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Hu Y, Huang J, Wang S, Sun X, Wang X, Yu H. Deciphering Autoimmune Diseases: Unveiling the Diagnostic, Therapeutic, and Prognostic Potential of Immune Repertoire Sequencing. Inflammation 2024:10.1007/s10753-024-02079-2. [PMID: 38914737 DOI: 10.1007/s10753-024-02079-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/08/2024] [Indexed: 06/26/2024]
Abstract
Autoimmune diseases (AIDs) are immune system disorders where the body exhibits an immune response to its own antigens, causing damage to its own tissues and organs. The pathogenesis of AIDs is incompletely understood. However, recent advances in immune repertoire sequencing (IR-seq) technology have opened-up a new avenue to study the IR. These studies have revealed the prevalence in IR alterations, potentially inducing AIDs by disrupting immune tolerance and thereby contributing to our comprehension of AIDs. IR-seq harbors significant potential for the clinical diagnosis, personalized treatment, and prognosis of AIDs. This article reviews the application and progress of IR-seq in diseases, such as multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, and type 1 diabetes, to enhance our understanding of the pathogenesis of AIDs and offer valuable references for the diagnosis and treatment of AIDs.
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Affiliation(s)
- Yuelin Hu
- Department of Immunology, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Jialing Huang
- Department of Immunology, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Shuqing Wang
- Department of Immunology, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Xin Sun
- School of Basic Medical Sciences, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Xin Wang
- School of Basic Medical Sciences, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Hongsong Yu
- Department of Immunology, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China.
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2
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Zhang L, Jiao W, Deng H, Hu C, Xu J, Yu J, Liu L, Zhang M, Liu J, Chen G. High-throughput Treg cell receptor sequencing reveals differential immune repertoires in rheumatoid arthritis with kidney deficiency. PeerJ 2023; 11:e14837. [PMID: 36751634 PMCID: PMC9899432 DOI: 10.7717/peerj.14837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Background Regulatory T (Treg) cells are important immune cells that are regulated by adaptive immunity in the composition of Treg-cell subsets and T-cell receptors (TCRs). Treg cells are related to most autoimmune diseases, such as rheumatoid arthritis (RA). In traditional Chinese medicine (TCM), RA is typically attributed to kidney deficiency (KD) associated with the immunosenescence that causes immune dysfunction and the impaired function of Treg cells. So far, however, no mechanism related to KD and immune repertoires has been identified in RA. Methods Flow cytometry and high-throughput Treg-cell receptor sequencing were used to investigate the amount of different Treg-cell subsets and the diversity of TCRs between RA patients and healthy subjects, as well as between KD RA and non-KD RA patients. RT-qPCR was used to validate the high-throughput sequencing results. Results The data showed that the amount of naïve Treg cells in KD patients was less than in non-KD RA patients (P = 0.004) with no significant differences observed between other subsets. In the TCR of Treg cells, the length of complementarity determining region 3 (CDR3) was low and clonotypes increased in the KD group compared with the non-KD group. The diversity and abundance of Treg TCRs were low, as determined by the Hill number. In addition, several V(D)J combinations, such as T-cell receptor beta variable 7-2 (TRBV7-2), TRBV11-1, TRBV13, TRBV15, and TRBJ2-3, varied significantly between the two groups, indicating that KD causes Treg dysfunction. RT-qPCR shows that FOXP3 expression in peripheral blood Treg is lower in KD than in non-KD. Conclusion The results demonstrate the close correlation between KD and immune repertoires in RA and provide a new evaluation method for RA in TCM.
