1
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Beigi YZ, Lanjanian H, Fayazi R, Salimi M, Hoseyni BHM, Noroozizadeh MH, Masoudi-Nejad A. Heterogeneity and molecular landscape of melanoma: implications for targeted therapy. MOLECULAR BIOMEDICINE 2024; 5:17. [PMID: 38724687 PMCID: PMC11082128 DOI: 10.1186/s43556-024-00182-2] [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: 11/19/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Uveal cancer (UM) offers a complex molecular landscape characterized by substantial heterogeneity, both on the genetic and epigenetic levels. This heterogeneity plays a critical position in shaping the behavior and response to therapy for this uncommon ocular malignancy. Targeted treatments with gene-specific therapeutic molecules may prove useful in overcoming radiation resistance, however, the diverse molecular makeups of UM call for a patient-specific approach in therapy procedures. We need to understand the intricate molecular landscape of UM to develop targeted treatments customized to each patient's specific genetic mutations. One of the promising approaches is using liquid biopsies, such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), for detecting and monitoring the disease at the early stages. These non-invasive methods can help us identify the most effective treatment strategies for each patient. Single-cellular is a brand-new analysis platform that gives treasured insights into diagnosis, prognosis, and remedy. The incorporation of this data with known clinical and genomics information will give a better understanding of the complicated molecular mechanisms that UM diseases exploit. In this review, we focused on the heterogeneity and molecular panorama of UM, and to achieve this goal, the authors conducted an exhaustive literature evaluation spanning 1998 to 2023, using keywords like "uveal melanoma, "heterogeneity". "Targeted therapies"," "CTCs," and "single-cellular analysis".
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Affiliation(s)
- Yasaman Zohrab Beigi
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hossein Lanjanian
- Software Engineering Department, Engineering Faculty, Istanbul Topkapi University, Istanbul, Turkey
| | - Reyhane Fayazi
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mahdieh Salimi
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Behnaz Haji Molla Hoseyni
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Masoudi-Nejad
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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2
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Tan CL, Lindner K, Boschert T, Meng Z, Rodriguez Ehrenfried A, De Roia A, Haltenhof G, Faenza A, Imperatore F, Bunse L, Lindner JM, Harbottle RP, Ratliff M, Offringa R, Poschke I, Platten M, Green EW. Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy. Nat Biotechnol 2024:10.1038/s41587-024-02161-y. [PMID: 38454173 DOI: 10.1038/s41587-024-02161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
The identification of patient-derived, tumor-reactive T cell receptors (TCRs) as a basis for personalized transgenic T cell therapies remains a time- and cost-intensive endeavor. Current approaches to identify tumor-reactive TCRs analyze tumor mutations to predict T cell activating (neo)antigens and use these to either enrich tumor infiltrating lymphocyte (TIL) cultures or validate individual TCRs for transgenic autologous therapies. Here we combined high-throughput TCR cloning and reactivity validation to train predicTCR, a machine learning classifier that identifies individual tumor-reactive TILs in an antigen-agnostic manner based on single-TIL RNA sequencing. PredicTCR identifies tumor-reactive TCRs in TILs from diverse cancers better than previous gene set enrichment-based approaches, increasing specificity and sensitivity (geometric mean) from 0.38 to 0.74. By predicting tumor-reactive TCRs in a matter of days, TCR clonotypes can be prioritized to accelerate the manufacture of personalized T cell therapies.
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Affiliation(s)
- C L Tan
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - K Lindner
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
- Immune Monitoring Unit, National Center for Tumor Diseases, Heidelberg, Germany
| | - T Boschert
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Helmholtz Institute for Translational Oncology, Mainz, Germany
| | - Z Meng
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Heidelberg, Germany
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - A Rodriguez Ehrenfried
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Helmholtz Institute for Translational Oncology, Mainz, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Heidelberg, Germany
| | - A De Roia
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- DNA Vector Laboratory, German Cancer Research Center, Heidelberg, Germany
| | - G Haltenhof
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
| | | | | | - L Bunse
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
| | | | - R P Harbottle
- DNA Vector Laboratory, German Cancer Research Center, Heidelberg, Germany
| | - M Ratliff
- Department of Neurosurgery, University Hospital Mannheim, Mannheim, Germany
| | - R Offringa
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Heidelberg, Germany
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - I Poschke
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Immune Monitoring Unit, National Center for Tumor Diseases, Heidelberg, Germany
| | - M Platten
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany.
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany.
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany.
- Immune Monitoring Unit, National Center for Tumor Diseases, Heidelberg, Germany.
- Helmholtz Institute for Translational Oncology, Mainz, Germany.
- German Cancer Research Center-Hector Cancer Institute at the Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.
| | - E W Green
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany.
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany.
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany.
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3
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Bryushkova EA, Mushenkova NV, Turchaninova MA, Lukyanov DK, Chudakov DM, Serebrovskaya EO. B cell clonality in cancer. Semin Immunol 2024; 72:101874. [PMID: 38508089 DOI: 10.1016/j.smim.2024.101874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 03/22/2024]
Abstract
Carcinogenesis in the process of long-term co-evolution of tumor cells and immune environment essentially becomes possible due to incorrect decisions made, remembered, and reproduced by the immune system at the level of clonal populations of antigen-specific T- and B-lymphocytes. Tumor-immunity interaction determines the nature of such errors and, consequently, delineates the possible ways of successful immunotherapeutic intervention. It is generally recognized that tumor-infiltrating B cells (TIL-B) can play both pro-tumor and anti-tumor roles. However, the exact mechanisms that determine the contribution of clonal B cell lineages with different specificities and functions remain largely unclear. This is due to the variability of cancer types, the molecular heterogeneity of tumor cells, and, to a large extent, the individual pattern of each immune response. Further progress requires detailed investigation of the functional properties and phenotypes of clonally heterogeneous B cells in relation to their antigenic specificities, which determine the functionality of both effector B lymphocytes and immunoglobulins produced in the tumor environment. Based on a real understanding of the role of clonal antigen-specific populations of B lymphocytes in the tumor microenvironment, we need to learn how to develop new methods of targeted immunotherapy, as well as adapt existing treatment options to the specific needs of different patients and patient subgroups. In this review, we will cover B cells functional diversity and their multifaceted roles in the tumor environment.
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Affiliation(s)
- E A Bryushkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, Moscow, Russia
| | - N V Mushenkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Unicorn Capital Partners, Moscow, Russia
| | - M A Turchaninova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - D K Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - D M Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - E O Serebrovskaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Current position: Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
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4
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Baudouin R, Tartour E, Badoual C, Hans S. Hypothesis of a CD137/Eomes activating axis for effector T cells in HPV oropharyngeal cancers. Mol Med 2024; 30:26. [PMID: 38355394 PMCID: PMC10868089 DOI: 10.1186/s10020-024-00796-w] [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: 07/17/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
Chronic Human Papilloma Virus (HPV) infection is supplanting alcohol and tobacco intoxications as the leading cause of oropharyngeal cancer in developed countries. HPV-related squamous cell carcinomas of the oropharynx (HPV + OSC) present better survival and respond better to radiotherapy and chemotherapy. Regulatory T cells (TREG) are mainly described as immunosuppressive and protumoral in most solid cancers. However, TREG are paradoxically associated with a better prognosis in HPV + OSCs. The transcription factor FoxP3 is the basis for the identification of TREG. Among CD4 + FoxP3 + T cells, some have effector functions. A medical hypothesis is formulated here: the existence of a CD137 (4.1BB)-Eomesodermin (Eomes) activated pathway downstream of TCR-specific activation in a subpopulation of CD4 + FoxP3 + T cells may explain this effector function. Evidence suggest that this axis may exist either in CD4 + FoxP3 + T cells or CD8 + T cells. This pathway could lead T cells to strong antitumor cytotoxic activity in a tumor-specific manner. Furthermore, CD137 is one of the most expected targets for the development of agonist immunotherapies. The identification of CD137 + Eomes + FoxP3+/- T cells could be a key element in the selective activation of the most anti-tumor cells in the HPV + OSC microenvironment.
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Affiliation(s)
- Robin Baudouin
- Department of Otolaryngology-Head & Neck Surgery, Foch Hospital, 40 rue Worth, 92 150, Suresnes, France.
- School of Medicine, UFR Simone Veil, Université Versailles Saint-Quentin-en- Yvelines (Paris Saclay University), 2 Av. de la Source de la Bièvre, Montigny- le-Bretonneux, 78 180, France.
| | - Eric Tartour
- Université Paris Cite, INSERM, PARCC, Hôpital européen Georges Pompidou, Service d'Immunologie biologique, 20, Rue Leblanc, Paris, 75015, France
| | - Cécile Badoual
- Hôpital européen Georges Pompidou, Service d'anatomopathologie, 20, Rue Leblanc, Paris, 75015, France
| | - Stéphane Hans
- Department of Otolaryngology-Head & Neck Surgery, Foch Hospital, 40 rue Worth, 92 150, Suresnes, France
- School of Medicine, UFR Simone Veil, Université Versailles Saint-Quentin-en- Yvelines (Paris Saclay University), 2 Av. de la Source de la Bièvre, Montigny- le-Bretonneux, 78 180, France
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5
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Liu Y, Altreuter J, Bodapati S, Cristea S, Wong CJ, Wu CJ, Michor F. Predicting patient outcomes after treatment with immune checkpoint blockade: A review of biomarkers derived from diverse data modalities. CELL GENOMICS 2024; 4:100444. [PMID: 38190106 PMCID: PMC10794784 DOI: 10.1016/j.xgen.2023.100444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/12/2023] [Accepted: 10/24/2023] [Indexed: 01/09/2024]
Abstract
Immune checkpoint blockade (ICB) therapy targeting cytotoxic T-lymphocyte-associated protein 4, programmed death 1, and programmed death ligand 1 has shown durable remission and clinical success across different cancer types. However, patient outcomes vary among disease indications. Studies have identified prognostic biomarkers associated with immunotherapy response and patient outcomes derived from diverse data types, including next-generation bulk and single-cell DNA, RNA, T cell and B cell receptor sequencing data, liquid biopsies, and clinical imaging. Owing to inter- and intra-tumor heterogeneity and the immune system's complexity, these biomarkers have diverse efficacy in clinical trials of ICB. Here, we review the genetic and genomic signatures and image features of ICB studies for pan-cancer applications and specific indications. We discuss the advantages and disadvantages of computational approaches for predicting immunotherapy effectiveness and patient outcomes. We also elucidate the challenges of immunotherapy prognostication and the discovery of novel immunotherapy targets.
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Affiliation(s)
- Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jennifer Altreuter
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sudheshna Bodapati
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Simona Cristea
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Cheryl J Wong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 20115, USA
| | - Catherine J Wu
- Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 20115, USA; The Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02138, USA; The Ludwig Center at Harvard, Boston, MA 02115, USA.
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6
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Nenclares P, Larkeryd A, Manodoro F, Lee JY, Lalondrelle S, Gilbert DC, Punta M, O’Leary B, Rullan A, Sadanandam A, Chain B, Melcher A, Harrington KJ, Bhide SA. T-cell receptor determinants of response to chemoradiation in locally-advanced HPV16-driven malignancies. Front Oncol 2024; 13:1296948. [PMID: 38234396 PMCID: PMC10791873 DOI: 10.3389/fonc.2023.1296948] [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: 09/19/2023] [Accepted: 11/28/2023] [Indexed: 01/19/2024] Open
Abstract
Background The effect of chemoradiation on the anti-cancer immune response is being increasingly acknowledged; however, its clinical implications in treatment responses are yet to be fully understood. Human papillomavirus (HPV)-driven malignancies express viral oncogenic proteins which may serve as tumor-specific antigens and represent ideal candidates for monitoring the peripheral T-cell receptor (TCR) changes secondary to chemoradiotherapy (CRT). Methods We performed intra-tumoral and pre- and post-treatment peripheral TCR sequencing in a cohort of patients with locally-advanced HPV16-positive cancers treated with CRT. An in silico computational pipeline was used to cluster TCR repertoire based on epitope-specificity and to predict affinity between these clusters and HPV16-derived epitopes. Results Intra-tumoral repertoire diversity, intra-tumoral and post-treatment peripheral CDR3β similarity clustering were predictive of response. In responders, CRT triggered an increase peripheral TCR clonality and clonal relatedness. Post-treatment expansion of baseline peripheral dominant TCRs was associated with response. Responders showed more baseline clustered structures of TCRs maintained post-treatment and displayed significantly more maintained clustered structures. When applying clustering by TCR-specificity methods, responders displayed a higher proportion of intra-tumoral TCRs predicted to recognise HPV16 peptides. Conclusions Baseline TCR characteristics and changes in the peripheral T-cell clones triggered by CRT are associated with treatment outcome. Maintenance and boosting of pre-existing clonotypes are key elements of an effective anti-cancer immune response driven by CRT, supporting a paradigm in which the immune system plays a central role in the success of CRT in current standard-of-care protocols.
