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Zuleger CL, Schwartz RW, Ong IM, Newton MA, Vail DM, Albertini MR. Development of a next-generation sequencing protocol for the canine T cell receptor beta chain repertoire. Vet Immunol Immunopathol 2024; 268:110702. [PMID: 38183837 PMCID: PMC10872364 DOI: 10.1016/j.vetimm.2023.110702] [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: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 01/08/2024]
Abstract
Profiling the T cell receptor (TCR) repertoire using next-generation sequencing has become common in both human and translational research. Companion dogs with spontaneous tumors, including canine melanoma, share several features, e.g., natural occurrence, shared environmental exposures, natural outbred population, and immunocompetence. T cells play an important role in the adaptive immune system by recognizing specific antigens via a surface TCR. As such, understanding the canine T cell response to vaccines, cancer, immunotherapies, and infectious diseases is critically important for both dog and human health. Off-the-shelf commercial reagents, kits and services are readily available for human, non-human primate, and mouse in this context. However, these resources are limited for the canine. In this study, we present a cost-effective protocol for analysis of canine TCR beta chain genes. Workflow can be accomplished in 1-2 days starting with total RNA and resulting in libraries ready for sequencing on Illumina platforms.
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Affiliation(s)
- Cindy L Zuleger
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Rene Welch Schwartz
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Irene M Ong
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States; Department of Obstetrics and Gynecology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Michael A Newton
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - David M Vail
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Mark R Albertini
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States; Department of Dermatology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States; The Medical Service, William S. Middleton Memorial Veterans Hospital, Madison, WI, United States.
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Paschold L, Gottschick C, Langer S, Klee B, Diexer S, Aksentijevich I, Schultheiß C, Purschke O, Riese P, Trittel S, Haase R, Dressler F, Eberl W, Hübner J, Strowig T, Guzman CA, Mikolajczyk R, Binder M. T cell repertoire breadth is associated with the number of acute respiratory infections in the LoewenKIDS birth cohort. Sci Rep 2023; 13:9516. [PMID: 37308563 DOI: 10.1038/s41598-023-36144-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/30/2023] [Indexed: 06/14/2023] Open
Abstract
We set out to gain insight into peripheral blood B and T cell repertoires from 120 infants of the LoewenKIDS birth cohort to investigate potential determinants of early life respiratory infections. Low antigen-dependent somatic hypermutation of B cell repertoires, as well as low T and B cell repertoire clonality, high diversity, and high richness especially in public T cell clonotypes reflected the immunological naivety at 12 months of age when high thymic and bone marrow output are associated with relatively few prior antigen encounters. Infants with inadequately low T cell repertoire diversity or high clonality showed higher numbers of acute respiratory infections over the first 4 years of life. No correlation of T or B cell repertoire metrics with other parameters such as sex, birth mode, older siblings, pets, the onset of daycare, or duration of breast feeding was noted. Together, this study supports that-regardless of T cell functionality-the breadth of the T cell repertoire is associated with the number of acute respiratory infections in the first 4 years of life. Moreover, this study provides a valuable resource of millions of T and B cell receptor sequences from infants with available metadata for researchers in the field.
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Affiliation(s)
- Lisa Paschold
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany
| | - Cornelia Gottschick
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Susan Langer
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Bianca Klee
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Sophie Diexer
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christoph Schultheiß
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany
| | - Oliver Purschke
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Peggy Riese
- Department Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Stephanie Trittel
- Department Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Roland Haase
- Department of Neonatology and Pediatric Intensive Care, Hospital St. Elisabeth und St. Barbara, 06110, Halle (Saale), Germany
| | - Frank Dressler
- Department of Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, 30625, Hannover, Germany
| | - Wolfgang Eberl
- Department of Paediatrics, Hospital Braunschweig, 38118, Braunschweig, Germany
| | - Johannes Hübner
- Department of Paediatrics, Dr. von Hauner Children's Hospital, Ludwig- Maximilians-University Munich, 80337, Munich, Germany
| | - Till Strowig
- Department Microbial Immune Regulation, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Carlos A Guzman
- Department Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Rafael Mikolajczyk
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany.
- Division of Medical Oncology, University Hospital Basel, Petersgraben 4, 40314031, Basel, Switzerland.
