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Longhini ALF, Fernández-Maestre I, Kennedy MC, Wereski MG, Mowla S, Xiao W, Lowe SW, Levine RL, Gardner R. Development of a customizable mouse backbone spectral flow cytometry panel to delineate immune cell populations in normal and tumor tissues. Front Immunol 2024; 15:1374943. [PMID: 38605953 PMCID: PMC11008467 DOI: 10.3389/fimmu.2024.1374943] [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: 01/23/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024] Open
Abstract
Introduction In vivo studies of cancer biology and assessment of therapeutic efficacy are critical to advancing cancer research and ultimately improving patient outcomes. Murine cancer models have proven to be an invaluable tool in pre-clinical studies. In this context, multi-parameter flow cytometry is a powerful method for elucidating the profile of immune cells within the tumor microenvironment and/or play a role in hematological diseases. However, designing an appropriate multi-parameter panel to comprehensively profile the increasing diversity of immune cells across different murine tissues can be extremely challenging. Methods To address this issue, we designed a panel with 13 fixed markers that define the major immune populations -referred to as the backbone panel- that can be profiled in different tissues but with the option to incorporate up to seven additional fluorochromes, including any marker specific to the study in question. Results This backbone panel maintains its resolution across different spectral flow cytometers and organs, both hematopoietic and non-hematopoietic, as well as tumors with complex immune microenvironments. Discussion Having a robust backbone that can be easily customized with pre-validated drop-in fluorochromes saves time and resources and brings consistency and standardization, making it a versatile solution for immuno-oncology researchers. In addition, the approach presented here can serve as a guide to develop similar types of customizable backbone panels for different research questions requiring high-parameter flow cytometry panels.
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Affiliation(s)
- Ana Leda F. Longhini
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, United States
| | - Inés Fernández-Maestre
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Margaret C. Kennedy
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Shoron Mowla
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Wenbin Xiao
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Scott W. Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Ross L. Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Rui Gardner
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, United States
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Zhu L, Wu J, Gao H, Wang T, Xiao G, Hu C, Lin Q, Zhou Q. Tumor immune microenvironment-modulated nanostrategy for the treatment of lung cancer metastasis. Chin Med J (Engl) 2023; 136:2787-2801. [PMID: 37442772 PMCID: PMC10686602 DOI: 10.1097/cm9.0000000000002525] [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: 03/16/2023] [Indexed: 07/15/2023] Open
Abstract
ABSTRACT As one of the most malignant tumors worldwide, lung cancer, fueled by metastasis, has shown rising mortality rates. However, effective clinical strategies aimed at preventing metastasis are lacking owing to its dynamic multi-step, complicated, and progressive nature. Immunotherapy has shown promise in treating cancer metastasis by reversing the immunosuppressive network of the tumor microenvironment. However, drug resistance inevitably develops due to inadequate delivery of immunostimulants and an uncontrolled immune response. Consequently, adverse effects occur, such as autoimmunity, from the non-specific immune activation and non-specific inflammation in off-target organs. Nanocarriers that improve drug solubility, permeability, stability, bioavailability, as well as sustained, controlled, and targeted delivery can effectively overcome drug resistance and enhance the therapeutic effect while reducing adverse effects. In particular, nanomedicine-based immunotherapy can be utilized to target tumor metastasis, presenting a promising therapeutic strategy for lung cancer. Nanotechnology strategies that boost the immunotherapy effect are classified based on the metastatic cascade related to the tumor immune microenvironment; the breaking away of primary tumors, circulating tumor cell dissemination, and premetastatic niche formation cause distant secondary site colonization. In this review, we focus on the opportunities and challenges of integrating immunotherapy with nanoparticle formulation to establish nanotechnology-based immunotherapy by modulating the tumor microenvironment for preclinical and clinical applications in the management of patients with metastatic lung cancer. We also discuss prospects for the emerging field and the clinical translation potential of these techniques.