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Affiliation(s)
- Pablo Nenclares
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Adrian Larkeryd
- Bioinformatics Unit, The Centre for Translational Immunotherapy, The Institute of Cancer Research, London, United Kingdom
| | - Floriana Manodoro
- Genomics Facility, The Institute of Cancer Research, London, United Kingdom
| | - Jen Y. Lee
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
| | - Susan Lalondrelle
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
| | - Duncan C. Gilbert
- Sussex Cancer Centre, University Hospitals Sussex NHS Foundation Trust, Brighton, United Kingdom
| | - Marco Punta
- Unit of Immunogenetic, Leukemia Genomics and Immunobiology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Ben O’Leary
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Antonio Rullan
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Anguraj Sadanandam
- Systems and Precision Cancer Medicine Team, The Institute of Cancer Research, London, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Alan Melcher
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
| | - Kevin J. Harrington
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Shreerang A. Bhide
- Radiotherapy and Imaging Division, The Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital, London, United Kingdom
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7
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Walsh LA, Quail DF. Decoding the tumor microenvironment with spatial technologies. Nat Immunol 2023; 24:1982-1993. [PMID: 38012408 DOI: 10.1038/s41590-023-01678-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/10/2023] [Indexed: 11/29/2023]
Abstract
Visualization of the cellular heterogeneity and spatial architecture of the tumor microenvironment (TME) is becoming increasingly important to understand mechanisms of disease progression and therapeutic response. This is particularly relevant in the era of cancer immunotherapy, in which the contexture of immune cell positioning within the tumor landscape has been proven to affect efficacy. Although single-cell technologies have mostly replaced conventional approaches to analyze specific cellular subsets within tumors, those that integrate a spatial dimension are now on the rise. In this Review, we assess the strengths and limitations of emerging spatial technologies with a focus on their applications in tumor immunology, as well as forthcoming opportunities for artificial intelligence (AI) and the value of integrating multiomics datasets to achieve a holistic picture of the TME.
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Affiliation(s)
- Logan A Walsh
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada.
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
| | - Daniela F Quail
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada.
- Department of Physiology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.
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8
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Kang W, Mo Z, Li W, Ma H, Zhang Q. Heterogeneity and individualized treatment of microenvironment in glioblastoma (Review). Oncol Rep 2023; 50:217. [PMID: 37888767 PMCID: PMC10636722 DOI: 10.3892/or.2023.8654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
The heterogeneity of glioblastoma can suppress immune cell function and lead to immune evasion, which presents a challenge in developing effective molecular therapies for tumor cells. However, the study of tumor immune heterogeneity holds great potential for clinical immunotherapy. Liquid biopsy is a useful tool for accurately monitoring dynamic changes in tumor immune heterogeneity and the tumor microenvironment. This paper explores the heterogeneity of glioblastoma and the immune microenvironment, providing a therapeutic basis for individualized treatment. Using liquid biopsy technology as a new diagnostic method, innovative treatment strategies may be implemented for patients with glioblastoma to improve their outcomes.
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Affiliation(s)
- Wei Kang
- Department of Neurosurgery, Qinghai Provincial People's Hospital, Xining, Qinghai 810001, P.R. China
| | - Zhixiao Mo
- Department of Neurosurgery, Qinghai Cardio-Cerebrovascular Hospital, Xining, Qinghai 810099, P.R. China
| | - Wenshan Li
- Department of Neurosurgery, Qinghai Provincial People's Hospital, Xining, Qinghai 810001, P.R. China
- Key Laboratory of Neurology of Gansu Province, Department of Neurosurgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Haifeng Ma
- Department of Neurosurgery, Qinghai Provincial People's Hospital, Xining, Qinghai 810001, P.R. China
| | - Qiang Zhang
- Department of Neurosurgery, Qinghai Provincial People's Hospital, Xining, Qinghai 810001, P.R. China
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9
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Li H, Yang Z, Tu F, Deng L, Han Y, Fu X, Wang L, Gu D, Werner B, Huang W. Mutation divergence over space in tumour expansion. J R Soc Interface 2023; 20:20230542. [PMID: 37989227 PMCID: PMC10681009 DOI: 10.1098/rsif.2023.0542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
Mutation accumulation in tumour evolution is one major cause of intra-tumour heterogeneity (ITH), which often leads to drug resistance during treatment. Previous studies with multi-region sequencing have shown that mutation divergence among samples within the patient is common, and the importance of spatial sampling to obtain a complete picture in tumour measurements. However, quantitative comparisons of the relationship between mutation heterogeneity and tumour expansion modes, sampling distances as well as the sampling methods are still few. Here, we investigate how mutations diverge over space by varying the sampling distance and tumour expansion modes using individual-based simulations. We measure ITH by the Jaccard index between samples and quantify how ITH increases with sampling distance, the pattern of which holds in various sampling methods and sizes. We also compare the inferred mutation rates based on the distributions of variant allele frequencies under different tumour expansion modes and sampling sizes. In exponentially fast expanding tumours, a mutation rate can always be inferred for any sampling size. However, the accuracy compared with the true value decreases when the sampling size decreases, where small sampling sizes result in a high estimate of the mutation rate. In addition, such an inference becomes unreliable when the tumour expansion is slow, such as in surface growth.
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Affiliation(s)
- Haiyang Li
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
- Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Zixuan Yang
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Fengyu Tu
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Lijuan Deng
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Yuqing Han
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Xing Fu
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Long Wang
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Di Gu
- The first affiliated hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Benjamin Werner
- Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Weini Huang
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
- School of Mathematical Sciences, Queen Mary University of London, London, UK
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10
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Assing K, Jørgensen SE, Sandgaard KS, De Keukeleere K, B-Hansen M, Petersen MS, Hartling UB, Vaal TMKD, Nielsen C, Jakobsen MA, Watt E, Adams S, Hao Q, Fagerberg C, Mogensen TH. A Novel CDC42 Variant with Impaired Thymopoiesis, IL-7R Signaling, PAK1 Binding, and TCR Repertoire Diversity. J Clin Immunol 2023; 43:1927-1940. [PMID: 37581646 PMCID: PMC10661826 DOI: 10.1007/s10875-023-01561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/30/2023] [Indexed: 08/16/2023]
Abstract
Genetic variants in cell division cycle 42 (CDC42) can manifest with dysmorphic features, autoinflammation, hemophagocytic lymphohistiocytosis, and thrombocytopenia, whereas defective thymopoiesis is a rare disease manifestation. We report a novel CDC42 missense variant (c.46A > G, p.Lys16Glu) resulting in infection and HPV-driven carcinogenesis in the mosaic mother and impaired thymopoiesis and profound T cell lymphopenia in the heterozygous daughter identified through newborn screening for SCID. We found that surface expression of IL-7Rα (CD127) was decreased, consistent with reduced IL-7-induced STAT5 phosphorylation and accelerated apoptotic T cell death. Consistent with the vital role of IL-7 in regulating thymopoiesis, both patients displayed reduced T cell receptor CDR3 repertoires. Moreover, the CDC42 variant prevented binding to the downstream effector, p21-activated kinase (PAK)1, suggesting this impaired interaction to underlie reduced IL-7Rα expression and signaling. Here, we provide the first report of severely compromised thymopoiesis and perturbed IL-7Rα signaling caused by a novel CDC42 variant and presenting with diverging clinical and immunological phenotypes in patients.
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Affiliation(s)
- Kristian Assing
- Department of Clinical Immunology, Odense University Hospital (OUH), Odense, Denmark.
| | | | | | | | - Marie B-Hansen
- Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Mikkel S Petersen
- Department of Clinical Immunology, Aarhus University Hospital (AUH), Aarhus, Denmark
| | - Ulla B Hartling
- Department of Pediatrics, Odense University Hospital (OUH), Odense, Denmark
| | | | - Christian Nielsen
- Department of Clinical Immunology, Odense University Hospital (OUH), Odense, Denmark
| | - Marianne A Jakobsen
- Department of Clinical Immunology, Odense University Hospital (OUH), Odense, Denmark
| | - Eleanor Watt
- Infection, Immunity and Inflammation Section, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Stuart Adams
- Infection, Immunity and Inflammation Section, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Qin Hao
- Department of Clinical Genetics, Odense University Hospital (OUH), Odense, Denmark
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital (OUH), Odense, Denmark
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University (AU), Aarhus, Denmark.
- Department of Infectious Diseases, Aarhus University Hospital (AUH), Aarhus, Denmark.
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11
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Nagano Y, Chain B. tidytcells: standardizer for TR/MH nomenclature. Front Immunol 2023; 14:1276106. [PMID: 37954585 PMCID: PMC10634431 DOI: 10.3389/fimmu.2023.1276106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
T cell receptors (TR) underpin the diversity and specificity of T cell activity. As such, TR repertoire data is valuable both as an adaptive immune biomarker, and as a way to identify candidate therapeutic TR. Analysis of TR repertoires relies heavily on computational analysis, and therefore it is of vital importance that the data is standardized and computer-readable. However in practice, the usage of different abbreviations and non-standard nomenclature in different datasets makes this data pre-processing non-trivial. tidytcells is a lightweight, platform-independent Python package that provides easy-to-use standardization tools specifically designed for TR nomenclature. The software is open-sourced under the MIT license and is available to install from the Python Package Index (PyPI). At the time of publishing, tidytcells is on version 2.0.0.
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Affiliation(s)
- Yuta Nagano
- Division of Medicine, Faculty of Medical Scienecs, University College London (UCL), London, United Kingdom
| | - Benjamin Chain
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London (UCL), London, United Kingdom
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12
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Suay G, Garcia-Cañaveras JC, Aparisi F, Lahoz A, Juan-Vidal O. Sex Differences in the Efficacy of Immune Checkpoint Inhibitors in Neoadjuvant Therapy of Non-Small Cell Lung Cancer: A Meta-Analysis. Cancers (Basel) 2023; 15:4433. [PMID: 37760403 PMCID: PMC10526439 DOI: 10.3390/cancers15184433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is one of the world's leading causes of morbidity and mortality. ICIs alone or combined with chemotherapy have become the standard first-line treatment of metastatic NSCLC. The impressive results obtained have stimulated our interest in applying these therapies in early disease stage treatments, as neoadjuvant immunotherapy has shown promising results. Among many of the factors that may influence responses, the role played by sex is attracting increased interest and needs to be addressed. Here, we aim to first review the state of the art regarding neoadjuvant ICIs, whether they are administered in monotherapy or in combination with chemotherapy at stages IB-IIIA, particularly at stage IIIA, before analyzing whether sex may influence responses. To this end, a meta-analysis of publicly available data comparing male and female major pathological responses (MPR) and pathological complete responses (pCR) was performed. In our meta-analysis, MPR was found to be significantly higher in females than in males, with an odds ratio (OR) of 1.82 (95% CI 1.13-2.93; p = 0.01), while pCR showed a trend to be more favorable in females than in males, but the OR of 1.62 was not statistically significant (95% CI 0.97-2.75; p = 0.08). Overall, our results showed that sex should be systematically considered in future clinical trials settings in order to establish the optimal treatment sequence.
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Affiliation(s)
- Guillermo Suay
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Av. Fernando Abril Martorell, 106, 46026 Valencia, Spain; (G.S.); (J.-C.G.-C.); (F.A.)
| | - Juan-Carlos Garcia-Cañaveras
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Av. Fernando Abril Martorell, 106, 46026 Valencia, Spain; (G.S.); (J.-C.G.-C.); (F.A.)
| | - Francisco Aparisi
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Av. Fernando Abril Martorell, 106, 46026 Valencia, Spain; (G.S.); (J.-C.G.-C.); (F.A.)
| | - Agustin Lahoz
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Av. Fernando Abril Martorell, 106, 46026 Valencia, Spain; (G.S.); (J.-C.G.-C.); (F.A.)
| | - Oscar Juan-Vidal
- Medical Oncology Department, La Fe University and Polytechnic Hospital, Av. Fernando Abril Martorell, 106, 46026 Valencia, Spain
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13
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Haraguchi M, Kiyotani K, Tate T, Sakata S, Sagawa R, Takagi S, Nagayama S, Takeuchi K, Takahashi K, Katayama R. Spatiotemporal commonality of the TCR repertoire in a T-cell memory murine model and in metastatic human colorectal cancer. Cancer Immunol Immunother 2023; 72:2971-2989. [PMID: 37270735 DOI: 10.1007/s00262-023-03473-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/22/2023] [Indexed: 06/05/2023]
Abstract
Immune checkpoint inhibitors (ICIs) have shown superior clinical responses and significantly prolong overall survival (OS) for many types of cancer. However, some patients exhibit long-term OS, whereas others do not respond to ICI therapy at all. To develop more effective and long-lasting ICI therapy, understanding the host immune response to tumors and the development of biomarkers are imperative. In this study, we established an MC38 immunological memory mouse model by administering an anti-PD-L1 antibody and evaluating the detailed characteristics of the immune microenvironment including the T cell receptor (TCR) repertoire. In addition, we found that the memory mouse can be established by surgical resection of residual tumor following anti-PD-L1 antibody treatment with a success rate of > 40%. In this model, specific depletion of CD8 T cells revealed that they were responsible for the rejection of reinoculated MC38 cells. Analysis of the tumor microenvironment (TME) of memory mice using RNA-seq and flow cytometry revealed that memory mice had a quick and robust immune response to MC38 cells compared with naïve mice. A TCR repertoire analysis indicated that T cells with a specific TCR repertoire were expanded in the TME, systemically distributed, and preserved in the host for a long time period. We also identified shared TCR clonotypes between serially resected tumors in patients with colorectal cancer (CRC). Our results suggest that memory T cells are widely preserved in patients with CRC, and the MC38 memory model is potentially useful for the analysis of systemic memory T-cell behavior.
