1
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Bo H, Jiang H, Xiong J, Zhang W, Shi Y, Pan C, Wang H. T cell receptor repertoire deciphers anti-tuberculosis immunity. Int Immunopharmacol 2024; 138:112252. [PMID: 38976948 DOI: 10.1016/j.intimp.2024.112252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 07/10/2024]
Abstract
T cell induced cellular immunity is considered to be extremely important for the control of tuberculosis (TB). T cell receptor (TCR), the key component responsible for the specificity and clustering of T cells, holds the potential to advance our understanding of T cell immunity against TB infection. This review systematically expounded the study progressions made in the field of TB-relevant TCRs based on single cell sequencing together with GLIPH2 technology and initiated a comparison of the T cell distribution between peripheral blood and infected organs. We divided clonal expanded T cell clones into recirculation subsets and local subsets to summarize their distinctions in clonal abundance, TCR sequences and antigenic specificity. Notably, local expansion appears to drive the primary variances in T cell subsets between these two contexts, indicating the necessity for further exploration into the functions and specificity of local subsets.
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Affiliation(s)
- Haohui Bo
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Haiqin Jiang
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China.
| | - Jingshu Xiong
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Wenyue Zhang
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Ying Shi
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Chun Pan
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Hongsheng Wang
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China; Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
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2
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Borcherding N, Kim W, Quinn M, Han F, Zhou JQ, Sturtz AJ, Schmitz AJ, Lei T, Schattgen SA, Klebert MK, Suessen T, Middleton WD, Goss CW, Liu C, Crawford JC, Thomas PG, Teefey SA, Presti RM, O'Halloran JA, Turner JS, Ellebedy AH, Mudd PA. CD4 + T cells exhibit distinct transcriptional phenotypes in the lymph nodes and blood following mRNA vaccination in humans. Nat Immunol 2024:10.1038/s41590-024-01888-9. [PMID: 39164479 DOI: 10.1038/s41590-024-01888-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 06/06/2024] [Indexed: 08/22/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and mRNA vaccination induce robust CD4+ T cell responses. Using single-cell transcriptomics, here, we evaluated CD4+ T cells specific for the SARS-CoV-2 spike protein in the blood and draining lymph nodes (dLNs) of individuals 3 months and 6 months after vaccination with the BNT162b2 mRNA vaccine. We analyzed 1,277 spike-specific CD4+ T cells, including 238 defined using Trex, a deep learning-based reverse epitope mapping method to predict antigen specificity. Human dLN spike-specific CD4+ follicular helper T (TFH) cells exhibited heterogeneous phenotypes, including germinal center CD4+ TFH cells and CD4+IL-10+ TFH cells. Analysis of an independent cohort of SARS-CoV-2-infected individuals 3 months and 6 months after infection found spike-specific CD4+ T cell profiles in blood that were distinct from those detected in blood 3 months and 6 months after BNT162b2 vaccination. Our findings provide an atlas of human spike-specific CD4+ T cell transcriptional phenotypes in the dLNs and blood following SARS-CoV-2 vaccination or infection.
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Affiliation(s)
- Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Wooseob Kim
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Microbiology, Korea University College of Medicine, Seoul, Korea
| | - Michael Quinn
- Division of Infectious Diseases, Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Fangjie Han
- Department of Emergency Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Julian Q Zhou
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Alexandria J Sturtz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Aaron J Schmitz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Tingting Lei
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Stefan A Schattgen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael K Klebert
- Clinical Trials Unit, Washington University School of Medicine, Saint Louis, MO, USA
| | - Teresa Suessen
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - William D Middleton
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Charles W Goss
- Division of Biostatistics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Chang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | | | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sharlene A Teefey
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Rachel M Presti
- Clinical Trials Unit, Washington University School of Medicine, Saint Louis, MO, USA
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jane A O'Halloran
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jackson S Turner
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Philip A Mudd
- Department of Emergency Medicine, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA.
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3
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Perez MAS, Chiffelle J, Bobisse S, Mayol-Rullan F, Bugnon M, Bragina ME, Arnaud M, Sauvage C, Barras D, Laniti DD, Huber F, Bassani-Sternberg M, Coukos G, Harari A, Zoete V. Predicting Antigen-Specificities of Orphan T Cell Receptors from Cancer Patients with TCRpcDist. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405949. [PMID: 39159239 DOI: 10.1002/advs.202405949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/19/2024] [Indexed: 08/21/2024]
Abstract
Approaches to analyze and cluster T-cell receptor (TCR) repertoires to reflect antigen specificity are critical for the diagnosis and prognosis of immune-related diseases and the development of personalized therapies. Sequence-based approaches showed success but remain restrictive, especially when the amount of experimental data used for the training is scarce. Structure-based approaches which represent powerful alternatives, notably to optimize TCRs affinity toward specific epitopes, show limitations for large-scale predictions. To handle these challenges, TCRpcDist is presented, a 3D-based approach that calculates similarities between TCRs using a metric related to the physico-chemical properties of the loop residues predicted to interact with the epitope. By exploiting private and public datasets and comparing TCRpcDist with competing approaches, it is demonstrated that TCRpcDist can accurately identify groups of TCRs that are likely to bind the same epitopes. Importantly, the ability of TCRpcDist is experimentally validated to determine antigen specificities (neoantigens and tumor-associated antigens) of orphan tumor-infiltrating lymphocytes (TILs) in cancer patients. TCRpcDist is thus a promising approach to support TCR repertoire analysis and TCR deorphanization for individualized treatments including cancer immunotherapies.
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Affiliation(s)
- Marta A S Perez
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, University of Lausanne, Quartier UNIL-Sorge, Bâtiment Amphipole, Lausanne, CH-1015, Switzerland
| | - Johanna Chiffelle
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, CH-1011, Switzerland
| | - Sara Bobisse
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, CH-1011, Switzerland
| | - Francesca Mayol-Rullan
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, University of Lausanne, Quartier UNIL-Sorge, Bâtiment Amphipole, Lausanne, CH-1015, Switzerland
| | - Marine Bugnon
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, University of Lausanne, Quartier UNIL-Sorge, Bâtiment Amphipole, Lausanne, CH-1015, Switzerland
| | - Maiia E Bragina
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, University of Lausanne, Quartier UNIL-Sorge, Bâtiment Amphipole, Lausanne, CH-1015, Switzerland
| | - Marion Arnaud
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, CH-1011, Switzerland
| | - Christophe Sauvage
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, CH-1011, Switzerland
| | - David Barras
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, CH-1011, Switzerland
| | - Denarda Dangaj Laniti
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, CH-1011, Switzerland
| | - Florian Huber
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, CH-1011, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, CH-1011, Switzerland
| | - George Coukos
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, CH-1011, Switzerland
- Department of Oncology, Immuno-Oncology Service, Lausanne University Hospital, Lausanne, CH-1011, Switzerland
| | - Alexandre Harari
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, CH-1011, Switzerland
| | - Vincent Zoete
- Department of Oncology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, CH-1005, Switzerland
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, University of Lausanne, Quartier UNIL-Sorge, Bâtiment Amphipole, Lausanne, CH-1015, Switzerland
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4
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Leong SP. Immune responses and immunotherapeutic approaches in the treatment against cancer. Clin Exp Metastasis 2024:10.1007/s10585-024-10300-7. [PMID: 39155358 DOI: 10.1007/s10585-024-10300-7] [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: 03/04/2024] [Accepted: 06/15/2024] [Indexed: 08/20/2024]
Abstract
Cancer cells within a population are heterogeneous due to genomic mutations or epigenetic changes. The immune response to cancer especially the T cell repertoire within the cancer microenvionment is important to the control and growth of cancer cells. When a cancer clone breaks through the surveillance of the immune system, it wins the battle to overcome the host's immune system. In this review, the complicated profile of the cancer microenvironment is emphasized. The molecular evidence of immune responses to cancer has been recently established. Based on these molecular mechanisms of immune interactions with cancer, clinical trials based on checkpoint inhibition therapy against CTLA-4 and/or PD-1 versus PD-L1 have been successful in the treatment of melanoma, lung cancer and other types of cancer. The diversity of the T cell repertoire is described and the tumor infiltrating lymphocytes within the cancer may be expanded ex vivo and infused back to the patient as a treatment modality for adoptive immunotherapy.
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Affiliation(s)
- Stanley P Leong
- California Pacific Medical Center and Research Institute, University of California School of Medicine, San Francisco, USA.
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5
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Markov NS, Ren Z, Senkow KJ, Grant RA, Gao CA, Malsin ES, Sichizya L, Kihshen H, Helmin KA, Jovisic M, Arnold JM, Pérez-Leonor XG, Abdala-Valencia H, Swaminathan S, Nwaezeapu J, Kang M, Rasmussen L, Ozer EA, Lorenzo-Redondo R, Hultquist JF, Simons LM, Rios-Guzman E, Misharin AV, Wunderink RG, Budinger GRS, Singer BD, Morales-Nebreda L. Distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia. Nat Immunol 2024:10.1038/s41590-024-01914-w. [PMID: 39138384 DOI: 10.1038/s41590-024-01914-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 07/03/2024] [Indexed: 08/15/2024]
Abstract
The evolution of T cell molecular signatures in the distal lung of patients with severe pneumonia is understudied. Here, we analyzed T cell subsets in longitudinal bronchoalveolar lavage fluid samples from 273 patients with severe pneumonia, including unvaccinated patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or with respiratory failure not linked to pneumonia. In patients with SARS-CoV-2 pneumonia, activation of interferon signaling pathways, low activation of the NF-κB pathway and preferential targeting of spike and nucleocapsid proteins early after intubation were associated with favorable outcomes, whereas loss of interferon signaling, activation of NF-κB-driven programs and specificity for the ORF1ab complex late in disease were associated with mortality. These results suggest that in patients with severe SARS-CoV-2 pneumonia, alveolar T cell interferon responses targeting structural SARS-CoV-2 proteins characterize individuals who recover, whereas responses against nonstructural proteins and activation of NF-κB are associated with poor outcomes.
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Affiliation(s)
- Nikolay S Markov
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ziyou Ren
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Karolina J Senkow
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rogan A Grant
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Catherine A Gao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Elizabeth S Malsin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lango Sichizya
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Hermon Kihshen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kathryn A Helmin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Milica Jovisic
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jason M Arnold
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xóchitl G Pérez-Leonor
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Suchitra Swaminathan
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Julu Nwaezeapu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mengjia Kang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Luke Rasmussen
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ramon Lorenzo-Redondo
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Judd F Hultquist
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lacy M Simons
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Estefany Rios-Guzman
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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6
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Stary V, Pandey RV, List J, Kleissl L, Deckert F, Kabiljo J, Laengle J, Gerakopoulos V, Oehler R, Watzke L, Farlik M, Lukowski SW, Vogt AB, Stary G, Stockinger H, Bergmann M, Pilat N. Dysfunctional tumor-infiltrating Vδ1 + T lymphocytes in microsatellite-stable colorectal cancer. Nat Commun 2024; 15:6949. [PMID: 39138181 PMCID: PMC11322529 DOI: 10.1038/s41467-024-51025-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/24/2024] [Indexed: 08/15/2024] Open
Abstract
Although γδ T cells are known to participate in immune dysregulation in solid tumors, their relevance to human microsatellite-stable (MSS) colorectal cancer (CRC) is still undefined. Here, using integrated gene expression analysis and T cell receptor sequencing, we characterized γδ T cells in MSS CRC, with a focus on Vδ1 + T cells. We identified Vδ1+ T cells with shared motifs in the third complementarity-determining region of the δ-chain, reflective of antigen recognition. Changes in gene and protein expression levels suggested a dysfunctional effector state of Vδ1+ T cells in MSS CRC, distinct from Vδ1+ T cells in microsatellite-instable (MSI). Interaction analysis highlighted an immunosuppressive role of fibroblasts in the dysregulation of Vδ1+ T cells in MSS CRC via the TIGIT-NECTIN2 axis. Blocking this pathway with a TIGIT antibody partially restored cytotoxicity of the dysfunctional Vδ1 phenotype. These results define an operative pathway in γδ T cells in MSS CRC.
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MESH Headings
- Humans
- Colorectal Neoplasms/immunology
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/pathology
- Lymphocytes, Tumor-Infiltrating/immunology
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Receptors, Immunologic/immunology
- Microsatellite Instability
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Microsatellite Repeats/genetics
- Gene Expression Regulation, Neoplastic
- Female
- Male
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
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Affiliation(s)
- Victoria Stary
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria.
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria.
| | - Ram V Pandey
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Julia List
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Lisa Kleissl
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Florian Deckert
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Julijan Kabiljo
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Johannes Laengle
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Vasileios Gerakopoulos
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Rudolf Oehler
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Lukas Watzke
- Medical University of Vienna, Department of Pathology, Vienna, Austria
| | - Matthias Farlik
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Samuel W Lukowski
- Department of Human Cancer Immunology, Boehringer Ingelheim RCV GmBH & Co KG., Dr. Boehringer Gasse 5-11, 1120, Vienna, Austria
| | - Anne B Vogt
- Department of Human Cancer Immunology, Boehringer Ingelheim RCV GmBH & Co KG., Dr. Boehringer Gasse 5-11, 1120, Vienna, Austria
| | - Georg Stary
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Hannes Stockinger
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
| | - Michael Bergmann
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Nina Pilat
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
- Medical University of Vienna, Department of Cardiac Surgery, Vienna, Austria
- Medical University of Vienna, Center for Biomedical Research and Translational Surgery, Vienna, Austria
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7
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Huang Q, Zhu J. Regulatory T cell-based therapy in type 1 diabetes: Latest breakthroughs and evidence. Int Immunopharmacol 2024; 140:112724. [PMID: 39098233 DOI: 10.1016/j.intimp.2024.112724] [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: 06/07/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 08/06/2024]
Abstract
Autoimmune diseases (ADs) are among the most significant health complications, with their incidence rising in recent years. Type 1 diabetes (T1D), an AD, targets the insulin-producing β cells in the pancreas, leading to chronic insulin deficiency in genetically susceptible individuals. Regulatory immune cells, particularly T-cells (Tregs), have been shown to play a crucial role in the pathogenesis of diabetes by modulating immune responses. In diabetic patients, Tregs often exhibit diminished effectiveness due to various factors, such as instability in forkhead box P3 (Foxp3) expression or abnormal production of the proinflammatory cytokine interferon-gamma (IFN-γ) by autoreactive T-cells. Consequently, Tregs represent a potential therapeutic target for diabetes treatment. Building on the successful clinical outcomes of chimeric antigen receptor (CAR) T-cell therapy in cancer treatment, particularly in leukemias, the concept of designing and utilizing CAR Tregs for ADs has emerged. This review summarizes the findings on Treg targeting in T1D and discusses the benefits and limitations of this treatment approach for patients suffering from T1D.