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Affiliation(s)
- Lingling Zhu
- Lung Cancer Center, Lung Cancer Institute, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, College of Polymer Science and Engineering, Sichuan University, Chengdu, Sichuan 610041, China
| | - Juan Wu
- Out-patient Department, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Honglin Gao
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, College of Polymer Science and Engineering, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ting Wang
- Lung Cancer Center, Lung Cancer Institute, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Guixiu Xiao
- Lung Cancer Center, Lung Cancer Institute, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Chenggong Hu
- Department of Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Qing Lin
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, College of Polymer Science and Engineering, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qinghua Zhou
- Lung Cancer Center, Lung Cancer Institute, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
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3
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Hawley JE, Obradovic AZ, Dallos MC, Lim EA, Runcie K, Ager CR, McKiernan J, Anderson CB, Decastro GJ, Weintraub J, Virk R, Lowy I, Hu J, Chaimowitz MG, Guo XV, Zhang Y, Haffner MC, Worley J, Stein MN, Califano A, Drake CG. Anti-PD-1 immunotherapy with androgen deprivation therapy induces robust immune infiltration in metastatic castration-sensitive prostate cancer. Cancer Cell 2023; 41:1972-1988.e5. [PMID: 37922910 PMCID: PMC11184948 DOI: 10.1016/j.ccell.2023.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 09/19/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
Abstract
When compared to other malignancies, the tumor microenvironment (TME) of primary and castration-resistant prostate cancer (CRPC) is relatively devoid of immune infiltrates. While androgen deprivation therapy (ADT) induces a complex immune infiltrate in localized prostate cancer, the composition of the TME in metastatic castration-sensitive prostate cancer (mCSPC), and the effects of ADT and other treatments in this context are poorly understood. Here, we perform a comprehensive single-cell RNA sequencing (scRNA-seq) profiling of metastatic sites from patients participating in a phase 2 clinical trial (NCT03951831) that evaluated standard-of-care chemo-hormonal therapy combined with anti-PD-1 immunotherapy. We perform a longitudinal, protein activity-based analysis of TME subpopulations, revealing immune subpopulations conserved across multiple metastatic sites. We also observe dynamic changes in these immune subpopulations in response to treatment and a correlation with clinical outcomes. Our study uncovers a therapy-resistant, transcriptionally distinct tumor subpopulation that expands in cell number in treatment-refractory patients.
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Affiliation(s)
- Jessica E Hawley
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Aleksandar Z Obradovic
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Matthew C Dallos
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Emerson A Lim
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Karie Runcie
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Casey R Ager
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - James McKiernan
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Christopher B Anderson
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Guarionex J Decastro
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Joshua Weintraub
- Department of Interventional Radiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Renu Virk
- Department of Pathology, Columbia University Irving Medical Center, New York, NY, USA
| | - Israel Lowy
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Jianhua Hu
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Matthew G Chaimowitz
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Xinzheng V Guo
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ya Zhang
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA; Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jeremy Worley
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Mark N Stein
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry & Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032 USA; Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032 USA; Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032 USA; J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032 USA.
| | - Charles G Drake
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA; Department of Interventional Radiology, Columbia University Irving Medical Center, New York, NY, USA.
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4
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Ager CR, Zhang M, Chaimowitz M, Bansal S, Tagore S, Obradovic A, Jugler C, Rogava M, Melms JC, McCann P, Spina C, Drake CG, Dallos MC, Izar B. KLRG1 marks tumor-infiltrating CD4 T cell subsets associated with tumor progression and immunotherapy response. J Immunother Cancer 2023; 11:e006782. [PMID: 37657842 PMCID: PMC10476134 DOI: 10.1136/jitc-2023-006782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2023] [Indexed: 09/03/2023] Open
Abstract
Current methods for biomarker discovery and target identification in immuno-oncology rely on static snapshots of tumor immunity. To thoroughly characterize the temporal nature of antitumor immune responses, we developed a 34-parameter spectral flow cytometry panel and performed high-throughput analyses in critical contexts. We leveraged two distinct preclinical models that recapitulate cancer immunoediting (NPK-C1) and immune checkpoint blockade (ICB) response (MC38), respectively, and profiled multiple relevant tissues at and around key inflection points of immune surveillance and escape and/or ICB response. Machine learning-driven data analysis revealed a pattern of KLRG1 expression that uniquely identified intratumoral effector CD4 T cell populations that constitutively associate with tumor burden across tumor models, and are lost in tumors undergoing regression in response to ICB. Similarly, a Helios-KLRG1+ subset of tumor-infiltrating regulatory T cells was associated with tumor progression from immune equilibrium to escape and was also lost in tumors responding to ICB. Validation studies confirmed KLRG1 signatures in human tumor-infiltrating CD4 T cells associate with disease progression in renal cancer. These findings nominate KLRG1+ CD4 T cell populations as subsets for further investigation in cancer immunity and demonstrate the utility of longitudinal spectral flow profiling as an engine of dynamic biomarker discovery.