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Affiliation(s)
- Mizuki Haraguchi
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-Ku, Tokyo, 135-8550, Japan
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Kazuma Kiyotani
- Immunopharmacogenomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tomohiro Tate
- Immunopharmacogenomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seiji Sakata
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ray Sagawa
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-Ku, Tokyo, 135-8550, Japan
| | - Satoshi Takagi
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-Ku, Tokyo, 135-8550, Japan
| | - Satoshi Nagayama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Surgery, Uji-Tokushukai Medical Center, Kyoto, Japan
| | - Kengo Takeuchi
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kazuhisa Takahashi
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-Ku, Tokyo, 135-8550, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
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14
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Goyette MA, Lipsyc-Sharf M, Polyak K. Clinical and translational relevance of intratumor heterogeneity. Trends Cancer 2023; 9:726-737. [PMID: 37248149 PMCID: PMC10524913 DOI: 10.1016/j.trecan.2023.05.001] [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: 04/12/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/31/2023]
Abstract
Intratumor heterogeneity (ITH) is a driver of tumor evolution and a main cause of therapeutic resistance. Despite its importance, measures of ITH are still not incorporated into clinical practice. Consequently, standard treatment is frequently ineffective for patients with heterogeneous tumors as changes to treatment regimens are made only after recurrence and disease progression. More effective combination therapies require a mechanistic understanding of ITH and ways to assess it in clinical samples. The growth of technologies enabling the spatially intact analysis of tumors at the single-cell level and the development of sophisticated preclinical models give us hope that ITH will not simply be used as a predictor of a poor outcome but will guide treatment decisions from diagnosis through treatment.
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Affiliation(s)
- Marie-Anne Goyette
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Marla Lipsyc-Sharf
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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15
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Schina A, Sztupinszki Z, Marie Svane I, Szallasi Z, Jönsson G, Donia M. Intratumoral T-cell and B-cell receptor architecture associates with distinct immune tumor microenvironment features and clinical outcomes of anti-PD-1/L1 immunotherapy. J Immunother Cancer 2023; 11:e006941. [PMID: 37604641 PMCID: PMC10445359 DOI: 10.1136/jitc-2023-006941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Effective cooperation between B-cells and T-cells within the tumor microenvironment may lead to the regression of established tumors. B-cells and T-cells can recognize tumor antigens with exquisite specificity via their receptor complexes. Nevertheless, whether a diverse intratumoral B-cells and T-cell receptor (BCR, TCR) repertoire affects the tumor immune microenvironment (TIME) and clinical outcomes in patients treated with immunotherapy is unclear. METHODS We extracted information on BCR and TCR repertoire diversity from large clinical datasets and measured the association between immune receptor diversity features, the TIME, and clinical outcomes of patients treated with anti-PD-1/PD-L1 immunotherapy. RESULTS In multiple tumor types, an increasingly diverse TCR repertoire was strongly associated with a highly activated TIME, while BCR diversity was more associated with antibody responses but not with the overall B-cell infiltration nor with measures related to intratumoral CD8+T cell activity. Neither TCR nor BCR diversity was independent prognostic biomarkers of survival across multiple cancer types. However, both TCR and BCR diversity improved the performance of predictive models combined with established biomarkers of response to immunotherapy. CONCLUSION Overall, these data indicate a currently unexplored immunological role of intratumoral B-cells associated with BCR diversity and antibody responses but independent of classical anticancer T-cells intratumoral activities.
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Affiliation(s)
- Aimilia Schina
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Herlev, Denmark
| | | | - Inge Marie Svane
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Herlev, Denmark
| | | | - Göran Jönsson
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Marco Donia
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Herlev, Denmark
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16
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Earland N, Chen K, Semenkovich NP, Chauhan PS, Zevallos JP, Chaudhuri AA. Emerging Roles of Circulating Tumor DNA for Increased Precision and Personalization in Radiation Oncology. Semin Radiat Oncol 2023; 33:262-278. [PMID: 37331781 DOI: 10.1016/j.semradonc.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Recent breakthroughs in circulating tumor DNA (ctDNA) technologies present a compelling opportunity to combine this emerging liquid biopsy approach with the field of radiogenomics, the study of how tumor genomics correlate with radiotherapy response and radiotoxicity. Canonically, ctDNA levels reflect metastatic tumor burden, although newer ultrasensitive technologies can be used after curative-intent radiotherapy of localized disease to assess ctDNA for minimal residual disease (MRD) detection or for post-treatment surveillance. Furthermore, several studies have demonstrated the potential utility of ctDNA analysis across various cancer types managed with radiotherapy or chemoradiotherapy, including sarcoma and cancers of the head and neck, lung, colon, rectum, bladder, and prostate . Additionally, because peripheral blood mononuclear cells are routinely collected alongside ctDNA to filter out mutations associated with clonal hematopoiesis, these cells are also available for single nucleotide polymorphism analysis and could potentially be used to detect patients at high risk for radiotoxicity. Lastly, future ctDNA assays will be utilized to better assess locoregional MRD in order to more precisely guide adjuvant radiotherapy after surgery in cases of localized disease, and guide ablative radiotherapy in cases of oligometastatic disease.
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Affiliation(s)
- Noah Earland
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - Kevin Chen
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - Nicholas P Semenkovich
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Pradeep S Chauhan
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - Jose P Zevallos
- Department of Otolaryngology, University of Pittsburgh Medical School, Pittsburgh, PA
| | - Aadel A Chaudhuri
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO; Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, MO; Department of Genetics, Washington University School of Medicine, St. Louis, MO; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO; Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO.
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17
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Xie X, Li L, Xie L, Liu Z, Zhang G, Gao X, Peng W, Deng H, Yang Y, Yang M, Chang L, Yi X, Xia X, He Z, Zhou C. Stratification of non-small cell lung adenocarcinoma patients with EGFR actionable mutations based on drug-resistant stem cell genes. iScience 2023; 26:106584. [PMID: 37288343 PMCID: PMC10241979 DOI: 10.1016/j.isci.2023.106584] [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: 09/28/2022] [Revised: 01/02/2023] [Accepted: 03/30/2023] [Indexed: 06/09/2023] Open
Abstract
EGFR-TKIs were used in NSCLC patients with actionable EGFR mutations and prolong prognosis. However, most patients treated with EGFR-TKIs developed resistance within around one year. This suggests that residual EGFR-TKIs resistant cells may eventually lead to relapse. Predicting resistance risk in patients will facilitate individualized management. Herein, we built an EGFR-TKIs resistance prediction (R-index) model and validate in cell line, mice, and cohort. We found significantly higher R-index value in resistant cell lines, mice models and relapsed patients. Patients with an elevated R-index had significantly shorter relapse time. We also found that the glycolysis pathway and the KRAS upregulation pathway were related to EGFR-TKIs resistance. MDSC is a significant immunosuppression factor in the resistant microenvironment. Our model provides an executable method for assessing patient resistance status based on transcriptional reprogramming and may contribute to the clinical translation of patient individual management and the study of unclear resistance mechanisms.
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Affiliation(s)
- Xiaohong Xie
- Pulmonary and Critical Care Medicine, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Lifeng Li
- Geneplus-Beijing, Beijing 102206, China
| | - Liang Xie
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital/Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | | | | | - Xuan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Geneplus-Shenzhen Clinical Laboratory, Shenzhen, Guangdong 518122, China
| | - Wenying Peng
- The Second Department of Oncology, Yunnan Cancer Hospital & The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Center, Kunming 650000, China
| | - Haiyi Deng
- Pulmonary and Critical Care Medicine, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Yilin Yang
- Pulmonary and Critical Care Medicine, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Meiling Yang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | | | - Xin Yi
- Geneplus-Beijing, Beijing 102206, China
| | | | - Zhiyi He
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Chengzhi Zhou
- Pulmonary and Critical Care Medicine, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
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18
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Milighetti M, Peng Y, Tan C, Mark M, Nageswaran G, Byrne S, Ronel T, Peacock T, Mayer A, Chandran A, Rosenheim J, Whelan M, Yao X, Liu G, Felce SL, Dong T, Mentzer AJ, Knight JC, Balloux F, Greenstein E, Reich-Zeliger S, Pade C, Gibbons JM, Semper A, Brooks T, Otter A, Altmann DM, Boyton RJ, Maini MK, McKnight A, Manisty C, Treibel TA, Moon JC, Noursadeghi M, Chain B. Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection. iScience 2023; 26:106937. [PMID: 37275518 PMCID: PMC10201888 DOI: 10.1016/j.isci.2023.106937] [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: 02/08/2023] [Revised: 04/14/2023] [Accepted: 05/17/2023] [Indexed: 06/07/2023] Open
Abstract
T cell responses precede antibody and may provide early control of infection. We analyzed the clonal basis of this rapid response following SARS-COV-2 infection. We applied T cell receptor (TCR) sequencing to define the trajectories of individual T cell clones immediately. In SARS-COV-2 PCR+ individuals, a wave of TCRs strongly but transiently expand, frequently peaking the same week as the first positive PCR test. These expanding TCR CDR3s were enriched for sequences functionally annotated as SARS-COV-2 specific. Epitopes recognized by the expanding TCRs were highly conserved between SARS-COV-2 strains but not with circulating human coronaviruses. Many expanding CDR3s were present at high frequency in pre-pandemic repertoires. Early response TCRs specific for lymphocytic choriomeningitis virus epitopes were also found at high frequency in the preinfection naive repertoire. High-frequency naive precursors may allow the T cell response to respond rapidly during the crucial early phases of acute viral infection.
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Affiliation(s)
- Martina Milighetti
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Cedric Tan
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Michal Mark
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gayathri Nageswaran
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Suzanne Byrne
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Tom Peacock
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Andreas Mayer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Aneesh Chandran
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Joshua Rosenheim
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Matthew Whelan
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Xuan Yao
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Guihai Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | | | - Julian C Knight
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Francois Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Erez Greenstein
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shlomit Reich-Zeliger
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Corinna Pade
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - Joseph M Gibbons
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - Amanda Semper
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Tim Brooks
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Ashley Otter
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Daniel M Altmann
- Department of Immunology and Inflammation, Imperial College London, London SW7 2BX, UK
| | - Rosemary J Boyton
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Lung Division, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Mala K Maini
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Aine McKnight
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - Charlotte Manisty
- Institute of Cardiovascular Sciences, University College London, London WC1E 6BT, UK
| | - Thomas A Treibel
- Institute of Cardiovascular Sciences, University College London, London WC1E 6BT, UK
| | - James C Moon
- Institute of Cardiovascular Sciences, University College London, London WC1E 6BT, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
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19
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Li X, Liang H, Fan J. Prospects of Cytomegalovirus-Specific T-Cell Receptors in Clinical Diagnosis and Therapy. Viruses 2023; 15:1334. [PMID: 37376633 DOI: 10.3390/v15061334] [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: 04/29/2023] [Revised: 06/03/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Human cytomegalovirus (HCMV) is responsible for widespread infections worldwide. In immunocompetent individuals it is typically latent, while infection or reactivation in immunocompromised individuals can result in severe clinical symptoms or even death. Although there has been significant progress in the treatment and diagnosis of HCMV infection in recent years, numerous shortcomings and developmental limitations persist. There is an urgent need to develop innovative, safe, and effective treatments, as well as to explore early and timely diagnostic strategies for HCMV infection. Cell-mediated immune responses are the primary factor controlling HCMV infection and replication, but the protective role of humoral immune responses remains controversial. T-cells, key effector cells of the cellular immune system, are critical for clearing and preventing HCMV infection. The T-cell receptor (TCR) lies at the heart of T-cell immune responses, and its diversity enables the immune system to differentiate between self and non-self. Given the significant influence of cellular immunity on human health and the indispensable role of the TCR in T-cell immune responses, we posit that the impact of TCR on the development of novel diagnostic and prognostic methods, as well as on patient monitoring and management of clinical HCMV infection, will be far-reaching and profound. High-throughput and single-cell sequencing technologies have facilitated unprecedented quantitative detection of TCR diversity. With these current sequencing technologies, researchers have already obtained a vast number of TCR sequences. It is plausible that in the near future studies on TCR repertoires will be instrumental in assessing vaccine efficacy, immunotherapeutic strategies, and the early diagnosis of HCMV infection.
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Affiliation(s)
- Xuejie Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Hanying Liang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Jun Fan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
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20
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Xie S, Yan R, Zheng A, Shi M, Tang L, Li X, Liu J, Gan Y, Wang Y, Jiang D, Liu L, Wu H, Wang Z. T cell receptor and B cell receptor exhibit unique signatures in tumor and adjacent non-tumor tissues of hepatocellular carcinoma. Front Immunol 2023; 14:1161417. [PMID: 37313417 PMCID: PMC10258310 DOI: 10.3389/fimmu.2023.1161417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/16/2023] [Indexed: 06/15/2023] Open
Abstract
Background The tumor microenvironment in hepatocellular carcinoma (HCC) is complicated. Tumor-infiltrating T and B cells play a pivotal role in anti-tumor immunity. T cell receptor (TCR) and B cell receptor (BCR) features may reflect the disease-associated antigen response. Methods By combining bulk TCR/BCR-sequencing, RNA-sequencing, whole exome-sequencing, and human leukocyte antigen-sequencing, we examined the immune repertoire (IR) features of tumor and adjacent non-tumor tissues obtained from 64 HCC patients. Results High IR heterogeneity with weak similarity was discovered between tumor and non-tumor tissues. Higher BCR diversity, richness, and somatic hypermutation (SHM) were found in non-tumor tissues, while TCRα and TCRβ diversity and richness were comparable or higher in tumor. Additionally, lower immune infiltration was found in tumor than non-tumor tissues; the microenvironment in tumor appeared to keep stably inhibited and changed slightly with tumor progression. Moreover, BCR SHM was stronger, whereas TCR/BCR diversity declined with HCC progression. Importantly, we found that higher IR evenness in tumor and lower TCR richness in non-tumor tissues indicated better survival in HCC patients. Collectively, the results revealed that TCR and BCR exhibited distinct features in tumor and non-tumor tissues. Conclusions We demonstrated that IR features vary between different tissues of HCC. IR features may represent a biomarker for the diagnosis and treatment of HCC patients, providing references for subsequent immunotherapy research and strategy selection.
