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Bhargava M, Crouser ED. Application of laboratory models for sarcoidosis research. J Autoimmun 2024:103184. [PMID: 38443221 DOI: 10.1016/j.jaut.2024.103184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/07/2024]
Abstract
This manuscript will review the implications and applications of sarcoidosis models towards advancing our understanding of sarcoidosis disease mechanisms, identification of biomarkers, and preclinical testing of novel therapies. Emerging disease models and innovative research tools will also be considered.
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Affiliation(s)
- Maneesh Bhargava
- University of Minnesota Medical Center, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, 420 Delaware Street SE, MMC 276. Minneapolis, MN 55455, USA
| | - Elliott D Crouser
- Ohio State University Wexner Medicine Center, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, 241 W. 11th Street, Suite 5000, Columbus, OH 43201, USA.
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2
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Tippalagama R, Chihab LY, Kearns K, Lewis S, Panda S, Willemsen L, Burel JG, Lindestam Arlehamn CS. Antigen-specificity measurements are the key to understanding T cell responses. Front Immunol 2023; 14:1127470. [PMID: 37122719 PMCID: PMC10140422 DOI: 10.3389/fimmu.2023.1127470] [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: 12/19/2022] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
Antigen-specific T cells play a central role in the adaptive immune response and come in a wide range of phenotypes. T cell receptors (TCRs) mediate the antigen-specificities found in T cells. Importantly, high-throughput TCR sequencing provides a fingerprint which allows tracking of specific T cells and their clonal expansion in response to particular antigens. As a result, many studies have leveraged TCR sequencing in an attempt to elucidate the role of antigen-specific T cells in various contexts. Here, we discuss the published approaches to studying antigen-specific T cells and their specific TCR repertoire. Further, we discuss how these methods have been applied to study the TCR repertoire in various diseases in order to characterize the antigen-specific T cells involved in the immune control of disease.
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3
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Sun X, Nguyen T, Achour A, Ko A, Cifello J, Ling C, Sharma J, Hiroi T, Zhang Y, Chia CW, Wood Iii W, Wu WW, Zukley L, Phue JN, Becker KG, Shen RF, Ferrucci L, Weng NP. Longitudinal analysis reveals age-related changes in the T cell receptor repertoire of human T cell subsets. J Clin Invest 2022; 132:158122. [PMID: 35708913 PMCID: PMC9433102 DOI: 10.1172/jci158122] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
A diverse T cell receptor (TCR) repertoire is essential for protection against a variety of pathogens, and TCR repertoire size is believed to decline with age. However, the precise size of human TCR repertoires, in both total and subsets of T cells, as well as their changes with age, are not fully characterized. We conducted a longitudinal analysis of the human blood TCRα and TCRβ repertoire of CD4+ and CD8+ T cell subsets using a unique molecular identifier–based (UMI-based) RNA-seq method. Thorough analysis of 1.9 × 108 T cells yielded the lower estimate of TCR repertoire richness in an adult at 3.8 × 108. Alterations of the TCR repertoire with age were observed in all 4 subsets of T cells. The greatest reduction was observed in naive CD8+ T cells, while the greatest clonal expansion was in memory CD8+ T cells, and the highest increased retention of TCR sequences was in memory CD8+ T cells. Our results demonstrated that age-related TCR repertoire attrition is subset specific and more profound for CD8+ than CD4+ T cells, suggesting that aging has a more profound effect on cytotoxic as opposed to helper T cell functions. This may explain the increased susceptibility of older adults to novel infections.
