - Murray Christian
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Lars-Olaf Cardell
- Division of ENT Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.,Department of Otorhinolaryngology, Karolinska University Hospital, Stockholm, Sweden
| | - Claus Bachert
- Division of ENT Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.,Upper Airways Research Laboratory and Department of Oto-Rhino-Laryngology, Ghent University, Ghent, Belgium.,First Affiliated Hospital, Sun Yat-sen University, International Airway Research Center, Guangzhou, China
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.
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25
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Lei Y, Tang R, Xu J, Wang W, Zhang B, Liu J, Yu X, Shi S. Applications of single-cell sequencing in cancer research: progress and perspectives. J Hematol Oncol 2021; 14:91. [PMID: 34108022 PMCID: PMC8190846 DOI: 10.1186/s13045-021-01105-2] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023] Open
Abstract
Single-cell sequencing, including genomics, transcriptomics, epigenomics, proteomics and metabolomics sequencing, is a powerful tool to decipher the cellular and molecular landscape at a single-cell resolution, unlike bulk sequencing, which provides averaged data. The use of single-cell sequencing in cancer research has revolutionized our understanding of the biological characteristics and dynamics within cancer lesions. In this review, we summarize emerging single-cell sequencing technologies and recent cancer research progress obtained by single-cell sequencing, including information related to the landscapes of malignant cells and immune cells, tumor heterogeneity, circulating tumor cells and the underlying mechanisms of tumor biological behaviors. Overall, the prospects of single-cell sequencing in facilitating diagnosis, targeted therapy and prognostic prediction among a spectrum of tumors are bright. In the near future, advances in single-cell sequencing will undoubtedly improve our understanding of the biological characteristics of tumors and highlight potential precise therapeutic targets for patients.
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Affiliation(s)
- Yalan Lei
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Rong Tang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wei Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Bo Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jiang Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China. .,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China. .,Pancreatic Cancer Institute, Fudan University, Shanghai, China.
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China. .,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China. .,Pancreatic Cancer Institute, Fudan University, Shanghai, China.
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26
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Andreatta M, Carmona SJ. STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data. Bioinformatics 2021; 37:882-884. [PMID: 32845323 PMCID: PMC8098019 DOI: 10.1093/bioinformatics/btaa755] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/19/2020] [Indexed: 12/03/2022] Open
Abstract
Summary STACAS is a computational method for the identification of integration anchors in the Seurat environment, optimized for the integration of single-cell (sc) RNA-seq datasets that share only a subset of cell types. We demonstrate that by (i) correcting batch effects while preserving relevant biological variability across datasets, (ii) filtering aberrant integration anchors with a quantitative distance measure and (iii) constructing optimal guide trees for integration, STACAS can accurately align scRNA-seq datasets composed of only partially overlapping cell populations. Availability and implementation Source code and R package available at https://github.com/carmonalab/STACAS; Docker image available at https://hub.docker.com/repository/docker/mandrea1/stacas_demo.
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Affiliation(s)
- Massimo Andreatta
- Ludwig Institute for Cancer Research Lausanne, University of Lausanne, CH-1066 Epalinges, Switzerland.,Department of Oncology, CHUV, UNIL CHUV, CH-1066 Epalinges, Lausanne, Switzerland.,University of Lausanne, Lausanne, Switzerland
| | - Santiago J Carmona
- Ludwig Institute for Cancer Research Lausanne, University of Lausanne, CH-1066 Epalinges, Switzerland.,Department of Oncology, CHUV, UNIL CHUV, CH-1066 Epalinges, Lausanne, Switzerland.,University of Lausanne, Lausanne, Switzerland
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27
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Schreiber S, Hammers CM, Kaasch AJ, Schraven B, Dudeck A, Kahlfuss S. Metabolic Interdependency of Th2 Cell-Mediated Type 2 Immunity and the Tumor Microenvironment. Front Immunol 2021; 12:632581. [PMID: 34135885 PMCID: PMC8201396 DOI: 10.3389/fimmu.2021.632581] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
The function of T cells is critically dependent on their ability to generate metabolic building blocks to fulfil energy demands for proliferation and consecutive differentiation into various T helper (Th) cells. Th cells then have to adapt their metabolism to specific microenvironments within different organs during physiological and pathological immune responses. In this context, Th2 cells mediate immunity to parasites and are involved in the pathogenesis of allergic diseases including asthma, while CD8+ T cells and Th1 cells mediate immunity to viruses and tumors. Importantly, recent studies have investigated the metabolism of Th2 cells in more detail, while others have studied the influence of Th2 cell-mediated type 2 immunity on the tumor microenvironment (TME) and on tumor progression. We here review recent findings on the metabolism of Th2 cells and discuss how Th2 cells contribute to antitumor immunity. Combining the evidence from both types of studies, we provide here for the first time a perspective on how the energy metabolism of Th2 cells and the TME interact. Finally, we elaborate how a more detailed understanding of the unique metabolic interdependency between Th2 cells and the TME could reveal novel avenues for the development of immunotherapies in treating cancer.