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Affiliation(s)
- Qiongxiao Huang
- Center for Reproductive Medicine, Department of Reproductive Endocrinology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang 310014, China
| | - Jing Zhu
- Center for Reproductive Medicine, Department of Reproductive Endocrinology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang 310014, China.
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8
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Santos AJM, van Unen V, Lin Z, Chirieleison SM, Ha N, Batish A, Chan JE, Cedano J, Zhang ET, Mu Q, Guh-Siesel A, Tomaske M, Colburg D, Varma S, Choi SS, Christophersen A, Baghdasaryan A, Yost KE, Karlsson K, Ha A, Li J, Dai H, Sellers ZM, Chang HY, Dunn JCY, Zhang BM, Mellins ED, Sollid LM, Fernandez-Becker NQ, Davis MM, Kuo CJ. A human autoimmune organoid model reveals IL-7 function in coeliac disease. Nature 2024; 632:401-410. [PMID: 39048815 DOI: 10.1038/s41586-024-07716-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/14/2024] [Indexed: 07/27/2024]
Abstract
In vitro models of autoimmunity are constrained by an inability to culture affected epithelium alongside the complex tissue-resident immune microenvironment. Coeliac disease (CeD) is an autoimmune disease in which dietary gluten-derived peptides bind to the major histocompatibility complex (MHC) class II human leukocyte antigen molecules (HLA)-DQ2 or HLA-DQ8 to initiate immune-mediated duodenal mucosal injury1-4. Here, we generated air-liquid interface (ALI) duodenal organoids from intact fragments of endoscopic biopsies that preserve epithelium alongside native mesenchyme and tissue-resident immune cells as a unit without requiring reconstitution. The immune diversity of ALI organoids spanned T cells, B and plasma cells, natural killer (NK) cells and myeloid cells, with extensive T-cell and B-cell receptor repertoires. HLA-DQ2.5-restricted gluten peptides selectively instigated epithelial destruction in HLA-DQ2.5-expressing organoids derived from CeD patients, and this was antagonized by blocking MHC-II or NKG2C/D. Gluten epitopes stimulated a CeD organoid immune network response in lymphoid and myeloid subsets alongside anti-transglutaminase 2 (TG2) autoantibody production. Functional studies in CeD organoids revealed that interleukin-7 (IL-7) is a gluten-inducible pathogenic modulator that regulates CD8+ T-cell NKG2C/D expression and is necessary and sufficient for epithelial destruction. Furthermore, endogenous IL-7 was markedly upregulated in patient biopsies from active CeD compared with remission disease from gluten-free diets, predominantly in lamina propria mesenchyme. By preserving the epithelium alongside diverse immune populations, this human in vitro CeD model recapitulates gluten-dependent pathology, enables mechanistic investigation and establishes a proof of principle for the organoid modelling of autoimmunity.
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MESH Headings
- Humans
- Autoantibodies/immunology
- Autoimmunity
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- Biopsy
- Celiac Disease/immunology
- Celiac Disease/pathology
- Celiac Disease/metabolism
- Duodenum/immunology
- Duodenum/pathology
- Duodenum/metabolism
- Epitopes/immunology
- Glutens/immunology
- Glutens/metabolism
- GTP-Binding Proteins/metabolism
- GTP-Binding Proteins/immunology
- HLA-DQ Antigens/immunology
- HLA-DQ Antigens/metabolism
- Interleukin-7/metabolism
- Intestinal Mucosa/immunology
- Intestinal Mucosa/metabolism
- Intestinal Mucosa/pathology
- Killer Cells, Natural/immunology
- Models, Biological
- Myeloid Cells/immunology
- Organoids/immunology
- Organoids/metabolism
- Organoids/pathology
- Protein Glutamine gamma Glutamyltransferase 2/immunology
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, B-Cell/metabolism
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
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Affiliation(s)
- António J M Santos
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Vincent van Unen
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhongqi Lin
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven M Chirieleison
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nhi Ha
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Arpit Batish
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Joshua E Chan
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jose Cedano
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Elisa T Zhang
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Qinghui Mu
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexander Guh-Siesel
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Madeline Tomaske
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Deana Colburg
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shannon S Choi
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Asbjørn Christophersen
- K. G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Department of Rheumatology, Dermatology and Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Ani Baghdasaryan
- Department of Chemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kasper Karlsson
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew Ha
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jing Li
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongjie Dai
- Department of Chemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Zachary M Sellers
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - James C Y Dunn
- Department of Pediatric Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Bing M Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth D Mellins
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ludvig M Sollid
- K. G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Nielsen Q Fernandez-Becker
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Calvin J Kuo
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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9
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Ye W, Clark EA, Sheng Q, Colaianni CA, Rohde SL, Gelbard A. Primary tracheal adenoid cystic carcinoma: A case report and analysis of the tumor immune microenvironment using single cell RNA sequencing. Head Neck 2024. [PMID: 39039710 DOI: 10.1002/hed.27879] [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: 11/04/2023] [Revised: 04/01/2024] [Accepted: 07/07/2024] [Indexed: 07/24/2024] Open
Abstract
BACKGROUND Tracheal adenoid cystic carcinoma (ACC) is a slow growing yet aggressive malignancy with high rates of local recurrence as well as distant metastasis. Tracheal ACC exhibit a low mutation burden along with high mutational diversity, and generally do not respond well to chemotherapeutics. METHODS We present a rare case of primary tracheal ACC initially presenting with nonspecific cervicalgia and globus sensation that was ultimately treated with tracheal resection followed by chemoradiation. Immune profiling of intratumoral T-cell receptor (TCR) repertoire was subsequently performed using single cell RNA sequencing (scRNAseq). RESULTS We describe a rare case of primary tracheal adenoid cystic carcinoma highlighting several management principles as well as providing new insights into intratumor T cell populations. CONCLUSIONS Primary tracheal ACC is most commonly treated with surgical resection followed by adjuvant therapy. Further characterization of the tumor immune microenvironment is necessary to better understand ACC disease biology and to identify potential therapeutic targets.
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Affiliation(s)
- Wenda Ye
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Evan A Clark
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - C Alessandra Colaianni
- Department of Otolaryngology-Head and Neck Surgery, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Sarah L Rohde
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexander Gelbard
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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10
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Yeh AC, Koyama M, Waltner OG, Minnie SA, Boiko JR, Shabaneh TB, Takahashi S, Zhang P, Ensbey KS, Schmidt CR, Legg SRW, Sekiguchi T, Nelson E, Bhise SS, Stevens AR, Goodpaster T, Chakka S, Furlan SN, Markey KA, Bleakley ME, Elson CO, Bradley PH, Hill GR. Microbiota dictate T cell clonal selection to augment graft-versus-host disease after stem cell transplantation. Immunity 2024; 57:1648-1664.e9. [PMID: 38876098 PMCID: PMC11236519 DOI: 10.1016/j.immuni.2024.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/09/2024] [Accepted: 05/20/2024] [Indexed: 06/16/2024]
Abstract
Allogeneic T cell expansion is the primary determinant of graft-versus-host disease (GVHD), and current dogma dictates that this is driven by histocompatibility antigen disparities between donor and recipient. This paradigm represents a closed genetic system within which donor T cells interact with peptide-major histocompatibility complexes (MHCs), though clonal interrogation remains challenging due to the sparseness of the T cell repertoire. We developed a Bayesian model using donor and recipient T cell receptor (TCR) frequencies in murine stem cell transplant systems to define limited common expansion of T cell clones across genetically identical donor-recipient pairs. A subset of donor CD4+ T cell clonotypes differentially expanded in identical recipients and were microbiota dependent. Microbiota-specific T cells augmented GVHD lethality and could target microbial antigens presented by gastrointestinal epithelium during an alloreactive response. The microbiota serves as a source of cognate antigens that contribute to clonotypic T cell expansion and the induction of GVHD independent of donor-recipient genetics.
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MESH Headings
- Graft vs Host Disease/immunology
- Graft vs Host Disease/microbiology
- Animals
- Mice
- Mice, Inbred C57BL
- CD4-Positive T-Lymphocytes/immunology
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Microbiota/immunology
- Clonal Selection, Antigen-Mediated
- Transplantation, Homologous
- Bayes Theorem
- Stem Cell Transplantation/adverse effects
- Mice, Inbred BALB C
- Gastrointestinal Microbiome/immunology
- Hematopoietic Stem Cell Transplantation/adverse effects
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Affiliation(s)
- Albert C Yeh
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA.
| | - Motoko Koyama
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Olivia G Waltner
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Simone A Minnie
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Julie R Boiko
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tamer B Shabaneh
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Shuichiro Takahashi
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ping Zhang
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kathleen S Ensbey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Christine R Schmidt
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Samuel R W Legg
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tomoko Sekiguchi
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ethan Nelson
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Shruti S Bhise
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Andrew R Stevens
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tracy Goodpaster
- Experimental Histopathology Core, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Saranya Chakka
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Scott N Furlan
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kate A Markey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Marie E Bleakley
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Division of Hematology, Oncology, and Bone Marrow Transplantation, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Charles O Elson
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Philip H Bradley
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Geoffrey R Hill
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA.
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11
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Wang Z, Zhao Y, Wo Y, Peng Y, Hu W, Wu Z, Liu P, Shang Y, Liu C, Chen X, Huang K, Chen Y, Hong H, Li F, Sun Y. The single cell immunogenomic landscape after neoadjuvant immunotherapy combined chemotherapy in esophageal squamous cell carcinoma. Cancer Lett 2024; 593:216951. [PMID: 38734159 DOI: 10.1016/j.canlet.2024.216951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Neoadjuvant immunotherapy represents promising strategy in the treatment of esophageal squamous cell carcinoma (ESCC). However, the mechanisms underlying its impact on treatment sensitivity or resistance remain a subject of controversy. In this study, we conducted single-cell RNA and T/B cell receptor (scTCR/scBCR) sequencing of CD45+ immune cells on samples from 10 patients who received neoadjuvant immunotherapy and chemotherapy. We also validated our findings using multiplexed immunofluorescence and analyzed bulk RNA-seq from other cohorts in public database. By integrating analysis of 87357 CD45+ cells, we found GZMK + effector memory T cells (Tem) were relatively enriched and CXCL13+ exhausted T cells (Tex) and regulator T cells (Treg) decreased among responders, indicating a persistent anti-tumor memory process. Additionally, the enhanced presence of BCR expansion and somatic hypermutation process within TNFRSF13B + memory B cells (Bmem) suggested their roles in antigen presentation. This was further corroborated by the evidence of the T-B co-stimulation pattern and CXCL13-CXCR5 axis. The complexity of myeloid cell heterogeneity was also particularly pronounced. The elevated expression of S100A7 in ESCC, as detected by bulk RNA-seq, was associated with an exhausted and immunosuppressive tumor microenvironment. In summary, this study has unveiled a potential regulatory network among immune cells and the clonal dynamics of their functions, and the mechanisms of exhaustion and memory conversion between GZMK + Tem and TNFRSF13B + Bmem from antigen presentation and co-stimulation perspectives during neoadjuvant PD-1 blockade treatment in ESCC.
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MESH Headings
- Humans
- Neoadjuvant Therapy/methods
- Esophageal Squamous Cell Carcinoma/immunology
- Esophageal Squamous Cell Carcinoma/genetics
- Esophageal Squamous Cell Carcinoma/therapy
- Esophageal Squamous Cell Carcinoma/drug therapy
- Esophageal Squamous Cell Carcinoma/pathology
- Esophageal Neoplasms/immunology
- Esophageal Neoplasms/genetics
- Esophageal Neoplasms/therapy
- Esophageal Neoplasms/drug therapy
- Esophageal Neoplasms/pathology
- Immunotherapy/methods
- Single-Cell Analysis/methods
- Female
- Male
- Tumor Microenvironment/immunology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Chemokine CXCL13/genetics
- Chemokine CXCL13/metabolism
- Middle Aged
- Aged
- Memory T Cells/immunology
- Memory T Cells/metabolism
- Leukocyte Common Antigens/metabolism
- Leukocyte Common Antigens/genetics
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/drug effects
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Receptors, Antigen, B-Cell/immunology
- Receptors, CXCR5/metabolism
- Receptors, CXCR5/genetics
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Affiliation(s)
- Zheyi Wang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue Zhao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Wo
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yizhou Peng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weilei Hu
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China; State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Zhigang Wu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pengcheng Liu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan Shang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chunnan Liu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kan Huang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuting Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hui Hong
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fei Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Yihua Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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12
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Clark EA, Talatala ER, Ye W, Davis RJ, Collins SL, Hillel AT, Ramirez-Solano M, Sheng Q, Wanjalla CN, Mallal SA, Gelbard A. Similarity Network Analysis of the Adaptive Immune Response in the Proximal Airway. Laryngoscope 2024; 134:3245-3252. [PMID: 38450771 PMCID: PMC11182723 DOI: 10.1002/lary.31376] [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: 05/02/2023] [Revised: 01/23/2024] [Accepted: 02/12/2024] [Indexed: 03/08/2024]
Abstract
OBJECTIVES Recent immunologic study of the adaptive immune repertoire in the subglottic airway demonstrated high-frequency T cell clones that do not overlap between individuals. However, the anatomic distribution and antigenic target of the T cell repertoire in the proximal airway mucosa remain unresolved. METHODS Single-cell RNA sequencing of matched scar and unaffected mucosa from idiopathic subglottic stenosis patients (iSGS, n = 32) was performed and compared with airway mucosa from healthy controls (n = 10). T cell receptor (TCR) sequences were interrogated via similarity network analysis to explore antigenic targets using the published algorithm: Grouping of Lymphocyte Interactions by Paratope Hotspots (GLIPH2). RESULTS The mucosal T cell repertoire in healthy control airways consisted of highly expressed T cell clones conserved across anatomic subsites (trachea, bronchi, bronchioles, and lung). In iSGS, high-frequency clones were equally represented in both scar and adjacent non-scar tissue. Significant differences in repertoire structure between iSGS scar and unaffected mucosa was observed, driven by unique low-frequency clones. GLIPH2 results suggest low-frequency clones share targets between multiple iSGS patients. CONCLUSION Healthy airway mucosa has a highly conserved T cell repertoire across multiple anatomic subsites. Similarly, iSGS patients have highly expressed T cell clones present in both scar and unaffected mucosa. iSGS airway scar possesses an abundance of less highly expanded clones with predicted antigen targets shared between patients. Interrogation of these shared motifs suggests abundant adaptive immunity to viral targets in iSGS airway scar. These results provide insight into disease pathogenesis and illuminate new treatment strategies in iSGS. LEVEL OF EVIDENCE NA Laryngoscope, 134:3245-3252, 2024.
