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Genetic Bias, Diversity Indices, Physiochemical Properties and CDR3 Motifs Divide Auto-Reactive from Allo-Reactive T-Cell Repertoires. Int J Mol Sci 2021; 22:ijms22041625. [PMID: 33562731 PMCID: PMC7915266 DOI: 10.3390/ijms22041625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 12/26/2022] Open
Abstract
The distinct properties of allo-reactive T-cell repertoires are not well understood. To investigate whether auto-reactive and allo-reactive T-cell repertoires encoded distinct properties, we used dextramer enumeration, enrichment, single-cell T-cell receptor (TCR) sequencing and multiparameter analysis. We found auto-reactive and allo-reactive T-cells differed in mean ex vivo frequency which was antigen dependent. Allo-reactive T-cells showed clear differences in TCR architecture, with enriched usage of specific T-cell receptor variable (TRBJ) genes and broader use of T-cell receptor variable joining (TRBJ) genes. Auto-reactive T-cell repertoires exhibited complementary determining regions three (CDR3) lengths using a Gaussian distribution whereas allo-reactive T-cell repertoires exhibited distorted patterns in CDR3 length. CDR3 loops from allo-reactive T-cells showed distinct physical-chemical properties, tending to encode loops that were more acidic in charge. Allo-reactive T-cell repertoires differed in diversity metrics, tending to show increased overall diversity and increased homogeneity between repertoires. Motif analysis of CDR3 loops showed allo-reactive T-cell repertoires differed in motif preference which included broader motif use. Collectively, these data conclude that allo-reactive T-cell repertoires are indeed different to auto-reactive repertoires and provide tangible metrics for further investigations and validation. Given that the antigens studied here are overexpressed on multiple cancers and that allo-reactive TCRs often show increased ligand affinity, this new TCR bank also has translational potential for adoptive cell therapy, soluble TCR-based therapy and rational TCR design.
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Abecassis M, Bridges N, Clancy C, Dew M, Eldadah B, Englesbe M, Flessner M, Frank J, Friedewald J, Gill J, Gries C, Halter J, Hartmann E, Hazzard W, Horne F, Hosenpud J, Jacobson P, Kasiske B, Lake J, Loomba R, Malani P, Moore T, Murray A, Nguyen MH, Powe N, Reese P, Reynolds H, Samaniego M, Schmader K, Segev D, Shah A, Singer L, Sosa J, Stewart Z, Tan J, Williams W, Zaas D, High K. Solid-organ transplantation in older adults: current status and future research. Am J Transplant 2012; 12:2608-22. [PMID: 22958872 PMCID: PMC3459231 DOI: 10.1111/j.1600-6143.2012.04245.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
An increasing number of patients older than 65 years are referred for and have access to organ transplantation, and an increasing number of older adults are donating organs. Although short-term outcomes are similar in older versus younger transplant recipients, older donor or recipient age is associated with inferior long-term outcomes. However, age is often a proxy for other factors that might predict poor outcomes more strongly and better identify patients at risk for adverse events. Approaches to transplantation in older adults vary across programs, but despite recent gains in access and the increased use of marginal organs, older patients remain less likely than other groups to receive a transplant, and those who do are highly selected. Moreover, few studies have addressed geriatric issues in transplant patient selection or management, or the implications on health span and disability when patients age to late life with a transplanted organ. This paper summarizes a recent trans-disciplinary workshop held by ASP, in collaboration with NHLBI, NIA, NIAID, NIDDK and AGS, to address issues related to kidney, liver, lung, or heart transplantation in older adults and to propose a research agenda in these areas.