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Affiliation(s)
- Lu Zhang
- First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei Jiao
- First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hui Deng
- First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Congqi Hu
- Department of Rheumatology, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jia Xu
- First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiahui Yu
- First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lijuan Liu
- Department of Rheumatology, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Mingying Zhang
- Department of Rheumatology, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiduo Liu
- Department of Rheumatology, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Guangxing Chen
- Department of Rheumatology, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China,Baiyun Hospital of the First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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3
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Song J, Hu L, Liu B, Jiang N, Huang H, Luo J, Wang L, Zeng J, Huang F, Huang M, Cai L, Tang L, Chen S, Chen Y, Wu A, Zheng S, Chen Q. The Emerging Role of Immune Cells and Targeted Therapeutic Strategies in Diabetic Wounds Healing. J Inflamm Res 2022; 15:4119-4138. [PMID: 35898820 PMCID: PMC9309318 DOI: 10.2147/jir.s371939] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/07/2022] [Indexed: 11/23/2022] Open
Abstract
Poor wound healing in individuals with diabetes has long plagued clinicians, and immune cells play key roles in the inflammation, proliferation and remodeling that occur in wound healing. When skin integrity is damaged, immune cells migrate to the wound bed through the actions of chemokines and jointly restore tissue homeostasis and barrier function by exerting their respective biological functions. An imbalance of immune cells often leads to ineffective and disordered inflammatory responses. Due to the maladjusted microenvironment, the wound is unable to smoothly transition to the proliferation and remodeling stage, causing it to develop into a chronic refractory wound. However, chronic refractory wounds consistently lead to negative outcomes, such as long treatment cycles, high hospitalization rates, high medical costs, high disability rates, high mortality rates, and many adverse consequences. Therefore, strategies that promote the rational distribution and coordinated development of immune cells during wound healing are very important for the treatment of diabetic wounds (DW). Here, we explored the following aspects by performing a literature review: 1) the current situation of DW and an introduction to the biological functions of immune cells; 2) the role of immune cells in DW; and 3) existing (or undeveloped) therapies targeting immune cells to promote wound healing to provide new ideas for basic research, clinical treatment and nursing of DW.
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Affiliation(s)
- Jianying Song
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, People’s Republic of China
- School of Nursing, Southwest Medical University, Luzhou, People’s Republic of China
| | - Lixin Hu
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, People’s Republic of China
- School of Nursing, Southwest Medical University, Luzhou, People’s Republic of China
| | - Bo Liu
- School of Nursing, Southwest Medical University, Luzhou, People’s Republic of China
| | - Nan Jiang
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, People’s Republic of China
| | - Houqiang Huang
- Department of Nursing, the Affiliated Hospital of Southwest Medical University, Luzhou, People’s Republic of China
| | - JieSi Luo
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, People’s Republic of China
| | - Long Wang
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, People’s Republic of China
| | - Jing Zeng
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, People’s Republic of China
| | - Feihong Huang
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, People’s Republic of China
| | - Min Huang
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, People’s Republic of China
| | - Luyao Cai
- School of Nursing, Southwest Medical University, Luzhou, People’s Republic of China
| | - Lingyu Tang
- School of Nursing, Southwest Medical University, Luzhou, People’s Republic of China
| | - Shunli Chen
- School of Nursing, Southwest Medical University, Luzhou, People’s Republic of China
| | - Yinyi Chen
- School of Nursing, Southwest Medical University, Luzhou, People’s Republic of China
| | - Anguo Wu
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, People’s Republic of China
| | - Silin Zheng
- Department of Nursing, the Affiliated Hospital of Southwest Medical University, Luzhou, People’s Republic of China
| | - Qi Chen
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, People’s Republic of China
- School of Nursing, Southwest Medical University, Luzhou, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Luzhou, People’s Republic of China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, People’s Republic of China
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4
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Amoriello R, Mariottini A, Ballerini C. Immunosenescence and Autoimmunity: Exploiting the T-Cell Receptor Repertoire to Investigate the Impact of Aging on Multiple Sclerosis. Front Immunol 2021; 12:799380. [PMID: 34925384 PMCID: PMC8673061 DOI: 10.3389/fimmu.2021.799380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/16/2021] [Indexed: 01/08/2023] Open
Abstract
T-cell receptor (TCR) repertoire diversity is a determining factor for the immune system capability in fighting infections and preventing autoimmunity. During life, the TCR repertoire diversity progressively declines as a physiological aging progress. The investigation of TCR repertoire dynamics over life represents a powerful tool unraveling the impact of immunosenescence in health and disease. Multiple Sclerosis (MS) is a demyelinating, inflammatory, T-cell mediated autoimmune disease of the Central Nervous System in which age is crucial: it is the most widespread neurological disease among young adults and, furthermore, patients age may impact on MS progression and treatments outcome. Crossing knowledge on the TCR repertoire dynamics over MS patients' life is fundamental to investigate disease mechanisms, and the advent of high- throughput sequencing (HTS) has significantly increased our knowledge on the topic. Here we report an overview of current literature about the impact of immunosenescence and age-related TCR dynamics variation in autoimmunity, including MS.