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Affiliation(s)
- Xiaoping Sun
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Thomas Nguyen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Achouak Achour
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Annette Ko
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Jeffrey Cifello
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Chen Ling
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Jay Sharma
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Toyoko Hiroi
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Yongqing Zhang
- Gene expression and Genomics Unit, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, United States of America
| | - Chee W Chia
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, United States of America
| | - William Wood Iii
- Gene expression and Genomics Unit, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, United States of America
| | - Wells W Wu
- Facility for Biotechnology Resources, Food and Drug Administration, Silver Spring, United States of America
| | - Linda Zukley
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, United States of America
| | - Je-Nie Phue
- Facility for Biotechnology Resources, Food and Drug Administration, Silver Spring, United States of America
| | - Kevin G Becker
- Gene expression and Genomics Unit, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, United States of America
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Food and Drug Administration, Silver Spring, United States of America
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, United States of America
| | - Nan-Ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
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4
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The CSF in neurosarcoidosis contains consistent clonal expansion of CD8 T cells, but not CD4 T cells. J Neuroimmunol 2022; 367:577860. [DOI: 10.1016/j.jneuroim.2022.577860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/01/2022] [Accepted: 03/29/2022] [Indexed: 01/02/2023]
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Abstract
Löfgren’s syndrome is an acute form of sarcoidosis that is characterized by the activation of CD4+ T helper cells. In this issue of JEM, Greaves et al. (2021. J. Exp. Med.https://doi.org/10.1084/jem.20210785) identified a peptide derived from an airborne mold species that stimulates T cells of Löfgren’s syndrome patients in an HLA-DR3–restricted manner. An increased serum IgG antibody response to the full-length protein was also observed in those patients, indicating that the fungus Aspergillus nidulans might be the elusive microbial agent that drives acute sarcoidosis.
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Affiliation(s)
- Clarice X Lim
- Center for Pathobiochemistry & Genetics, Medical University of Vienna, Vienna, Austria
| | - Thomas Weichhart
- Center for Pathobiochemistry & Genetics, Medical University of Vienna, Vienna, Austria
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6
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Greaves SA, Ravindran A, Santos RG, Chen L, Falta MT, Wang Y, Mitchell AM, Atif SM, Mack DG, Tinega AN, Maier LA, Dai S, Pinilla C, Grunewald J, Fontenot AP. CD4+ T cells in the lungs of acute sarcoidosis patients recognize an Aspergillus nidulans epitope. J Exp Med 2021; 218:212583. [PMID: 34410304 PMCID: PMC8383815 DOI: 10.1084/jem.20210785] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/18/2021] [Accepted: 07/22/2021] [Indexed: 11/05/2022] Open
Abstract
Löfgren’s syndrome (LS) is an acute form of sarcoidosis characterized by a genetic association with HLA-DRB1*03 (HLA-DR3) and an accumulation of CD4+ T cells of unknown specificity in the bronchoalveolar lavage (BAL). Here, we screened related LS-specific TCRs for antigen specificity and identified a peptide derived from NAD-dependent histone deacetylase hst4 (NDPD) of Aspergillus nidulans that stimulated these CD4+ T cells in an HLA-DR3–restricted manner. Using ELISPOT analysis, a greater number of IFN-γ– and IL-2–secreting T cells in the BAL of DR3+ LS subjects compared with DR3+ control subjects was observed in response to the NDPD peptide. Finally, increased IgG antibody responses to A. nidulans NDPD were detected in the serum of DR3+ LS subjects. Thus, our findings identify a ligand for CD4+ T cells derived from the lungs of LS patients and suggest a role of A. nidulans in the etiology of LS.
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Affiliation(s)
- Sarah A Greaves
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Avinash Ravindran
- Department of Medicine, Solna, Karolinska University Hospital, Stockholm, Sweden.,Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Radleigh G Santos
- Department of Mathematics, Nova Southeastern University, Ft. Lauderdale, FL
| | - Lan Chen
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Michael T Falta
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Yang Wang
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Angela M Mitchell
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Shaikh M Atif
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Douglas G Mack
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Alex N Tinega
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Lisa A Maier
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Medicine, National Jewish Health, Denver, CO
| | - Shaodong Dai
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Clemencia Pinilla
- Center for Translational Science, Florida International University, Port St. Lucie, FL
| | - Johan Grunewald
- Department of Medicine, Solna, Karolinska University Hospital, Stockholm, Sweden
| | - Andrew P Fontenot
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO
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7
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Liu H, Pan W, Tang C, Tang Y, Wu H, Yoshimura A, Deng Y, He N, Li S. The methods and advances of adaptive immune receptors repertoire sequencing. Theranostics 2021; 11:8945-8963. [PMID: 34522220 PMCID: PMC8419057 DOI: 10.7150/thno.61390] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022] Open
Abstract
The adaptive immune response is a powerful tool, capable of recognizing, binding to, and neutralizing a vast number of internal and external threats via T or B lymphatic receptors with widespread sets of antigen specificities. The emergence of high-throughput sequencing technology and bioinformatics provides opportunities for research in the fields of life sciences and medicine. The analysis and annotation for immune repertoire data can reveal biologically meaningful information, including immune prediction, target antigens, and effective evaluation. Continuous improvements of the immunological repertoire sequencing methods and analysis tools will help to minimize the experimental and calculation errors and realize the immunological information to meet the clinical requirements. That said, the clinical application of adaptive immune repertoire sequencing requires appropriate experimental methods and standard analytical tools. At the population cell level, we can acquire the overview of cell groups, but the information about a single cell is not obtained accurately. The information that is ignored may be crucial for understanding the heterogeneity of each cell, gene expression and drug response. The combination of high-throughput sequencing and single-cell technology allows us to obtain single-cell information with low-cost and high-throughput. In this review, we summarized the current methods and progress in this area.