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Paschold L, Stein A, Thiele B, Tintelnot J, Henkes SS, Coith C, Schultheiß C, Pantel K, Riethdorf S, Binder M. First-line treatment of unresectable or metastatic HER2 positive esophagogastric adenocarcinoma: liquid biomarker analysis of the phase 2 INTEGA trial. J Immunother Cancer 2023; 11:e006678. [PMID: 37328285 PMCID: PMC10277145 DOI: 10.1136/jitc-2023-006678] [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: 05/30/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND The addition of nivolumab to trastuzumab and chemotherapy in first-line unresectable or metastatic HER2 positive esophagogastric adenocarcinoma (HER2+ EGA) results in long progression-free and overall survival as shown by the INTEGA (ipilimumab or FOLFOX in combination with nivolumab and trastuzumab in HER2 positive esophagogastric adenocarcinoma) trial. This trial suggested that the chemotherapy backbone is needed in an unselected HER2+ patient population. Yet, it remains an open question if there are specific patient subsets that may benefit from an enhanced immunotherapeutic but chemotherapy-free approach. METHODS We analyzed blood T cell repertoire metrics determined by next-generation sequencing, circulating tumor cell (CTC) counts detected by CellSearch and their expression of HER2 and PD-L1 as potential liquid biomarkers predicting outcomes on ipilimumab versus FOLFOX (folinic acid, FOL, fluorouracil, F, oxaliplatin, OX) chemotherapy added to a backbone of trastuzumab and nivolumab in patients with HER2+ EGA in the INTEGA trial population. RESULTS Patients with two out of three baseline-determined liquid biomarkers-high T cell repertoire richness, absence of CTCs or HER2-expression on CTCs-made up approximately 44% of HER2+ EGA cases and did not show compromise in efficacy if treated with a chemotherapy-free regimen. Long-term responders showing a progression-free survival of >12 months were enriched in this biomarker triad, especially if treated on the chemotherapy-free arm. CONCLUSION Prospective validation of this liquid biomarker triad is needed to molecularly define HER2+ EGA patient subsets with different needs in the first-line systemic treatment setting.
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Affiliation(s)
- Lisa Paschold
- Internal Medicine IV, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Alexander Stein
- Hematology-Oncology Practice Eppendorf (HOPE), Hamburg, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Thiele
- Department of Internal Medicine II and Clinic of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joseph Tintelnot
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Cornelia Coith
- Institute of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Christoph Schultheiß
- Internal Medicine IV, Martin-Luther-University Halle-Wittenberg, Halle, Germany
- Division of Medical Oncology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, Laboratory of Translational Immuno-Oncology, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Klaus Pantel
- Institute of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Sabine Riethdorf
- Institute of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Mascha Binder
- Division of Medical Oncology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, Laboratory of Translational Immuno-Oncology, University of Basel and University Hospital Basel, Basel, Switzerland
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Chen S, Zhang L, Chen L, Huang Q, Wang Y, Liang Y. Comprehensive analysis of glycoprotein VI-mediated platelet activation signaling pathway for predicting pan-cancer survival and response to anti-PD-1 immunotherapy. Comput Struct Biotechnol J 2023; 21:2873-2883. [PMID: 37206616 PMCID: PMC10189353 DOI: 10.1016/j.csbj.2023.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 05/21/2023] Open
Abstract
Platelets play a vital role in cancer and immunity. However, few comprehensive studies have been conducted on the role of platelet-related signaling pathways in various cancers and their responses to immune checkpoint blockade (ICB) therapy. In the present study, we focused on the glycoprotein VI-mediated platelet activation (GMPA) signaling pathway and comprehensively evaluated its roles in 19 types of cancers listed in The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO). Cox regression and meta-analyses showed that for all 19 types of cancers, patients with high GMPA scores tended to have a good prognosis. Furthermore, the GMPA signature score could serve as an independent prognostic factor for patients with skin cutaneous melanoma (SKCM). The GMPA signature was linked to tumor immunity in all 19 types of cancers, and was correlated with SKCM tumor histology. Compared to other signature scores, the GMPA signature scores for on-treatment samples were more robust predictors of the response to anti-PD-1 blockade in metastatic melanoma. Moreover, the GMPA signature scores were significantly negatively correlated with EMMPRIN (CD147) and positively correlated with CD40LG expression at the transcriptomic level in most cancer patient samples from the TCGA cohort and on-treatment samples from anti-PD1 therapy cohorts. The results of this study provide an important theoretical basis for the use of GMPA signatures, as well as GPVI-EMMPRIN and GPVI-CD40LG pathways, to predict the responses of cancer patients to various types of ICB therapy.