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Affiliation(s)
- Roberta Amoriello
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), Laboratory of Neuroimmunology, University of Florence, Florence, Italy
| | - Alice Mariottini
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Clara Ballerini
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), Laboratory of Neuroimmunology, University of Florence, Florence, Italy
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5
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Nakayama M, Michels AW. Using the T Cell Receptor as a Biomarker in Type 1 Diabetes. Front Immunol 2021; 12:777788. [PMID: 34868047 PMCID: PMC8635517 DOI: 10.3389/fimmu.2021.777788] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/26/2021] [Indexed: 12/20/2022] Open
Abstract
T cell receptors (TCRs) are unique markers that define antigen specificity for a given T cell. With the evolution of sequencing and computational analysis technologies, TCRs are now prime candidates for the development of next-generation non-cell based T cell biomarkers, which provide a surrogate measure to assess the presence of antigen-specific T cells. Type 1 diabetes (T1D), the immune-mediated form of diabetes, is a prototypical organ specific autoimmune disease in which T cells play a pivotal role in targeting pancreatic insulin-producing beta cells. While the disease is now predictable by measuring autoantibodies in the peripheral blood directed to beta cell proteins, there is an urgent need to develop T cell markers that recapitulate T cell activity in the pancreas and can be a measure of disease activity. This review focuses on the potential and challenges of developing TCR biomarkers for T1D. We summarize current knowledge about TCR repertoires and clonotypes specific for T1D and discuss challenges that are unique for autoimmune diabetes. Ultimately, the integration of large TCR datasets produced from individuals with and without T1D along with computational 'big data' analysis will facilitate the development of TCRs as potentially powerful biomarkers in the development of T1D.
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Affiliation(s)
- Maki Nakayama
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Aaron W Michels
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
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6
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Song R, Jia X, Zhao J, Du P, Zhang JA. T cell receptor revision and immune repertoire changes in autoimmune diseases. Int Rev Immunol 2021; 41:517-533. [PMID: 34243694 DOI: 10.1080/08830185.2021.1929954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Autoimmune disease (AID) is a condition in which the immune system breaks down and starts to attack the body. Some common AIDs include systemic lupus erythematosus, rheumatoid arthritis, type 1 diabetes mellitus and so forth. The changes in T-cell receptor (TCR) repertoire have been found in several autoimmune diseases, and may be responsible for the breakdown of peripheral immune tolerance. In this review, we discussed the processes of TCR revision in peripheral immune environment, the changes in TCR repertoire that occurred in various AIDs, and the specifically expanded T cell clones. We hope our discussion can provide insights for the future studies, helping with the discovery of disease biomarkers and expanding the strategies of immune-targeted therapy. HighlightsRestricted TCR repertoire and biased TCR-usage are found in a variety of AIDs.TCR repertoire shows tissue specificity in a variety of AID diseases.The relationship between TCR repertoire diversity and disease activity is still controversial in AIDs.Dominant TCR clonotypes may help to discover new disease biomarkers and expand the strategies of immune-targeted therapy.