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Affiliation(s)
- Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Congli Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Yujie Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hu-nan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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8
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Hassman LM, Paley MA, Esaulova E, Paley GL, Ruzycki PA, Linskey N, Laurent J, Feigl-Lenzen L, Springer L, Montana CL, Hong K, Enright J, James H, Artyomov MN, Yokoyama WM. Clinicomolecular Identification of Conserved and Individualized Features of Granulomatous Uveitis. OPHTHALMOLOGY SCIENCE 2021; 1:100010. [PMID: 35937550 PMCID: PMC9352144 DOI: 10.1016/j.xops.2021.100010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/17/2021] [Accepted: 03/08/2021] [Indexed: 12/17/2022]
Abstract
Objective To identify molecular features that distinguish individuals with shared clinical features of granulomatous uveitis. Design Cross-sectional, observational study. Participants Four eyes from patients with active granulomatous uveitis. Methods We performed single-cell RNA-sequencing with antigen-receptor sequence analysis to obtain an unbiased gene expression survey of ocular immune cells and identify clonally expanded lymphocytes. Main Outcomes Measures For each inflamed eye, we measured the proportion of distinct immune cell types, the amount of B or T cell clonal expansion, and the transcriptional profile of T and B cells. Results Each individual had robust clonal expansion arising from a single T or B cell lineage, suggesting distinct, antigen-driven pathogenic processes in each patient. This variability in clonal expansion was mirrored by individual variability in CD4 T cell populations, whereas ocular CD8 T cells and B cells were more transcriptionally similar between patients. Finally, ocular B cells displayed evidence of class-switching and plasmablast differentiation within the ocular microenvironment, providing additional support for antigen-driven immune responses in granulomatous uveitis. Conclusions Collectively, our study identified both conserved and individualized features of granulomatous uveitis, illuminating parallel pathophysiologic mechanisms, and suggesting that future personalized therapeutic approaches may be warranted.
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Affiliation(s)
- Lynn M. Hassman
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Michael A. Paley
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Ekaterina Esaulova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Grace L. Paley
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Philip A. Ruzycki
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Nicole Linskey
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Jennifer Laurent
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Lacey Feigl-Lenzen
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Luke Springer
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Cynthia L. Montana
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Karen Hong
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Jennifer Enright
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Hayley James
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Maxim N. Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Wayne M. Yokoyama
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
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9
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Abstract
T cells are an integral component of the adaptive immune response via the recognition of peptides by the cell surface-expressed T cell receptor (TCR). Rearrangement of the TCR genes results in a highly polymorphic repertoire on the T cells within a given individual. Although the diverse repertoire is beneficial for immune responses to foreign pathogens, recognition of self-peptides by T cells can contribute to the development of autoimmune disorders. Increasing evidence supports a pathogenic role for T cells in autoimmune pathology, and it is of interest to determine the TCR repertoires involved in autoimmune disease development. In this review, we summarize methodologies and advancements in the TCR sequencing field and discuss recent studies focused on TCR sequencing in a variety of autoimmune conditions. The rapidly evolving methodology of TCR sequencing has the potential to allow for a better understanding of autoimmune disease pathogenesis, identify disease-specific biomarkers, and aid in developing therapies to prevent and treat a number of these disorders.