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Affiliation(s)
- Casey R Ager
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Urology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Mingxuan Zhang
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Molecular Pathology and Therapeutics, Columbia University Irving Medical Center, New York, New York, USA
| | - Matthew Chaimowitz
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York, USA
| | - Shruti Bansal
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York, USA
| | - Somnath Tagore
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Aleksandar Obradovic
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Collin Jugler
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Patrick McCann
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York, USA
| | - Catherine Spina
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York, USA
| | - Charles G Drake
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Urology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
- Janssen Research and Development, Janssen Pharmaceuticals, Spring House, Pennsylvania, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA
| | - Matthew C Dallos
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA
- Department of Urology, Columbia University Irving Medical Center, New York, New York, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA
- Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
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Pruitt HC, Guan Y, Liu H, Carey AE, Brennen WN, Lu J, Joshu C, Weeraratna A, Lotan TL, Karin Eisinger-Mathason TS, Gerecht S. Collagen VI deposition mediates stromal T cell trapping through inhibition of T cell motility in the prostate tumor microenvironment. Matrix Biol 2023; 121:90-104. [PMID: 37331435 DOI: 10.1016/j.matbio.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/11/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
The tumor extracellular matrix (ECM) is a barrier to anti-tumor immunity in solid tumors by disrupting T cell-tumor cell interaction underlying the need for elucidating mechanisms by which specific ECM proteins impact T cell motility and activity within the desmoplastic stroma of solid tumors. Here, we show that Collagen VI (Col VI) deposition correlates with stromal T cell density in human prostate cancer specimens. Furthermore, motility of CD4+ T cells is completely ablated on purified Col VI surfaces when compared with Fibronectin and Collagen I. Importantly, T cells adhered to Col VI surfaces displayed reduced cell spreading and fibrillar actin, indicating a reduction in traction force generation accompanied by a decrease in integrin β1 clustering. We found that CD4+ T cells largely lack expression of integrin α1 in the prostate tumor microenvironment and that blockade of α1β1 integrin heterodimers inhibited CD8+ T cell motility on prostate fibroblast-derived matrix, while re-expression of ITGA1 improved motility. Taken together, we show that the Col VI-rich microenvironment in prostate cancer reduces the motility of CD4+ T cells lacking integrin α1, leading to their accumulation in the stroma, thus putatively inhibiting anti-tumor T cell responses.
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Affiliation(s)
- Hawley C Pruitt
- Institute for NanoBioTechnology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Ya Guan
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Hudson Liu
- Institute for NanoBioTechnology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Alexis E Carey
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - W Nathaniel Brennen
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jiayun Lu
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Corrine Joshu
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Ashani Weeraratna
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - T S Karin Eisinger-Mathason
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sharon Gerecht
- Institute for NanoBioTechnology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
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6
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Tshering LF, Luo F, Russ S, Szenk M, Rubel D, Tutuska K, Rail JG, Balázsi G, Shen MM, Talos F. Immune mechanisms shape the clonal landscape during early progression of prostate cancer. Dev Cell 2023; 58:1071-1086.e8. [PMID: 37148881 PMCID: PMC10330387 DOI: 10.1016/j.devcel.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 12/18/2022] [Accepted: 04/14/2023] [Indexed: 05/08/2023]
Abstract
Understanding the role of the immune microenvironment in modulating intratumor heterogeneity is essential for effective cancer therapies. Using multicolor lineage tracing in genetically engineered mouse models and single-cell transcriptomics, we show that slowly progressing tumors contain a multiclonal landscape of relatively homogeneous subpopulations within a well-organized tumor microenvironment. In more advanced and aggressive tumors, however, the multiclonal landscape develops into competing dominant and minor clones accompanied by a disordered microenvironment. We demonstrate that this dominant/minor landscape is associated with differential immunoediting, in which minor clones are marked by an increased expression of IFNγ-response genes and the T cell-activating chemokines Cxcl9 and Cxcl11. Furthermore, immunomodulation of the IFNγ pathway can rescue minor clones from elimination. Notably, the immune-specific gene signature of minor clones exhibits a prognostic value for biochemical recurrence-free survival in human prostate cancer. These findings suggest new immunotherapy approaches for modulating clonal fitness and tumor progression in prostate cancer.