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Affiliation(s)
- Evan A. Clark
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Edward R.R. Talatala
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Wenda Ye
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Ruth J. Davis
- Department of Otolaryngology-Head & Neck Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Samuel L. Collins
- Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alexander T. Hillel
- Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Celestine N. Wanjalla
- Department of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Simon A. Mallal
- Department of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alexander Gelbard
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
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13
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Hao Q, Long Y, Yang Y, Deng Y, Ding Z, Yang L, Shu Y, Xu H. Development and Clinical Applications of Therapeutic Cancer Vaccines with Individualized and Shared Neoantigens. Vaccines (Basel) 2024; 12:717. [PMID: 39066355 PMCID: PMC11281709 DOI: 10.3390/vaccines12070717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Neoantigens, presented as peptides on the surfaces of cancer cells, have recently been proposed as optimal targets for immunotherapy in clinical practice. The promising outcomes of neoantigen-based cancer vaccines have inspired enthusiasm for their broader clinical applications. However, the individualized tumor-specific antigens (TSA) entail considerable costs and time due to the variable immunogenicity and response rates of these neoantigens-based vaccines, influenced by factors such as neoantigen response, vaccine types, and combination therapy. Given the crucial role of neoantigen efficacy, a number of bioinformatics algorithms and pipelines have been developed to improve the accuracy rate of prediction through considering a series of factors involving in HLA-peptide-TCR complex formation, including peptide presentation, HLA-peptide affinity, and TCR recognition. On the other hand, shared neoantigens, originating from driver mutations at hot mutation spots (e.g., KRASG12D), offer a promising and ideal target for the development of therapeutic cancer vaccines. A series of clinical practices have established the efficacy of these vaccines in patients with distinct HLA haplotypes. Moreover, increasing evidence demonstrated that a combination of tumor associated antigens (TAAs) and neoantigens can also improve the prognosis, thus expand the repertoire of shared neoantigens for cancer vaccines. In this review, we provide an overview of the complex process involved in identifying personalized neoantigens, their clinical applications, advances in vaccine technology, and explore the therapeutic potential of shared neoantigen strategies.
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Affiliation(s)
- Qing Hao
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Yuhang Long
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Yi Yang
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Yiqi Deng
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
- Colorectal Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhenyu Ding
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Li Yang
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Yang Shu
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
- Gastric Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Heng Xu
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
- Institute of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- Research Center of Clinical Laboratory Medicine, Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
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14
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Dintwe OB, Ballweber Fleming L, Voillet V, McNevin J, Seese A, Naidoo A, Omarjee S, Bekker LG, Kublin JG, De Rosa SC, Newell EW, Fiore-Gartland A, Andersen-Nissen E, McElrath MJ. Adolescent BCG revaccination induces a phenotypic shift in CD4 + T cell responses to Mycobacterium tuberculosis. Nat Commun 2024; 15:5191. [PMID: 38890283 PMCID: PMC11189459 DOI: 10.1038/s41467-024-49050-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
A recent clinical trial demonstrated that Bacille Calmette-Guérin (BCG) revaccination of adolescents reduced the risk of sustained infection with Mycobacterium tuberculosis (M.tb). In a companion phase 1b trial, HVTN 602/Aeras A-042, we characterize in-depth the cellular responses to BCG revaccination or to a H4:IC31 vaccine boost to identify T cell subsets that could be responsible for the protection observed. High-dimensional clustering analysis of cells profiled using a 26-color flow cytometric panel show marked increases in five effector memory CD4+ T cell subpopulations (TEM) after BCG revaccination, two of which are highly polyfunctional. CITE-Seq single-cell analysis shows that the activated subsets include an abundant cluster of Th1 cells with migratory potential. Additionally, a small cluster of Th17 TEM cells induced by BCG revaccination expresses high levels of CD103; these may represent recirculating tissue-resident memory cells that could provide pulmonary immune protection. Together, these results identify unique populations of CD4+ T cells with potential to be immune correlates of protection conferred by BCG revaccination.
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Affiliation(s)
- One B Dintwe
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | | | - Valentin Voillet
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | - John McNevin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Aaron Seese
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Anneta Naidoo
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | - Saleha Omarjee
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | - Linda-Gail Bekker
- The Desmond Tutu HIV Centre, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - James G Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Erica Andersen-Nissen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa.
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.
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15
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Dunlap G, Wagner A, Meednu N, Wang R, Zhang F, Ekabe JC, Jonsson AH, Wei K, Sakaue S, Nathan A, Bykerk VP, Donlin LT, Goodman SM, Firestein GS, Boyle DL, Holers VM, Moreland LW, Tabechian D, Pitzalis C, Filer A, Raychaudhuri S, Brenner MB, Thakar J, McDavid A, Rao DA, Anolik JH. Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium. Nat Commun 2024; 15:4991. [PMID: 38862501 PMCID: PMC11167034 DOI: 10.1038/s41467-024-49186-0] [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: 06/04/2023] [Accepted: 05/20/2024] [Indexed: 06/13/2024] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease involving antigen-specific T and B cells. Here, we perform single-cell RNA and repertoire sequencing on paired synovial tissue and blood samples from 12 seropositive RA patients. We identify clonally expanded CD4 + T cells, including CCL5+ cells and T peripheral helper (Tph) cells, which show a prominent transcriptomic signature of recent activation and effector function. CD8 + T cells show higher oligoclonality than CD4 + T cells, with the largest synovial clones enriched in GZMK+ cells. CD8 + T cells with possibly virus-reactive TCRs are distributed across transcriptomic clusters. In the B cell compartment, NR4A1+ activated B cells, and plasma cells are enriched in the synovium and demonstrate substantial clonal expansion. We identify synovial plasma cells that share BCRs with synovial ABC, memory, and activated B cells. Receptor-ligand analysis predicted IFNG and TNFRSF members as mediators of synovial Tph-B cell interactions. Together, these results reveal clonal relationships between functionally distinct lymphocyte populations that infiltrate the synovium of patients with RA.
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Grants
- UH2 AR067685 NIAMS NIH HHS
- UM2 AR067678 NIAMS NIH HHS
- K08 AR081412 NIAMS NIH HHS
- UH2 AR067681 NIAMS NIH HHS
- UH2 AR067688 NIAMS NIH HHS
- UH2 AR067689 NIAMS NIH HHS
- UH2 AR067690 NIAMS NIH HHS
- UH2 AR067677 NIAMS NIH HHS
- UH2 AR067694 NIAMS NIH HHS
- UH2 AR067679 NIAMS NIH HHS
- UH2 AR067676 NIAMS NIH HHS
- UH2 AR067691 NIAMS NIH HHS
- Funding for AMP RA/SLE work was provided through grants from the National Institutes of Health (UH2-AR067676, UH2-AR067677, UH2-AR067679, UH2-AR067681, UH2-AR067685, UH2-AR067688, UH2-AR067689, UH2-AR067690, UH2-AR067691, UH2-AR067694, and UM2-AR067678).
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Affiliation(s)
- Garrett Dunlap
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Aaron Wagner
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Nida Meednu
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Ruoqiao Wang
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jabea Cyril Ekabe
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vivian P Bykerk
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Laura T Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Susan M Goodman
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Gary S Firestein
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego;, La Jolla, CA, USA
| | - David L Boyle
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego;, La Jolla, CA, USA
| | - V Michael Holers
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Larry W Moreland
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Darren Tabechian
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Costantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, EULAR Centre of Excellence, William Harvey Research Institute, Queen Mary University of London, London, UK
- Barts Health NHS Trust, Barts Biomedical Research Centre (BRC), National Institute for Health and Care Research (NIHR), London, UK
- Department of Biomedical Sciences, Humanitas University and Humanitas Research Hospital, Milan, Italy
| | - Andrew Filer
- Rheumatology Research Group, Institute for Inflammation and Ageing, University of Birmingham, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- Birmingham Tissue Analytics, Institute of Translational Medicine, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Juilee Thakar
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Jennifer H Anolik
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA.
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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16
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Shen M, Chen S, Han X, Hao Y, Wang J, Li L, Chen T, Wang B, Zou L, Zhang T, Zhang W, Han X, Wang W, Yu H, Li K, Liu S, Jin A. Identification of an HLA-A*11:01-restricted neoepitope of mutant PIK3CA and its specific T cell receptors for cancer immunotherapy targeting hotspot driver mutations. Cancer Immunol Immunother 2024; 73:150. [PMID: 38832948 PMCID: PMC11150344 DOI: 10.1007/s00262-024-03729-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/10/2024] [Indexed: 06/06/2024]
Abstract
Hotspot driver mutations presented by human leukocyte antigens might be recognized by anti-tumor T cells. Based on their advantages of tumor-specificity and immunogenicity, neoantigens derived from hotspot mutations, such as PIK3CAH1047L, may serve as emerging targets for cancer immunotherapies. NetMHCpan V4.1 was utilized for predicting neoepitopes of PIK3CA hotspot mutation. Using in vitro stimulation, antigen-specific T cells targeting the HLA-A*11:01-restricted PIK3CA mutation were isolated from healthy donor-derived peripheral blood mononuclear cells. T cell receptors (TCRs) were cloned using single-cell PCR and sequencing. Their functionality was assessed through T cell activation markers, cytokine production and cytotoxic response to cancer cell lines pulsed with peptides or transduced genes of mutant PIK3CA. Immunogenic mutant antigens from PIK3CA and their corresponding CD8+ T cells were identified. These PIK3CA mutation-specific CD8+ T cells were subsequently enriched, and their TCRs were isolated. The TCR clones exhibited mutation-specific and HLA-restricted reactivity, demonstrating varying degrees of functional avidity. Identified TCR genes were transferred into CD8+ Jurkat cells and primary T cells deficient of endogenous TCRs. TCR-expressing cells demonstrated specific recognition and reactivity against the PIK3CAH1047L peptide presented by HLA-A*11:01-expressing K562 cells. Furthermore, mutation-specific TCR-T cells demonstrated an elevation in cytokine production and profound cytotoxic effects against HLA-A*11:01+ malignant cell lines harboring PIK3CAH1047L. Our data demonstrate the immunogenicity of an HLA-A*11:01-restricted PIK3CA hotspot mutation and its targeting therapeutic potential, together with promising candidates of TCR-T cell therapy.
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Affiliation(s)
- Meiying Shen
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Siyin Chen
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Xiaojian Han
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Yanan Hao
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Junfan Wang
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Luo Li
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Tong Chen
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Bozhi Wang
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Lin Zou
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Tong Zhang
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Wanli Zhang
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Xiaxia Han
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Wang Wang
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Haochen Yu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Kang Li
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shengchun Liu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Aishun Jin
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China.
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17
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Johansson AM, Kwok WW. T-cell receptor sequencing in interrogating antigen-specific T-cell responses to foreign and self-antigens. J Allergy Clin Immunol 2024; 153:1540-1542. [PMID: 38657797 DOI: 10.1016/j.jaci.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024]
Affiliation(s)
- Alexandra M Johansson
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Wash
| | - William W Kwok
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Wash.
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18
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Delmonte OM, Oguz C, Dobbs K, Myint-Hpu K, Palterer B, Abers MS, Draper D, Truong M, Kaplan IM, Gittelman RM, Zhang Y, Rosen LB, Snow AL, Dalgard CL, Burbelo PD, Imberti L, Sottini A, Quiros-Roldan E, Castelli F, Rossi C, Brugnoni D, Biondi A, Bettini LR, D'Angio M, Bonfanti P, Anderson MV, Saracino A, Chironna M, Di Stefano M, Fiore JR, Santantonio T, Castagnoli R, Marseglia GL, Magliocco M, Bosticardo M, Pala F, Shaw E, Matthews H, Weber SE, Xirasagar S, Barnett J, Oler AJ, Dimitrova D, Bergerson JRE, McDermott DH, Rao VK, Murphy PM, Holland SM, Lisco A, Su HC, Lionakis MS, Cohen JI, Freeman AF, Snyder TM, Lack J, Notarangelo LD. Perturbations of the T-cell receptor repertoire in response to SARS-CoV-2 in immunocompetent and immunocompromised individuals. J Allergy Clin Immunol 2024; 153:1655-1667. [PMID: 38154666 PMCID: PMC11162338 DOI: 10.1016/j.jaci.2023.12.011] [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: 05/29/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND Functional T-cell responses are essential for virus clearance and long-term protection after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, whereas certain clinical factors, such as older age and immunocompromise, are associated with worse outcome. OBJECTIVE We sought to study the breadth and magnitude of T-cell responses in patients with coronavirus disease 2019 (COVID-19) and in individuals with inborn errors of immunity (IEIs) who had received COVID-19 mRNA vaccine. METHODS Using high-throughput sequencing and bioinformatics tools to characterize the T-cell receptor β repertoire signatures in 540 individuals after SARS-CoV-2 infection, 31 IEI recipients of COVID-19 mRNA vaccine, and healthy controls, we quantified HLA class I- and class II-restricted SARS-CoV-2-specific responses and also identified several HLA allele-clonotype motif associations in patients with COVID-19, including a subcohort of anti-type 1 interferon (IFN-1)-positive patients. RESULTS Our analysis revealed that elderly patients with COVID-19 with critical disease manifested lower SARS-CoV-2 T-cell clonotype diversity as well as T-cell responses with reduced magnitude, whereas the SARS-CoV-2-specific clonotypes targeted a broad range of HLA class I- and class II-restricted epitopes across the viral proteome. The presence of anti-IFN-I antibodies was associated with certain HLA alleles. Finally, COVID-19 mRNA immunization induced an increase in the breadth of SARS-CoV-2-specific clonotypes in patients with IEIs, including those who had failed to seroconvert. CONCLUSIONS Elderly individuals have impaired capacity to develop broad and sustained T-cell responses after SARS-CoV-2 infection. Genetic factors may play a role in the production of anti-IFN-1 antibodies. COVID-19 mRNA vaccines are effective in inducing T-cell responses in patients with IEIs.