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Affiliation(s)
- Angela M Mitchell
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO, USA, 80045
| | - Aaron W Michels
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO, USA, 80045
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10
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Abstract
PURPOSE OF REVIEW Sarcoidosis is a systemic disease characterized by granulomatous inflammation of unknown cause. There is extensive heterogeneity between patients with respect to the number and types of organs involved, disease course, and response to therapy. Recent research in the field has leveraged 'omics' techniques such as transcriptomics to identify important 'molecular profiles' in the disease. These tools may help in identifying clinically useful biomarkers and targets for therapy. RECENT FINDINGS Several studies have used gene expression profiling of predesignated lists or the entire genome to find genes and markers that differentiate sarcoidosis from healthy controls, but only a few have compared sarcoidosis patients based on disease phenotypes and organ involvement. The common gene pathways that have been repeatedly identified include those related to the interferon response, T-cell receptor signaling, and the major histocompatibility complex. SUMMARY While the molecular profiling studies to date offer the ability to compare sarcoidosis and health as well as across tissues, further longitudinal studies that include sarcoidosis patients with varying outcomes with respect to organ involvement and response to treatment are needed to identify clinically important phenotypes in the disease that can then be differentiated based on molecular features.
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Affiliation(s)
- Nicholas K. Arger
- University of California, San Francisco, Division of Pulmonary and Critical Care, 505 Parnassus Ave, San Francisco, CA 94143, USA
| | - Brian O’Connor
- National Jewish Health, Center for Genes, Environment, & Health, 1400 Jackson St, Denver, CO 80206, USA
| | - Laura L. Koth
- University of California, San Francisco, Division of Pulmonary and Critical Care, 505 Parnassus Ave, San Francisco, CA 94143, USA
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11
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Tanno H, McDaniel JR, Stevens CA, Voss WN, Li J, Durrett R, Lee J, Gollihar J, Tanno Y, Delidakis G, Pothukuchy A, Ellefson JW, Goronzy JJ, Maynard JA, Ellington AD, Ippolito GC, Georgiou G. A facile technology for the high-throughput sequencing of the paired VH:VL and TCRβ:TCRα repertoires. SCIENCE ADVANCES 2020; 6:eaay9093. [PMID: 32426460 PMCID: PMC7176429 DOI: 10.1126/sciadv.aay9093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/27/2020] [Indexed: 05/27/2023]
Abstract
Natively paired sequencing (NPS) of B cell receptors [variable heavy (VH) and light (VL)] and T cell receptors (TCRb and TCRa) is essential for the understanding of adaptive immunity in health and disease. Despite many recent technical advances, determining the VH:VL or TCRb:a repertoire with high accuracy and throughput remains challenging. We discovered that the recently engineered xenopolymerase, RTX, is exceptionally resistant to cell lysate inhibition in single-cell emulsion droplets. We capitalized on the characteristics of this enzyme to develop a simple, rapid, and inexpensive in-droplet overlap extension reverse transcription polymerase chain reaction method for NPS not requiring microfluidics or other specialized equipment. Using this technique, we obtained high yields (5000 to >20,000 per sample) of paired VH:VL or TCRb:a clonotypes at low cost. As a demonstration, we performed NPS on peripheral blood plasmablasts and T follicular helper cells following seasonal influenza vaccination and discovered high-affinity influenza-specific antibodies and TCRb:a.
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Affiliation(s)
- Hidetaka Tanno
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Jonathan R. McDaniel
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | | | - William N. Voss
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Jie Li
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Russell Durrett
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Jiwon Lee
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Jimmy Gollihar
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- U.S. Army Research Laboratory South, Austin, TX, USA
| | - Yuri Tanno
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - George Delidakis
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Arti Pothukuchy
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Jared W. Ellefson
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Jörg J. Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Jennifer A. Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Andrew D. Ellington
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Gregory C. Ippolito
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
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12
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Greaves SA, Atif SM, Fontenot AP. Adaptive Immunity in Pulmonary Sarcoidosis and Chronic Beryllium Disease. Front Immunol 2020; 11:474. [PMID: 32256501 PMCID: PMC7093490 DOI: 10.3389/fimmu.2020.00474] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 02/28/2020] [Indexed: 12/11/2022] Open
Abstract
Pulmonary sarcoidosis and chronic beryllium disease (CBD) are inflammatory granulomatous lung diseases defined by the presence of non-caseating granulomas in the lung. CBD results from beryllium exposure in the workplace, while the cause of sarcoidosis remains unknown. CBD and sarcoidosis are both immune-mediated diseases that involve Th1-polarized inflammation in the lung. Beryllium exposure induces trafficking of dendritic cells to the lung in a mechanism dependent on MyD88 and IL-1α. B cells are also recruited to the lung in a MyD88 dependent manner after beryllium exposure in order to protect the lung from beryllium-induced injury. Similar to most immune-mediated diseases, disease susceptibility in CBD and sarcoidosis is driven by the expression of certain MHCII molecules, primarily HLA-DPB1 in CBD and several HLA-DRB1 alleles in sarcoidosis. One of the defining features of both CBD and sarcoidosis is an infiltration of activated CD4+ T cells in the lung. CD4+ T cells in the bronchoalveolar lavage (BAL) of CBD and sarcoidosis patients are highly Th1 polarized, and there is a significant increase in inflammatory Th1 cytokines present in the BAL fluid. In sarcoidosis, there is also a significant population of Th17 cells in the lungs that is not present in CBD. Due to persistent antigen exposure and chronic inflammation in the lung, these activated CD4+ T cells often display either an exhausted or anergic phenotype. Evidence suggests that these T cells are responding to common antigens in the lung. In CBD there is an expansion of beryllium-responsive TRBV5.1+ TCRs expressed on pathogenic CD4+ T cells derived from the BAL of CBD patients that react with endogenous human peptides derived from the plexin A protein. In an acute form of sarcoidosis, there are expansions of specific TRAV12-1/TRBV2 T cell receptors expressed on BAL CD4+ T cells, indicating that these T cells are trafficking to and expanding in the lung in response to common antigens. The specificity of these pathogenic CD4+T cells in sarcoidosis are currently unknown.