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Affiliation(s)
- Ronghua Song
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Xi Jia
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Jing Zhao
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Peng Du
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Jin-An Zhang
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
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7
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Khatun A, Kasmani MY, Zander R, Schauder DM, Snook JP, Shen J, Wu X, Burns R, Chen YG, Lin CW, Williams MA, Cui W. Single-cell lineage mapping of a diverse virus-specific naive CD4 T cell repertoire. J Exp Med 2021; 218:e20200650. [PMID: 33201171 PMCID: PMC7676493 DOI: 10.1084/jem.20200650] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 08/24/2020] [Accepted: 10/22/2020] [Indexed: 12/21/2022] Open
Abstract
Tracking how individual naive T cells from a natural TCR repertoire clonally expand, differentiate, and make lineage choices in response to an infection has not previously been possible. Here, using single-cell sequencing technology to identify clones by their unique TCR sequences, we were able to trace the clonal expansion, differentiation trajectory, and lineage commitment of individual virus-specific CD4 T cells during an acute lymphocytic choriomeningitis virus (LCMV) infection. Notably, we found previously unappreciated clonal diversity and cellular heterogeneity among virus-specific helper T cells. Interestingly, although most naive CD4 T cells gave rise to multiple lineages at the clonal level, ∼28% of naive cells exhibited a preferred lineage choice toward either Th1 or TFH cells. Mechanistically, we found that TCR structure, in particular the CDR3 motif of the TCR α chain, skewed lineage decisions toward the TFH cell fate.
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Affiliation(s)
- Achia Khatun
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Moujtaba Y. Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Ryan Zander
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - David M. Schauder
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Jeremy P. Snook
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Jian Shen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Xiaopeng Wu
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Robert Burns
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Yi-Guang Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
- Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI
| | - Chien-Wei Lin
- Institute for Health and Equity, Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI
| | - Matthew A. Williams
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
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Ahmed S, Cerosaletti K, James E, Long SA, Mannering S, Speake C, Nakayama M, Tree T, Roep BO, Herold KC, Brusko TM. Standardizing T-Cell Biomarkers in Type 1 Diabetes: Challenges and Recent Advances. Diabetes 2019; 68:1366-1379. [PMID: 31221801 PMCID: PMC6609980 DOI: 10.2337/db19-0119] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/20/2019] [Indexed: 12/17/2022]
Abstract
Type 1 diabetes (T1D) results from the progressive destruction of pancreatic β-cells in a process mediated primarily by T lymphocytes. The T1D research community has made dramatic progress in understanding the genetic basis of the disease as well as in the development of standardized autoantibody assays that inform both disease risk and progression. Despite these advances, there remains a paucity of robust and accepted biomarkers that can effectively inform on the activity of T cells during the natural history of the disease or in response to treatment. In this article, we discuss biomarker development and validation efforts for evaluation of T-cell responses in patients with and at risk for T1D as well as emerging technologies. It is expected that with systematic planning and execution of a well-conceived biomarker development pipeline, T-cell-related biomarkers would rapidly accelerate disease progression monitoring efforts and the evaluation of intervention therapies in T1D.
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Affiliation(s)
- Simi Ahmed
- Immunotherapies Program, Research, JDRF, New York, NY
| | | | - Eddie James
- Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - S Alice Long
- Benaroya Research Institute at Virginia Mason, Seattle, WA
| | | | - Cate Speake
- Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - Maki Nakayama
- Departments of Pediatrics and Integrated Immunology, Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO
| | - Timothy Tree
- Department of Immunobiology, King's College London, London, U.K
| | - Bart O Roep
- Department of Diabetes Immunobiology, City of Hope Diabetes & Metabolism Research Institute, Duarte, CA
| | - Kevan C Herold
- Departments of Immunobiology and Medicine, Yale School of Medicine, New Haven, CT
| | - Todd M Brusko
- Department of Pathology, University of Florida Diabetes Institute, Gainesville, FL
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9
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Fink K. Can We Improve Vaccine Efficacy by Targeting T and B Cell Repertoire Convergence? Front Immunol 2019; 10:110. [PMID: 30814993 PMCID: PMC6381292 DOI: 10.3389/fimmu.2019.00110] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/15/2019] [Indexed: 01/31/2023] Open
Abstract
Traditional vaccine development builds on the assumption that healthy individuals have virtually unlimited antigen recognition repertoires of receptors in B cells and T cells [the B cell receptor (BCR) and TCR respectively]. However, there are indications that there are "holes" in the breadth of repertoire diversity, where no or few B or T cell are able to bind to a given antigen. Repertoire diversity may in these cases be a limiting factor for vaccine efficacy. Assuming that it is possible to predict which B and T cell receptors will respond to a given immunogen, vaccine strategies could be optimized and personalized. In addition, vaccine testing could be simplified if we could predict responses through sequencing BCR and TCRs. Bulk sequencing has shown putatively specific converging sequences after infection or vaccination. However, only single cell technologies have made it possible to capture the sequence of both heavy and light chains of a BCR or the alpha and beta chains the TCR. This has enabled the cloning of receptors and the functional validation of a predicted specificity. This review summarizes recent evidence of converging sequences in infectious diseases. Current and potential future applications of single cell technology in immune repertoire analysis are then discussed. Finally, possible short- and long- term implications for vaccine research are highlighted.