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Affiliation(s)
- Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
| | - Cihan Oguz
- Integrated Data Sciences Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Katherine Myint-Hpu
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Boaz Palterer
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michael S Abers
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Deborah Draper
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Meng Truong
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | | | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Lindsey B Rosen
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrew L Snow
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md; Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, Md; The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Peter D Burbelo
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Md
| | - Luisa Imberti
- Section of Microbiology, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Alessandra Sottini
- Section of Microbiology, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Francesco Castelli
- Department of Infectious and Tropical Diseases, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Camillo Rossi
- Direzione Sanitaria, ASST Spedali Civili, Brescia, Italy
| | - Duilio Brugnoni
- Laboratorio Analisi Chimico-Cliniche, ASST Spedali Civili, Brescia, Italy
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Laura Rachele Bettini
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Mariella D'Angio
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Megan V Anderson
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Annalisa Saracino
- Clinic of Infectious Diseases, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, University of Bari, Bari, Italy
| | - Maria Chironna
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Mariantonietta Di Stefano
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Jose Ramon Fiore
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Teresa Santantonio
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Riccardo Castagnoli
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Gian Luigi Marseglia
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Mary Magliocco
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Elana Shaw
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Helen Matthews
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sarah E Weber
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sandhya Xirasagar
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Jason Barnett
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Dimana Dimitrova
- Center for Immuno-Oncology, National Cancer Institute, National Institutes of Health, Bethesda, Md
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - David H McDermott
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - V Koneti Rao
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Philip M Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrea Lisco
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | | | - Justin Lack
- Integrated Data Sciences Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
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19
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Wen Z, Wang L, Ma H, Li L, Wan L, Shi L, Li H, Chen H, Hao W, Song S, Xue Q, Wei Y, Li F, Xu J, Zhang S, Wong KW, Song Y. Integrated single-cell transcriptome and T cell receptor profiling reveals defects of T cell exhaustion in pulmonary tuberculosis. J Infect 2024; 88:106158. [PMID: 38642678 DOI: 10.1016/j.jinf.2024.106158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/07/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024]
Abstract
Tuberculosis-affected lungs with chronic inflammation harbor abundant immunosuppressive immune cells but the nature of such inflammation is unclear. Dysfunction in T cell exhaustion, while implicated in chronic inflammatory diseases, remains unexplored in tuberculosis. Given that immunotherapy targeting exhaustion checkpoints exacerbates tuberculosis, we speculate that T cell exhaustion is dysfunctional in tuberculosis. Using integrated single-cell RNA sequencing and T cell receptor profiling we reported defects in exhaustion responses within inflamed tuberculosis-affected lungs. Tuberculosis lungs demonstrated significantly reduced levels of exhausted CD8+ T cells and exhibited diminished expression of exhaustion-related transcripts among clonally expanded CD4+ and CD8+ T cells. Additionally, clonal expansion of CD4+ and CD8+ T cells bearing T cell receptors specific for CMV was observed. Expanded CD8+ T cells expressed the cytolytic marker GZMK. Hence, inflamed tuberculosis-affected lungs displayed dysfunction in T cell exhaustion. Our findings likely hold implications for understanding the reactivation of tuberculosis observed in patients undergoing immunotherapy targeting the exhaustion checkpoint.
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Affiliation(s)
- Zilu Wen
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lin Wang
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hui Ma
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Leilei Li
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Laiyi Wan
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lei Shi
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hongwei Li
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hui Chen
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Wentao Hao
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shu Song
- Department of Pathology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qinghua Xue
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yutong Wei
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Feng Li
- Department of Respiratory Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jianqing Xu
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shulin Zhang
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Ka-Wing Wong
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Yanzheng Song
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
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20
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Takahashi M, So TY, Chamberlain-Evans V, Hughes R, Yam-Puc JC, Kania K, Ruhle M, Mann T, Schuijs MJ, Coupland P, Naisbitt D, Halim TY, Lyons PA, Lio P, Roychoudhuri R, Okkenhaug K, Adams DJ, Smith KG, Jodrell DI, Chapman MA, Thaventhiran JED. Intratumoral antigen signaling traps CD8 + T cells to confine exhaustion to the tumor site. Sci Immunol 2024; 9:eade2094. [PMID: 38787961 PMCID: PMC7616235 DOI: 10.1126/sciimmunol.ade2094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
Immunotherapy advances have been hindered by difficulties in tracking the behaviors of lymphocytes after antigen signaling. Here, we assessed the behavior of T cells active within tumors through the development of the antigen receptor signaling reporter (AgRSR) mouse, fate-mapping lymphocytes responding to antigens at specific times and locations. Contrary to reports describing the ready egress of T cells out of the tumor, we find that intratumoral antigen signaling traps CD8+ T cells in the tumor. These clonal populations expand and become increasingly exhausted over time. By contrast, antigen-signaled regulatory T cell (Treg) clonal populations readily recirculate out of the tumor. Consequently, intratumoral antigen signaling acts as a gatekeeper to compartmentalize CD8+ T cell responses, even within the same clonotype, thus enabling exhausted T cells to remain confined to a specific tumor tissue site.
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Affiliation(s)
- Munetomo Takahashi
- Medical Research Council Toxicology Unit, University of Cambridge; Gleeson Building, Tennis Court Road,
Cambridge,
CB2 1QR, UK
- Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo,
113-0033, Japan
| | - Tsz Y. So
- Medical Research Council Toxicology Unit, University of Cambridge; Gleeson Building, Tennis Court Road,
Cambridge,
CB2 1QR, UK
- University of Cambridge, CRUK Cambridge Institute; Cambridge,
CB2 0RE, UK
| | - Vitalina Chamberlain-Evans
- Medical Research Council Toxicology Unit, University of Cambridge; Gleeson Building, Tennis Court Road,
Cambridge,
CB2 1QR, UK
| | - Robert Hughes
- Medical Research Council Toxicology Unit, University of Cambridge; Gleeson Building, Tennis Court Road,
Cambridge,
CB2 1QR, UK
| | - Juan Carlos Yam-Puc
- Medical Research Council Toxicology Unit, University of Cambridge; Gleeson Building, Tennis Court Road,
Cambridge,
CB2 1QR, UK
| | - Katarzyna Kania
- University of Cambridge, CRUK Cambridge Institute; Cambridge,
CB2 0RE, UK
| | - Michelle Ruhle
- University of Cambridge, CRUK Cambridge Institute; Cambridge,
CB2 0RE, UK
| | - Tiffeney Mann
- Medical Research Council Toxicology Unit, University of Cambridge; Gleeson Building, Tennis Court Road,
Cambridge,
CB2 1QR, UK
| | - Martijn J. Schuijs
- University of Cambridge, CRUK Cambridge Institute; Cambridge,
CB2 0RE, UK
| | - Paul Coupland
- University of Cambridge, CRUK Cambridge Institute; Cambridge,
CB2 0RE, UK
- Altos Labs Cambridge Institute, Cambridge CB21 6GP, UK
| | - Dean Naisbitt
- Department of Pharmacology and Therapeutics, University of Liverpool; Sherrington Building, Ashton Street,
Liverpool,
L69 3G, UK
| | | | - Paul A. Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious
Disease, University of Cambridge; Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus,
Cambridge, UK
- Department of Medicine, University of Cambridge, School of Clinical Medicine; Cambridge Biomedical Campus,
Cambridge, UK
| | - Pietro Lio
- Department of Computer Science and Technology, University of Cambridge; Cambridge,
CB3 0FD, UK
| | | | - Klaus Okkenhaug
- Department of Pathology, University of Cambridge; Cambridge, UK
| | - David J. Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute; Hinxton, Cambridge,
CB10 1SA
| | - Ken G.C. Smith
- Cambridge Institute of Therapeutic Immunology and Infectious
Disease, University of Cambridge; Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus,
Cambridge, UK
- Department of Medicine, University of Cambridge, School of Clinical Medicine; Cambridge Biomedical Campus,
Cambridge, UK
- The Walter and Eliza Hall Institute of Medical
Research, Parkville, VIC 3052,
Australia
- The University of Melbourne, Parkville, VIC 3052,
Australia
| | - Duncan I. Jodrell
- Department of Oncology, University of Cambridge, School of Clinical Medicine; Box 197, Cambridge
Biomedical Campus, Cambridge, CB2
0XZ, UK
| | - Michael A. Chapman
- Medical Research Council Toxicology Unit, University of Cambridge; Gleeson Building, Tennis Court Road,
Cambridge,
CB2 1QR, UK
- Department of Hematology, University of Cambridge, Cambridge,
CB2 0RE, UK
| | - James E. D. Thaventhiran
- Medical Research Council Toxicology Unit, University of Cambridge; Gleeson Building, Tennis Court Road,
Cambridge,
CB2 1QR, UK
- University of Cambridge, CRUK Cambridge Institute; Cambridge,
CB2 0RE, UK
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21
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Leary AY, Scott D, Gupta NT, Waite JC, Skokos D, Atwal GS, Hawkins PG. Designing meaningful continuous representations of T cell receptor sequences with deep generative models. Nat Commun 2024; 15:4271. [PMID: 38769289 PMCID: PMC11106309 DOI: 10.1038/s41467-024-48198-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
T Cell Receptor (TCR) antigen binding underlies a key mechanism of the adaptive immune response yet the vast diversity of TCRs and the complexity of protein interactions limits our ability to build useful low dimensional representations of TCRs. To address the current limitations in TCR analysis we develop a capacity-controlled disentangling variational autoencoder trained using a dataset of approximately 100 million TCR sequences, that we name TCR-VALID. We design TCR-VALID such that the model representations are low-dimensional, continuous, disentangled, and sufficiently informative to provide high-quality TCR sequence de novo generation. We thoroughly quantify these properties of the representations, providing a framework for future protein representation learning in low dimensions. The continuity of TCR-VALID representations allows fast and accurate TCR clustering and is benchmarked against other state-of-the-art TCR clustering tools and pre-trained language models.
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Affiliation(s)
- Allen Y Leary
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA.
| | - Darius Scott
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Namita T Gupta
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Janelle C Waite
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Dimitris Skokos
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Gurinder S Atwal
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Peter G Hawkins
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA.
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22
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Peng X, Zhu X, Liu X, Huang Y, Zhu B. Increase in HIV reservoir and T cell immune response after CoronaVac vaccination in people living with HIV. Heliyon 2024; 10:e30394. [PMID: 38720759 PMCID: PMC11076980 DOI: 10.1016/j.heliyon.2024.e30394] [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: 01/16/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
Introduction CoronaVac, an inactivated vaccine developed by Sinovac Life Sciences, has been widely used for protection against Coronavirus Disease 2019 (COVID-19). This study investigates its effect on the HIV reservoir and T cell repertoires in people living with HIV (PLWHs). Methods Blood samples were collected from fifteen PLWHs who were administered at least two doses of CoronaVac between April 2021 and February 2022. The levels of cell-associated HIV RNA (CA HIV RNA) and HIV DNA, as well as the T cell receptor (TCR) repertoire profiles, TCR clustering and TCRβ annotation, were studied. Results A significant increase was observed in CA HIV RNA at 2 weeks (431.5 ± 164.2 copies/106 cells, P = 0.039) and 12 weeks (330.2 ± 105.9 copies/106 cells, P = 0.019) after the second dose, when compared to the baseline (0 weeks) (73.6 ± 23.7 copies/106 cells). Various diversity indices of the TCRβ repertoire, including Shannon index, Pielou's evenness index, and Hvj Index, revealed a slight increase (P < 0.05) following CoronaVac vaccination. The proportion of overlapping TCRβ clonotypes increased from baseline (31.9 %) to 2 weeks (32.5 %) and 12 weeks (40.4 %) after the second dose. We also found that the breadth and depth of COVID-19-specific T cells increased from baseline (0.003 and 0.0035) to 12 weeks (0.0066 and 0.0058) post the second dose. Conclusions Our study demonstrated an initial increase in HIV reservoir and TCR repertoire diversity, as well as an expansion in the depth and breadth of COVID-19-specific T-cell clones among CoronaVac-vaccinated PLWHs. These findings provide important insights into the effects of COVID-19 vaccination in PLWHs.
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Affiliation(s)
- Xiaorong Peng
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Xueling Zhu
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Xiang Liu
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Ying Huang
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Biao Zhu
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
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23
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Qian W, Ma N, Zeng X, Shi M, Wang M, Yang Z, Tsui SKW. Identification of novel single nucleotide variants in the drug resistance mechanism of Mycobacterium tuberculosis isolates by whole-genome analysis. BMC Genomics 2024; 25:478. [PMID: 38745294 PMCID: PMC11094924 DOI: 10.1186/s12864-024-10390-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) represents a major global health challenge. Drug resistance in Mycobacterium tuberculosis (MTB) poses a substantial obstacle to effective TB treatment. Identifying genomic mutations in MTB isolates holds promise for unraveling the underlying mechanisms of drug resistance in this bacterium. METHODS In this study, we investigated the roles of single nucleotide variants (SNVs) in MTB isolates resistant to four antibiotics (moxifloxacin, ofloxacin, amikacin, and capreomycin) through whole-genome analysis. We identified the drug-resistance-associated SNVs by comparing the genomes of MTB isolates with reference genomes using the MuMmer4 tool. RESULTS We observed a strikingly high proportion (94.2%) of MTB isolates resistant to ofloxacin, underscoring the current prevalence of drug resistance in MTB. An average of 3529 SNVs were detected in a single ofloxacin-resistant isolate, indicating a mutation rate of approximately 0.08% under the selective pressure of ofloxacin exposure. We identified a set of 60 SNVs associated with extensively drug-resistant tuberculosis (XDR-TB), among which 42 SNVs were non-synonymous mutations located in the coding regions of nine key genes (ctpI, desA3, mce1R, moeB1, ndhA, PE_PGRS4, PPE18, rpsA, secF). Protein structure modeling revealed that SNVs of three genes (PE_PGRS4, desA3, secF) are close to the critical catalytic active sites in the three-dimensional structure of the coding proteins. CONCLUSION This comprehensive study elucidates novel resistance mechanisms in MTB against antibiotics, paving the way for future design and development of anti-tuberculosis drugs.
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Affiliation(s)
- Weiye Qian
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Nan Ma
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mingqiang Wang
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Zhiyuan Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China.
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24
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Dzanibe S, Wilk AJ, Canny S, Ranganath T, Alinde B, Rubelt F, Huang H, Davis MM, Holmes SP, Jaspan HB, Blish CA, Gray CM. Premature skewing of T cell receptor clonality and delayed memory expansion in HIV-exposed infants. Nat Commun 2024; 15:4080. [PMID: 38744812 PMCID: PMC11093981 DOI: 10.1038/s41467-024-47955-5] [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: 05/25/2023] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
While preventing vertical HIV transmission has been very successful, HIV-exposed uninfected infants (iHEU) experience an elevated risk to infections compared to HIV-unexposed and uninfected infants (iHUU). Here we present a longitudinal multimodal analysis of infant immune ontogeny that highlights the impact of HIV/ARV exposure. Using mass cytometry, we show alterations in T cell memory differentiation between iHEU and iHUU being significant from week 15 of life. The altered memory T cell differentiation in iHEU was preceded by lower TCR Vβ clonotypic diversity and linked to TCR clonal depletion within the naïve T cell compartment. Compared to iHUU, iHEU had elevated CD56loCD16loPerforin+CD38+CD45RA+FcεRIγ+ NK cells at 1 month postpartum and whose abundance pre-vaccination were predictive of vaccine-induced pertussis and rotavirus antibody responses post 3 months of life. Collectively, HIV/ARV exposure disrupted the trajectory of innate and adaptive immunity from birth which may underlie relative vulnerability to infections in iHEU.