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Affiliation(s)
- Simon Schreiber
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | | | - Achim J. Kaasch
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI-3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Burkhart Schraven
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI-3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Anne Dudeck
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI-3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Sascha Kahlfuss
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI-3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
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28
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Andreatta M, Corria-Osorio J, Müller S, Cubas R, Coukos G, Carmona SJ. Interpretation of T cell states from single-cell transcriptomics data using reference atlases. Nat Commun 2021; 12:2965. [PMID: 34017005 PMCID: PMC8137700 DOI: 10.1038/s41467-021-23324-4] [Citation(s) in RCA: 198] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 04/22/2021] [Indexed: 02/07/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has revealed an unprecedented degree of immune cell diversity. However, consistent definition of cell subtypes and cell states across studies and diseases remains a major challenge. Here we generate reference T cell atlases for cancer and viral infection by multi-study integration, and develop ProjecTILs, an algorithm for reference atlas projection. In contrast to other methods, ProjecTILs allows not only accurate embedding of new scRNA-seq data into a reference without altering its structure, but also characterizing previously unknown cell states that "deviate" from the reference. ProjecTILs accurately predicts the effects of cell perturbations and identifies gene programs that are altered in different conditions and tissues. A meta-analysis of tumor-infiltrating T cells from several cohorts reveals a strong conservation of T cell subtypes between human and mouse, providing a consistent basis to describe T cell heterogeneity across studies, diseases, and species.
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Affiliation(s)
- Massimo Andreatta
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, Lausanne, Epalinges, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jesus Corria-Osorio
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, Lausanne, Epalinges, Switzerland
| | - Sören Müller
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA
| | - Rafael Cubas
- Department of Translational Oncology, Genentech, South San Francisco, CA, USA
| | - George Coukos
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, Lausanne, Epalinges, Switzerland
| | - Santiago J Carmona
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, Lausanne, Epalinges, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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29
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Baseline Frequency of Inflammatory Cxcl9-Expressing Tumor-Associated Macrophages Predicts Response to Avelumab Treatment. Cell Rep 2021; 32:107873. [PMID: 32640238 DOI: 10.1016/j.celrep.2020.107873] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 03/30/2020] [Accepted: 06/15/2020] [Indexed: 12/25/2022] Open
Abstract
The tumor microenvironment is rich with immune-suppressive macrophages that are associated with cancer progression and resistance to immune checkpoint therapy. Using pre-treatment tumor biopsies complemented with single-cell RNA sequencing (RNA-seq), we characterize intratumoral immune heterogeneity to unveil potential mechanisms of resistance to avelumab (anti-PD-L1). We identify a proinflammatory F480+MHCII+Ly6Clo macrophage population that is associated with response rather than resistance to avelumab. These macrophages are the primary source of the interferon-inducible chemokine Cxcl9, which facilitates the recruitment of protective Cxcr3+ T cells. Consequently, the efficacy of avelumab in mouse tumor models is dependent on Cxcr3 and Cxcl9, and baseline levels of Cxcl9 in patients treated with avelumab are associated with clinical response and overall survival. These data suggest that, within the broadly immune-suppressive macrophage compartment, a pro-inflammatory population exists that promotes responsiveness to PD-L1 blockade.