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Affiliation(s)
- Katja Fink
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
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10
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Werner L, Nunberg MY, Rechavi E, Lev A, Braun T, Haberman Y, Lahad A, Shteyer E, Schvimer M, Somech R, Weiss B, Lee YN, Shouval DS. Altered T cell receptor beta repertoire patterns in pediatric ulcerative colitis. Clin Exp Immunol 2019; 196:1-11. [PMID: 30556140 DOI: 10.1111/cei.13247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2018] [Indexed: 01/06/2023] Open
Abstract
The antigenic specificity of T cells occurs via generation and rearrangement of different gene segments producing a functional T cell receptor (TCR). High-throughput sequencing (HTS) allows in-depth assessment of TCR repertoire patterns. There are limited data concerning whether TCR repertoires are altered in inflammatory bowel disease. We hypothesized that pediatric ulcerative colitis (UC) patients possess unique TCR repertoires, resulting from clonotypical expansions in the gut. Paired blood and rectal samples were collected from nine newly diagnosed treatment-naive pediatric UC patients and four healthy controls. DNA was isolated to determine the TCR-β repertoire by HTS. Significant clonal expansion was demonstrated in UC patients, with inverse correlation between clinical disease severity and repertoire diversity in the gut. Using different repertoire variables in rectal biopsies, a clear segregation was observed between patients with severe UC, those with mild-moderate disease and healthy controls. Moreover, the overlap between autologous blood-rectal samples in UC patients was significantly higher compared with overlap among controls. Finally, we identified several clonotypes that were shared in either all or the majority of UC patients in the colon. Clonal expansion of TCR-β-expressing T cells among UC patients correlates with disease severity and highlights their involvement in mediating intestinal inflammation.
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Affiliation(s)
- L Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - M Y Nunberg
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - E Rechavi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - A Lev
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - T Braun
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Y Haberman
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - A Lahad
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - E Shteyer
- Juliet Keidan Institute of Pediatric Gastroenterology, Hepatology and Nutrition, Shaare Zedek Medical Center and The Hebrew University of Jerusalem, Jerusalem, Israel
| | - M Schvimer
- Institute of Pathology, Sheba Medical Center, Tel Hashomer, Israel
| | - R Somech
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - B Weiss
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Y N Lee
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - D S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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11
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Jia X, Wang B, Zhai T, Yao Q, Li Q, Zhang JA. WITHDRAWN: T cell receptor revision and immune repertoire changes in autoimmune diseases. Clin Immunol 2018:S1521-6616(18)30724-1. [PMID: 30543918 DOI: 10.1016/j.clim.2018.12.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Xi Jia
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai 201508, China
| | - Bing Wang
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai 201508, China
| | - Tianyu Zhai
- Department of Endocrinology, Zhongshan Hospital of Fudan University, Shanghai 201508, China
| | - Qiuming Yao
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai 201508, China
| | - Qian Li
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai 201508, China
| | - Jin-An Zhang
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, China.