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Affiliation(s)
- Sonwabile Dzanibe
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Aaron J Wilk
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Susan Canny
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
- Division of Rheumatology, Department of Pediatrics, Seattle Children's Hospital, Seattle, WA, USA
| | - Thanmayi Ranganath
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Berenice Alinde
- Division of Immunology, Department of Biomedical Sciences, Biomedical Research Institute, Stellenbosch University, Cape Town, South Africa
| | - Florian Rubelt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Huang Huang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Heather B Jaspan
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Seattle Children's Research Institute and Department of Paediatrics and Global Health, University of Washington, Seattle, WA, USA.
| | - Catherine A Blish
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA.
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Clive M Gray
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Immunology, Department of Biomedical Sciences, Biomedical Research Institute, Stellenbosch University, Cape Town, South Africa.
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25
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Gupta T, Antanaviciute A, Hyun-Jung Lee C, Ottakandathil Babu R, Aulicino A, Christoforidou Z, Siejka-Zielinska P, O'Brien-Ball C, Chen H, Fawkner-Corbett D, Geros AS, Bridges E, McGregor C, Cianci N, Fryer E, Alham NK, Jagielowicz M, Santos AM, Fellermeyer M, Davis SJ, Parikh K, Cheung V, Al-Hillawi L, Sasson S, Slevin S, Brain O, Fernandes RA, Koohy H, Simmons A. Tracking in situ checkpoint inhibitor-bound target T cells in patients with checkpoint-induced colitis. Cancer Cell 2024; 42:797-814.e15. [PMID: 38744246 DOI: 10.1016/j.ccell.2024.04.010] [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: 05/23/2023] [Revised: 02/09/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
The success of checkpoint inhibitors (CPIs) for cancer has been tempered by immune-related adverse effects including colitis. CPI-induced colitis is hallmarked by expansion of resident mucosal IFNγ cytotoxic CD8+ T cells, but how these arise is unclear. Here, we track CPI-bound T cells in intestinal tissue using multimodal single-cell and subcellular spatial transcriptomics (ST). Target occupancy was increased in inflamed tissue, with drug-bound T cells located in distinct microdomains distinguished by specific intercellular signaling and transcriptional gradients. CPI-bound cells were largely CD4+ T cells, including enrichment in CPI-bound peripheral helper, follicular helper, and regulatory T cells. IFNγ CD8+ T cells emerged from both tissue-resident memory (TRM) and peripheral populations, displayed more restricted target occupancy profiles, and co-localized with damaged epithelial microdomains lacking effective regulatory cues. Our multimodal analysis identifies causal pathways and constitutes a resource to inform novel preventive strategies.
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Affiliation(s)
- Tarun Gupta
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Agne Antanaviciute
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.
| | - Chloe Hyun-Jung Lee
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Rosana Ottakandathil Babu
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Anna Aulicino
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Zoe Christoforidou
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Paulina Siejka-Zielinska
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Caitlin O'Brien-Ball
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - Hannah Chen
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - David Fawkner-Corbett
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Academic Paediatric Surgery Unit (APSU), Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Ana Sousa Geros
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Esther Bridges
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Colleen McGregor
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Nicole Cianci
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Eve Fryer
- Pathology, Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Nasullah Khalid Alham
- Nuffield Department of Surgical Sciences and Oxford NIHR Biomedical Research Centre (BRC), University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Marta Jagielowicz
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ana Mafalda Santos
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Martin Fellermeyer
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Simon J Davis
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Kaushal Parikh
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Vincent Cheung
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Lulia Al-Hillawi
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Sarah Sasson
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Stephanie Slevin
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Oliver Brain
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ricardo A Fernandes
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - Hashem Koohy
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.
| | - Alison Simmons
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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26
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Tsuda S, Shichino S, Tilburgs T, Shima T, Morita K, Yamaki-Ushijima A, Roskin K, Tomura M, Sameshima A, Saito S, Nakashima A. CD4 + T cell heterogeneity in gestational age and preeclampsia using single-cell RNA sequencing. Front Immunol 2024; 15:1401738. [PMID: 38774869 PMCID: PMC11106458 DOI: 10.3389/fimmu.2024.1401738] [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: 03/15/2024] [Accepted: 04/23/2024] [Indexed: 05/24/2024] Open
Abstract
A balance between pro-inflammatory decidual CD4+ T cells and FOXP3+ regulatory T cells (FOXP3+ Tregs) is important for maintaining fetomaternal tolerance. Using single-cell RNA-sequencing and T cell receptor repertoire analysis, we determined that diversity and clonality of decidual CD4+ T cell subsets depend on gestational age. Th1/Th2 intermediate and Th1 subsets of CD4+ T cells were clonally expanded in both early and late gestation, whereas FOXP3+ Tregs were clonally expanded in late gestation. Th1/Th2 intermediate and FOXP3+ Treg subsets showed altered gene expression in preeclampsia (PE) compared to healthy late gestation. The Th1/Th2 intermediate subset exhibited elevated levels of cytotoxicity-related gene expression in PE. Moreover, increased Treg exhaustion was observed in the PE group, and FOXP3+ Treg subcluster analysis revealed that the effector Treg like subset drove the Treg exhaustion signatures in PE. The Th1/Th2 intermediate and effector Treg like subsets are possible inflammation-driving subsets in PE.
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Affiliation(s)
- Sayaka Tsuda
- Department of Obstetrics and Gynecology, University of Toyama, Toyama, Japan
- Division of Immunobiology, Center for Inflammation and Tolerance, Cincinnati Children’s Hospital, Cincinnati, OH, United States
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Tamara Tilburgs
- Division of Immunobiology, Center for Inflammation and Tolerance, Cincinnati Children’s Hospital, Cincinnati, OH, United States
| | - Tomoko Shima
- Department of Obstetrics and Gynecology, University of Toyama, Toyama, Japan
| | - Keiko Morita
- Department of Obstetrics and Gynecology, University of Toyama, Toyama, Japan
| | | | - Krishna Roskin
- Divisions of Biomedical Informatics & Immunobiology, Cincinnati Children’s Hospital, Cincinnati, OH, United States
| | - Michio Tomura
- Laboratory of Immunology, Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
| | - Azusa Sameshima
- Department of Obstetrics and Gynecology, University of Toyama, Toyama, Japan
- Ladies’ Clinic We! Toyama, Toyama, Japan
| | | | - Akitoshi Nakashima
- Department of Obstetrics and Gynecology, University of Toyama, Toyama, Japan
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27
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Irac SE, Soon MSF, Borcherding N, Tuong ZK. Single-cell immune repertoire analysis. Nat Methods 2024; 21:777-792. [PMID: 38637691 DOI: 10.1038/s41592-024-02243-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/12/2024] [Indexed: 04/20/2024]
Abstract
Single-cell T cell and B cell antigen receptor-sequencing data analysis can potentially perform in-depth assessments of adaptive immune cells that inform on understanding immune cell development to tracking clonal expansion in disease and therapy. However, it has been extremely challenging to analyze and interpret T cells and B cells and their adaptive immune receptor repertoires at the single-cell level due to not only the complexity of the data but also the underlying biology. In this Review, we delve into the computational breakthroughs that have transformed the analysis of single-cell T cell and B cell antigen receptor-sequencing data.
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Affiliation(s)
- Sergio E Irac
- Cancer Immunoregulation and Immunotherapy, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Megan Sioe Fei Soon
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Omniscope, Palo Alto, CA, USA
| | - Zewen Kelvin Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
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28
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Long X, Zhang Z, Li Y, Deng K, Gao W, Huang M, Wang X, Lin X, She X, Zhao Y, Zhang M, Huang C, Wang S, Du Y, Du P, Chen S, Liu Q, Wu M. ScRNA-seq reveals novel immune-suppressive T cells and investigates CMV-TCR-T cells cytotoxicity against GBM. J Immunother Cancer 2024; 12:e008967. [PMID: 38688579 PMCID: PMC11086384 DOI: 10.1136/jitc-2024-008967] [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: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Glioblastoma (GBM) is a fatal primary brain malignancy in adults. Previous studies have shown that cytomegalovirus (CMV) is a risk factor for tumorigenesis and aggressiveness for glioblastoma. However, little is known about how CMV infection affects immune cells in the tumor microenvironment of GBM. Furthermore, there has been almost no engineered T-cell receptor (TCR)-T targeting CMV for GBM research to date. METHODS We evaluated the CMV infection status of patients with GBM's tumor tissue by immune electron microscopy, immunofluorescence, and droplet digital PCR. We performed single-cell RNA sequencing for CMV-infected GBM to investigate the effects of CMV on the GBM immune microenvironment. CellChat was applied to analyze the interaction between cells in the GBM tumor microenvironment. Additionally, we conducted single-cell TCR/B cell receptor (BCR) sequencing and Grouping of Lymphocyte Interactions with Paratope Hotspots 2 algorithms to acquire specific CMV-TCR sequences. Genetic engineering was used to introduce CMV-TCR into primary T cells derived from patients with CMV-infected GBM. Flow cytometry was used to measure the proportion and cytotoxicity status of T cells in vitro. RESULTS We identified two novel immune cell subpopulations in CMV-infected GBM, which were bipositive CD68+SOX2+ tumor-associated macrophages and FXYD6+ T cells. We highlighted that the interaction between bipositive TAMs or cancer cells and T cells was predominantly focused on FXYD6+ T cells rather than regulatory T cells (Tregs), whereas, FXYD6+ T cells were further identified as a group of novel immunosuppressive T cells. CMV-TCR-T cells showed significant therapeutic effects on the human-derived orthotopic GBM mice model. CONCLUSIONS These findings provided an insight into the underlying mechanism of CMV infection promoting the GBM immunosuppression, and provided a novel potential immunotherapy strategy for patients with GBM.
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Affiliation(s)
- Xinmiao Long
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- FuRong Laboratory, Central South University, Changsha, Hunan, China
| | - Zuping Zhang
- Department of Pathogeny Biology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Yuzhe Li
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, Hunan, China
- Chinese Academy of Medical Sciences and Peking Union Medical College, Peking University, Beijing, China
| | - Kun Deng
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- FuRong Laboratory, Central South University, Changsha, Hunan, China
| | - Wei Gao
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- FuRong Laboratory, Central South University, Changsha, Hunan, China
| | - Meng Huang
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, Hunan, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiangyu Wang
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiang Lin
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Xiaoling She
- Department of Pathology in Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yiming Zhao
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Department of Pathogeny Biology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Minfu Zhang
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Cheng Huang
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- FuRong Laboratory, Central South University, Changsha, Hunan, China
| | - Shiyi Wang
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- FuRong Laboratory, Central South University, Changsha, Hunan, China
| | - Yinfei Du
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- FuRong Laboratory, Central South University, Changsha, Hunan, China
| | - Peng Du
- Department of Neurosurgery, The Second Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Shuai Chen
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Qing Liu
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Minghua Wu
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- FuRong Laboratory, Central South University, Changsha, Hunan, China
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29
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Chang L, Zheng Z, Xiao F, Zhou Y, Zhong B, Ni Q, Qian C, Chen C, Che T, Zhou Y, Zhao Z, Zou Q, Li J, Lu L, Zou L, Wu Y. Single-cell clonal tracing of glandular and circulating T cells identifies a population of CD9+ CD8+ T cells in primary Sjogren's syndrome. J Leukoc Biol 2024; 115:804-818. [PMID: 37395700 DOI: 10.1093/jleuko/qiad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 07/04/2023] Open
Abstract
Primary Sjogren's syndrome (pSS) is a complex chronic autoimmune disease in which local tissue damage in exocrine glands is combined with broader systemic involvement across the body in tissues including the skin. These combined manifestations negatively impact patient health and quality of life. While studies have previously reported differences in immune cell composition in the peripheral blood of pSS patients relative to healthy control subjects, a detailed immune cell landscape of the damaged exocrine glands of these patients remains lacking. Through single-cell transcriptomics and repertoire sequencing of immune cells in paired peripheral blood samples and salivary gland biopsies, we present here a preliminary picture of adaptive immune response in pSS. We characterize a number of points of divergence between circulating and glandular immune responses that have been hitherto underappreciated, and identify a novel population of CD8+ CD9+ cells with tissue-residential properties that are highly enriched in the salivary glands of pSS patients. Through comparative analyses with other sequencing data, we also observe a potential connection between these cells and the tissue-resident memory cells found in cutaneous vasculitis lesions. Together, these results indicate a potential role for CD8+ CD9+ cells in mediating glandular and systemic effects associated with pSS and other autoimmune disorders.
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Affiliation(s)
- Ling Chang
- Institute of Immunology, Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
| | - Zihan Zheng
- Institute of Immunology, Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
- Biomedical Analysis Center, Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
- Department of Autoimmune Diseases, Chongqing International Institute for Immunology, 13 Tianchi Avenue, Banan District, Chongqing, China
| | - Fan Xiao
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, China
| | - Yingbo Zhou
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, China
| | - Bing Zhong
- Department of Rheumatology and Immunology, First Affiliated Hospital of Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
| | - Qingshan Ni
- Biomedical Analysis Center, Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
| | - Can Qian
- Department of Rheumatology and Immunology, First Affiliated Hospital of Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
| | - Chengshun Chen
- Department of Rheumatology and Immunology, First Affiliated Hospital of Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
| | - Tiantian Che
- Institute of Immunology, Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
| | - Yiwen Zhou
- Institute of Immunology, Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
| | - Zihua Zhao
- Institute of Immunology, Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
| | - Qinghua Zou
- Department of Rheumatology and Immunology, First Affiliated Hospital of Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
| | - Jingyi Li
- Department of Rheumatology and Immunology, First Affiliated Hospital of Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
| | - Liwei Lu
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, China
| | - Liyun Zou
- Institute of Immunology, Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
| | - Yuzhang Wu
- Institute of Immunology, Army Medical University, 30 Gaotanyan Avenue, Shapingba District, Chongqing, China
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30
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Hoang MH, Skidmore ZL, Rindt H, Chu S, Fisk B, Foltz JA, Fronick C, Fulton R, Zhou M, Bivens NJ, Reinero CN, Fehniger TA, Griffith M, Bryan JN, Griffith OL. Single-cell T-cell receptor repertoire profiling in dogs. Commun Biol 2024; 7:484. [PMID: 38649520 PMCID: PMC11035579 DOI: 10.1038/s42003-024-06174-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Spontaneous cancers in companion dogs are robust models of human disease. Tracking tumor-specific immune responses in these models requires reagents to perform species-specific single cell T cell receptor sequencing (scTCRseq). scTCRseq and integration with scRNA data have not been demonstrated on companion dogs with cancer. Here, five healthy dogs, two dogs with T cell lymphoma and four dogs with melanoma are selected to demonstrate applicability of scTCRseq in a cancer immunotherapy setting. Single-cell suspensions of PBMCs or lymph node aspirates are profiled using scRNA and dog-specific scTCRseq primers. In total, 77,809 V(D)J-expressing cells are detected, with an average of 3498 (348 - 5,971) unique clonotypes identified per sample. In total, 29/34, 40/40, 22/22 and 9/9 known functional TRAV, TRAJ, TRBV and TRBJ gene segments are observed respectively. Pseudogene or otherwise defective gene segments are also detected supporting re-annotation of several as functional. Healthy dogs exhibit highly diverse repertoires, T cell lymphomas exhibit clonal repertoires, and vaccine-treated melanoma dogs are dominated by a small number of highly abundant clonotypes. scRNA libraries define large clusters of V(D)J-expressing CD8+ and CD4 + T cells. Dominant clonotypes observed in melanoma PBMCs are predominantly CD8 + T cells, with activated phenotypes, suggesting possible anti-tumor T cell populations.