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Affiliation(s)
- Shi Xie
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rong Yan
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Anqi Zheng
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mengfen Shi
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | | | - Xueying Li
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiabang Liu
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yifan Gan
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yu Wang
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Deke Jiang
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Li Liu
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hongkai Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zhanhui Wang
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
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21
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Feng Z, Lin H, Liu Z, Yan L, Wang Y, Li B, Liu E, Han C, Shi Z, Lu C, Liu Z, Pang C, Li Z, Cui Y, Pan X, Chen X. Artificial intelligence-quantified tumour-lymphocyte spatial interaction predicts disease-free survival in resected lung adenocarcinoma: A graph-based, multicentre study. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 238:107617. [PMID: 37235970 DOI: 10.1016/j.cmpb.2023.107617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 05/01/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND OBJECTIVE A high degree of lymphocyte infiltration is related to superior outcomes amongst patients with lung adenocarcinoma. Recent evidence indicates that the spatial interactions between tumours and lymphocytes also influence the anti-tumour immune responses, but the spatial analysis at the cellular level remains insufficient. METHODS We proposed an artificial intelligence-quantified Tumour-Lymphocyte Spatial Interaction score (TLSI-score) by calculating the ratio between the number of spatial adjacent tumour-lymphocyte and the number of tumour cells based on topology cell graph constructed using H&E-stained whole-slide images. The association of TLSI-score with disease-free survival (DFS) was explored in 529 patients with lung adenocarcinoma across three independent cohorts (D1, 275; V1, 139; V2, 115). RESULTS After adjusting for pTNM stage and other clinicopathologic risk factors, a higher TLSI-score was independently associated with longer DFS than a low TLSI-score in the three cohorts [D1, adjusted hazard ratio (HR), 0.674; 95% confidence interval (CI) 0.463-0.983; p = 0.040; V1, adjusted HR, 0.408; 95% CI 0.223-0.746; p = 0.004; V2, adjusted HR, 0.294; 95% CI 0.130-0.666; p = 0.003]. By integrating the TLSI-score with clinicopathologic risk factors, the integrated model (full model) improves the prediction of DFS in three independent cohorts (C-index, D1, 0.716 vs. 0.701; V1, 0.666 vs. 0.645; V2, 0.708 vs. 0.662) CONCLUSIONS: TLSI-score shows the second highest relative contribution to the prognostic prediction model, next to the pTNM stage. TLSI-score can assist in the characterising of tumour microenvironment and is expected to promote individualized treatment and follow-up decision-making in clinical practice.
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Affiliation(s)
- Zhengyun Feng
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, 541004, China
| | - Huan Lin
- Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China; School of Medicine, South China University of Technology, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China
| | - Zaiyi Liu
- Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China; Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China
| | - Lixu Yan
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Yumeng Wang
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, 541004, China
| | - Bingbing Li
- Department of Pathology, Guangdong Provincial People's Hospital Ganzhou Hospital (Ganzhou Municipal Hospital), Ganzhou, 341000, China
| | - Entao Liu
- WeiLun PET Center, Department of Nuclear Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Chu Han
- Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China; Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China
| | - Zhenwei Shi
- Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China; Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China; Guangdong Cardiovascular Institute, Guangzhou, 510080, China
| | - Cheng Lu
- Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China; Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China
| | - Zhenbing Liu
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, 541004, China
| | - Cheng Pang
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, 541004, China
| | - Zhenhui Li
- Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China; Department of Radiology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Centre, Kunming, 650118, China.
| | - Yanfen Cui
- Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China; Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China; Guangdong Cardiovascular Institute, Guangzhou, 510080, China; Department of Radiology, Shanxi Province Cancer Hospital; Shanxi Hospital Affiliated to Cancer Hospital; Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013, China.
| | - Xipeng Pan
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, 541004, China; Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China; Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China.
| | - Xin Chen
- Department of Radiology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, China.
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22
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Lv X, Mao Z, Sun X, Liu B. Intratumoral Heterogeneity in Lung Cancer. Cancers (Basel) 2023; 15:2709. [PMID: 37345046 DOI: 10.3390/cancers15102709] [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: 04/19/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
The diagnosis and treatment of lung cancer (LC) is always a challenge. The difficulty in the decision of therapeutic schedule and diagnosis is directly related to intratumoral heterogeneity (ITH) in the progression of LC. It has been proven that most tumors emerge and evolve under the pressure of their living microenvironment, which involves genetic, immunological, metabolic, and therapeutic components. While most research on ITH revealed multiple mechanisms and characteristic, a systemic exposition of ITH in LC is still hard to find. In this review, we describe how ITH in LC develops from the perspective of space and time. We discuss elaborate details and affection of every aspect of ITH in LC and the relationship between them. Based on ITH in LC, we describe a more accurate multidisciplinary therapeutic strategy on LC and provide the newest opinion on the potential approach of LC therapy.
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Affiliation(s)
- Xiaodi Lv
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai 200437, China
| | - Zixian Mao
- Pujiang Community Health Center of Minhang District of Shanghai, Shanghai 201114, China
| | - Xianjun Sun
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai 200437, China
- Institutes of Integrative Medicine, Fudan University, Shanghai 200437, China
| | - Baojun Liu
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai 200437, China
- Institutes of Integrative Medicine, Fudan University, Shanghai 200437, China
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23
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Weeden CE, Gayevskiy V, Marceaux C, Batey D, Tan T, Yokote K, Ribera NT, Clatch A, Christo S, Teh CE, Mitchell AJ, Trussart M, Rankin LC, Obers A, McDonald JA, Sutherland KD, Sharma VJ, Starkey G, D'Costa R, Antippa P, Leong T, Steinfort D, Irving L, Swanton C, Gordon CL, Mackay LK, Speed TP, Gray DHD, Asselin-Labat ML. Early immune pressure initiated by tissue-resident memory T cells sculpts tumor evolution in non-small cell lung cancer. Cancer Cell 2023; 41:837-852.e6. [PMID: 37086716 DOI: 10.1016/j.ccell.2023.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/05/2023] [Accepted: 03/24/2023] [Indexed: 04/24/2023]
Abstract
Tissue-resident memory T (TRM) cells provide immune defense against local infection and can inhibit cancer progression. However, it is unclear to what extent chronic inflammation impacts TRM activation and whether TRM cells existing in tissues before tumor onset influence cancer evolution in humans. We performed deep profiling of healthy lungs and lung cancers in never-smokers (NSs) and ever-smokers (ESs), finding evidence of enhanced immunosurveillance by cells with a TRM-like phenotype in ES lungs. In preclinical models, tumor-specific or bystander TRM-like cells present prior to tumor onset boosted immune cell recruitment, causing tumor immune evasion through loss of MHC class I protein expression and resistance to immune checkpoint inhibitors. In humans, only tumors arising in ES patients underwent clonal immune evasion, unrelated to tobacco-associated mutagenic signatures or oncogenic drivers. These data demonstrate that enhanced TRM-like activity prior to tumor development shapes the evolution of tumor immunogenicity and can impact immunotherapy outcomes.
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Affiliation(s)
- Clare E Weeden
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Velimir Gayevskiy
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Claire Marceaux
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Daniel Batey
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Tania Tan
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Kenta Yokote
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Nina Tubau Ribera
- Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Allison Clatch
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Susan Christo
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Charis E Teh
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Andrew J Mitchell
- Materials Characterisation and Fabrication Platform, Department of Chemical Engineering, the University of Melbourne, Parkville, VIC, Australia
| | - Marie Trussart
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Lucille C Rankin
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Andreas Obers
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jackson A McDonald
- ACRF Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Kate D Sutherland
- ACRF Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Varun J Sharma
- Department of Surgery, University of Melbourne, Parkville, VIC, Australia; Liver and Intestinal Transplant Unit, Austin Health, Heidelberg, VIC, Australia; Department of Cardiothoracic Surgery, Austin Health, Heidelberg, VIC, Australia
| | - Graham Starkey
- Department of Surgery, University of Melbourne, Parkville, VIC, Australia; Liver and Intestinal Transplant Unit, Austin Health, Heidelberg, VIC, Australia
| | - Rohit D'Costa
- DonateLife Victoria, Carlton, VIC, Australia; Department of Intensive Care Medicine, Melbourne Health, Melbourne, VIC, Australia
| | - Phillip Antippa
- Department of Surgery, University of Melbourne, Parkville, VIC, Australia; The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Tracy Leong
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia; Department of Respiratory and Sleep Medicine, Austin Health, Heidelberg, VIC, Australia
| | - Daniel Steinfort
- Department of Medicine, the University of Melbourne, Parkville, VIC, Australia; The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Louis Irving
- Department of Medicine, the University of Melbourne, Parkville, VIC, Australia; The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK
| | - Claire L Gordon
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia; North Eastern Public Health Unit, Austin Health, Heidelberg, VIC, Australia
| | - Laura K Mackay
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Terence P Speed
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; School of Mathematics and Statistics, the University of Melbourne, Parkville, VIC, Australia
| | - Daniel H D Gray
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia.
| | - Marie-Liesse Asselin-Labat
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia.
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24
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Frank ML, Lu K, Erdogan C, Han Y, Hu J, Wang T, Heymach JV, Zhang J, Reuben A. T-Cell Receptor Repertoire Sequencing in the Era of Cancer Immunotherapy. Clin Cancer Res 2023; 29:994-1008. [PMID: 36413126 PMCID: PMC10011887 DOI: 10.1158/1078-0432.ccr-22-2469] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/07/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022]
Abstract
T cells are integral components of the adaptive immune system, and their responses are mediated by unique T-cell receptors (TCR) that recognize specific antigens from a variety of biological contexts. As a result, analyzing the T-cell repertoire offers a better understanding of immune responses and of diseases like cancer. Next-generation sequencing technologies have greatly enabled the high-throughput analysis of the TCR repertoire. On the basis of our extensive experience in the field from the past decade, we provide an overview of TCR sequencing, from the initial library preparation steps to sequencing and analysis methods and finally to functional validation techniques. With regards to data analysis, we detail important TCR repertoire metrics and present several computational tools for predicting antigen specificity. Finally, we highlight important applications of TCR sequencing and repertoire analysis to understanding tumor biology and developing cancer immunotherapies.
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Affiliation(s)
- Meredith L Frank
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, Texas
| | - Kaylene Lu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, Texas.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Can Erdogan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Rice University, Houston, Texas
| | - Yi Han
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jian Hu
- The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, Texas.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas.,Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, Texas.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, Texas
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25
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Merz M, Hu Q, Merz AMA, Wang J, Hutson N, Rondeau C, Celotto K, Belal A, Alberico R, Block AW, Mohammadpour H, Wallace PK, Tario J, Luce J, Glenn ST, Singh P, Samur M, Munshi N, Liu S, McCarthy PL, Wei L, Hillengass J. Spatiotemporal assessment of immunogenomic heterogeneity in multiple myeloma. Blood Adv 2023; 7:718-733. [PMID: 35868022 PMCID: PMC9984963 DOI: 10.1182/bloodadvances.2022007457] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 11/20/2022] Open
Abstract
Spatial heterogeneity is a common phenomenon in metastatic solid tumors and an evolving concept in multiple myeloma (MM). The interplay between malignant plasma cells (PCs) and the microenvironment has not yet been analyzed in MM. For this purpose, we performed bone marrow aspirates and imaging-guided biopsies of corresponding lesions in newly diagnosed MM (NDMM) and relapsed/refractory MM (RRMM) patients. PCs were isolated and subjected to whole-exome sequencing (WES). Non-PCs were studied with next-generation flow (NGF) and T-cell receptor sequencing (TCRseq) to analyze the connection between malignant and nonmalignant cells in the bone marrow and in lesions. Although we observed a strong overlap from WES, NGF, and TCRseq in patients with intramedullary disease, WES revealed significant spatial heterogeneity in patients with extramedullary disease. NGF showed significant immunosuppression in RRMM compared with NDMM as indicated by fewer myeloid dendritic cells, unswitched memory B cells, Th9 cells, and CD8 effector memory T cells but more natural killer and regulatory T cells. Additionally, fewer T-cell receptor (TCR) sequences were detected in RRMM compared with NDMM and healthy individuals. After induction therapy, TCR repertoire richness increased to levels of healthy individuals, and NGF showed more regulatory T cells and myeloid-derived suppressor cells, regardless of depth of response. Clinical significance of imaging-guided biopsies of lesions was demonstrated by detection of monoclonal PCs in patients without measurable residual disease (MRD) in aspirates from the iliac crest as well as identification of secondary primary malignancies in MRD- patients. Furthermore, site-specific clones with different drug susceptibilities and genetically defined high-risk features were detected by our workflow.