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5
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Mou W, Zhu L, Yang T, Lin A, Lyu Q, Guo L, Liu Z, Cheng Q, Zhang J, Luo P. Relationship between ATOH1 and tumor microenvironment in colon adenocarcinoma patients with different microsatellite instability status. Cancer Cell Int 2022; 22:229. [PMID: 35836254 PMCID: PMC9281179 DOI: 10.1186/s12935-022-02651-6] [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: 04/23/2022] [Accepted: 07/05/2022] [Indexed: 11/19/2022] Open
Abstract
Background Colon adenocarcinoma (COAD) is one of the major varieties of malignant tumors threatening human health today. Immune checkpoint inhibitors (ICIs) have recently begun to emerge as an effective option for the treatment of COAD patients, but not all patients can benefit from ICI treatment. Previous studies have suggested that ICIs boast significant clinical effects on patients with microsatellite instability-high (MSI-H), while conversely patients with microsatellite-stable/microsatellite instability-low (MSS/MSI-L) have shown limited response. Methods We used ATAC-seq, RNA-seq, and mutation data from The Cancer Genome Atlas Colon adenocarcinoma (TCGA-COAD) cohort to perform multi-omics differential analysis on COAD samples with different MSI statuses, then further screened genes by additionally combining these results with survival analysis. We analyzed the effects of the screened genes on the tumor microenvironment and immunogenicity of COAD patients, and subsequently determined their influence on the efficacy of ICIs in COAD patients using a series of predictive indexes. Results Twelve genes were screened in the TCGA-COAD cohort, and after the combined survival analysis, we identified ATOH1 as having significant effects. ATOH1 is characterized by high chromatin accessibility, high expression, and high mutation in COAD patients in the MSI-H group. COAD patients with high ATOH1 expression are associated with a better prognosis, unique immune microenvironment, and higher efficacy in ICI treatment. Enrichment analysis showed that COAD patients with high ATOH1 expression displayed significant upregulation in their humoral immunity and other related pathways. Conclusions We speculate that ATOH1 may influence the efficacy of ICIs therapy in patients with COAD by affecting the immune microenvironment and immunogenicity of the tumor. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02651-6.
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Affiliation(s)
- Weiming Mou
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.,The First Clinical Medical School, Southern Medical University, 1023 Shatai South Road, Guangzhou, 510515, Guangdong, China
| | - Lingxuan Zhu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.,The First Clinical Medical School, Southern Medical University, 1023 Shatai South Road, Guangzhou, 510515, Guangdong, China
| | - Tao Yang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.,The First Clinical Medical School, Southern Medical University, 1023 Shatai South Road, Guangzhou, 510515, Guangdong, China
| | - Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Qiong Lyu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, Guangdong, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.
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Cerqueira OLD, Antunes F, Assis NG, Cardoso EC, Clavijo-Salomón MA, Domingues AC, Tessarollo NG, Strauss BE. Perspectives for Combining Viral Oncolysis With Additional Immunotherapies for the Treatment of Melanoma. Front Mol Biosci 2022; 9:777775. [PMID: 35495634 PMCID: PMC9048901 DOI: 10.3389/fmolb.2022.777775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/22/2022] [Indexed: 12/19/2022] Open
Abstract
Melanoma is the deadliest type of skin cancer with steadily increasing incidence worldwide during the last few decades. In addition to its tumor associated antigens (TAAs), melanoma has a high mutation rate compared to other tumors, which promotes the appearance of tumor specific antigens (TSAs) as well as increased lymphocytic infiltration, inviting the use of therapeutic tools that evoke new or restore pre-existing immune responses. Innovative therapeutic proposals, such as immune checkpoint inhibitors (ICIs), have emerged as effective options for melanoma. However, a significant portion of these patients relapse and become refractory to treatment. Likewise, strategies using viral vectors, replicative or not, have garnered confidence and approval by different regulatory agencies around the world. It is possible that further success of immune therapies against melanoma will come from synergistic combinations of different approaches. In this review we outline molecular features inherent to melanoma and how this supports the use of viral oncolysis and immunotherapies when used as monotherapies or in combination.