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30
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Blass E, Ott PA. Advances in the development of personalized neoantigen-based therapeutic cancer vaccines. Nat Rev Clin Oncol 2021; 18:215-229. [PMID: 33473220 PMCID: PMC7816749 DOI: 10.1038/s41571-020-00460-2] [Citation(s) in RCA: 445] [Impact Index Per Article: 148.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2020] [Indexed: 01/31/2023]
Abstract
Within the past decade, the field of immunotherapy has revolutionized the treatment of many cancers with the development and regulatory approval of various immune-checkpoint inhibitors and chimeric antigen receptor T cell therapies in diverse indications. Another promising approach to cancer immunotherapy involves the use of personalized vaccines designed to trigger de novo T cell responses against neoantigens, which are highly specific to tumours of individual patients, in order to amplify and broaden the endogenous repertoire of tumour-specific T cells. Results from initial clinical studies of personalized neoantigen-based vaccines, enabled by the availability of rapid and cost-effective sequencing and bioinformatics technologies, have demonstrated robust tumour-specific immunogenicity and preliminary evidence of antitumour activity in patients with melanoma and other cancers. Herein, we provide an overview of the complex process that is necessary to generate a personalized neoantigen vaccine, review the types of vaccine-induced T cells that are found within tumours and outline strategies to enhance the T cell responses. In addition, we discuss the current status of clinical studies testing personalized neoantigen vaccines in patients with cancer and considerations for future clinical investigation of this novel, individualized approach to immunotherapy.
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Affiliation(s)
- Eryn Blass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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31
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ElTanbouly MA, Noelle RJ. Rethinking peripheral T cell tolerance: checkpoints across a T cell's journey. Nat Rev Immunol 2021; 21:257-267. [PMID: 33077935 DOI: 10.1038/s41577-020-00454-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2020] [Indexed: 01/10/2023]
Abstract
Following their exit from the thymus, T cells are endowed with potent effector functions but must spare host tissue from harm. The fate of these cells is dictated by a series of checkpoints that regulate the quality and magnitude of T cell-mediated immunity, known as tolerance checkpoints. In this Perspective, we discuss the mediators and networks that control the six main peripheral tolerance checkpoints throughout the life of a T cell: quiescence, ignorance, anergy, exhaustion, senescence and death. At the naive T cell stage, two intrinsic checkpoints that actively maintain tolerance are quiescence and ignorance. In the presence of co-stimulation-deficient T cell activation, anergy is a dominant hallmark that mandates T cell unresponsiveness. When T cells are successfully stimulated and reach the effector stage, exhaustion and senescence can limit excessive inflammation and prevent immunopathology. At every stage of the T cell's journey, cell death exists as a checkpoint to limit clonal expansion and to terminate unrestrained responses. Here, we compare and contrast the T cell tolerance checkpoints and discuss their specific roles, with the aim of providing an integrated view of T cell peripheral tolerance and fate regulation.
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Affiliation(s)
- Mohamed A ElTanbouly
- Department of Microbiology and Immunology, Geisel School of Medicine, Norris Cotton Cancer Center, Dartmouth College, Hanover, NH, USA
| | - Randolph J Noelle
- Department of Microbiology and Immunology, Geisel School of Medicine, Norris Cotton Cancer Center, Dartmouth College, Hanover, NH, USA.
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32
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Blass E, Ott PA. Advances in the development of personalized neoantigen-based therapeutic cancer vaccines. Nat Rev Clin Oncol 2021. [PMID: 33473220 DOI: 10.1038/s41571-020-00460-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Within the past decade, the field of immunotherapy has revolutionized the treatment of many cancers with the development and regulatory approval of various immune-checkpoint inhibitors and chimeric antigen receptor T cell therapies in diverse indications. Another promising approach to cancer immunotherapy involves the use of personalized vaccines designed to trigger de novo T cell responses against neoantigens, which are highly specific to tumours of individual patients, in order to amplify and broaden the endogenous repertoire of tumour-specific T cells. Results from initial clinical studies of personalized neoantigen-based vaccines, enabled by the availability of rapid and cost-effective sequencing and bioinformatics technologies, have demonstrated robust tumour-specific immunogenicity and preliminary evidence of antitumour activity in patients with melanoma and other cancers. Herein, we provide an overview of the complex process that is necessary to generate a personalized neoantigen vaccine, review the types of vaccine-induced T cells that are found within tumours and outline strategies to enhance the T cell responses. In addition, we discuss the current status of clinical studies testing personalized neoantigen vaccines in patients with cancer and considerations for future clinical investigation of this novel, individualized approach to immunotherapy.