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Affiliation(s)
- My H Hoang
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Zachary L Skidmore
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Hans Rindt
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA
| | - Shirley Chu
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA
| | - Bryan Fisk
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Jennifer A Foltz
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Catrina Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Robert Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Mingyi Zhou
- Genomics Technology Core, University of Missouri, Columbia, MO, USA
| | - Nathan J Bivens
- Genomics Technology Core, University of Missouri, Columbia, MO, USA
| | - Carol N Reinero
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA
| | - Todd A Fehniger
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO, USA
| | - Malachi Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Jeffrey N Bryan
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA.
| | - Obi L Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.
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31
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Ben Hamza A, Welters C, Stadler S, Brüggemann M, Dietze K, Brauns O, Brümmendorf TH, Winkler T, Bullinger L, Blankenstein T, Rosenberger L, Leisegang M, Kammertöns T, Herr W, Moosmann A, Strobel J, Hackstein H, Dornmair K, Beier F, Hansmann L. Virus-reactive T cells expanded in aplastic anemia eliminate hematopoietic progenitor cells by molecular mimicry. Blood 2024; 143:1365-1378. [PMID: 38277625 DOI: 10.1182/blood.2023023142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
ABSTRACT Acquired aplastic anemia is a bone marrow failure syndrome characterized by hypocellular bone marrow and peripheral blood pancytopenia. Frequent clinical responses to calcineurin inhibition and antithymocyte globulin strongly suggest critical roles for hematopoietic stem/progenitor cell-reactive T-cell clones in disease pathophysiology; however, their exact contribution and antigen specificities remain unclear. We determined differentiation states and targets of dominant T-cell clones along with their potential to eliminate hematopoietic progenitor cells in the bone marrow of 15 patients with acquired aplastic anemia. Single-cell sequencing and immunophenotyping revealed oligoclonal expansion and effector differentiation of CD8+ T-cell compartments. We reexpressed 28 dominant T-cell receptors (TCRs) of 9 patients in reporter cell lines to determine reactivity with (1) in vitro-expanded CD34+ bone marrow, (2) CD34- bone marrow, or (3) peptide pools covering immunodominant epitopes of highly prevalent viruses. Besides 5 cytomegalovirus-reactive TCRs, we identified 3 TCRs that recognized antigen presented on hematopoietic progenitor cells. T cells transduced with these TCRs eliminated hematopoietic progenitor cells of the respective patients in vitro. One progenitor cell-reactive TCR (11A5) also recognized an epitope of the Epstein-Barr virus-derived latent membrane protein 1 (LMP1) presented on HLA-A∗02:01. We identified 2 LMP1-related mimotopes within the human proteome as activating targets of TCR 11A5, providing proof of concept that molecular mimicry of viral and self-epitopes can drive T cell-mediated elimination of hematopoietic progenitor cells in aplastic anemia.
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Affiliation(s)
- Amin Ben Hamza
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Carlotta Welters
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Serena Stadler
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, Partner Site Berlin, and German Cancer Research Center, Heidelberg, Germany
| | - Monika Brüggemann
- Department of Medicine II, Hematology and Oncology, University Hospital Schleswig Holstein, Kiel, Germany
| | - Kerstin Dietze
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Olaf Brauns
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology, Aachen Bonn Cologne Düsseldorf, Aachen, Germany
| | - Thomas Winkler
- Division of Genetics, Department of Biology, Friedrich Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, Partner Site Berlin, and German Cancer Research Center, Heidelberg, Germany
| | - Thomas Blankenstein
- Molecular Immunology and Gene Therapy, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Leonie Rosenberger
- Institute of Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Leisegang
- German Cancer Consortium, Partner Site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Institute of Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- David and Etta Jonas Center for Cellular Therapy, The University of Chicago, Chicago, IL
| | - Thomas Kammertöns
- Institute of Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Wolfgang Herr
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Andreas Moosmann
- Department of Medicine III, Klinikum der Universität München, Munich, Germany
- German Center for Infection Research, Munich, Germany
- Helmholtz Munich, Munich, Germany
| | - Julian Strobel
- Department of Transfusion Medicine and Hemostaseology, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Holger Hackstein
- Department of Transfusion Medicine and Hemostaseology, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig Maximilian University Munich, Munich, Germany
- Biomedical Center, Faculty of Medicine, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology, Aachen Bonn Cologne Düsseldorf, Aachen, Germany
| | - Leo Hansmann
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, Partner Site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
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Clark EA, Talatala ER, Ye W, Davis RJ, Collins SL, Hillel AT, Ramirez-Solano M, Sheng Q, Wanjalla CN, Mallal SA, Gelbard A. Characterizing the T Cell Repertoire in the Proximal Airway in Health and Disease. Laryngoscope 2024; 134:1757-1764. [PMID: 37787469 PMCID: PMC10947968 DOI: 10.1002/lary.31088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
OBJECTIVES Recent translational scientific efforts in subglottic stenosis (SGS) support a disease model where epithelial alterations facilitate microbiome displacement, dysregulated immune activation, and localized fibrosis. Given the observed immune cell infiltrate in SGS, we sought to test the hypothesis that SGS cases possessed a low diversity (highly clonal) adaptive immune response when compared with healthy controls. METHODS Single cell RNA sequencing (scRNA-seq) of subglottic mucosal scar in iSGS (n = 24), iLTS (n = 8), and healthy controls (n = 7) was performed. T cell receptor (TCR) sequences were extracted, analyzed, and used to construct repertoire structure, compare diversity, interrogate overlap, and define antigenic targets using the Immunarch bioinformatics pipeline. RESULTS The proximal airway mucosa in health and disease are equally diverse via Hill framework quantitation (iSGS vs. iLTS vs. Control, p > 0.05). Repertoires do not significantly overlap between individuals (Morisita <0.02). Among iSGS patients, clonality of the TCR repertoire is driven by CD8+ T cells, and iSGS patients possess numerous TCRs targeting viral and intercellular pathogens. High frequency clonotypes do not map to known targets in public datasets. CONCLUSION SGS cases do not possess a lower diversity adaptive immune infiltrate when compared with healthy controls. Interestingly, the TCR repertoire in both health and disease contains a restricted number of high frequency clonotypes that do not significantly overlap between individuals. The target of the high frequency clonotypes in health and disease remain unresolved. LEVEL OF EVIDENCE NA Laryngoscope, 134:1757-1764, 2024.
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Affiliation(s)
- Evan A. Clark
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Edward R.R. Talatala
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Wenda Ye
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Ruth J. Davis
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Samuel L. Collins
- Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alexander T. Hillel
- Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Celestine N. Wanjalla
- Department of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Simon A. Mallal
- Department of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alexander Gelbard
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
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Ye X, Shih DJH, Ku Z, Hong J, Barrett DF, Rupp RE, Zhang N, Fu TM, Zheng WJ, An Z. Transcriptional signature of durable effector T cells elicited by a replication defective HCMV vaccine. NPJ Vaccines 2024; 9:70. [PMID: 38561339 PMCID: PMC10984989 DOI: 10.1038/s41541-024-00860-w] [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: 01/13/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Human cytomegalovirus (HCMV) is a leading infectious cause of birth defects and the most common opportunistic infection that causes life-threatening diseases post-transplantation; however, an effective vaccine remains elusive. V160 is a live-attenuated replication defective HCMV vaccine that showed a 42.4% efficacy against primary HCMV infection among seronegative women in a phase 2b clinical trial. Here, we integrated the multicolor flow cytometry, longitudinal T cell receptor (TCR) sequencing, and single-cell RNA/TCR sequencing approaches to characterize the magnitude, phenotype, and functional quality of human T cell responses to V160. We demonstrated that V160 de novo induces IE-1 and pp65 specific durable polyfunctional effector CD8 T cells that are comparable to those induced by natural HCMV infection. We identified a variety of V160-responsive T cell clones which exhibit distinctive "transient" and "durable" expansion kinetics, and revealed a transcriptional signature that marks durable CD8 T cells post-vaccination. Our study enhances the understanding of human T-cell immune responses to V160 vaccination.
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Affiliation(s)
- Xiaohua Ye
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Infectious Disease Research, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - David J H Shih
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Junping Hong
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Diane F Barrett
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Richard E Rupp
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Tong-Ming Fu
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - W Jim Zheng
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.
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34
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Ji H, Wang XX, Zhang Q, Zhang C, Zhang HM. Predicting TCR sequences for unseen antigen epitopes using structural and sequence features. Brief Bioinform 2024; 25:bbae210. [PMID: 38711371 PMCID: PMC11074592 DOI: 10.1093/bib/bbae210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/04/2024] [Accepted: 04/22/2024] [Indexed: 05/08/2024] Open
Abstract
T-cell receptor (TCR) recognition of antigens is fundamental to the adaptive immune response. With the expansion of experimental techniques, a substantial database of matched TCR-antigen pairs has emerged, presenting opportunities for computational prediction models. However, accurately forecasting the binding affinities of unseen antigen-TCR pairs remains a major challenge. Here, we present convolutional-self-attention TCR (CATCR), a novel framework tailored to enhance the prediction of epitope and TCR interactions. Our approach utilizes convolutional neural networks to extract peptide features from residue contact matrices, as generated by OpenFold, and a transformer to encode segment-based coded sequences. We introduce CATCR-D, a discriminator that can assess binding by analyzing the structural and sequence features of epitopes and CDR3-β regions. Additionally, the framework comprises CATCR-G, a generative module designed for CDR3-β sequences, which applies the pretrained encoder to deduce epitope characteristics and a transformer decoder for predicting matching CDR3-β sequences. CATCR-D achieved an AUROC of 0.89 on previously unseen epitope-TCR pairs and outperformed four benchmark models by a margin of 17.4%. CATCR-G has demonstrated high precision, recall and F1 scores, surpassing 95% in bidirectional encoder representations from transformers score assessments. Our results indicate that CATCR is an effective tool for predicting unseen epitope-TCR interactions. Incorporating structural insights enhances our understanding of the general rules governing TCR-epitope recognition significantly. The ability to predict TCRs for novel epitopes using structural and sequence information is promising, and broadening the repository of experimental TCR-epitope data could further improve the precision of epitope-TCR binding predictions.
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MESH Headings
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/genetics
- Humans
- Epitopes/chemistry
- Epitopes/immunology
- Computational Biology/methods
- Neural Networks, Computer
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/chemistry
- Antigens/chemistry
- Antigens/immunology
- Amino Acid Sequence
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Affiliation(s)
- Hongchen Ji
- Department of Oncology of Xijing Hospital, Air Force Medical University, Xi’an, Shaanxi, China
| | - Xiang-Xu Wang
- Department of Oncology of Xijing Hospital, Air Force Medical University, Xi’an, Shaanxi, China
| | - Qiong Zhang
- Department of Oncology of Xijing Hospital, Air Force Medical University, Xi’an, Shaanxi, China
| | - Chengkai Zhang
- Department of Oncology of Xijing Hospital, Air Force Medical University, Xi’an, Shaanxi, China
| | - Hong-Mei Zhang
- Department of Oncology of Xijing Hospital, Air Force Medical University, Xi’an, Shaanxi, China
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35
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Roy P, Suthahar SSA, Makings J, Ley K. Identification of apolipoprotein B-reactive CDR3 motifs allows tracking of atherosclerosis-related memory CD4 +T cells in multiple donors. Front Immunol 2024; 15:1302031. [PMID: 38571941 PMCID: PMC10988780 DOI: 10.3389/fimmu.2024.1302031] [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: 09/25/2023] [Accepted: 02/02/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction Atherosclerosis is a major pathological condition that underlies many cardiovascular diseases (CVDs). Its etiology involves breach of tolerance to self, leading to clonal expansion of autoreactive apolipoprotein B (APOB)-reactive CD4+T cells that correlates with clinical CVD. The T-cell receptor (TCR) sequences that mediate activation of APOB-specific CD4+T cells are unknown. Methods In a previous study, we had profiled the hypervariable complementarity determining region 3 (CDR3) of CD4+T cells that respond to six immunodominant APOB epitopes in most donors. Here, we comprehensively analyze this dataset of 149,065 APOB-reactive and 199,211 non-reactive control CDR3s from six human leukocyte antigen-typed donors. Results We identified 672 highly expanded (frequency threshold > 1.39E-03) clones that were significantly enriched in the APOB-reactive group as compared to the controls (log10 odds ratio ≥1, Fisher's test p < 0.01). Analysis of 114,755 naïve, 91,001 central memory (TCM) and 29,839 effector memory (TEM) CDR3 sequences from the same donors revealed that APOB+ clones can be traced to the complex repertoire of unenriched blood T cells. The fraction of APOB+ clones that overlapped with memory CDR3s ranged from 2.2% to 46% (average 16.4%). This was significantly higher than their overlap with the naïve pool, which ranged from 0.7% to 2% (average 1.36%). CDR3 motif analysis with the machine learning-based in-silico tool, GLIPHs (grouping of lymphocyte interactions by paratope hotspots), identified 532 APOB+ motifs. Analysis of naïve and memory CDR3 sequences with GLIPH revealed that ~40% (209 of 532) of these APOB+ motifs were enriched in the memory pool. Network analysis with Cytoscape revealed extensive sharing of the memory-affiliated APOB+ motifs across multiple donors. We identified six motifs that were present in TCM and TEM CDR3 sequences from >80% of the donors and were highly enriched in the APOB-reactive TCR repertoire. Discussion The identified APOB-reactive expanded CD4+T cell clones and conserved motifs can be used to annotate and track human atherosclerosis-related autoreactive CD4+T cells and measure their clonal expansion.