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Affiliation(s)
- Otto Luiz Dutra Cerqueira
- Centro de Investigação Translacional em Oncologia (CTO)/LIM, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Fernanda Antunes
- Centro de Investigação Translacional em Oncologia (CTO)/LIM, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Nadine G Assis
- Centro de Investigação Translacional em Oncologia (CTO)/LIM, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Elaine C Cardoso
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Maria A Clavijo-Salomón
- Centro de Investigação Translacional em Oncologia (CTO)/LIM, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Ana C Domingues
- Centro de Investigação Translacional em Oncologia (CTO)/LIM, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Nayara G Tessarollo
- Centro de Investigação Translacional em Oncologia (CTO)/LIM, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Bryan E Strauss
- Centro de Investigação Translacional em Oncologia (CTO)/LIM, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
- *Correspondence: Bryan E Strauss,
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Aran A, Garrigós L, Curigliano G, Cortés J, Martí M. Evaluation of the TCR Repertoire as a Predictive and Prognostic Biomarker in Cancer: Diversity or Clonality? Cancers (Basel) 2022; 14:cancers14071771. [PMID: 35406543 PMCID: PMC8996954 DOI: 10.3390/cancers14071771] [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: 02/14/2022] [Revised: 03/22/2022] [Accepted: 03/29/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The TCR is the T cell antigen receptor, and it is responsible of the T cell activation, through the HLA-antigen complex recognition. Studying the TCR repertoire in patients with cancer can help to better understand the anti-tumoural responses and it has been suggested to have predictive and or/prognostic values, both for the disease and in response to treatments. The aim of this review is to summarize TCR repertoire studies performed in patients with cancer found in the literature, thoroughly analyse the different factors that can be involved in shaping the TCR repertoire, and draw the current conclusions in this field, especially focusing on whether the TCR diversity—or its opposite, the clonality—can be used as predictors or prognostic biomarkers of the disease. Abstract T cells play a vital role in the anti-tumoural response, and the presence of tumour-infiltrating lymphocytes has shown to be directly correlated with a good prognosis in several cancer types. Nevertheless, some patients presenting tumour-infiltrating lymphocytes do not have favourable outcomes. The TCR determines the specificities of T cells, so the analysis of the TCR repertoire has been recently considered to be a potential biomarker for patients’ progression and response to therapies with immune checkpoint inhibitors. The TCR repertoire is one of the multiple elements comprising the immune system and is conditioned by several factors, including tissue type, tumour mutational burden, and patients’ immunogenetics. Its study is crucial to understanding the anti-tumoural response, how to beneficially modulate the immune response with current or new treatments, and how to better predict the prognosis. Here, we present a critical review including essential studies on TCR repertoire conducted in patients with cancer with the aim to draw the current conclusions and try to elucidate whether it is better to encounter higher clonality with few TCRs at higher frequencies, or higher diversity with many different TCRs at lower frequencies.
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Affiliation(s)
- Andrea Aran
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia I Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain;
| | - Laia Garrigós
- International Breast Cancer Center (IBCC), 08017 Barcelona, Spain; (L.G.); (J.C.)
| | - Giuseppe Curigliano
- Division of Early Drug Development, European Institute of Oncology, IRCCS, 20141 Milano, Italy;
- Department of Oncology and Hemato-Oncology, University of Milano, 20122 Milano, Italy
| | - Javier Cortés
- International Breast Cancer Center (IBCC), 08017 Barcelona, Spain; (L.G.); (J.C.)
- Medica Scientia Innovation Research (MedSIR), 08018 Barcelona, Spain
- Medica Scientia Innovation Research (MedSIR), Ridgewood, NJ 07450, USA
- Department of Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Madrid, Spain
| | - Mercè Martí
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia I Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain;
- Correspondence: ; Tel.: +34-935812409
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Bowen SR, Hippe DS, Thomas HM, Sasidharan B, Lampe PD, Baik CS, Eaton KD, Lee S, Martins RG, Santana-Davila R, Chen DL, Kinahan PE, Miyaoka RS, Vesselle HJ, Houghton AM, Rengan R, Zeng J. Prognostic Value of Early Fluorodeoxyglucose-Positron Emission Tomography Response Imaging and Peripheral Immunologic Biomarkers: Substudy of a Phase II Trial of Risk-Adaptive Chemoradiation for Unresectable Non-Small Cell Lung Cancer. Adv Radiat Oncol 2022; 7:100857. [PMID: 35387421 PMCID: PMC8977846 DOI: 10.1016/j.adro.2021.100857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/29/2021] [Indexed: 11/24/2022] Open