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Affiliation(s)
- Lara F Tshering
- Department of Urology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Fu Luo
- Department of Urology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Savanah Russ
- Department of Urology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mariola Szenk
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Diana Rubel
- Department of Urology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Karis Tutuska
- Department of Urology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - James G Rail
- Department of Urology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Gábor Balázsi
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael M Shen
- Departments of Medicine, Genetics & Development, Urology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Flaminia Talos
- Department of Urology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA; Departments of Medicine, Genetics & Development, Urology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA.
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7
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Vasciaveo A, Arriaga JM, de Almeida FN, Zou M, Douglass EF, Picech F, Shibata M, Rodriguez-Calero A, de Brot S, Mitrofanova A, Chua CW, Karan C, Realubit R, Pampou S, Kim JY, Afari SN, Mukhammadov T, Zanella L, Corey E, Alvarez MJ, Rubin MA, Shen MM, Califano A, Abate-Shen C. OncoLoop: A Network-Based Precision Cancer Medicine Framework. Cancer Discov 2023; 13:386-409. [PMID: 36374194 PMCID: PMC9905319 DOI: 10.1158/2159-8290.cd-22-0342] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/22/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Prioritizing treatments for individual patients with cancer remains challenging, and performing coclinical studies using patient-derived models in real time is often unfeasible. To circumvent these challenges, we introduce OncoLoop, a precision medicine framework that predicts drug sensitivity in human tumors and their preexisting high-fidelity (cognate) model(s) by leveraging drug perturbation profiles. As a proof of concept, we applied OncoLoop to prostate cancer using genetically engineered mouse models (GEMM) that recapitulate a broad spectrum of disease states, including castration-resistant, metastatic, and neuroendocrine prostate cancer. Interrogation of human prostate cancer cohorts by Master Regulator (MR) conservation analysis revealed that most patients with advanced prostate cancer were represented by at least one cognate GEMM-derived tumor (GEMM-DT). Drugs predicted to invert MR activity in patients and their cognate GEMM-DTs were successfully validated in allograft, syngeneic, and patient-derived xenograft (PDX) models of tumors and metastasis. Furthermore, OncoLoop-predicted drugs enhanced the efficacy of clinically relevant drugs, namely, the PD-1 inhibitor nivolumab and the AR inhibitor enzalutamide. SIGNIFICANCE OncoLoop is a transcriptomic-based experimental and computational framework that can support rapid-turnaround coclinical studies to identify and validate drugs for individual patients, which can then be readily adapted to clinical practice. This framework should be applicable in many cancer contexts for which appropriate models and drug perturbation data are available. This article is highlighted in the In This Issue feature, p. 247.