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Affiliation(s)
- Maximilian Merz
- Department of Medicine, Roswell Park Comprehensive Cancer Center (Roswell Park), Buffalo, NY
- Department of Hematology, Cellular Therapy and Hemostaseology, Univeristy Hospital of Leipzig, Leipzig, Germany
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park, Buffalo, NY
| | - Almuth Maria Anni Merz
- Department of Medicine, Roswell Park Comprehensive Cancer Center (Roswell Park), Buffalo, NY
| | - Jie Wang
- Department of Biostatistics and Bioinformatics, Roswell Park, Buffalo, NY
| | - Nicholas Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park, Buffalo, NY
| | - Cherie Rondeau
- Department of Medicine, Roswell Park Comprehensive Cancer Center (Roswell Park), Buffalo, NY
| | - Kimberly Celotto
- Department of Medicine, Roswell Park Comprehensive Cancer Center (Roswell Park), Buffalo, NY
| | - Ahmed Belal
- Department of Diagnostic Radiology, Roswell Park, Buffalo, NY
| | - Ronald Alberico
- Department of Diagnostic Radiology, Roswell Park, Buffalo, NY
| | - AnneMarie W. Block
- Clinical Cytogenetics Laboratory, Department of Pathology and Laboratory Medicine, Roswell Park, Buffalo, NY
| | | | - Paul K. Wallace
- Flow and Image Cytometry, Department of Pathology and Laboratory Medicine, Roswell Park, Buffalo, NY
| | - Joseph Tario
- Flow and Image Cytometry, Department of Pathology and Laboratory Medicine, Roswell Park, Buffalo, NY
| | - Jesse Luce
- Genomics Shared Resources, Roswell Park, Buffalo, NY
| | - Sean T. Glenn
- Genomics Shared Resources, Roswell Park, Buffalo, NY
| | | | - Mehmet Samur
- Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Nikhil Munshi
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
- VA Boston Healthcare System, Boston, MA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park, Buffalo, NY
| | - Philip L. McCarthy
- Transplant and Cellular Therapy Program, Department of Medicine, Roswell Park, Buffalo, NY
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park, Buffalo, NY
| | - Jens Hillengass
- Department of Medicine, Roswell Park Comprehensive Cancer Center (Roswell Park), Buffalo, NY
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26
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Sanromán ÁF, Joshi K, Au L, Chain B, Turajlic S. TCR sequencing: applications in immuno-oncology research. IMMUNO-ONCOLOGY TECHNOLOGY 2023; 17:100373. [PMID: 36908996 PMCID: PMC9996383 DOI: 10.1016/j.iotech.2023.100373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
•T-cell receptor (TCR) interaction with major histocompatibility complex-antigen complexes leads to antitumour responses.•TCR sequencing analysis allows characterisation of T cells that recognise tumour neoantigens.•T-cell clonal revival and clonal replacement potentially underpin immunotherapy responses.
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Affiliation(s)
- Á F Sanromán
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - K Joshi
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK.,Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - L Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Australia
| | - B Chain
- Division of Infection and Immunity, University College London, London, UK.,Department of Computer Science, University College London, London, UK
| | - S Turajlic
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London, UK.,Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
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27
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Balbach ML, Axelrod ML, Balko JM, Bankhead A, Shaffer T, Lim L, Guo J, Hernandez J, Li M, Iams WT. Peripheral T-cell receptor repertoire dynamics in small cell lung cancer. Transl Lung Cancer Res 2023; 12:257-265. [PMID: 36895920 PMCID: PMC9989808 DOI: 10.21037/tlcr-22-666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/21/2022] [Indexed: 02/25/2023]
Abstract
Background Identifying a circulating biomarker predictive of immune checkpoint inhibitor (ICI) benefit in patients with small cell lung cancer (SCLC) remains an unmet need. Characteristics of peripheral and intratumoral T-cell receptor (TCR) repertoires have been shown to predict clinical outcomes in non-small cell lung cancer (NSCLC). Recognizing a knowledge gap, we sought to characterize circulating TCR repertoires and their relationship with clinical outcomes in SCLC. Methods SCLC patients with limited (n=4) and extensive (n=10) stage disease were prospectively enrolled for blood collection and chart review. Targeted next-generation sequencing of TCR beta and alpha chains of peripheral blood samples was performed. Unique TCR clonotypes were defined by identical CDR3, V gene, and J gene nucleotide sequences of the beta chain and subsequently used to calculate TCR diversity indices. Results Patients with stable versus progressive and limited versus extensive stage disease did not demonstrate significant differences in V gene usage. Kaplan-Meier curve and log-rank analysis did not identify a statistical difference in progression-free survival (PFS) (P=0.900) or overall survival (OS) (P=0.200) between high and low on-treatment TCR diversity groups, although the high diversity group exhibited a trend toward increased OS. Conclusions We report the second study investigating peripheral TCR repertoire diversity in SCLC. With a limited sample size, no statistically significant associations between peripheral TCR diversity and clinical outcomes were observed, though further study is warranted.
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Affiliation(s)
- Meridith L. Balbach
- Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margaret L. Axelrod
- Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Justin M. Balko
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | | | | | - Lee Lim
- Resolution Bioscience, Kirkland, WA, USA
| | | | | | - Mark Li
- Resolution Bioscience, Kirkland, WA, USA
| | - Wade T. Iams
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
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Abstract
The theory that cancer-associated fibroblasts (CAFs) are immunosuppressive cells has prevailed throughout the past decade. However, recent high-throughput, high-resolution mesenchyme-directed single-cell studies have harnessed computational advances to functionally characterize cell states, highlighting the existence of immunostimulatory CAFs. Our group and others have uncovered and experimentally substantiated key functions of cancer antigen-presenting CAFs in T cell immunity, both in vitro and in vivo, refuting the conventional assumption that CAFs impede adaptive immune rejection of tumours. In this Perspective, I unify the follicular and non-follicular, non-endothelial stroma of tumours under the 'peripheral adaptive immune mesenchyme' framework and position subsets of CAFs as direct positive regulators of the adaptive immune system. Building on the understanding of cancer antigen presentation by CAFs and the second touch hypothesis, which postulates that full T cell polarization requires interaction with antigen-presenting cells in the non-lymphoid tissue where the antigen resides, I re-design the 'cancer-immunity cycle' to incorporate intratumoural activation of cancer-specific CD4+ T cells. Lastly, a road map to therapeutic harnessing of immunostimulatory CAF states is proposed.
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Affiliation(s)
- Maria Tsoumakidou
- Institute of Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece.
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Hudson WH, Wieland A. Technology meets TILs: Deciphering T cell function in the -omics era. Cancer Cell 2023; 41:41-57. [PMID: 36206755 PMCID: PMC9839604 DOI: 10.1016/j.ccell.2022.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/15/2022] [Accepted: 09/15/2022] [Indexed: 01/17/2023]
Abstract
T cells are at the center of cancer immunology because of their ability to recognize mutations in tumor cells and directly mediate cancer cell killing. Immunotherapies to rejuvenate exhausted T cell responses have transformed the clinical management of several malignancies. In parallel, the development of novel multidimensional analysis platforms, such as single-cell RNA sequencing and high-dimensional flow cytometry, has yielded unprecedented insights into immune cell biology. This convergence has revealed substantial heterogeneity of tumor-infiltrating immune cells in single tumors, across tumor types, and among individuals with cancer. Here we discuss the opportunities and challenges of studying the complex tumor microenvironment with -omics technologies that generate vast amounts of data, highlighting the opportunities and limitations of these technologies with a particular focus on interpreting high-dimensional studies of CD8+ T cells in the tumor microenvironment.
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Affiliation(s)
- William H Hudson
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Andreas Wieland
- Department of Otolaryngology, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH 43210, USA.
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30
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Shu T, Zhou Z, Bai J, Xiao X, Gao M, Zhang N, Wang H, Xia X, Gao Y, Zheng H. Circulating T-cell receptor diversity as predictive biomarker for PARP inhibitors maintenance therapy in high grade serous ovarian cancer. Gynecol Oncol 2023; 168:135-143. [PMID: 36442424 DOI: 10.1016/j.ygyno.2022.11.013] [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: 06/17/2022] [Revised: 10/17/2022] [Accepted: 11/13/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVE T-cell receptor (TCR) repertoire diversity is getting increasing attention as a predictive biomarker in cancer patients. However, the characteristics of the TCR together with its predictive significance for high grade serous ovarian cancer (HGSOC) patients receiving poly (ADP-ribose) polymerase inhibitor (PARPi) maintenance therapy remain unknown. METHODS Twenty-seven patients with HGSOC were analyzed including 22 patients receiving PARPi maintenance therapy and 5 untreated patients as control. Peripheral blood samples were collected for TCR sequencing at baseline as well as one month and three months after the exposure to PARPi. To determine whether TCR diversity was related to PARPi efficacy, we compared the TCR repertoire between patients who had received PARPi and those who had not. RESULTS For patients receiving PARPi treatment or not, we evaluated changes in clone abundance during PARPi maintenance and the similarity of the TCR repertoire before and after the treatment. The results revealed that patients receiving PARPi had TCR repertoires that were more stable than those of untreated cases. We next correlated TCR diversity with the efficacy of PARPi in the treatment group. The rising trend of TCR diversity after three months with PARPi treatment was associated with a longer PFS (21.7 vs 7.4 months, hazard ratio = 0.19, p < 0.001) and a better response to PARPi (91.7% vs 25.0%, p = 0.004). Furthermore, we discovered that the primary characteristic with predictive value for the effectiveness of PARPi is the considerable reduction of the high-frequency T cell clones. CONCLUSION We suggested that the circulating TCR diversity could be a potential predictive biomarker for PARPi maintenance therapy in HGSOC.
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Affiliation(s)
- Tong Shu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gynecologic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhipeng Zhou
- Geneplus-Beijing Institute, Beijing 102206, China
| | - Jing Bai
- Geneplus-Beijing Institute, Beijing 102206, China
| | - Xiao Xiao
- Geneplus-Shenzhen Institute, Guangdong 518118, China
| | - Min Gao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gynecologic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Nan Zhang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gynecologic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Hongguo Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gynecologic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xuefeng Xia
- Geneplus-Beijing Institute, Beijing 102206, China
| | - Yunong Gao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gynecologic Oncology, Peking University Cancer Hospital & Institute, Beijing, China.
| | - Hong Zheng
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gynecologic Oncology, Peking University Cancer Hospital & Institute, Beijing, China.
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31
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Huang B, Zhang J, Zong W, Chen S, Zong Z, Zeng X, Zhang H. Myeloidcells in the immunosuppressive microenvironment in glioblastoma: The characteristics and therapeutic strategies. Front Immunol 2023; 14:994698. [PMID: 36923402 PMCID: PMC10008967 DOI: 10.3389/fimmu.2023.994698] [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: 07/15/2022] [Accepted: 01/31/2023] [Indexed: 03/03/2023] Open
Abstract
Glioblastoma (GBM) is the most common and lethal malignant tumor of the central nervous system in adults. Conventional therapies, including surgery, radiotherapy, and chemotherapy, have limited success in ameliorating patient survival. The immunosuppressive tumor microenvironment, which is infiltrated by a variety of myeloid cells, has been considered a crucial obstacle to current treatment. Recently, immunotherapy, which has achieved great success in hematological malignancies and some solid cancers, has garnered extensive attention for the treatment of GBM. In this review, we will present evidence on the features and functions of different populations of myeloid cells, and on current clinical advances in immunotherapies for glioblastoma.
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Affiliation(s)
- Boyuan Huang
- Department of Neurosurgery, Capital Medical University Electric Power Teaching Hospital/State Grid Beijing Electric Power Hospital, Beijing, China
| | - Jin Zhang
- Department of Neurosurgery, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Wenjing Zong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Sisi Chen
- Department of neurosurgery, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang, China
| | - Zhitao Zong
- Department of neurosurgery, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang, China
| | - Xiaojun Zeng
- Department of Neurosurgery, Shenzhen Key Laboratory of Neurosurgery, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Hongbo Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Francisco-Cruz A, Rocha P, Reuben A, Krishnan SN, Das P, Chen R, Quek K, Li J, Parra ER, Solis LM, Barua S, Jiang M, Lazcano R, Chow CW, Behrens C, Gumb C, Little L, Fukuoka J, Kalhor N, Weissferdt A, Kadara H, Heymach JV, Swisher S, Sepesi B, Rao A, Moran C, Zhang J, Lee JJ, Fujimoto J, Futreal PA, Wistuba II, Peterson CB, Zhang J. Analysis of Immune Intratumor Heterogeneity Highlights Immunoregulatory and Coinhibitory Lymphocytes as Hallmarks of Recurrence in Stage I Non-Small Cell Lung Cancer. Mod Pathol 2023; 36:100028. [PMID: 36788067 PMCID: PMC10251498 DOI: 10.1016/j.modpat.2022.100028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 07/19/2022] [Accepted: 09/01/2022] [Indexed: 01/19/2023]
Abstract
Our understanding of the molecular mechanisms underlying postsurgical recurrence of non-small cell lung cancer (NSCLC) is rudimentary. Molecular and T cell repertoire intratumor heterogeneity (ITH) have been reported to be associated with postsurgical relapse; however, how ITH at the cellular level impacts survival is largely unknown. Here we report the analysis of 2880 multispectral images representing 14.2% to 27% of tumor areas from 33 patients with stage I NSCLC, including 17 cases (relapsed within 3 years after surgery) and 16 controls (without recurrence ≥5 years after surgery) using multiplex immunofluorescence. Spatial analysis was conducted to quantify the minimum distance between different cell types and immune cell infiltration around malignant cells. Immune ITH was defined as the variance of immune cells from 3 intratumor regions. We found that tumors from patients having relapsed display different immune biology compared with nonrecurrent tumors, with a higher percentage of tumor cells and macrophages expressing PD-L1 (P =.031 and P =.024, respectively), along with an increase in regulatory T cells (Treg) (P =.018), antigen-experienced T cells (P =.025), and effector-memory T cells (P =.041). Spatial analysis revealed that a higher level of infiltration of PD-L1+ macrophages (CD68+PD-L1+) or antigen-experienced cytotoxic T cells (CD3+CD8+PD-1+) in the tumor was associated with poor overall survival (P =.021 and P =.006, respectively). A higher degree of Treg ITH was associated with inferior recurrence-free survival regardless of tumor mutational burden (P =.022), neoantigen burden (P =.021), genomic ITH (P =.012) and T cell repertoire ITH (P =.001). Using multiregion multiplex immunofluorescence, we characterized ITH at the immune cell level along with whole exome and T cell repertoire sequencing from the same tumor regions. This approach highlights the role of immunoregulatory and coinhibitory signals as well as their spatial distribution and ITH that define the hallmarks of tumor relapse of stage I NSCLC.