Abstract
Purpose We sought to examine the prognostic value of fluorodeoxyglucose-positron emission tomography (PET) imaging during chemoradiation for unresectable non-small cell lung cancer for survival and hypothesized that tumor PET response is correlated with peripheral T-cell function. Methods and Materials Forty-five patients with American Joint Committee on Cancer version 7 stage IIB-IIIB non-small cell lung cancer enrolled in a phase II trial and received platinum-doublet chemotherapy concurrent with 6 weeks of radiation (NCT02773238). Fluorodeoxyglucose-PET was performed before treatment start and after 24 Gy of radiation (week 3). PET response status was prospectively defined by multifactorial radiologic interpretation. PET responders received 60 Gy in 30 fractions, while nonresponders received concomitant boosts to 74 Gy in 30 fractions. Peripheral blood was drawn synchronously with PET imaging, from which germline DNA sequencing, T-cell receptor sequencing, and plasma cytokine analysis were performed. Results Median follow-up was 18.8 months, 1-year overall survival (OS) 82%, 1-year progression-free survival 53%, and 1-year locoregional control 88%. Higher midtreatment PET total lesion glycolysis was detrimental to OS (1 year 87% vs 63%, P < .001), progression-free survival (1 year 60% vs 26%, P = .044), and locoregional control (1 year 94% vs 65%, P = .012), even after adjustment for clinical/treatment factors. Twenty-nine of 45 patients (64%) were classified as PET responders based on a priori definition. Higher tumor programmed death-ligand 1 expression was correlated with response on PET (P = .017). Higher T-cell receptor richness and clone distribution slope were associated with improved OS (P = .018-0.035); clone distribution slope was correlated with PET response (P = .031). Conclusions Midchemoradiation PET imaging is prognostic for survival; PET response may be linked to tumor and peripheral T-cell biomarkers.
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Affiliation(s)
- Stephen R. Bowen
- Radiation Oncology and
- Radiology, University of Washington School of Medicine, Seattle, Washington
| | - Daniel S. Hippe
- Radiology, University of Washington School of Medicine, Seattle, Washington
| | - Hannah M. Thomas
- Department of Radiation Oncology, Christian Medical College, Vellore, India
| | | | - Paul D. Lampe
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Christina S. Baik
- Division of Medical Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Keith D. Eaton
- Division of Medical Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Sylvia Lee
- Division of Medical Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Renato G. Martins
- Division of Medical Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Rafael Santana-Davila
- Division of Medical Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Delphine L. Chen
- Radiology, University of Washington School of Medicine, Seattle, Washington
| | - Paul E. Kinahan
- Radiology, University of Washington School of Medicine, Seattle, Washington
| | - Robert S. Miyaoka
- Radiology, University of Washington School of Medicine, Seattle, Washington
| | - Hubert J. Vesselle
- Radiology, University of Washington School of Medicine, Seattle, Washington
| | - A. McGarry Houghton
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ramesh Rengan
- Radiation Oncology and
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
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Shao MM, Yi FS, Huang ZY, Peng P, Wu FY, Shi HZ, Zhai K. T Cell Receptor Repertoire Analysis Reveals Signatures of T Cell Responses to Human Mycobacterium tuberculosis. Front Microbiol 2022; 13:829694. [PMID: 35197957 PMCID: PMC8859175 DOI: 10.3389/fmicb.2022.829694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/03/2022] [Indexed: 11/17/2022] Open
Abstract
Characterization of T cell receptor (TCR) repertoires is essential for understanding the mechanisms of Mycobacterium tuberculosis (Mtb) infection involving T cell adaptive immunity. The characteristics of TCR sequences and distinctive signatures of T cell subsets in tuberculous patients are still unclear. By combining single-cell TCR sequencing (sc-TCR seq) with single-cell RNA sequencing (sc-RNA seq) and flow cytometry to characterize T cells in tuberculous pleural effusions (TPEs), we identified 41,718 CD3+ T cells in TPEs and paired blood samples, including 30,515 CD4+ T cells and 11,203 CD8+ T cells. Compared with controls, no differences in length and profile of length distribution were observed in complementarity determining region 3 (CDR3) in both CD4+ and CD8+ T cells in TPE. Altered hydrophobicity was demonstrated in CDR3 in CD8+ T cells and a significant imbalance in the TCR usage pattern of T cells with preferential expression of TRBV4-1 in TPE. A significant increase in clonality was observed in TCR repertoires in CD4+ T cells, but not in CD8+ T cells, although both enriched CD4+ and CD8+ T cells showed TH1 and cytotoxic signatures. Furthermore, we identified a new subset of polyfunctional CD4+ T cells with CD1-restricted, TH1, and cytotoxic characteristics, and this subset might provide protective immunity against Mtb.