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Affiliation(s)
- Payel Roy
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, United States
- Immunology Center of Georgia, Augusta University, Augusta, GA, United States
| | | | - Jeffrey Makings
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Klaus Ley
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, United States
- Immunology Center of Georgia, Augusta University, Augusta, GA, United States
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36
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Gail DP, Suzart VG, Carpenter SM. Analyzing human CD4 + T cells activated in response to macrophages infected with Mycobacterium tuberculosis. STAR Protoc 2024; 5:102939. [PMID: 38451821 PMCID: PMC10937946 DOI: 10.1016/j.xpro.2024.102939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/24/2024] [Accepted: 02/21/2024] [Indexed: 03/09/2024] Open
Abstract
M1- and M2-like macrophages infected with Mycobacterium tuberculosis (Mtb) have been found to differ in their capacity to elicit memory CD4+ T cell activation. Here, we present a protocol to quantify and isolate the subset of human memory CD4+ T cells activated in response to autologous monocyte-derived macrophages (MDMs) infected with virulent Mtb. We describe steps for CD14+ monocyte isolation, generating MDMs, culturing Mtb and infection of macrophages, and identifying activated CD4+ T cells by flow cytometry. For complete details on the use and execution of this protocol, please refer to Gail et al.1.
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Affiliation(s)
- Daniel P Gail
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Vinicius G Suzart
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Biomedical Sciences Training Program, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Stephen M Carpenter
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Biomedical Sciences Training Program, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA.
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37
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Li X, Zhang Y, Guo S, Wu Z, Wang H, Huang Y, Wang Y, Qiu M, Lang J, Xiao Y, Zhu Y, Jin G, Hu L, Kong X. Global analysis of T-cell groups reveals immunological features and common antigen targets of digestive tract tumors. J Cancer Res Clin Oncol 2024; 150:129. [PMID: 38488909 PMCID: PMC10943170 DOI: 10.1007/s00432-024-05645-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/05/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND T cells are key players in the tumor immune microenvironment (TIME), as they can recognize and eliminate cancer cells that express neoantigens derived from somatic mutations. However, the diversity and specificity of T-cell receptors (TCRs) that recognize neoantigens are largely unknown, due to the high variability of TCR sequences among individuals. METHODS To address this challenge, we applied GLIPH2, a novel algorithm that groups TCRs based on their predicted antigen specificity and HLA restriction, to cluster the TCR repertoire of 1,702 patients with digestive tract cancer. The patients were divided into five groups based on whether they carried tumor-infiltrating or clonal-expanded TCRs and calculated their TCR diversity. The prognosis, tumor subtype, gene mutation, gene expression, and immune microenvironment of these groups were compared. Viral specificity inference and immunotherapy relevance analysis performed for the TCR groups. RESULTS This approach reduced the complexity of TCR sequences to 249 clonally expanded and 150 tumor-infiltrating TCR groups, which revealed distinct patterns of TRBV usage, HLA association, and TCR diversity. In gastric adenocarcinoma (STAD), patients with tumor-infiltrating TCRs (Patients-TI) had significantly worse prognosis than other patients (Patients-nonTI). Patients-TI had richer CD8+ T cells in the immune microenvironment, and their gene expression features were positively correlated with immunotherapy response. We also found that tumor-infiltrating TCR groups were associated with four distinct tumor subtypes, 26 common gene mutations, and 39 gene expression signatures. We discovered that tumor-infiltrating TCRs had cross-reactivity with viral antigens, indicating a possible link between viral infections and tumor immunity. CONCLUSION By applying GLIPH2 to TCR sequences from digestive tract tumors, we uncovered novel insights into the tumor immune landscape and identified potential candidates for shared TCRs and neoantigens.
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Affiliation(s)
- Xiaoxue Li
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yuchao Zhang
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
| | - Shiwei Guo
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Shanghai, China
| | - Zhenchuan Wu
- Anda Biology Medicine Development (Shenzhen) Co., Ltd., Shenzhen, China
| | - Hailong Wang
- Anda Biology Medicine Development (Shenzhen) Co., Ltd., Shenzhen, China
| | - Yi Huang
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yue Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Mengni Qiu
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Jingyu Lang
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
| | - Yichuan Xiao
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
| | - Yufei Zhu
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Shanghai, China.
| | - Landian Hu
- Anda Biology Medicine Development (Shenzhen) Co., Ltd., Shenzhen, China.
| | - Xiangyin Kong
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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Pothuri VS, Hogg GD, Conant L, Borcherding N, James CA, Mudd J, Williams G, Seo YD, Hawkins WG, Pillarisetty VG, DeNardo DG, Fields RC. Intratumoral T-cell receptor repertoire composition predicts overall survival in patients with pancreatic ductal adenocarcinoma. Oncoimmunology 2024; 13:2320411. [PMID: 38504847 PMCID: PMC10950267 DOI: 10.1080/2162402x.2024.2320411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/14/2024] [Indexed: 03/21/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy that is refractory to immune checkpoint inhibitor therapy. However, intratumoral T-cell infiltration correlates with improved overall survival (OS). Herein, we characterized the diversity and antigen specificity of the PDAC T-cell receptor (TCR) repertoire to identify novel immune-relevant biomarkers. Demographic, clinical, and TCR-beta sequencing data were collated from 353 patients across three cohorts that underwent surgical resection for PDAC. TCR diversity was calculated using Shannon Wiener index, Inverse Simpson index, and "True entropy." Patients were clustered by shared repertoire specificity. TCRs predictive of OS were identified and their associated transcriptional states were characterized by single-cell RNAseq. In multivariate Cox regression models controlling for relevant covariates, high intratumoral TCR diversity predicted OS across multiple cohorts. Conversely, in peripheral blood, high abundance of T-cells, but not high diversity, predicted OS. Clustering patients based on TCR specificity revealed a subset of TCRs that predicts OS. Interestingly, these TCR sequences were more likely to encode CD8+ effector memory and CD4+ T-regulatory (Tregs) T-cells, all with the capacity to recognize beta islet-derived autoantigens. As opposed to T-cell abundance, intratumoral TCR diversity was predictive of OS in multiple PDAC cohorts, and a subset of TCRs enriched in high-diversity patients independently correlated with OS. These findings emphasize the importance of evaluating peripheral and intratumoral TCR repertoires as distinct and relevant biomarkers in PDAC.
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Affiliation(s)
- Vikram S. Pothuri
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Graham D. Hogg
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Leah Conant
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Nicholas Borcherding
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - C. Alston James
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacqueline Mudd
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Greg Williams
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Yongwoo David Seo
- Department of Surgery, University of Washington School of Medicine, Seattle, WA, USA
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - William G. Hawkins
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MOUSA
| | - Venu G. Pillarisetty
- Department of Surgery, University of Washington School of Medicine, Seattle, WA, USA
- Fred Hutchinson Cancer Center, Seattle, WAUSA
| | - David G. DeNardo
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MOUSA
| | - Ryan C. Fields
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MOUSA
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Voogd L, Drittij AM, Dingenouts CK, Franken KL, Unen VV, van Meijgaarden KE, Ruibal P, Hagedoorn RS, Leitner JA, Steinberger P, Heemskerk MH, Davis MM, Scriba TJ, Ottenhoff TH, Joosten SA. Mtb HLA-E-tetramer-sorted CD8 + T cells have a diverse TCR repertoire. iScience 2024; 27:109233. [PMID: 38439958 PMCID: PMC10909886 DOI: 10.1016/j.isci.2024.109233] [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: 10/18/2023] [Revised: 01/05/2024] [Accepted: 02/09/2024] [Indexed: 03/06/2024] Open
Abstract
HLA-E molecules can present self- and pathogen-derived peptides to both natural killer (NK) cells and T cells. T cells that recognize HLA-E peptides via their T cell receptor (TCR) are termed donor-unrestricted T cells due to restricted allelic variation of HLA-E. The composition and repertoire of HLA-E TCRs is not known so far. We performed TCR sequencing on CD8+ T cells from 21 individuals recognizing HLA-E tetramers (TMs) folded with two Mtb-HLA-E-restricted peptides. We sorted HLA-E Mtb TM+ and TM- CD8+ T cells directly ex vivo and performed bulk RNA-sequencing and single-cell TCR sequencing. The identified TCR repertoire was diverse and showed no conservation between and within individuals. TCRs selected from our single-cell TCR sequencing data could be activated upon HLA-E/peptide stimulation, although not robust, reflecting potentially weak interactions between HLA-E peptide complexes and TCRs. Thus, HLA-E-Mtb-specific T cells have a highly diverse TCR repertoire.
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Affiliation(s)
- Linda Voogd
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Anne M.H.F. Drittij
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Calinda K.E. Dingenouts
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Kees L.M.C. Franken
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Vincent van Unen
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Paula Ruibal
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Renate S. Hagedoorn
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Judith A. Leitner
- Centre for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Medical University of Vienna, Vienna, Austria
| | - Peter Steinberger
- Centre for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Mark M. Davis
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Palo Alto, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Tom H.M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Simone A. Joosten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
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40
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Aterido A, López-Lasanta M, Blanco F, Juan-Mas A, García-Vivar ML, Erra A, Pérez-García C, Sánchez-Fernández SÁ, Sanmartí R, Fernández-Nebro A, Alperi-López M, Tornero J, Ortiz AM, Fernández-Cid CM, Palau N, Pan W, Byrne-Steele M, Starenki D, Weber D, Rodriguez-Nunez I, Han J, Myers RM, Marsal S, Julià A. Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes. Genome Biol 2024; 25:68. [PMID: 38468286 PMCID: PMC10926600 DOI: 10.1186/s13059-024-03210-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/04/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND In rheumatoid arthritis (RA), the activation of T and B cell clones specific for self-antigens leads to the chronic inflammation of the synovium. Here, we perform an in-depth quantitative analysis of the seven chains that comprise the adaptive immune receptor repertoire (AIRR) in RA. RESULTS In comparison to controls, we show that RA patients have multiple and strong differences in the B cell receptor repertoire including reduced diversity as well as altered isotype, chain, and segment frequencies. We demonstrate that therapeutic tumor necrosis factor inhibition partially restores this alteration but find a profound difference in the underlying biochemical reactivities between responders and non-responders. Combining the AIRR with HLA typing, we identify the specific T cell receptor repertoire associated with disease risk variants. Integrating these features, we further develop a molecular classifier that shows the utility of the AIRR as a diagnostic tool. CONCLUSIONS Simultaneous sequencing of the seven chains of the human AIRR reveals novel features associated with the disease and clinically relevant phenotypes, including response to therapy. These findings show the unique potential of AIRR to address precision medicine in immune-related diseases.
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Affiliation(s)
- Adrià Aterido
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | - María López-Lasanta
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | - Francisco Blanco
- Rheumatology Department, Hospital Juan Canalejo, A Coruña, Spain
| | | | | | - Alba Erra
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
- Rheumatology Department, Hospital Sant Rafael, Barcelona, Spain
| | | | | | - Raimon Sanmartí
- Rheumatology Department, Hospital Clínic de Barcelona and IDIBAPS, Barcelona, Spain
| | | | | | - Jesús Tornero
- Rheumatology Department, Hospital Universitario Guadalajara, Guadalajara, Spain
| | - Ana María Ortiz
- Rheumatology Department, Hospital Universitario La Princesa, IIS La Princesa, Madrid, Spain
| | | | - Núria Palau
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | | | | | | | | | | | - Jian Han
- iRepertoire Inc, Huntsville, AL, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sara Marsal
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain.
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41
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Chugh S, Bahal RK, Dhiman R, Singh R. Antigen identification strategies and preclinical evaluation models for advancing tuberculosis vaccine development. NPJ Vaccines 2024; 9:57. [PMID: 38461350 PMCID: PMC10924964 DOI: 10.1038/s41541-024-00834-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/05/2024] [Indexed: 03/11/2024] Open
Abstract
In its myriad devastating forms, Tuberculosis (TB) has existed for centuries, and humanity is still affected by it. Mycobacterium tuberculosis (M. tuberculosis), the causative agent of TB, was the foremost killer among infectious agents until the COVID-19 pandemic. One of the key healthcare strategies available to reduce the risk of TB is immunization with bacilli Calmette-Guerin (BCG). Although BCG has been widely used to protect against TB, reports show that BCG confers highly variable efficacy (0-80%) against adult pulmonary TB. Unwavering efforts have been made over the past 20 years to develop and evaluate new TB vaccine candidates. The failure of conventional preclinical animal models to fully recapitulate human response to TB, as also seen for the failure of MVA85A in clinical trials, signifies the need to develop better preclinical models for TB vaccine evaluation. In the present review article, we outline various approaches used to identify protective mycobacterial antigens and recent advancements in preclinical models for assessing the efficacy of candidate TB vaccines.
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Affiliation(s)
- Saurabh Chugh
- Centre for Tuberculosis Research, Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, 121001, Haryana, India
| | - Ritika Kar Bahal
- Marshall Centre, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Ramandeep Singh
- Centre for Tuberculosis Research, Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, 121001, Haryana, India.
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42
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Jensen MF, Nielsen M. Enhancing TCR specificity predictions by combined pan- and peptide-specific training, loss-scaling, and sequence similarity integration. eLife 2024; 12:RP93934. [PMID: 38437160 PMCID: PMC10942633 DOI: 10.7554/elife.93934] [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] [Indexed: 03/06/2024] Open
Abstract
Predicting the interaction between Major Histocompatibility Complex (MHC) class I-presented peptides and T-cell receptors (TCR) holds significant implications for vaccine development, cancer treatment, and autoimmune disease therapies. However, limited paired-chain TCR data, skewed towards well-studied epitopes, hampers the development of pan-specific machine-learning (ML) models. Leveraging a larger peptide-TCR dataset, we explore various alterations to the ML architectures and training strategies to address data imbalance. This leads to an overall improved performance, particularly for peptides with scant TCR data. However, challenges persist for unseen peptides, especially those distant from training examples. We demonstrate that such ML models can be used to detect potential outliers, which when removed from training, leads to augmented performance. Integrating pan-specific and peptide-specific models alongside with similarity-based predictions, further improves the overall performance, especially when a low false positive rate is desirable. In the context of the IMMREP22 benchmark, this modeling framework attained state-of-the-art performance. Moreover, combining these strategies results in acceptable predictive accuracy for peptides characterized with as little as 15 positive TCRs. This observation places great promise on rapidly expanding the peptide covering of the current models for predicting TCR specificity. The NetTCR 2.2 model incorporating these advances is available on GitHub (https://github.com/mnielLab/NetTCR-2.2) and as a web server at https://services.healthtech.dtu.dk/services/NetTCR-2.2/.
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Affiliation(s)
- Mathias Fynbo Jensen
- Department of Health Technology, Section for Bioinformatics, Technical University of DenmarkLyngbyDenmark
| | - Morten Nielsen
- Department of Health Technology, Section for Bioinformatics, Technical University of DenmarkLyngbyDenmark
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43
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Hudson D, Lubbock A, Basham M, Koohy H. A comparison of clustering models for inference of T cell receptor antigen specificity. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2024; 13:None. [PMID: 38525047 PMCID: PMC10955519 DOI: 10.1016/j.immuno.2024.100033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 03/26/2024]
Abstract
The vast potential sequence diversity of TCRs and their ligands has presented an historic barrier to computational prediction of TCR epitope specificity, a holy grail of quantitative immunology. One common approach is to cluster sequences together, on the assumption that similar receptors bind similar epitopes. Here, we provide the first independent evaluation of widely used clustering algorithms for TCR specificity inference, observing some variability in predictive performance between models, and marked differences in scalability. Despite these differences, we find that different algorithms produce clusters with high degrees of similarity for receptors recognising the same epitope. Our analysis strengthens the case for use of clustering models to identify signals of common specificity from large repertoires, whilst highlighting scope for improvement of complex models over simple comparators.