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Affiliation(s)
- Eryn Blass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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33
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Wang Y, Chen Z, Wang T, Guo H, Liu Y, Dang N, Hu S, Wu L, Zhang C, Ye K, Shi B. A novel CD4+ CTL subtype characterized by chemotaxis and inflammation is involved in the pathogenesis of Graves' orbitopathy. Cell Mol Immunol 2021; 18:735-745. [PMID: 33514849 PMCID: PMC8027210 DOI: 10.1038/s41423-020-00615-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 02/08/2023] Open
Abstract
Graves' orbitopathy (GO), the most severe manifestation of Graves' hyperthyroidism (GH), is an autoimmune-mediated inflammatory disorder, and treatments often exhibit a low efficacy. CD4+ T cells have been reported to play vital roles in GO progression. To explore the pathogenic CD4+ T cell types that drive GO progression, we applied single-cell RNA sequencing (scRNA-Seq), T cell receptor sequencing (TCR-Seq), flow cytometry, immunofluorescence and mixed lymphocyte reaction (MLR) assays to evaluate CD4+ T cells from GO and GH patients. scRNA-Seq revealed the novel GO-specific cell type CD4+ cytotoxic T lymphocytes (CTLs), which are characterized by chemotactic and inflammatory features. The clonal expansion of this CD4+ CTL population, as demonstrated by TCR-Seq, along with their strong cytotoxic response to autoantigens, localization in orbital sites, and potential relationship with disease relapse provide strong evidence for the pathogenic roles of GZMB and IFN-γ-secreting CD4+ CTLs in GO. Therefore, cytotoxic pathways may become potential therapeutic targets for GO.
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Affiliation(s)
- Yue Wang
- grid.452438.cDepartment of Endocrinology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China ,grid.43169.390000 0001 0599 1243MOE Key Lab for Intelligent Networks & Networks Security, School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China ,grid.452438.cGenome Institute, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China ,grid.452438.cPrecision Medicine Center, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Ziyi Chen
- grid.452438.cDepartment of Endocrinology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Tingjie Wang
- grid.452438.cDepartment of Endocrinology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China ,grid.43169.390000 0001 0599 1243MOE Key Lab for Intelligent Networks & Networks Security, School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
| | - Hui Guo
- grid.452438.cDepartment of Endocrinology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yufeng Liu
- grid.43169.390000 0001 0599 1243MOE Key Lab for Intelligent Networks & Networks Security, School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China ,grid.452438.cGenome Institute, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China ,grid.452438.cBioBank, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Ningxin Dang
- grid.452438.cGenome Institute, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Shiqian Hu
- grid.452438.cDepartment of Endocrinology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Liping Wu
- grid.452438.cDepartment of Endocrinology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Chengsheng Zhang
- grid.452438.cPrecision Medicine Center, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China ,grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Kai Ye
- grid.43169.390000 0001 0599 1243MOE Key Lab for Intelligent Networks & Networks Security, School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China ,grid.452438.cGenome Institute, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China ,grid.43169.390000 0001 0599 1243The School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Bingyin Shi
- grid.452438.cDepartment of Endocrinology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
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Abstract
Single-cell sequencing techniques enable the decades-old T helper subset dogma to be approached in an unsupervised manner, bringing nuances to the definition of known subsets, while simultaneously identifying interesting novel cell states.
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Affiliation(s)
| | - Maria Rescigno
- Humanitas Cinical and Research Center - IRCCS, Rozzano, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Enrico Lugli
- Humanitas Cinical and Research Center - IRCCS, Rozzano, Milan, Italy.
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35
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Guruprasad P, Lee YG, Kim KH, Ruella M. The current landscape of single-cell transcriptomics for cancer immunotherapy. J Exp Med 2021; 218:e20201574. [PMID: 33601414 PMCID: PMC7754680 DOI: 10.1084/jem.20201574] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/28/2020] [Accepted: 12/02/2020] [Indexed: 12/28/2022] Open
Abstract
Immunotherapies such as immune checkpoint blockade and adoptive cell transfer have revolutionized cancer treatment, but further progress is hindered by our limited understanding of tumor resistance mechanisms. Emerging technologies now enable the study of tumors at the single-cell level, providing unprecedented high-resolution insights into the genetic makeup of the tumor microenvironment and immune system that bulk genomics cannot fully capture. Here, we highlight the recent key findings of the use of single-cell RNA sequencing to deconvolute heterogeneous tumors and immune populations during immunotherapy. Single-cell RNA sequencing has identified new crucial factors and cellular subpopulations that either promote tumor progression or leave tumors vulnerable to immunotherapy. We anticipate that the strategic use of single-cell analytics will promote the development of the next generation of successful, rationally designed immunotherapeutics.