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Affiliation(s)
- Ming-Ming Shao
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Feng-Shuang Yi
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Zhong-Yin Huang
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Peng Peng
- Department of Respiratory and Critical Care Medicine, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, China
| | - Feng-Yao Wu
- Department of Tuberculosis, Nanning Fourth People’s Hospital, Nanning, China
| | - Huan-Zhong Shi
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Kan Zhai
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- *Correspondence: Kan Zhai,
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10
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Storkus WJ, Maurer D, Lin Y, Ding F, Bose A, Lowe D, Rose A, DeMark M, Karapetyan L, Taylor JL, Chelvanambi M, Fecek RJ, Filderman JN, Looney TJ, Miller L, Linch E, Lowman GM, Kalinski P, Butterfield LH, Tarhini A, Tawbi H, Kirkwood JM. Dendritic cell vaccines targeting tumor blood vessel antigens in combination with dasatinib induce therapeutic immune responses in patients with checkpoint-refractory advanced melanoma. J Immunother Cancer 2021; 9:jitc-2021-003675. [PMID: 34782430 PMCID: PMC8593702 DOI: 10.1136/jitc-2021-003675] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2021] [Indexed: 01/12/2023] Open
Abstract
Background A first-in-human, randomized pilot phase II clinical trial combining vaccines targeting overexpressed, non-mutated tumor blood vessel antigens (TBVA) and tyrosine kinase inhibitor dasatinib was conducted in human leukocyte antigen (HLA)-A2+ patients with advanced melanoma. Methods Patient monocyte-derived type-1-polarized dendritic cells were loaded with HLA-A2-presented peptides derived from TBVA (DLK1, EphA2, HBB, NRP1, RGS5, TEM1) and injected intradermally as a vaccine into the upper extremities every other week. Patients were randomized into one of two treatment arms receiving oral dasatinib (70 mg two times per day) beginning in week 5 (Arm A) or in week 1 (Arm B). Trial endpoints included T cell response to vaccine peptides (interferon-γ enzyme-linked immunosorbent spot), objective clinical response (Response Evaluation Criteria in Solid Tumors V.1.1) and exploratory tumor, blood and serum profiling of immune-associated genes/proteins. Results Sixteen patients with advanced-stage cutaneous (n=10), mucosal (n=1) or uveal (n=5) melanoma were accrued, 15 of whom had previously progressed on programmed cell death protein 1 (PD-1) blockade. Of 13 evaluable patients, 6 patients developed specific peripheral blood T cell responses against ≥3 vaccine-associated peptides, with further evidence of epitope spreading. All six patients with specific CD8+ T cell response to vaccine-targeted antigens exhibited evidence of T cell receptor (TCR) convergence in association with preferred clinical outcomes (four partial response and two stabilization of disease (SD)). Seven patients failed to respond to vaccination (one SD and six progressive disease). Patients in Arm B (immediate dasatinib) outperformed those in Arm A (delayed dasatinib) for immune response rate (IRR; 66.7% vs 28.6%), objective response rate (ORR) (66.7% vs 0%), overall survival (median 15.45 vs 3.47 months; p=0.0086) and progression-free survival (median 7.87 vs 1.97 months; p=0.063). IRR (80% vs 25%) and ORR (60% vs 12.5%) was greater for females versus male patients. Tumors in patients exhibiting response to treatment displayed (1) evidence of innate and adaptive immune-mediated inflammation and TCR convergence at baseline, (2) on-treatment transcriptional changes associated with reduced hypoxia/acidosis/glycolysis, and (3) increased inflammatory immune cell infiltration and tertiary lymphoid structure neogenesis. Conclusions Combined vaccination against TBVA plus dasatinib was safe and resulted in coordinating immunologic and/or objective clinical responses in 6/13 (46%) evaluable patients with melanoma, particularly those initiating treatment with both agents. Trial registration number NCT01876212.