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Affiliation(s)
- Alejandro Francisco-Cruz
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pedro Rocha
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; University of Barcelona, Barcelona, Spain
| | - Alexandre Reuben
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Santhoshi N Krishnan
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas; Department of Computational Biology and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Priyam Das
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Runzhe Chen
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kelly Quek
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jun Li
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edwin R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luisa M Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Souptik Barua
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas
| | - Mei Jiang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chi-Wan Chow
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carmen Behrens
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Curtis Gumb
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Latasha Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Annikka Weissferdt
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John V Heymach
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Arvind Rao
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas; Department of Computational Biology and Bioinformatics, University of Michigan, Ann Arbor, Michigan; Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Cesar Moran
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Christine B Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Jianjun Zhang
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Porciello N, Franzese O, D’Ambrosio L, Palermo B, Nisticò P. T-cell repertoire diversity: friend or foe for protective antitumor response? JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:356. [PMID: 36550555 PMCID: PMC9773533 DOI: 10.1186/s13046-022-02566-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Profiling the T-Cell Receptor (TCR) repertoire is establishing as a potent approach to investigate autologous and treatment-induced antitumor immune response. Technical and computational breakthroughs, including high throughput next-generation sequencing (NGS) approaches and spatial transcriptomics, are providing unprecedented insight into the mechanisms underlying antitumor immunity. A precise spatiotemporal variation of T-cell repertoire, which dynamically mirrors the functional state of the evolving host-cancer interaction, allows the tracking of the T-cell populations at play, and may identify the key cells responsible for tumor eradication, the evaluation of minimal residual disease and the identification of biomarkers of response to immunotherapy. In this review we will discuss the relationship between global metrics characterizing the TCR repertoire such as T-cell clonality and diversity and the resultant functional responses. In particular, we will explore how specific TCR repertoires in cancer patients can be predictive of prognosis or response to therapy and in particular how a given TCR re-arrangement, following immunotherapy, can predict a specific clinical outcome. Finally, we will examine current improvements in terms of T-cell sequencing, discussing advantages and challenges of current methodologies.
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Affiliation(s)
- Nicla Porciello
- grid.417520.50000 0004 1760 5276Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Ornella Franzese
- grid.6530.00000 0001 2300 0941Department of Systems Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Lorenzo D’Ambrosio
- grid.417520.50000 0004 1760 5276Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Belinda Palermo
- grid.417520.50000 0004 1760 5276Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Paola Nisticò
- grid.417520.50000 0004 1760 5276Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
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Yang B, Li X, Zhang W, Fan J, Zhou Y, Li W, Yin J, Yang X, Guo E, Li X, Fu Y, Liu S, Hu D, Qin X, Dou Y, Xiao R, Lu F, Wang Z, Qin T, Wang W, Zhang Q, Li S, Ma D, Mills GB, Chen G, Sun C. Spatial heterogeneity of infiltrating T cells in high-grade serous ovarian cancer revealed by multi-omics analysis. Cell Rep Med 2022; 3:100856. [PMID: 36543113 PMCID: PMC9798026 DOI: 10.1016/j.xcrm.2022.100856] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 09/03/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022]
Abstract
Tumor-infiltrating lymphocytes (TILs), especially CD8+ TILs, represent a favorable prognostic factor in high-grade serous ovarian cancer (HGSOC) and other tumor lineages. Here, we analyze the spatial heterogeneity of different TIL subtypes in HGSOC. We integrated RNA sequencing, whole-genome sequencing, bulk T cell receptor (TCR) sequencing, as well as single-cell RNA/TCR sequencing to investigate the characteristics and differential composition of TILs across different HGSOC sites. Two immune "cold" patterns in ovarian cancer are identified: (1) ovarian lesions with low infiltration of mainly dysfunctional T cells and immunosuppressive Treg cells and (2) omental lesions infiltrated with non-tumor-specific bystander cells. Exhausted CD8 T cells that are preferentially enriched in ovarian tumors exhibit evidence for expansion and cytotoxic activity. Inherent tumor immune microenvironment characteristics appear to be the main contributor to the spatial differences in TIL status. The landscape of spatial heterogeneity of TILs may inform potential strategies for therapeutic manipulation in HGSOC.
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Affiliation(s)
- Bin Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiong Li
- Department of Gynecology & Obstetrics, the Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Zhang
- City University of Hong Kong, Shenzhen Research Institute, Shenzhen 518083, China
| | - Junpeng Fan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yong Zhou
- City University of Hong Kong, Shenzhen Research Institute, Shenzhen 518083, China
| | - Wenting Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jingjing Yin
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaohang Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ensong Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xi Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yu Fu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Si Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dianxing Hu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xu Qin
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yingyu Dou
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Rourou Xiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Funian Lu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zizhuo Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tianyu Qin
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Qinghua Zhang
- Department of Gynecology & Obstetrics, the Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuaicheng Li
- City University of Hong Kong, Shenzhen Research Institute, Shenzhen 518083, China
| | - Ding Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Gordon B Mills
- Department of Cell, Development and Cancer Biology, Oregon Health and Sciences University, Portland, OR 97201, USA; Knight Cancer Institute, Portland, OR 97201, USA; Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Spurr LF, Martinez CA, Kang W, Chen M, Zha Y, Hseu R, Gutiontov SI, Turchan WT, Lynch CM, Pointer KB, Chang P, Murgu S, Husain AN, Cody B, Vokes EE, Bestvina CM, Patel JD, Diehn M, Gajewski TF, Weichselbaum RR, Chmura SJ, Pitroda SP. Highly aneuploid non-small cell lung cancer shows enhanced responsiveness to concurrent radiation and immune checkpoint blockade. NATURE CANCER 2022; 3:1498-1512. [PMID: 36443406 DOI: 10.1038/s43018-022-00467-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 10/13/2022] [Indexed: 11/30/2022]
Abstract
Over 500 clinical trials are investigating combination radiotherapy and immune checkpoint blockade (ICB) as cancer treatments; however, the majority of trials have found no positive interaction. Here we perform a comprehensive molecular analysis of a randomized phase I clinical trial of patients with non-small cell lung cancer (NSCLC) treated with concurrent or sequential ablative radiotherapy and ICB. We show that concurrent treatment is superior to sequential treatment in augmenting local and distant tumor responses and in improving overall survival in a subset of patients with immunologically cold, highly aneuploid tumors, but not in those with less aneuploid tumors. In addition, radiotherapy alone decreases intratumoral cytotoxic T cell and adaptive immune signatures, whereas radiotherapy and ICB upregulates key immune pathways. Our findings challenge the prevailing paradigm that local ablative radiotherapy beneficially stimulates the immune response. We propose the use of tumor aneuploidy as a biomarker and therapeutic target in personalizing treatment approaches for patients with NSCLC treated with radiotherapy and ICB.
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Affiliation(s)
- Liam F Spurr
- Pritzker School of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA.,Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA
| | - Carlos A Martinez
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA
| | - Wenjun Kang
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA.,Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Mengjie Chen
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA.,Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Yuanyuan Zha
- Human Immunogenomic Monitoring Facility, The University of Chicago, Chicago, IL, USA
| | - Robyn Hseu
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA
| | - Stanley I Gutiontov
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA
| | - William T Turchan
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA
| | - Connor M Lynch
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA
| | - Kelli B Pointer
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA
| | - Paul Chang
- Department of Radiology, The University of Chicago, Chicago, IL, USA
| | - Septimiu Murgu
- Department of Anesthesia and Critical Care, The University of Chicago, Chicago, IL, USA
| | - Aliya N Husain
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Brittany Cody
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Everett E Vokes
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, IL, USA
| | - Christine M Bestvina
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, IL, USA
| | - Jyoti D Patel
- Division of Hematology and Oncology, Department of Medicine, Northwestern University, Chicago, IL, USA
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.,Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Thomas F Gajewski
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, IL, USA
| | - Ralph R Weichselbaum
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA.,Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, USA
| | - Steven J Chmura
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA
| | - Sean P Pitroda
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA. .,Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, USA.
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36
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Kandalaft LE, Dangaj Laniti D, Coukos G. Immunobiology of high-grade serous ovarian cancer: lessons for clinical translation. Nat Rev Cancer 2022; 22:640-656. [PMID: 36109621 DOI: 10.1038/s41568-022-00503-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
Treatment of high-grade serous ovarian cancer (HGSOC) remains challenging. Although HGSOC can potentially be responsive to immunotherapy owing to endogenous immunity at the molecular or T cell level, immunotherapy for this disease has fallen short of expectations to date. This Review proposes a working classification for HGSOC based on the presence or absence of intraepithelial T cells, and elaborates the putative mechanisms that give rise to such immunophenotypes. These differences might explain the failures of existing immunotherapies, and suggest that rational therapeutic approaches tailored to each immunophenotype might meet with improved success. In T cell-inflamed tumours, treatment could focus on mobilizing pre-existing immunity and strengthening the activation of T cells embedded in intraepithelial tumour myeloid niches. Conversely, in immune-excluded and immune-desert tumours, treatment could focus on restoring inflammation by reprogramming myeloid cells, stromal cells and vascular epithelial cells. Poly(ADP-ribose) polymerase (PARP) inhibitors, low-dose radiotherapy, epigenetic drugs and anti-angiogenesis therapy are among the tools available to restore T cell infiltration in HGSOC tumours and could be implemented in combination with vaccines and redirected T cells.
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Affiliation(s)
- Lana E Kandalaft
- Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Denarda Dangaj Laniti
- Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland.
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37
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Chen Z, Zhu Q, Deng X, Yao W, Zhang W, Liu W, Tang Y, Zhao S. Angioimmunoblastic T-cell lymphoma with predominant CD8+ tumor-infiltrating T-cells is a distinct immune pattern with an immunosuppressive microenvironment. Front Immunol 2022; 13:987227. [PMID: 36325319 PMCID: PMC9618886 DOI: 10.3389/fimmu.2022.987227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/27/2022] [Indexed: 11/19/2022] Open
Abstract
Background Angioimmunoblastic T-cell lymphoma (AITL) has a rich tumor microenvironment (TME) that typically harbors plenty of CD4+tumor infiltrating lymphocytes, (TIL)-T-cells (so called common AITL). Nonetheless, AITL with large numbers of CD8+TIL-Ts that outnumber CD4+cells have been observed (CD8-predominant AITL). However, detailed comparison of CD8-predominant AITL and common AITL are still lacking. Methods We compared clinicopathological features, TIL subsets, TME T cell receptor-β (TRB), and immunoglobulin heavy chain (IGH) repertoires, and gene expression profiles in six CD8-predominant and 12 common AITLs using case-control matching (2014 to 2019). Results Comparing with common AITLs, CD8-predominant AITLs showed more frequent edema (P = 0.011), effusion (P = 0.026), high elevated plasma EBV-DNA (P = 0.008), and shorter survival (P = 0.034). Moreover, they had more pronounced eosinophil increase (P = 0.004) and a higher Ki67 index (P = 0.041). Flow cytometry revealed an inverted CD4/CD8 ratio in TIL-Ts and lower TIL-B proportions (P = 0.041). TRB repertoire metrics deteriorated, including lower productive clones (P = 0.014) and higher clonality score (P = 0.019). The IGH repertoire was also narrowed, showing a higher proportion of the top 10 clones (P = 0.002) and lower entropy (P = 0.027). Gene expression analysis showed significant enrichment for upregulated negative regulation of immune system processes and downregulated T-cell activation and immune cell differentiation. Conclusion Our findings demonstrated that CD8-predominant AITL is a distinct immune pattern of AITL characterized by anti-tumor immunity impairment and an immunosuppressive microenvironment. These characteristics can interpret its severe clinical manifestations and poor outcomes.
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Affiliation(s)
| | | | | | | | | | | | - Yuan Tang
- *Correspondence: Sha Zhao, ; Yuan Tang,
| | - Sha Zhao
- *Correspondence: Sha Zhao, ; Yuan Tang,
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38
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Liu S, Iorgulescu JB, Li S, Borji M, Barrera-Lopez IA, Shanmugam V, Lyu H, Morriss JW, Garcia ZN, Murray E, Reardon DA, Yoon CH, Braun DA, Livak KJ, Wu CJ, Chen F. Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response. Immunity 2022; 55:1940-1952.e5. [PMID: 36223726 PMCID: PMC9745674 DOI: 10.1016/j.immuni.2022.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 06/21/2022] [Accepted: 08/31/2022] [Indexed: 12/15/2022]
Abstract
T cells mediate antigen-specific immune responses to disease through the specificity and diversity of their clonotypic T cell receptors (TCRs). Determining the spatial distributions of T cell clonotypes in tissues is essential to understanding T cell behavior, but spatial sequencing methods remain unable to profile the TCR repertoire. Here, we developed Slide-TCR-seq, a 10-μm-resolution method, to sequence whole transcriptomes and TCRs within intact tissues. We confirmed the ability of Slide-TCR-seq to map the characteristic locations of T cells and their receptors in mouse spleen. In human lymphoid germinal centers, we identified spatially distinct TCR repertoires. Profiling T cells in renal cell carcinoma and melanoma specimens revealed heterogeneous immune responses: T cell states and infiltration differed intra- and inter-clonally, and adjacent tumor and immune cells exhibited distinct gene expression. Altogether, our method yields insights into the spatial relationships between clonality, neighboring cell types, and gene expression that drive T cell responses.