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Affiliation(s)
- Sarah A Greaves
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Shaikh M Atif
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Andrew P Fontenot
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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13
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Kaiser Y, Eklund A, Grunewald J. Moving target: shifting the focus to pulmonary sarcoidosis as an autoimmune spectrum disorder. Eur Respir J 2019; 54:13993003.021532018. [PMID: 31000677 DOI: 10.1183/13993003.021532018] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 04/01/2019] [Indexed: 12/27/2022]
Abstract
Despite more than a century of research, the causative agent(s) in sarcoidosis, a heterogeneous granulomatous disorder mainly affecting the lungs, remain(s) elusive. Following identification of genetic factors underlying different clinical phenotypes, increased understanding of CD4+ T-cell immunology, which is believed to be central to sarcoid pathogenesis, as well as the role of B-cells and other cells bridging innate and adaptive immunity, contributes to novel insights into the mechanistic pathways influencing disease resolution or chronicity. Hopefully, new perspectives and state-of-the-art technology will help to shed light on the still-elusive enigma of sarcoid aetiology. This perspective article highlights a number of recent advances in the search for antigenic targets in sarcoidosis, as well as the main arguments for sarcoidosis as a spectrum of autoimmune conditions, either as a result of an external (microbial) trigger and/or due to defective control mechanisms regulating the balance between T-cell activation and inhibition.
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Affiliation(s)
- Ylva Kaiser
- Respiratory Medicine Unit, Dept of Medicine, Solna and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Anders Eklund
- Respiratory Medicine Unit, Dept of Medicine, Solna and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Johan Grunewald
- Respiratory Medicine Unit, Dept of Medicine, Solna and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
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14
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Abstract
Sarcoidosis is an inflammatory disorder of unknown cause that is characterized by granuloma formation in affected organs, most often in the lungs. Patients frequently suffer from cough, shortness of breath, chest pain and pronounced fatigue and are at risk of developing lung fibrosis or irreversible damage to other organs. The disease develops in genetically predisposed individuals with exposure to an as-yet unknown antigen. Genetic factors affect not only the risk of developing sarcoidosis but also the disease course, which is highly variable and difficult to predict. The typical T cell accumulation, local T cell immune response and granuloma formation in the lungs indicate that the inflammatory response in sarcoidosis is induced by specific antigens, possibly including self-antigens, which is consistent with an autoimmune involvement. Diagnosis can be challenging for clinicians because of the potential for almost any organ to be affected. As the aetiology of sarcoidosis is unknown, no specific treatment and no pathognomic markers exist. Thus, improved biomarkers to determine disease activity and to identify patients at risk of developing fibrosis are needed. Corticosteroids still constitute the first-line treatment, but new treatment strategies, including those targeting quality-of-life issues, are being evaluated and should yield appropriate, personalized and more effective treatments.