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Affiliation(s)
- Walter J Storkus
- Dermatology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Deena Maurer
- Translational and Regulatory Affairs, Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Yan Lin
- Biostatistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Fei Ding
- Biostatistics, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Anamika Bose
- Immunoregulation and Immunodiagnostics, Chittaranjan National Cancer Institute, Kolkata, West Bengal, India
| | - Devin Lowe
- Immunotherapeutics and Biotechnology, Texas Tech University Health Sciences Center, Abilene, Texas, USA
| | - Amy Rose
- Clinical Research Services, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Melissa DeMark
- Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lilit Karapetyan
- Medicine, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Jennifer L Taylor
- Dermatology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Manoj Chelvanambi
- Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ronald J Fecek
- Microbiology and Immunology, LECOM, Greensburg, Pennsylvania, USA
| | - Jessica N Filderman
- Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Lauren Miller
- Molecular Biology, Thermo Fisher Scientific, Santa Clara, Carlsbad, California, USA
| | - Elizabeth Linch
- Molecular Biology, Thermo Fisher Scientific, Santa Clara, Carlsbad, California, USA
| | - Geoffrey M Lowman
- Molecular Biology, Thermo Fisher Scientific, Santa Clara, Carlsbad, California, USA
| | - Pawel Kalinski
- Medical Oncology and Immunology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Lisa H Butterfield
- Research and Development, Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
- Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
| | - Ahmad Tarhini
- Cutaneous Oncology and Immunology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Hussein Tawbi
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John M Kirkwood
- Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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11
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Shevyrev D, Tereshchenko V, Kozlov V. Immune Equilibrium Depends on the Interaction Between Recognition and Presentation Landscapes. Front Immunol 2021; 12:706136. [PMID: 34394106 PMCID: PMC8362327 DOI: 10.3389/fimmu.2021.706136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/12/2021] [Indexed: 12/15/2022] Open
Abstract
In this review, we described the structure and organization of antigen-recognizing repertoires of B and T cells from the standpoint of modern immunology. We summarized the latest advances in bioinformatics analysis of sequencing data from T and B cell repertoires and also presented contemporary ideas about the mechanisms of clonal diversity formation at different stages of organism development. At the same time, we focused on the importance of the allelic variants of the HLA genes and spectra of presented antigens for the formation of T-cell receptors (TCR) landscapes. The main idea of this review is that immune equilibrium and proper functioning of immunity are highly dependent on the interaction between the recognition and the presentation landscapes of antigens. Certain changes in these landscapes can occur during life, which can affect the protective function of adaptive immunity. We described some mechanisms associated with these changes, for example, the conversion of effector cells into regulatory cells and vice versa due to the trans-differentiation or bystander effect, changes in the clonal organization of the general TCR repertoire due to homeostatic proliferation or aging, and the background for the altered presentation of some antigens due to SNP mutations of MHC, or the alteration of the presenting antigens due to post-translational modifications. The authors suggest that such alterations can lead to an increase in the risk of the development of oncological and autoimmune diseases and influence the sensitivity of the organism to different infectious agents.
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Affiliation(s)
- Daniil Shevyrev
- Laboratory of Clinical Immunopathology, Research Institute for Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - Valeriy Tereshchenko
- Laboratory of Molecular Immunology, Research Institute for Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - Vladimir Kozlov
- Laboratory of Clinical Immunopathology, Research Institute for Fundamental and Clinical Immunology, Novosibirsk, Russia
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12
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Wang J, Bie Z, Zhang Y, Li L, Zhu Y, Zhang Y, Nie X, Zhang P, Cheng G, Di X, Li X, Cheng S, Feng L. Prognostic value of the baseline circulating T cell receptor β chain diversity in advanced lung cancer. Oncoimmunology 2021; 10:1899609. [PMID: 33796410 PMCID: PMC7993185 DOI: 10.1080/2162402x.2021.1899609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
An indicator for systemic evaluation of the adaptive immune status is lacking. Peripheral blood is important in antitumour immunity, and the T-cell receptor (TCR) repertoire diversity is key for effective immunity. This study aimed to investigate changes in the circulating T cell receptor β chain (TCRB) diversity during the first few (1 ~ 4) treatment cycles and its clinical value in patients with advanced lung cancer. TCRB-enriched sequencing data combined with transcriptomic RNA sequencing data of peripheral blood leukocytes were obtained from 72 patients with advanced lung cancer before and after targeted therapy or chemotherapy. Changes in the circulating TCRB diversity during treatment and the relationship of the baseline circulating TCRB diversity with prognosis and therapeutic effects were evaluated. We found that targeted therapy or chemotherapy did not significantly affect the T lymphocyte composition or circulating TCRB diversity (3.83 vs 3.74, T-test, p = .16) in patients with advanced lung adenocarcinoma (LUAD) during the first few treatment cycles. The higher circulating TCRB diversity was linked to improved therapeutic effects (T-test, p = .00083) in LUAD patients receiving targeted therapy. Higher baseline circulating TCRB diversity was associated with better prognosis. In addition, a five-factor prognostic risk score model was built for more accurate prognosis prediction for LUAD patients. The chemotherapeutic agents for advanced lung cancer do not significantly affect adaptive immune function over the first few treatment cycles. The circulating TCRB diversity reflects the adaptive immunological repertoire and might be a convenient indicator for evaluating the adaptive immune status and prognosis.