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Affiliation(s)
- Sophia Liu
- Biophysics Program, Harvard University, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - J Bryan Iorgulescu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mehdi Borji
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Vignesh Shanmugam
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Haoxiang Lyu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Julia W Morriss
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zoe N Garcia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David A Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Charles H Yoon
- Department of Surgical Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David A Braun
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Yale Center of Cellular and Molecular Oncology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Stem Cell Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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39
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Characteristics and significance of peripheral blood T-cell receptor repertoire features in patients with indeterminate lung nodules. Signal Transduct Target Ther 2022; 7:348. [PMID: 36210387 PMCID: PMC9548502 DOI: 10.1038/s41392-022-01169-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 07/21/2022] [Accepted: 08/19/2022] [Indexed: 11/08/2022] Open
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40
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Wolf Y, Samuels Y. Intratumor Heterogeneity and Antitumor Immunity Shape One Another Bidirectionally. Clin Cancer Res 2022; 28:2994-3001. [PMID: 35380639 PMCID: PMC9306293 DOI: 10.1158/1078-0432.ccr-21-1355] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/10/2022] [Accepted: 03/28/2022] [Indexed: 01/07/2023]
Abstract
Over the last decade, it has become clear that the genomic landscapes of tumors profoundly impact their immunogenicity and how tumor cells interact with immune cells. Whereas past discoveries mainly focused on the interplay between tumor immunogenicity and tumor mutational burden (TMB), under the assumption that a higher mutation load would give rise to a better patient response to immune checkpoint blockade therapies, we and others have underlined intratumor heterogeneity (ITH) as an important determinant of the magnitude of the antitumor response and the nature of the tumor microenvironment. In this review, we define TMB versus ITH and how the two factors are being inferred from data, examine key findings in the cancer immunogenomics literature deciphering the complex cross-talk between TMB, ITH, and antitumor immunity in human cancers and in vivo models, and discuss the mutual influence of ITH and immunity-how the antitumor response can give rise to tumors with higher ITH, and how higher ITH can put shackles on the antitumor response.
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Affiliation(s)
- Yochai Wolf
- Ella Lemelbaum Institute for Immuno-Oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Corresponding Authors: Yochai Wolf, Ella Lemelbaum Institute for Immuno-Oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Ramat Gan 5265601, Israel. E-mail: ; and Yardena Samuels, Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761000, Israel. E-mail:
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Corresponding Authors: Yochai Wolf, Ella Lemelbaum Institute for Immuno-Oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Ramat Gan 5265601, Israel. E-mail: ; and Yardena Samuels, Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761000, Israel. E-mail:
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41
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Xu H, Clemenceau JR, Park S, Choi J, Lee SH, Hwang TH. Spatial heterogeneity and organization of tumor mutation burden with immune infiltrates within tumors based on whole slide images correlated with patient survival in bladder cancer. J Pathol Inform 2022; 13:100105. [PMID: 36268064 PMCID: PMC9577053 DOI: 10.1016/j.jpi.2022.100105] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023] Open
Abstract
Background High tumor mutation burden (TMB-H) could result in an increased number of neoepitopes from somatic mutations expressed by a patient's own tumor cell which can be recognized and targeted by neighboring tumor-infiltrating lymphocytes (TILs). Deeper understanding of spatial heterogeneity and organization of tumor cells and their neighboring immune infiltrates within tumors could provide new insights into tumor progression and treatment response. Methods Here we first developed computational approaches using whole slide images (WSIs) to predict bladder cancer patients' TMB status and TILs across tumor regions, and then investigate spatial heterogeneity and organization of regions harboring TMB-H tumor cells and TILs within tumors, as well as their prognostic utility. Results: In experiments using WSIs from The Cancer Genome Atlas (TCGA) bladder cancer (BLCA), our findings show that computational pathology can reliably predict patient-level TMB status and delineate spatial TMB heterogeneity and co-organization with TILs. TMB-H patients with low spatial heterogeneity enriched with high TILs show improved overall survival. Conclusions Computational approaches using WSIs have the potential to provide rapid and cost-effective TMB testing and TILs detection. Survival analysis illuminates potential clinical utility of spatial heterogeneity and co-organization of TMB and TILs as a prognostic biomarker in BLCA which warrants further validation in future studies.
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Affiliation(s)
- Hongming Xu
- School of Biomedical Engineering, Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian 116024, China
- Liaoning Key Laboratory of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian 116024, China
| | - Jean René Clemenceau
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Sunho Park
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Jinhwan Choi
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Sung Hak Lee
- Department of Hospital Pathology, Seoul St.Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, South Korea
| | - Tae Hyun Hwang
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Jacksonville, FL 32224, USA
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42
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Jhala G, Krishnamurthy B, Brodnicki TC, Ge T, Akazawa S, Selck C, Trivedi PM, Pappas EG, Mackin L, Principe N, Brémaud E, De George DJ, Boon L, Smyth I, Chee J, Kay TWH, Thomas HE. Interferons limit autoantigen-specific CD8 + T-cell expansion in the non-obese diabetic mouse. Cell Rep 2022; 39:110747. [PMID: 35476975 DOI: 10.1016/j.celrep.2022.110747] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/24/2022] [Accepted: 04/07/2022] [Indexed: 11/24/2022] Open
Abstract
Interferon gamma (IFNγ) is a proinflammatory cytokine implicated in autoimmune diseases. However, deficiency or neutralization of IFNγ is ineffective in reducing disease. We characterize islet antigen-specific T cells in non-obese diabetic (NOD) mice lacking all three IFN receptor genes. Diabetes is minimally affected, but at 125 days of age, antigen-specific CD8+ T cells, quantified using major histocompatibility complex class I tetramers, are present in 10-fold greater numbers in Ifngr-mutant NOD mice. T cells from Ifngr-mutant mice have increased proliferative responses to interleukin-2 (IL-2). They also have reduced phosphorylated STAT1 and its target gene, suppressor of cytokine signaling 1 (SOCS-1). IFNγ controls the expansion of antigen-specific CD8+ T cells by mechanisms which include increased SOCS-1 expression that regulates IL-2 signaling. The expanded CD8+ T cells are likely to contribute to normal diabetes progression despite reduced inflammation in Ifngr-mutant mice.
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Affiliation(s)
- Gaurang Jhala
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, VIC 3065, Australia
| | - Balasubramanian Krishnamurthy
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, VIC 3065, Australia; Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, VIC 3065, Australia
| | - Thomas C Brodnicki
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, VIC 3065, Australia; Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, VIC 3065, Australia; Department of Microbiology and Immunology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Tingting Ge
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, VIC 3065, Australia; Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, VIC 3065, Australia
| | - Satoru Akazawa
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, VIC 3065, Australia
| | - Claudia Selck
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, VIC 3065, Australia
| | - Prerak M Trivedi
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, VIC 3065, Australia
| | - Evan G Pappas
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, VIC 3065, Australia
| | - Leanne Mackin
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, VIC 3065, Australia
| | - Nicola Principe
- National Centre of Asbestos-Related Diseases, Institute of Respiratory Health, School of Biomedical Science, University of Western Australia, Nedlands, WA 6009, Australia
| | - Erwan Brémaud
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, VIC 3065, Australia
| | - David J De George
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, VIC 3065, Australia; Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, VIC 3065, Australia
| | - Louis Boon
- Polpharma Biologics, 3584 CM Utrecht, the Netherlands
| | - Ian Smyth
- Australian Phenomics Network, Monash Genome Modification Platform, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia
| | - Jonathan Chee
- National Centre of Asbestos-Related Diseases, Institute of Respiratory Health, School of Biomedical Science, University of Western Australia, Nedlands, WA 6009, Australia
| | - Thomas W H Kay
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, VIC 3065, Australia; Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, VIC 3065, Australia.
| | - Helen E Thomas
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, VIC 3065, Australia; Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, VIC 3065, Australia
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43
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Genomic and TCR profiling data reveal the distinct molecular traits in epithelial ovarian cancer histotypes. Oncogene 2022; 41:3093-3103. [PMID: 35468938 DOI: 10.1038/s41388-022-02277-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/24/2022] [Accepted: 03/11/2022] [Indexed: 11/08/2022]
Abstract
Epithelial ovarian cancer (EOC) is classified into five major histotypes: high-grade serous (HGSOC), low-grade serous (LGSOC), clear cell (CCOC), endometrioid (ENOC), and mucinous (MOC). However, the landscape of molecular and immunological alterations in these histotypes, especially LGSOC, CCOC, ENOC, and MOC, is largely uncharacterized. We collected 101 treatment-naive EOC patients. The resected tumor tissues and paired preoperative peripheral blood samples were collected and subjected to target sequencing of 1021 cancer-associated genes and T cell repertoire sequencing. Distinct characteristics of mutations were identified among the five histotypes. Furthermore, tumor mutation burden (TMB) was found to be higher in CCOC and ENOC, but lower in LGSOC and HGSOC. Alterations associated with DNA damage repair (DDR) pathways and homologous recombination deficiencies (HRD) were prevalent in five histotypes. CCOC demonstrated increased level of T cell clonality compared with HSGOC. Interestingly, the proportion of the 100 most common T cell clones was associated with TMB and tumor neoantigen burden in CCOC, highlighting more sensitive anti-tumor responses in this histotype, which was also evidenced by the enhanced convergent recombination of T cell clones. These findings shed light on the molecular traits of genomic alteration and T cell repertoire in the five major EOC histotypes and may help optimize clinical management of EOC with different histotypes.
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44
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Jia Q, Wang A, Yuan Y, Zhu B, Long H. Heterogeneity of the tumor immune microenvironment and its clinical relevance. Exp Hematol Oncol 2022; 11:24. [PMID: 35461288 PMCID: PMC9034473 DOI: 10.1186/s40164-022-00277-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/10/2022] [Indexed: 02/08/2023] Open
Abstract
During the course of tumorigenesis and subsequent metastasis, malignant cells gradually diversify and become more heterogeneous. Consequently, the tumor mass might be infiltrated by diverse immune-related components, including the cytokine/chemokine environment, cytotoxic activity, or immunosuppressive elements. This immunological heterogeneity is universally presented spatially or varies temporally along with tumor evolution or therapeutic intervention across almost all solid tumors. The heterogeneity of anti-tumor immunity shows a profound association with the progression of disease and responsiveness to treatment, particularly in the realm of immunotherapy. Therefore, an accurate understanding of tumor immunological heterogeneity is essential for the development of effective therapies. Facilitated by multi-regional and -omics sequencing, single cell sequencing, and longitudinal liquid biopsy approaches, recent studies have demonstrated the potential to investigate the complexity of immunological heterogeneity of the tumors and its clinical relevance in immunotherapy. Here, we aimed to review the mechanism underlying the heterogeneity of the immune microenvironment. We also explored how clinical assessments of tumor heterogeneity might facilitate the development of more effective personalized therapies.
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Affiliation(s)
- Qingzhu Jia
- Institute of Cancer, Xinqiao Hospital, Army Military Medical University, Xinqiao Main Street, Chongqing, 400037, China.,Chongqing Key Laboratory of Immunotherapy, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Aoyun Wang
- Institute of Cancer, Xinqiao Hospital, Army Military Medical University, Xinqiao Main Street, Chongqing, 400037, China.,Chongqing Key Laboratory of Immunotherapy, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Yixiao Yuan
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Bo Zhu
- Institute of Cancer, Xinqiao Hospital, Army Military Medical University, Xinqiao Main Street, Chongqing, 400037, China. .,Chongqing Key Laboratory of Immunotherapy, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.
| | - Haixia Long
- Institute of Cancer, Xinqiao Hospital, Army Military Medical University, Xinqiao Main Street, Chongqing, 400037, China. .,Chongqing Key Laboratory of Immunotherapy, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.
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45
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Cantini L, Laniado I, Murthy V, Sterman D, Aerts JGJV. Immunotherapy for mesothelioma: Moving beyond single immune check point inhibition. Lung Cancer 2022; 165:91-101. [PMID: 35114509 DOI: 10.1016/j.lungcan.2022.01.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 01/20/2022] [Indexed: 12/29/2022]
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive neoplasm with low survival rates. Platinum-based chemotherapy has represented the cornerstone of treatment for over a decade, prompting the investigation of new therapeutic strategies both in the early stage of the disease and in the advanced setting. The advent of immune check-point inhibitors (ICIs) has recently revamped the enthusiasm for using immunotherapy also in MPM. However, results from first clinical trials using single immune check-point inhibition have been conflicting, and this may be mainly attributed to the lack of specific biomarkers as well as to intra- and inter- patient heterogeneity. The phase III Checkmate743 firstly demonstrated the superiority of an ICI combination (nivolumab plus ipilimumab) over chemotherapy in the first-line treatment of unresectable MPM, leading to FDA approval of this regimen and showing that moving beyond single immune check point inhibition might be a successful strategy to overcome resistance in the majority of MPM patients. In this review, we describe the emerging immunotherapy strategies for the treatment of MPM. We also discuss how refining the approach in pre-clinical studies towards a more holistic perspective (which takes into account not only genetic but also pathophysiological vulnerabilities) and strengthening multi-institutional collaboration in clinical trials is finally helping the clinical development of immunotherapy in MPM.