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Affiliation(s)
- Alessandro Vasciaveo
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Juan Martín Arriaga
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Francisca Nunes de Almeida
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Min Zou
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Eugene F. Douglass
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Florencia Picech
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Maho Shibata
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
- Department of Urology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Antonio Rodriguez-Calero
- Department for Biomedical Research, University of Bern, Bern, Switzerland 3008
- Institute of Pathology, University of Bern and Inselspital, Bern, Switzerland 3008
| | - Simone de Brot
- COMPATH, Institute of Animal Pathology, University of Bern, Switzerland 3012
| | - Antonina Mitrofanova
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Chee Wai Chua
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
- Department of Urology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Charles Karan
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Ronald Realubit
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Sergey Pampou
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Jaime Y. Kim
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Stephanie N. Afari
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Timur Mukhammadov
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Luca Zanella
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA USA 98195
| | - Mariano J. Alvarez
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- DarwinHealth Inc, New York, NY
| | - Mark A. Rubin
- Department for Biomedical Research, University of Bern, Bern, Switzerland 3008
- Bern Center for Precision Medicine (BCPM) Bern, Switzerland 3008
| | - Michael M. Shen
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
- Department of Urology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
| | - Andrea Califano
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY USA 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
- Department of Biochemistry & Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Cory Abate-Shen
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Urology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY USA 10032
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8
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Meng Z, Niu X, Xia L, Chen Y, Wang Z, Wang H, Ji P, Cui W, Wang Y, Lu S. A 3D Ex Vivo Tumor-Immune Coculture System Mimicking In Vivo Tumor Environmental Stress on CD8+ T Cells Exhaustion. Adv Biol (Weinh) 2023:e2200264. [PMID: 36658782 DOI: 10.1002/adbi.202200264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/11/2022] [Indexed: 01/21/2023]
Abstract
Dissection of exhaustion trajectories of immune cells under tumor selection pressure in the tumor microenvironment (TME) elucidates the underlying machinery in anti-tumor immunity, which still lacks easy-to-use models to decipher. Herein, gelatin methacryloyl (GelMA)-poly (ethylene oxide) (PEO) based 3D hydrogel microspheroids are constructed with non-immunogenicity and controllable macroporous structure to establish a tumor-immune cell coculture (3D-HyGTIC) system. In 3D-HyGTIC system, when immune cells embarked, stepwise up-regulation of main immune checkpoints (ICs) molecules is observed with compromised cytokine production in CD8+ T cells, the trajectory of which is in lineage correlation with in vivo grafted tumors. Reinvigoration of CD8+ T cells is more obvious with the addition of an anti-PD-1 regimen at the early time point, which is recapitulated during the coculture of patient-derived tumor fragments (PDTF) and autologous T cells. Moreover, the upregulation of LAG-3 on CD8+ T cells after anti-PD-1 treatment is uncovered. Sequential addition of anti-LAG-3 successfully rescues the otherwise failed reactivation of CD8+ T cells. Therefore, the 3D-HyGTIC system is not only inclined to mimic the early differentiation trajectories of tumor-infiltrating CD8+ T cells but also may facilitate an evaluation of the efficacy of IC blockades and guide the designing of combination immunotherapy.
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Affiliation(s)
- Zhouwenli Meng
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
| | - Xiaomin Niu
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
| | - Liliang Xia
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
| | - Yingying Chen
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Zhen Wang
- Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, P. R. China
| | - Hui Wang
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
| | - Ping Ji
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Wenguo Cui
- Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, P. R. China
| | - Ying Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Shun Lu
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
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9
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Ager CR, Zhang M, Chaimowitz M, Bansal S, Obradovic A, Rogava M, Melms JC, McCann P, Spina C, Drake CG, Dallos MC, Izar B. KLRG1 marks tumor-infiltrating CD4 T cell subsets associated with tumor progression and immunotherapy response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.01.522340. [PMID: 36711647 PMCID: PMC9881861 DOI: 10.1101/2023.01.01.522340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Current methods for biomarker discovery and target identification in immuno-oncology rely on static snapshots of tumor immunity. To thoroughly characterize the temporal nature of antitumor immune responses, we developed a 34-parameter spectral flow cytometry panel and performed high-throughput analyses in critical contexts. We leveraged two distinct preclinical models that recapitulate cancer immunoediting (NPK-C1) and immune checkpoint blockade (ICB) response (MC38), respectively, and profiled multiple relevant tissues at and around key inflection points of immune surveillance and escape and/or ICB response. Machine learning-driven data analysis revealed a pattern of KLRG1 expression that uniquely identified intratumoral effector CD4 T cell populations that constitutively associate with tumor burden across tumor models, and are lost in tumors undergoing regression in response to ICB. Similarly, a Helios - KLRG1 + subset of tumor-infiltrating regulatory T cells (Tregs) was associated with tumor progression from immune equilibrium to escape, and were also lost in tumors responding to ICB. Validation studies confirmed KLRG1 signatures in human tumorinfiltrating CD4 T cells associate with disease progression in renal cancer. These findings nominate KLRG1 + CD4 T cell populations as subsets for further investigation in cancer immunity and demonstrate the utility of longitudinal spectral flow profiling as an engine of dynamic biomarker and/or target discovery.