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Affiliation(s)
- Jiaqi Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhixin Bie
- Minimally Invasive Tumor Therapies Center, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yajing Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Li
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yujie Zhu
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Nie
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ping Zhang
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Gang Cheng
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuebing Di
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoguang Li
- Minimally Invasive Tumor Therapies Center, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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13
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Wang Y, Liu Y, Chen L, Chen Z, Wang X, Jiang R, Zhao K, He X. T Cell Receptor Beta-Chain Profiling of Tumor Tissue, Peripheral Blood and Regional Lymph Nodes From Patients With Papillary Thyroid Carcinoma. Front Immunol 2021; 12:595355. [PMID: 33679738 PMCID: PMC7930746 DOI: 10.3389/fimmu.2021.595355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/25/2021] [Indexed: 11/29/2022] Open
Abstract
Objective: To study the characteristics of the T cell receptor (TCR) repertoire in cancer tissue, peripheral blood and regional lymph nodes (LNs) from patients with papillary thyroid carcinoma (PTC). Methods: PTC tissue, peripheral blood mononuclear cells (PBMCs) and regional LNs of six patients with papillary thyroid carcinoma were harvested. T cell receptor beta-chain (TCRβ) profiling was performed though high-throughput sequencing (HTS), and IMonitor, MiXCR and VDJtools were used to analyze the characteristics of the TCR repertoire. Results: The results of IMonitor and those of MiXCR and VDJtools were very similar. The unique CDR3 of TCRβ from LNs was higher than that of PBMCs, and the CDR3 of TCRβ from LNs was higher than that of PTC tissue. Shannon's diversity index, D50, inverse Simpson index_mean and normalized Shannon's diversity index_mean of CDR3 from LNs were higher than those of PTCs and PBMCs. The HEC (high expansion clones) rate of CDR3 sequences at the amino acid level in PTC tissue was higher than that of PBMCs, which was higher than that of LNs. The V-J HEC rate of CDR3 was highest in PTC tissue, followed by PBMCs and LNs. Conclusion: TCR CDR3 profiling showed differences among and within the PBMCs, PTC tissues and regional LNs of PTC, including unique CDR3, CDR3 HEC at the amino acid level, CDR3 V-J HEC at the amino acid level, Shannon's diversity index and D50. The TCRβ repertoire of PTC tissue, peripheral blood and regional LNs of PTC provide a reference for further study of immunity mechanisms against PTC.
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Affiliation(s)
- Yizeng Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Yuanchao Liu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Li Chen
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Zuoyu Chen
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Xiaoning Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Ruoyu Jiang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Ke Zhao
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Xianghui He
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
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14
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Ratnam NM, Frederico SC, Gonzalez JA, Gilbert MR. Clinical correlates for immune checkpoint therapy: significance for CNS malignancies. Neurooncol Adv 2021; 3:vdaa161. [PMID: 33506203 PMCID: PMC7813206 DOI: 10.1093/noajnl/vdaa161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) have revolutionized the field of cancer immunotherapy. Most commonly, inhibitors of PD-1 and CTLA4 are used having received approval for the treatment of many cancers like melanoma, non-small-cell lung carcinoma, and leukemia. In contrast, to date, clinical studies conducted in patients with CNS malignancies have not demonstrated promising results. However, patients with CNS malignancies have several underlying factors such as treatment with supportive medications like corticosteroids and cancer therapies including radiation and chemotherapy that may negatively impact response to ICIs. Although many clinical trials have been conducted with ICIs, measures that reproducibly and reliably indicate that treatment has evoked an effective immune response have not been fully developed. In this article, we will review the history of ICI therapy and the correlative biology that has been performed in the clinical trials testing these therapies in different cancers. It is our aim to help provide an overview of the assays that may be used to gauge immunologic response. This may be particularly germane for CNS tumors, where there is currently a great need for predictive biomarkers that will allow for the selection of patients with the highest likelihood of responding.
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Affiliation(s)
- Nivedita M Ratnam
- Neuro-Oncology Branch, CCR, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen C Frederico
- Neuro-Oncology Branch, CCR, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Javier A Gonzalez
- Neuro-Oncology Branch, CCR, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, CCR, NCI, National Institutes of Health, Bethesda, Maryland, USA
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