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15
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powerTCR: A model-based approach to comparative analysis of the clone size distribution of the T cell receptor repertoire. PLoS Comput Biol 2018; 14:e1006571. [PMID: 30485278 PMCID: PMC6287877 DOI: 10.1371/journal.pcbi.1006571] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 12/10/2018] [Accepted: 10/19/2018] [Indexed: 11/19/2022] Open
Abstract
Sequencing of the T cell receptor (TCR) repertoire is a powerful tool for deeper study of immune response, but the unique structure of this type of data makes its meaningful quantification challenging. We introduce a new method, the Gamma-GPD spliced threshold model, to address this difficulty. This biologically interpretable model captures the distribution of the TCR repertoire, demonstrates stability across varying sequencing depths, and permits comparative analysis across any number of sampled individuals. We apply our method to several datasets and obtain insights regarding the differentiating features in the T cell receptor repertoire among sampled individuals across conditions. We have implemented our method in the open-source R package powerTCR. A more detailed understanding of the immune response can unlock critical information concerning diagnosis and treatment of disease. Here, in particular, we study T cells through T cell receptor sequencing, as T cells play a vital role in immune response. One important feature of T cell receptor sequencing data is the frequencies of each receptor in a given sample. These frequencies harbor global information about the landscape of the immune response. We introduce a flexible method that extracts this information by modeling the distribution of these frequencies, and show that it can be used to quantify differences in samples from individuals of different biological conditions.
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16
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Kinloch AJ, Kaiser Y, Wolfgeher D, Ai J, Eklund A, Clark MR, Grunewald J. In Situ Humoral Immunity to Vimentin in HLA-DRB1*03 + Patients With Pulmonary Sarcoidosis. Front Immunol 2018; 9:1516. [PMID: 30038611 PMCID: PMC6046378 DOI: 10.3389/fimmu.2018.01516] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022] Open
Abstract
Vimentin has been implicated in pulmonary sarcoidosis as a T-cell autoantigen, particularly in the context of HLA-DRB1*03, the Vα2.3/Vβ22 T-cell receptor (TCR), and Löfgren’s syndrome. As vimentin is a known antigenic target in B-cell-mediated autoimmunity, we investigated in situ humoral anti-vimentin responses in pulmonary sarcoidosis and their relationship with HLA-DRB1*03. Sarcoid and healthy control (HC) lung biopsies were analyzed by multi-color confocal microscopy for B-cells, T-cells, proliferation, and vimentin, and compared to tonsillectomy tissue. Bronchoalveolar lavage fluid (BALF) and serum from 48 sarcoidosis patients and 15 healthy volunteers were typed for HLA-DRB1*03 and titrated for antibodies to full-length vimentin, vimentin truncations, and total IgG and IgA by ELISA. Presence of extracellular vimentin in BALF was determined by mass spectrometry and T-cell populations measured by flow cytometry. Sarcoid lung samples, especially from HLA-DRB1*03+ patients, contained vimentin-rich tertiary lymphoid structures and corresponding BALF was highly enriched for both IgG and IgA anti-vimentin antibody (AVA) titers. Furthermore, sarcoidosis patient BALF AVA concentrations (expressed as arbitrary units per milligram of total immunoglobulin isotype) correlated with the percentage of CD4+ T-cells expressing the Vα2.3/Vβ22 TCR. BALF antibody reactivity to the vimentin N-terminus was most prominent in HCs, whereas reactivity to the C-terminus (VimC-term) was enriched in the sarcoid lung. Specifically, HLA-DRB1*03+ patient BALF contained higher concentrations of anti-VimC-term antibodies than BALF from both HCs and HLA-DRB1*03− patients. Consistent with the lung as a site of AVA production, the concentration of AVAs in BALF was dramatically higher than in matched serum samples. Overall, there was a poor correlation between BALF and serum AVA concentrations. Together, these studies reveal the presence of linked in situ recognition of vimentin by both T- and B-cells in HLA-DRB1*03+ sarcoidosis patients, associated with a selective humoral immune response to the vimentin C-terminus.
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Affiliation(s)
- Andrew J Kinloch
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, United States
| | - Ylva Kaiser
- Respiratory Medicine Unit, Department of Medicine, Solna and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Don Wolfgeher
- Proteomics Core Laboratory, Cummings Life Science Center, University of Chicago, Chicago, IL, United States
| | - Junting Ai
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, United States
| | - Anders Eklund
- Respiratory Medicine Unit, Department of Medicine, Solna and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Marcus R Clark
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, United States
| | - Johan Grunewald
- Respiratory Medicine Unit, Department of Medicine, Solna and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
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