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Fähnrich A, Klein S, Sergé A, Nyhoegen C, Kombrink S, Möller S, Keller K, Westermann J, Kalies K. CD154 Costimulation Shifts the Local T-Cell Receptor Repertoire Not Only During Thymic Selection but Also During Peripheral T-Dependent Humoral Immune Responses. Front Immunol 2018; 9:1019. [PMID: 29867987 PMCID: PMC5966529 DOI: 10.3389/fimmu.2018.01019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/24/2018] [Indexed: 12/20/2022] Open
Abstract
CD154 is a transmembrane cytokine expressed transiently on activated CD4 T cells upon T-cell receptor (TCR) stimulation that interacts with CD40 on antigen-presenting cells. The signaling via CD154:CD40 is essential for B-cell maturation and germinal center formation and also for the final differentiation of CD4 T cells during T-dependent humoral immune responses. Recent data demonstrate that CD154 is critically involved in the selection of T-cell clones during the negative selection process in the thymus. Whether CD154 signaling influences the TCR repertoire during peripheral T-dependent humoral immune responses has not yet been elucidated. To find out, we used CD154-deficient mice and assessed the global TCRβ repertoire in T-cell zones (TCZ) of spleens by high-throughput sequencing after induction of a Th2 response to the multiepitopic antigen sheep red blood cells. Qualitative and quantitative comparison of the splenic TCZ-specific TCRβ repertoires revealed that CD154 deficiency shifts the distribution of Vβ-Jβ genes after antigen exposure. This data led to the conclusion that costimulation via CD154:CD40 during the interaction of T cells with CD40-matured B cells contributes to the recruitment of T-cell clones into the immune response and thereby shapes the peripheral TCR repertoire.
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Affiliation(s)
- Anke Fähnrich
- Institute of Anatomy, University of Luebeck, Luebeck, Germany
| | - Sebastian Klein
- Institute of Anatomy, University of Luebeck, Luebeck, Germany
| | - Arnauld Sergé
- Centre de Recherche en Cancérologie de Marseille (CRCM) U1068 INSERM - UMR7258 CNRS - Institut Paoli Calmette, Aix-Marseille University, UM105, Marseille, France
| | | | - Sabrina Kombrink
- Institute of Mathematics, University of Luebeck, Luebeck, Germany
| | - Steffen Möller
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock, Germany
| | - Karsten Keller
- Institute of Mathematics, University of Luebeck, Luebeck, Germany
| | | | - Kathrin Kalies
- Institute of Anatomy, University of Luebeck, Luebeck, Germany
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13
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Bhandage AK, Jin Z, Korol SV, Shen Q, Pei Y, Deng Q, Espes D, Carlsson PO, Kamali-Moghaddam M, Birnir B. GABA Regulates Release of Inflammatory Cytokines From Peripheral Blood Mononuclear Cells and CD4 + T Cells and Is Immunosuppressive in Type 1 Diabetes. EBioMedicine 2018; 30:283-294. [PMID: 29627388 PMCID: PMC5952354 DOI: 10.1016/j.ebiom.2018.03.019] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 12/31/2022] Open
Abstract
The neurotransmitter γ-aminobutyric acid (GABA) is an extracellular signaling molecule in the brain and in pancreatic islets. Here, we demonstrate that GABA regulates cytokine secretion from human peripheral blood mononuclear cells (PBMCs) and CD4+ T cells. In anti-CD3 stimulated PBMCs, GABA (100 nM) inhibited release of 47 cytokines in cells from patients with type 1 diabetes (T1D), but only 16 cytokines in cells from nondiabetic (ND) individuals. CD4+ T cells from ND individuals were grouped into responder or non-responder T cells according to effects of GABA (100 nM, 500 nM) on the cell proliferation. In the responder T cells, GABA decreased proliferation, and inhibited secretion of 37 cytokines in a concentration-dependent manner. In the non-responder T cells, GABA modulated release of 8 cytokines. GABA concentrations in plasma from T1D patients and ND individuals were correlated with 10 cytokines where 7 were increased in plasma of T1D patients. GABA inhibited secretion of 5 of these cytokines from both T1D PBMCs and ND responder T cells. The results identify GABA as a potent regulator of both Th1- and Th2-type cytokine secretion from human PBMCs and CD4+ T cells where GABA generally decreases the secretion. GABA regulates cytokine secretion in anti-CD3-stimulated peripheral blood mononuclear cells (PBMCs) and CD4+ T cells. GABA inhibits secretion of 47 cytokines in PBMCs from type 1 diabetes patients. GABA regulates secretion of pro- and anti-inflammatory cytokines in a concentration-dependent manner.