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Affiliation(s)
- Dan Hudson
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- The Rosalind Franklin Institute, Didcot, UK
| | | | | | - Hashem Koohy
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Alan Turning Fellow in Health and Medicine, UK
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44
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Akama-Garren EH, Yin X, Prestwood TR, Ma M, Utz PJ, Carroll MC. T cell help shapes B cell tolerance. Sci Immunol 2024; 9:eadj7029. [PMID: 38363829 DOI: 10.1126/sciimmunol.adj7029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/29/2023] [Indexed: 02/18/2024]
Abstract
T cell help is a crucial component of the normal humoral immune response, yet whether it promotes or restrains autoreactive B cell responses remains unclear. Here, we observe that autoreactive germinal centers require T cell help for their formation and persistence. Using retrogenic chimeras transduced with candidate TCRs, we demonstrate that a follicular T cell repertoire restricted to a single autoreactive TCR, but not a foreign antigen-specific TCR, is sufficient to initiate autoreactive germinal centers. Follicular T cell specificity influences the breadth of epitope spreading by regulating wild-type B cell entry into autoreactive germinal centers. These results demonstrate that TCR-dependent T cell help can promote loss of B cell tolerance and that epitope spreading is determined by TCR specificity.
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Affiliation(s)
- Elliot H Akama-Garren
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Xihui Yin
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tyler R Prestwood
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Minghe Ma
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Paul J Utz
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael C Carroll
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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45
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Savage TM, Fortson KT, de Los Santos-Alexis K, Oliveras-Alsina A, Rouanne M, Rae SS, Gamarra JR, Shayya H, Kornberg A, Cavero R, Li F, Han A, Haeusler RA, Adam J, Schwabe RF, Arpaia N. Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis. Immunity 2024; 57:303-318.e6. [PMID: 38309273 PMCID: PMC10922825 DOI: 10.1016/j.immuni.2024.01.009] [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: 09/23/2022] [Revised: 11/20/2023] [Accepted: 01/10/2024] [Indexed: 02/05/2024]
Abstract
Production of amphiregulin (Areg) by regulatory T (Treg) cells promotes repair after acute tissue injury. Here, we examined the function of Treg cells in non-alcoholic steatohepatitis (NASH), a setting of chronic liver injury. Areg-producing Treg cells were enriched in the livers of mice and humans with NASH. Deletion of Areg in Treg cells, but not in myeloid cells, reduced NASH-induced liver fibrosis. Chronic liver damage induced transcriptional changes associated with Treg cell activation. Mechanistically, Treg cell-derived Areg activated pro-fibrotic transcriptional programs in hepatic stellate cells via epidermal growth factor receptor (EGFR) signaling. Deletion of Areg in Treg cells protected mice from NASH-dependent glucose intolerance, which also was dependent on EGFR signaling on hepatic stellate cells. Areg from Treg cells promoted hepatocyte gluconeogenesis through hepatocyte detection of hepatic stellate cell-derived interleukin-6. Our findings reveal a maladaptive role for Treg cell-mediated tissue repair functions in chronic liver disease and link liver damage to NASH-dependent glucose intolerance.
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Affiliation(s)
- Thomas M Savage
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | - Katherine T Fortson
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | | | | | - Mathieu Rouanne
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | - Sarah S Rae
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | | | - Hani Shayya
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY, USA
| | - Adam Kornberg
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA; Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Renzo Cavero
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | - Fangda Li
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | - Arnold Han
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA; Columbia Center for Translational Immunology, Columbia University, New York, NY, USA; Department of Medicine, Columbia University, New York, NY, USA
| | - Rebecca A Haeusler
- Naomi Berrie Diabetes Center, Columbia University, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Julien Adam
- Pathology Department, Hopital Paris Saint-Joseph, Paris, France; INSERM U1186, Gustave Roussy, Villejuif, France
| | | | - Nicholas Arpaia
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
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46
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Ravishankar S, Towlerton AM, Mooka P, Kafeero J, Coffey DG, Aicher LD, Mubiru KR, Okoche L, Atwinirembabazi P, Okonye J, Phipps WT, Warren EH. The signature of a T-cell response to KSHV persists across space and time in individuals with epidemic and endemic KS from Uganda. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579223. [PMID: 38370623 PMCID: PMC10871354 DOI: 10.1101/2024.02.06.579223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Inadequate T-cell control of Kaposi sarcoma-associated herpesvirus (KSHV) infection predisposes to development of Kaposi sarcoma (KS), but little is known about the T-cell response to KSHV. Postulating that KS tumors contain abundant KSHV-specific T-cells, we performed transcriptional profiling and T-cell receptor (TCR) repertoire analysis of tumor biopsies from 144 Ugandan adults with KS. We show that CD8+ T-cells and M2-polarized macrophages dominate the tumor micro-environment (TME). The TCR repertoire of KS tumor infiltrating lymphocytes (TIL) is shared across non-contiguous tumors and persists across time. Clusters of T-cells with predicted shared specificity for uncharacterized antigens, potentially encoded by KSHV, comprise ~25% of KS TIL, and are shared across tumors from different time points and individuals. Single-cell RNA-sequencing of blood identifies a non-proliferating effector memory phenotype and captured the TCRs in 14,698 putative KSHV-specific T-cells. These results suggest that a polyspecific KSHV-specific T-cell response inhibited by M2 macrophages exists within the KS TME, and provide a foundation for studies to define its specificity at a large scale.
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Affiliation(s)
- Shashidhar Ravishankar
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Andrea M.H. Towlerton
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Hutchinson Centre Research Institute – Uganda, Kampala, Uganda
| | - Peter Mooka
- Hutchinson Centre Research Institute – Uganda, Kampala, Uganda
| | - James Kafeero
- Hutchinson Centre Research Institute – Uganda, Kampala, Uganda
| | - David G. Coffey
- Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States
| | - Lauri D. Aicher
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | | | - Lazarus Okoche
- Hutchinson Centre Research Institute – Uganda, Kampala, Uganda
| | | | - Joseph Okonye
- Hutchinson Centre Research Institute – Uganda, Kampala, Uganda
| | - Warren T. Phipps
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Edus H. Warren
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
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47
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Almalki WH. NEAT1 in inflammatory infectious diseases: An integrated perspective on molecular modulation. Pathol Res Pract 2024; 254:154956. [PMID: 38218038 DOI: 10.1016/j.prp.2023.154956] [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: 10/11/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 01/15/2024]
Abstract
The long non-coding RNA (lncRNA), NEAT1, has emerged as a central figure in the intricate network of molecular regulators in inflammatory infectious diseases (IIDs). The review initiates a comprehensive exploration of NEAT1's multifaceted roles and molecular interactions in the context of these complex diseases. The study begins by acknowledging the global health burden of IIDs, underscoring the urgency for innovative insights into their pathogenesis and therapeutic avenues. NEAT1 is introduced as a pivotal lncRNA with growing relevance in immune responses and inflammatory processes. The core of this review unravels the NEAT1 landscape, elucidating its involvement in the modulation of immune signalling pathways, regulation of inflammatory cytokines, and interactions with various immune cells during infection. It explores NEAT1's role in orchestrating immune responses and balancing host defence mechanisms with the risk of immunopathology. Furthermore, the review underscores the clinical significance of NEAT1 in infectious diseases, discussing its associations with disease severity, prognosis, and potential as a diagnostic and therapeutic target. It provides insights into ongoing research endeavours aimed at harnessing NEAT1 for innovative disease management strategies, including developing RNA-based therapeutics. Concluding on a forward-looking note, the review highlights the broader implications of NEAT1 in the context of emerging infectious diseases and the possibility for precision medicine approaches that leverage NEAT1's regulatory capacities. In summary, this review illuminates the pivotal role of NEAT1 in IIDs by navigating its complex landscape, offering profound insights into its implications for disease pathogenesis and the development of targeted therapies.
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Affiliation(s)
- Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.
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48
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Súkeníková L, Mallone A, Schreiner B, Ripellino P, Nilsson J, Stoffel M, Ulbrich SE, Sallusto F, Latorre D. Autoreactive T cells target peripheral nerves in Guillain-Barré syndrome. Nature 2024; 626:160-168. [PMID: 38233524 PMCID: PMC10830418 DOI: 10.1038/s41586-023-06916-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/30/2023] [Indexed: 01/19/2024]
Abstract
Guillain-Barré syndrome (GBS) is a rare heterogenous disorder of the peripheral nervous system, which is usually triggered by a preceding infection, and causes a potentially life-threatening progressive muscle weakness1. Although GBS is considered an autoimmune disease, the mechanisms that underlie its distinct clinical subtypes remain largely unknown. Here, by combining in vitro T cell screening, single-cell RNA sequencing and T cell receptor (TCR) sequencing, we identify autoreactive memory CD4+ cells, that show a cytotoxic T helper 1 (TH1)-like phenotype, and rare CD8+ T cells that target myelin antigens of the peripheral nerves in patients with the demyelinating disease variant. We characterized more than 1,000 autoreactive single T cell clones, which revealed a polyclonal TCR repertoire, short CDR3β lengths, preferential HLA-DR restrictions and recognition of immunodominant epitopes. We found that autoreactive TCRβ clonotypes were expanded in the blood of the same patient at distinct disease stages and, notably, that they were shared in the blood and the cerebrospinal fluid across different patients with GBS, but not in control individuals. Finally, we identified myelin-reactive T cells in the nerve biopsy from one patient, which indicates that these cells contribute directly to disease pathophysiology. Collectively, our data provide clear evidence of autoreactive T cell immunity in a subset of patients with GBS, and open new perspectives in the field of inflammatory peripheral neuropathies, with potential impact for biomedical applications.
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Affiliation(s)
- L Súkeníková
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - A Mallone
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - B Schreiner
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - P Ripellino
- Department of Neurology, Neurocenter of Southern Switzerland EOC, Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - J Nilsson
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - M Stoffel
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Medical Faculty, University of Zurich, Zurich, Switzerland
| | - S E Ulbrich
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - F Sallusto
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - D Latorre
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
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49
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Zhang J, Wang Y, Huang Y, Tan X, Xu J, Yan Q, Tan J, Zhang Y, Zhang J, Ma Q, Zhu H, Ye J, Zhu Z, Lan W. Characterization of T cell receptor repertoire in penile cancer. Cancer Immunol Immunother 2024; 73:24. [PMID: 38280010 PMCID: PMC10822009 DOI: 10.1007/s00262-023-03615-z] [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: 09/26/2023] [Accepted: 12/04/2023] [Indexed: 01/29/2024]
Abstract
Tumor-infiltrating lymphocytes (TILs) play a key role in regulating the host immune response and shaping tumor microenvironment. It has been previously shown that T cell infiltration in penile tumors was associated with clinical outcomes. However, few studies have reported the T cell receptor (TCR) repertoire in patients with penile cancer. In the present study, we evaluated the TCR repertoires in tumor and adjacent normal tissues from 22 patients with penile squamous cell carcinoma (PSCC). Analysis of the T cell receptor beta-variable (TRBV) and joining (TRBJ) genes usage and analysis of complementarity determining region 3 (CDR3) length distribution did not show significant differences between tumor and matched normal tissues. Moreover, analysis of the median Jaccard index indicated a limited overlap of TCR repertoire between these groups. Compared with normal tissues, a significantly lower diversity and higher clonality of TCR repertoire was observed in tumor samples, which was associated with clinical characteristics. Further analysis of transcriptional profiles demonstrated that tumor samples with high clonality showed increased expression of genes associated with CD8 + T cells. In addition, we analyzed the TCR repertoire of CD4 + T cells and CD8 + T cells isolated from tumor tissues. We identified that expanded clonotypes were predominantly in the CD8 + T cell compartment, which presented with an exhausted phenotype. Overall, we comprehensively compared TCR repertoire between penile tumor and normal tissues and demonstrated the presence of distinct T cell immune microenvironments in patients with PSCC.
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Affiliation(s)
- Junying Zhang
- Chongqing Key Laboratory of High Active Traditional Chinese Drug Delivery System, Chongqing Engineering Research Center of Pharmaceutical Sciences, Chongqing Medical and Pharmaceutical College, Chongqing, 401331, People's Republic of China
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Yapeng Wang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Yiqiang Huang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Xintao Tan
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Jing Xu
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Qian Yan
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Jiao Tan
- School of Pharmacy, Chongqing Medical and Pharmaceutical College, Chongqing, 401331, People's Republic of China
| | - Yao Zhang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Jun Zhang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Qiang Ma
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Hailin Zhu
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Jin Ye
- Urinary Nephropathy Center, The Thirteenth People's Hospital of Chongqing, Chongqing, 400053, People's Republic of China.
| | - Zhaojing Zhu
- Chongqing Key Laboratory of High Active Traditional Chinese Drug Delivery System, Chongqing Engineering Research Center of Pharmaceutical Sciences, Chongqing Medical and Pharmaceutical College, Chongqing, 401331, People's Republic of China.
| | - Weihua Lan
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China.
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Chang H, Ashlock DA, Graether SP, Keller SM. Anchor Clustering for million-scale immune repertoire sequencing data. BMC Bioinformatics 2024; 25:42. [PMID: 38273275 PMCID: PMC10809746 DOI: 10.1186/s12859-024-05659-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The clustering of immune repertoire data is challenging due to the computational cost associated with a very large number of pairwise sequence comparisons. To overcome this limitation, we developed Anchor Clustering, an unsupervised clustering method designed to identify similar sequences from millions of antigen receptor gene sequences. First, a Point Packing algorithm is used to identify a set of maximally spaced anchor sequences. Then, the genetic distance of the remaining sequences to all anchor sequences is calculated and transformed into distance vectors. Finally, distance vectors are clustered using unsupervised clustering. This process is repeated iteratively until the resulting clusters are small enough so that pairwise distance comparisons can be performed. RESULTS Our results demonstrate that Anchor Clustering is faster than existing pairwise comparison clustering methods while providing similar clustering quality. With its flexible, memory-saving strategy, Anchor Clustering is capable of clustering millions of antigen receptor gene sequences in just a few minutes. CONCLUSIONS This method enables the meta-analysis of immune-repertoire data from different studies and could contribute to a more comprehensive understanding of the immune repertoire data space.
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Affiliation(s)
- Haiyang Chang
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Daniel A Ashlock
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Stefan M Keller
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.
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