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10
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Zhao K, Jiang L, Si Y, Zhou S, Huang Z, Meng X. TIGIT blockade enhances tumor response to radiotherapy via a CD103 + dendritic cell-dependent mechanism. Cancer Immunol Immunother 2023; 72:193-209. [PMID: 35794399 DOI: 10.1007/s00262-022-03227-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/17/2022] [Indexed: 01/07/2023]
Abstract
Blockade of the T cell immunoreceptor with the immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT) can enhance innate and adaptive tumor immunity and radiotherapy (RT) can enhance anti-tumor immunity. However, our data suggest that TIGIT-mediated immune suppression may be an impediment to such goals. Herein, we report on the synergistic effects of RT combined with anti-TIGIT therapy and the mechanism of their interaction. Treatment efficacy was assessed by measuring primary and secondary tumor growth, survival, and immune memory capacity. The function of CD103 + dendritic cells (DCs) under the combined treatment was assessed in wild-type and BATF3-deficient (BATF3-/-) mice. FMS-like tyrosine kinase 3 ligand (Flt3L) was used to confirm the role of CD103 + DCs in RT combined with anti-TIGIT therapy. TIGIT was upregulated in immune cells following RT in both esophageal squamous cell carcinoma patients and mouse models. Administration of the anti-TIGIT antibody enhanced the efficacy of RT through a CD8 + T cell-dependent mechanism. It was observed that RT and the anti-TIGIT antibody synergistically enhanced the accumulation of tumor-infiltrating DCs, which activated CD8 + T cells. The efficacy of the combination therapy was negated in the BATF3-/- mouse model. CD103 + DCs were required to promote the anti-tumor effects of combination therapy. Additionally, Flt3L therapy enhanced tumor response to RT combined with TIGIT blockade. Our study demonstrated TIGIT blockade can synergistically enhance anti-tumor T cell responses to RT via CD8 + T cells (dependent on CD103 + DCs), suggesting the clinical potential of targeting the TIGIT pathway and expanding CD103 + DCs in RT.
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Affiliation(s)
- Kaikai Zhao
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Department of Radiation Oncology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Liyang Jiang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Youjiao Si
- Department of Radiology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Department of Radiology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Shujie Zhou
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhaoqin Huang
- Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Xiangjiao Meng
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.
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11
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Dual Effect of Immune Cells within Tumour Microenvironment: Pro- and Anti-Tumour Effects and Their Triggers. Cancers (Basel) 2022; 14:cancers14071681. [PMID: 35406451 PMCID: PMC8996887 DOI: 10.3390/cancers14071681] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
Our body is constantly exposed to pathogens or external threats, but with the immune response that our body can develop, we can fight off and defeat possible attacks or infections. Nevertheless, sometimes this threat comes from an internal factor. Situations such as the existence of a tumour also cause our immune system (IS) to be put on alert. Indeed, the link between immunology and cancer is evident these days, with IS being used as one of the important targets for treating cancer. Our IS is able to eliminate those abnormal or damaged cells found in our body, preventing the uncontrolled proliferation of tumour cells that can lead to cancer. However, in several cases, tumour cells can escape from the IS. It has been observed that immune cells, the extracellular matrix, blood vessels, fat cells and various molecules could support tumour growth and development. Thus, the developing tumour receives structural support, irrigation and energy, among other resources, making its survival and progression possible. All these components that accompany and help the tumour to survive and to grow are called the tumour microenvironment (TME). Given the importance of its presence in the tumour development process, this review will focus on one of the components of the TME: immune cells. Immune cells can support anti-tumour immune response protecting us against tumour cells; nevertheless, they can also behave as pro-tumoural cells, thus promoting tumour progression and survival. In this review, the anti-tumour and pro-tumour immunity of several immune cells will be discussed. In addition, the TME influence on this dual effect will be also analysed.
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