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Affiliation(s)
- Puneeth Guruprasad
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Department of Medicine, Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Yong Gu Lee
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Department of Medicine, Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Ki Hyun Kim
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Department of Medicine, Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Marco Ruella
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Department of Medicine, Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
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36
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Cardenas MA, Prokhnevska N, Kissick HT. Organized immune cell interactions within tumors sustain a productive T-cell response. Int Immunol 2020; 33:27-37. [PMID: 32827212 DOI: 10.1093/intimm/dxaa057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/18/2020] [Indexed: 12/11/2022] Open
Abstract
Tumor-infiltrating CD8 T cells are associated with improved patient survival and response to immunotherapy in various cancers. Persistent antigen leads to CD8 T-cell exhaustion, where proliferation/self-renewal and killing are divided within distinct subsets of CD8 T cells in the tumor. CD8 T-cell responses in chronic antigen settings must be maintained for long periods of time, suggesting that mechanisms that regulate chronic CD8 T-cell responses may differ from those in acute settings. Currently, factors that regulate the maintenance of stem-like CD8 T cells in the tumor or their differentiation into terminally differentiated cells are unknown. In this review, we discuss the role of dendritic cells in the activation and differentiation of CD8 T-cell subsets within secondary lymphoid tissue and tumors. In addition, we examine changes in CD4 T-cell differentiation in response to chronic antigens and consider how subset-specific mechanisms could assist the stem-like and terminally differentiated CD8 T-cell subsets. Finally, we highlight how tumor-infiltrating CD4 T cells and dendritic cells interact with CD8 T cells within organized lymphoid-like areas in the tumor and propose a CD8 T-cell differentiation model that requires the collaboration of CD4 T cells and dendritic cells. These organized interactions coordinate the anti-tumor response and control disease progression by mechanisms that regulate CD8 T-cell differentiation, which permit the maintenance of an effective balance of stem-like and terminally differentiated CD8 T cells.
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Affiliation(s)
| | | | - Haydn T Kissick
- Department of Urology, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA.,Emory Vaccine Centre, Atlanta, GA, USA
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37
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Immune Landscape in Tumor Microenvironment: Implications for Biomarker Development and Immunotherapy. Int J Mol Sci 2020; 21:ijms21155521. [PMID: 32752264 PMCID: PMC7432816 DOI: 10.3390/ijms21155521] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023] Open
Abstract
Integration of the tumor microenvironment as a fundamental part of the tumorigenic process has undoubtedly revolutionized our understanding of cancer biology. Increasing evidence indicates that neoplastic cells establish a dependency relationship with normal resident cells in the affected tissue and, furthermore, develop the ability to recruit new accessory cells that aid tumor development. In addition to normal stromal and tumor cells, this tumor ecosystem includes an infiltrated immune component that establishes complex interactions that have a critical effect during the natural history of the tumor. The process by which immune cells modulate tumor progression is known as immunoediting, a dynamic process that creates a selective pressure that finally leads to the generation of immune-resistant cells and the inability of the immune system to eradicate the tumor. In this context, the cellular and functional characterization of the immune compartment within the tumor microenvironment will help to understand tumor progression and, ultimately, will serve to create novel prognostic tools and improve patient stratification for cancer treatment. Here we review the impact of the immune system on tumor development, focusing particularly on its clinical implications and the current technologies used to analyze immune cell diversity within the tumor.
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Tang Y, He H, Hu P, Xu X. T lymphocytes in IgA nephropathy. Exp Ther Med 2020; 20:186-194. [PMID: 32509008 PMCID: PMC7271719 DOI: 10.3892/etm.2020.8673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 03/19/2020] [Indexed: 02/07/2023] Open
Abstract
Immunoglobulin A nephropathy (IgAN), the most common primary glomerulonephritis worldwide, is the main cause of end-stage renal disease. IgAN is characterized by the accumulation of immune complexes in the circulation, which contain abnormal levels of IgA. IgAN primarily results from galactose-deficient IgA1 (Gd-IgA1) and Gd-IgA1 deposition in the renal mesangium, causing local proliferation and matrix expansion. Gd-IgA1 has been confirmed as one of the key effectors in the pathogenesis of IgAN, but the origin of Gd-IgA1 is not clear. Recent studies have shown that Gd-IgA1 deposition could be the result of mucosally primed plasma cells and is associated with T cell dysregulation. T cells contribute to the IgA response and play an important role in the development of IgAN. In the present review, the latest discoveries regarding the role of T lymphocytes in the pathogenesis of IgAN have been summarized. Understanding these advances will allow novel therapeutic strategies for the treatment of IgAN.