GABA is a signal molecule in the brain, blood and pancreatic islets where it is secreted by the insulin-producing β cells. GABA has many roles in human islets including optimizing function and survival of β cells. Bhandage et al. now show that GABA is a potent regulator of secretion of both pro- and anti-inflammatory cytokines in stimulated immune cells. In type 1 diabetes the β-cell mass is diminished and thus the protective effect of GABA in the islets although not in blood. Targeting GABA signaling in diabetes mellitus is likely to be a part of the solution when curing diabetes.
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Affiliation(s)
- Amol K Bhandage
- Department of Neuroscience, Uppsala University, 75124 Uppsala, Sweden
| | - Zhe Jin
- Department of Neuroscience, Uppsala University, 75124 Uppsala, Sweden
| | - Sergiy V Korol
- Department of Neuroscience, Uppsala University, 75124 Uppsala, Sweden
| | - Qiujin Shen
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Yu Pei
- Department of Cell and Molecular Biology, Karolinska Institute, 17165 Stockholm, Sweden
| | - Qiaolin Deng
- Department of Cell and Molecular Biology, Karolinska Institute, 17165 Stockholm, Sweden
| | - Daniel Espes
- Department of Medical Cell Biology, Uppsala University, 75124 Uppsala, Sweden; Department of Medical Sciences, Uppsala University, 75124 Uppsala, Sweden
| | - Per-Ola Carlsson
- Department of Medical Cell Biology, Uppsala University, 75124 Uppsala, Sweden; Department of Medical Sciences, Uppsala University, 75124 Uppsala, Sweden
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Bryndis Birnir
- Department of Neuroscience, Uppsala University, 75124 Uppsala, Sweden.
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14
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Kosteria I, Kanaka-Gantenbein C, Anagnostopoulos AK, Chrousos GP, Tsangaris GT. Pediatric endocrine and metabolic diseases and proteomics. J Proteomics 2018; 188:46-58. [PMID: 29563068 DOI: 10.1016/j.jprot.2018.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/05/2018] [Accepted: 03/16/2018] [Indexed: 12/11/2022]
Abstract
The principles of Predictive, Preventive and Personalized Medicine (PPPM) dictate the need to recognize individual susceptibility to disease in a timely fashion and to offer targeted preventive interventions and treatments. Proteomics is a state-of-the art technology- driven science aiming at expanding our understanding of the pathophysiologic mechanisms that underlie disease, but also at identifying accurate predictive, diagnostic and therapeutic biomarkers, that will eventually promote the implementation of PPPM. In this review, we summarize the wide spectrum of the applications of Mass Spectrometry-based proteomics in the various fields of Pediatric Endocrinology, including Inborn Errors of Metabolism, type 1 diabetes, Adrenal Disease, Metabolic Syndrome and Thyroid disease, ranging from neonatal screening to early recognition of specific at-risk populations for disease manifestations or complications in adult life and to monitoring of disease progression and response to treatment. SIGNIFICANCE Proteomics is a state-of-the art technology- driven science aiming at expanding our understanding of the pathophysiologic mechanisms that underlie disease, but also at identifying accurate predictive, diagnostic and therapeutic biomarkers that will eventually lead to successful, targeted, patient-centric, individualized approach of each patient, as dictated by the principles of Predictive, Preventive and Personalized Medicine. In this review, we summarize the wide spectrum of the applications of Mass Spectrometry-based proteomics in the various fields of Pediatric Endocrinology, including Inborn Errors of Metabolism, type 1 diabetes, Adrenal Disease, Metabolic Syndrome and Thyroid disease, ranging from neonatal screening, accurate diagnosis, early recognition of specific at-risk populations for the prevention of disease manifestation or future complications.
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Affiliation(s)
- Ioanna Kosteria
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, Aghia Sophia Children's Hospital, Athens, Greece.
| | - Christina Kanaka-Gantenbein
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, Aghia Sophia Children's Hospital, Athens, Greece.
| | | | - George P Chrousos
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, Aghia Sophia Children's Hospital, Athens, Greece
| | - George Th Tsangaris
- Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
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