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Affiliation(s)
- Luca Cantini
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Clinical Oncology, Università Politecnica Delle Marche, AOU Ospedali Riuniti Ancona, Italy
| | - Isaac Laniado
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University (NYU), School of Medicine/NYU Langone Medical Center, New York, NY, United States
| | - Vivek Murthy
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University (NYU), School of Medicine/NYU Langone Medical Center, New York, NY, United States
| | - Daniel Sterman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University (NYU), School of Medicine/NYU Langone Medical Center, New York, NY, United States
| | - Joachim G J V Aerts
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
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46
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Chen X, Lin Y, Qu Q, Ning B, Chen H, Liao B, Li X. Analyzing Association between Expression Quantitative Trait and CNV for Breast Cancer Based on Gene Interaction Network Clustering and Group Sparse Learning. Curr Bioinform 2022. [DOI: 10.2174/1574893617666220207095117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aims:
The occurrence and development of tumor is accompanied by the change of pathogenic gene expression. Tumor cells avoid the damage of immune cells by regulating the expression of immune related genes.
Background:
Tracing the causes of gene expression variation is helpful to understand tumor evolution and metastasis.
Objective:
Current gene expression variation explanation methods are confronted with several main challenges: low explanation power, insufficient prediction accuracy, and lack of biological meaning.
Method:
In this study, we propose a novel method to analyze the mRNA expression variations of breast cancers risk genes. Firstly, we collected some high-confidence risk genes related to breast cancer and then designed a rank-based method to preprocess the breast cancers copy number variation (CNV) and mRNA data. Secondly, to elevate the biological meaning and narrow down the combinatorial space, we introduced a prior gene interaction network and applied a network clustering algorithm to generate high density subnetworks. Lastly, to describe the interlinked structure within and between subnetworks and target genes mRNA expression, we proposed a group sparse learning model to identify CNVs for pathogenic genes expression variations.
Result:
The performance of the proposed method is evaluated by both significantly improved predication accuracy and biological meaning of pathway enrichment analysis.
Conclusion:
The experimental results show that our method has practical significance
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Affiliation(s)
- Xia Chen
- College of Computer Science and Electronic Engineering, Hunan University, Changsha,
Hunan, China
- School of Basic Education, Changsha Aeronautical Vocational and Technical College,
Changsha, Hunan, China
| | - Yexiong Lin
- College of Computer Science and Electronic Engineering, Hunan University, Changsha,
Hunan, China
| | - Qiang Qu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha,
Hunan, China
| | - Bin Ning
- College of Computer Science and Electronic Engineering, Hunan University, Changsha,
Hunan, China
| | - Haowen Chen
- College of Computer Science and Electronic Engineering, Hunan University, Changsha,
Hunan, China
| | - Bo Liao
- Ministry of Education, Hainan Normal University, Haikou, China
| | - Xiong Li
- School of Software, East China Jiaotong University, Nanchang, 330013, China
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47
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Kerdidani D, Aerakis E, Verrou KM, Angelidis I, Douka K, Maniou MA, Stamoulis P, Goudevenou K, Prados A, Tzaferis C, Ntafis V, Vamvakaris I, Kaniaris E, Vachlas K, Sepsas E, Koutsopoulos A, Potaris K, Tsoumakidou M. Lung tumor MHCII immunity depends on in situ antigen presentation by fibroblasts. J Exp Med 2022; 219:212965. [PMID: 35029648 PMCID: PMC8764966 DOI: 10.1084/jem.20210815] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 11/18/2021] [Accepted: 12/16/2021] [Indexed: 12/14/2022] Open
Abstract
A key unknown of the functional space in tumor immunity is whether CD4 T cells depend on intratumoral MHCII cancer antigen recognition. MHCII-expressing, antigen-presenting cancer-associated fibroblasts (apCAFs) have been found in breast and pancreatic tumors and are considered to be immunosuppressive. This analysis shows that antigen-presenting fibroblasts are frequent in human lung non-small cell carcinomas, where they seem to actively promote rather than suppress MHCII immunity. Lung apCAFs directly activated the TCRs of effector CD4 T cells and at the same time produced C1q, which acted on T cell C1qbp to rescue them from apoptosis. Fibroblast-specific MHCII or C1q deletion impaired CD4 T cell immunity and accelerated tumor growth, while inducing C1qbp in adoptively transferred CD4 T cells expanded their numbers and reduced tumors. Collectively, we have characterized in the lungs a subset of antigen-presenting fibroblasts with tumor-suppressive properties and propose that cancer immunotherapies might be strongly dependent on in situ MHCII antigen presentation.
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Affiliation(s)
- Dimitra Kerdidani
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming," Vari, Greece
| | - Emmanouil Aerakis
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming," Vari, Greece
| | - Kleio-Maria Verrou
- Greek Research Infrastructure for Personalized Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Ilias Angelidis
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming," Vari, Greece
| | - Katerina Douka
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming," Vari, Greece
| | - Maria-Anna Maniou
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming," Vari, Greece
| | - Petros Stamoulis
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming," Vari, Greece
| | - Katerina Goudevenou
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming," Vari, Greece
| | - Alejandro Prados
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming," Vari, Greece
| | - Christos Tzaferis
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming," Vari, Greece.,Greek Research Infrastructure for Personalized Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Vasileios Ntafis
- Animal House Facility, Biomedical Sciences Research Center "Alexander Fleming," Vari, Greece
| | | | - Evangelos Kaniaris
- Department of Respiratory Medicine, Sotiria Chest Hospital, Athens, Greece
| | | | - Evangelos Sepsas
- Department of Thoracic Surgery, Sotiria Chest Hospital, Athens, Greece
| | | | | | - Maria Tsoumakidou
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming," Vari, Greece.,Greek Research Infrastructure for Personalized Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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48
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Joshi K, Milighetti M, Chain BM. Application of T cell receptor (TCR) repertoire analysis for the advancement of cancer immunotherapy. Curr Opin Immunol 2022; 74:1-8. [PMID: 34454284 DOI: 10.1016/j.coi.2021.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 12/14/2022]
Abstract
T cell receptor (TCR) sequencing has emerged as a powerful new technology in analysis of the host-tumour interaction. The advances in NextGen sequencing technologies, coupled with powerful novel bioinformatic tools, allow quantitative and reproducible characterisation of repertoires from tumour and blood samples from an increasing number of patients with a variety of solid cancers. In this review, we consider how global metrics such as T cell clonality and diversity can be extracted from these repertoires and used to give insight into the mechanism of action of immune checkpoint blockade. Furthermore, we explore how the analysis of TCR overlap between repertories can help define spatial and temporal heterogeneity of the anti-tumoural immune response. Finally, we review how analysis of TCR sequence and structure, either of individual TCRs or from sets of related TCRs can be used to annotate the antigenic specificity, with important implications for the development of personalised adoptive cellular immunotherapies.
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Affiliation(s)
- Kroopa Joshi
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Martina Milighetti
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Benjamin M Chain
- Division of Infection and Immunity, University College London, London, United Kingdom; Department of Computer Science, University College London, London, United Kingdom.
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49
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Wu J, Sun W, Yang X, Wang H, Liu X, Chi K, Zhou L, Huang X, Mao L, Zhao S, Ding T, Meng B, Lin D. Heterogeneity of programmed death-ligand 1 expression and infiltrating lymphocytes in paired resected primary and metastatic non-small cell lung cancer. Mod Pathol 2022; 35:218-227. [PMID: 34493824 DOI: 10.1038/s41379-021-00903-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/09/2022]
Abstract
Metastatic tumors (MTs) may show different characteristics of the immune microenvironment from primary tumors (PTs) in non-small cell lung cancer (NSCLC). The heterogeneity of immune markers in metastatic NSCLC and its associated factors has not been well demonstrated. In this study, 64 surgically resected specimens of paired PTs and MTs were obtained from 28 patients with NSCLC. Multiplex immunofluorescence (mIF; panel including programmed death-ligand 1 (PD-L1), Cytokeratin, CD8, and CD68) was performed on whole sections. The heterogeneity of the immune contexture of PD-L1 expression, infiltrating lymphocytes, and immune-to-tumor cell distances was quantified via digital image analysis. In a quantitative comparison of MTs and corresponding PTs, MTs showed higher PD-L1 expression levels, lower density of CD8+ cytotoxic T lymphocytes (CTLs), and longer spatial distance between CTLs and tumor cells. Subgroup analysis, which associated clinical factors, revealed that the heterogeneity of immune markers was more obvious in extrapulmonary, metachronous, and treated MTs, while fewer differences were observed in intrapulmonary, synchronous, and untreated MTs. In particular, MTs showed significantly higher PD-L1 expression and lower lymphocyte infiltration in metastatic NSCLC with EGFR mutations. Prognosis analysis showed that an increased density of CD8+ CTLs in MTs was associated with better overall survival (OS). Therefore, significant discrepancies in PD-L1 expression and lymphocyte infiltration in metastatic NSCLC are most likely associated with temporal heterogeneity with a history of anti-treatment and correlated with EGFR mutations. The detection of immune markers in re-obtained metastatic specimens may be required for immunotherapy prediction in these patients with metastatic NSCLC.
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Affiliation(s)
- Jianghua Wu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China.,Department of Pathology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center of Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center of Cancer, Tianjin, China
| | - Wei Sun
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xin Yang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Haiyue Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xinying Liu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Kaiwen Chi
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Lixin Zhou
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaozheng Huang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Luning Mao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Shuai Zhao
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center of Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center of Cancer, Tianjin, China
| | - Tingting Ding
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center of Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center of Cancer, Tianjin, China
| | - Bin Meng
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center of Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center of Cancer, Tianjin, China
| | - Dongmei Lin
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China.
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50
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Sandgaard KS, Gkouleli T, Attenborough T, Adams S, Gibbons D, Holm M, Eisen S, Baxendale H, De Rossi A, Pahwa S, Chain B, Gkazi AS, Klein N. The importance of taking ART appropriately in children and adolescents with HIV-1 to reach the highest capacity of immune function later in life. Front Immunol 2022; 13:860316. [PMID: 35967315 PMCID: PMC9364750 DOI: 10.3389/fimmu.2022.860316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/28/2022] [Indexed: 11/26/2022] Open
Abstract
Current antiretroviral therapy (ART) guidelines recommend treating all children with HIV-1 infection. This has changed from the broader use of ART to treat children to improve morbidity and minimise mortality. However, prior to current recommendations, not everyone with HIV-1 received timely treatment. What happens to the paediatric immune system when HIV-1 replication is not appropriately supressed remains unclear. 11 samples from adolescents with HIV-1 on ART and uninfected controls in the UK, aged 12-25 years, were examined; overall, adolescents with CD4+ counts > 500/μl and a viral load < 50 copies/ml were compared with adolescents with CD4+ counts < 500/μl and a viral load > 50 copies/ml at time of sampling. Measurements of thymic output were combined with high throughput next generation sequencing and bioinformatics to systematically organize CD4+ and CD8+ T cell receptor (TCR) repertoires. TCR repertoire diversity, clonal expansions, TCR sequence sharing, and formation of TCR clusters in HIV-1 infected adolescents with successful HIV-1 suppression were compared to adolescents with ineffective HIV-1 suppression. Thymic output and CD4+ T cell numbers were decreased in HIV-1 infected adolescents with poor HIV-1 suppression. A strong homeostatic TCR response, driven by the decreased CD4+ T cell compartment and reduced thymic output was observed in the virally uncontrolled HIV-1-infected adolescents. Formation of abundant robust TCR clusters and structurally related TCRs were found in the adolescents with effective HIV-1 suppression. Numerous CD4+ T cell numbers in the virally controlled adolescents emphasize the importance of high thymic output and formation of robust TCR clusters in the maintenance of HIV-1 suppression. While the profound capacity for immune recovery in children may allow better opportunity to deal with immunological stress, when ART is taken appropriately, this study demonstrates new insights into the unique paediatric immune system and the immunological changes when HIV-1 replication is ongoing.
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Affiliation(s)
- Katrine Schou Sandgaard
- Infection, Immunity and Inflammation, University College London (UCL) Great Ormond Street Institute of Child Health, London, United Kingdom.,Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Triantafylia Gkouleli
- Infection, Immunity and Inflammation, University College London (UCL) Great Ormond Street Institute of Child Health, London, United Kingdom.,University College London (UCL) Zayed Centre for Research into Rare Disease in Children, London, United Kingdom
| | - Teresa Attenborough
- Infection, Immunity and Inflammation, University College London (UCL) Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Stuart Adams
- Genetics and Rare Diseases, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Deena Gibbons
- Peter Gorer Department of Immunobiology, Kings College London, London, United Kingdom
| | - Mette Holm
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Sarah Eisen
- Tropical Diseases, University College London Hospital, London, United Kingdom
| | - Helen Baxendale
- Clinical Immunology Department, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Anita De Rossi
- Department of Mother and Child Health, University of Padova, Padova, Italy
| | - Savita Pahwa
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States
| | - Benny Chain
- University College London (UCL) Division of Infection and Immunity, University College London (UCL) Cruciform Building, London, United Kingdom
| | - Athina S Gkazi
- Genetics and Rare Diseases, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Nigel Klein
- Infection, Immunity and Inflammation, University College London (UCL) Great Ormond Street Institute of Child Health, London, United Kingdom
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