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Affiliation(s)
- Yuyan Tang
- Department of Nephrology, Minhang Hospital, Fudan University, Shanghai 201199, P.R. China
| | - Haidong He
- Department of Nephrology, Minhang Hospital, Fudan University, Shanghai 201199, P.R. China
| | - Pin Hu
- Department of Nephrology, Minhang Hospital, Fudan University, Shanghai 201199, P.R. China
| | - Xudong Xu
- Department of Nephrology, Minhang Hospital, Fudan University, Shanghai 201199, P.R. China
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Gibellini L, De Biasi S, Porta C, Lo Tartaro D, Depenni R, Pellacani G, Sabbatini R, Cossarizza A. Single-Cell Approaches to Profile the Response to Immune Checkpoint Inhibitors. Front Immunol 2020; 11:490. [PMID: 32265933 PMCID: PMC7100547 DOI: 10.3389/fimmu.2020.00490] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/03/2020] [Indexed: 12/26/2022] Open
Abstract
Novel treatments based upon the use of immune checkpoint inhibitors have an impressive efficacy in different types of cancer. Unfortunately, most patients do not derive benefit or lasting responses, and the reasons for the lack of therapeutic success are not known. Over the past two decades, a pressing need to deeply profile either the tumor microenvironment or cells responsible for the immune response has led investigators to integrate data obtained from traditional approaches with those obtained with new, more sophisticated, single-cell technologies, including high parameter flow cytometry, single-cell sequencing and high resolution imaging. The introduction and use of these technologies had, and still have a prominent impact in the field of cancer immunotherapy, allowing delving deeper into the molecular and cellular crosstalk between cancer and immune system, and fostering the identification of predictive biomarkers of response. In this review, besides the molecular and cellular cancer-immune system interactions, we are discussing how cutting-edge single-cell approaches are helping to point out the heterogeneity of immune cells in the tumor microenvironment and in blood.
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Affiliation(s)
- Lara Gibellini
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Sara De Biasi
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Camillo Porta
- Department of Internal Medicine and Therapeutics, Division of Translational Oncology, IRCCS Istituti Clinici Scientifici Maugeri, University of Pavia, Pavia, Italy
| | - Domenico Lo Tartaro
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Roberta Depenni
- Department of Oncology, Hematology, University of Modena and Reggio Emilia, Modena, Italy
| | - Giovanni Pellacani
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Roberto Sabbatini
- Department of Oncology, Hematology, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy.,Section of Modena, Istituto Nazionale per le Ricerche Cardiovascolari, Bologna, Italy
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Wen M, Cai G, Ye J, Liu X, Ding H, Zeng H. Single-cell transcriptomics reveals the alteration of peripheral blood mononuclear cells driven by sepsis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:125. [PMID: 32175418 DOI: 10.21037/atm.2020.02.35] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background Sepsis is a serious systemic inflammatory response syndrome caused by infection, with an extremely high mortality rate. Peripheral blood mononuclear cells (PBMCs) played a key role in the immune response against infection, whose components and functions were altered radically in Sepsis. Here, we wondered to characterize the alteration of PBMCs in sepsis at the single-cell transcriptional level. Methods We isolated PBMCs from seven septic patients and four donors. Based on BD Rhapsody, PBMCs were generated by single-cell RNA sequencing, and cell types were clustered and named by unsupervised clustering and annotation analysis. Results PBMCs were profiled for 6 kinds of cell types, the biological properties of T cell and monocytes were shown in a detailed manner. We noticed that monocytes could be clustered into 6 subsets, with great heterogeneity in the alteration of composition, gene profile, and signaling pathways driven by sepsis. Moreover, the expression of representative genes was high associated with septic clinical indicators in clusters of monocytes, such as NEAT1. Conclusions Although the study was preliminary, we revealed sepsis-specific alteration of PBMCs and associated pathways. These results give a panoramic picture of PBMCs in composition, genes profiles, and pathway signatures that are driven by sepsis, which offers a unique perspective to understand disease progression or treatment in clinical practice.
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Affiliation(s)
- Miaoyun Wen
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China.,Department of Emergency and Critical Care Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Gengxin Cai
- School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Jingkun Ye
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xinqiang Liu
- Department of Emergency and Critical Care Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Hongguang Ding
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Hongke Zeng
- Department of Emergency and Critical Care Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China.,The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
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