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Affiliation(s)
- M. Abecassis
- Departments of Surgery and Microbiology-Immunology, Northwestern University Feinberg School of Medicine
| | - N.D. Bridges
- Transplantation Immunobiology Branch and Clinical Transplantation Section, National Institute of Allergy and Infectious Diseases
| | | | - M.A. Dew
- Department of Psychiatry, University of Pittsburgh
| | - B. Eldadah
- Division of Geriatrics and Clinical Gerontology, National Institute on Aging
| | - M.J. Englesbe
- Division of Transplantation, Department of Surgery, University of Michigan Medical School
| | - M.F. Flessner
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases
| | - J.C. Frank
- Geffen School of Medicine at the University of California, Los Angeles
| | - J. Friedewald
- Departments of Medicine and Surgery, Northwestern University
| | - J Gill
- Division of Nephrology, University of British Columbia
| | - C. Gries
- University of Pittsburgh School of Medicine
| | - J.B. Halter
- Division of Geriatric and Palliative Medicine, University of Michigan Medical School
| | | | - W.R. Hazzard
- Division of Gerontology and Geriatric Medicine, University of Washington, VA Puget Sound Health Care System
| | | | | | - P. Jacobson
- Department of Experimental and Clinical Pharmacology, University of Minnesota
| | | | - J. Lake
- Liver Transplant Program, University of Minnesota
| | - R. Loomba
- University of California, San Diego School of Medicine
| | - P.N. Malani
- Department of Internal Medicine, University of Michigan Medical School
| | - T.M. Moore
- National Heart, Lung, and Blood Institute
| | - A. Murray
- Division of Geriatrics, University of Minnesota
| | | | - N.R. Powe
- University of California, San Francisco
| | | | | | | | - K.E. Schmader
- GRECC, Durham VA Medical Center and Division of Geriatric Medicine, Duke University School of Medicine
| | - D.L. Segev
- Division of Transplant Surgery, Johns Hopkins University School of Medicine
| | - A.S. Shah
- Division of Cardiac Surgery, Johns Hopkins University School of Medicine
| | - L.G. Singer
- Toronto Lung Transplant Program, University of Toronto
| | - J.A. Sosa
- Divisions of Endocrine Surgery and Surgical Oncology, Department of Surgery, Yale University School of Medicine
| | | | - J.C. Tan
- Adult Kidney and Pancreas Transplant Program, Stanford University
| | - W.W. Williams
- Harvard University and Massachusetts General Hospital
| | - D.W. Zaas
- Department of Medicine, Duke University School of Medicine
| | - K.P. High
- Wake Forest School of Medicine,To Whom Correspondence Should be Sent: Kevin P. High, M.D., M.S., Professor of Medicine and Translational Science, Chief, Section on Infectious Diseases, Department of Internal Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston Salem, NC 27157-1042, Phone: (336) 716-4584, Fax: (336) 716-3825,
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Wolfson MY, Nam K, Chakraborty AK. The effect of mutations on the alloreactive T cell receptor/peptide-MHC interface structure: a molecular dynamics study. J Phys Chem B 2011; 115:8317-27. [PMID: 21651302 PMCID: PMC3131071 DOI: 10.1021/jp202471d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
T cells orchestrate adaptive, pathogen-specific immune responses. T cells have a surface receptor (called TCR) whose ligands are complexes (pMHCs) of peptides (derived from pathogens or host proteins) and major histocompatibility complex proteins (MHCs). MHC proteins vary between hosts. During organ transplants, host TCRs interact with peptides present in complex with genetically different MHCs. This usually causes a vigorous immune response: alloreactivity. Studies of alloreactive protein interactions have yielded results that present a puzzle. Some crystallographic studies concluded that the alloreactive TCR/MHC interface is essentially unaffected by changing the TCR peptide-binding region, suggesting that the peptide does not influence the interface. Another biochemical study concluded from mutation data that different peptides can alter the binding interface with the same TCR. To explore the origin of this puzzle, we used molecular dynamics simulations to study the dependence of the TCR/pMHC interface on changes in both the peptide and the TCR. Our simulations show that the footprint of the TCR on the pMHC is insensitive to mutations of the TCR peptide-binding loops, but peptide mutations can make multiple local changes to TCR/pMHC contacts. Therefore, our results demonstrate that the structural and mutation data do not conflict and reveal how subtle, but important, characteristics of the alloreactive TCR/pMHC interface are influenced by the TCR and the peptide.
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Affiliation(s)
| | - Kwangho Nam
- To whom correspondence should be addressed: ; , Phone: +1 617 495 8997; +1 617 253 3890. Fax: +1 617 495 8755; +1 617 253 2272
| | - Arup K. Chakraborty
- To whom correspondence should be addressed: ; , Phone: +1 617 495 8997; +1 617 253 3890. Fax: +1 617 495 8755; +1 617 253 2272
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High KP, D'Aquila RT, Fuldner RA, Gerding DN, Halter JB, Haynes L, Hazzard WR, Jackson LA, Janoff E, Levin MJ, Nayfield SG, Nichol KL, Prabhudas M, Talbot HK, Clayton CP, Henderson R, Scott CM, Tarver ED, Woolard NF, Schmader KE. Workshop on immunizations in older adults: identifying future research agendas. J Am Geriatr Soc 2010; 58:765-76. [PMID: 20398161 DOI: 10.1111/j.1532-5415.2010.02772.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Goals for immunization in older adults may differ from those in young adults and children, in whom complete prevention of disease is the objective. Often, reduced hospitalization and death but also averting exacerbation of underlying chronic illness, functional decline, and frailty are important goals in the older age group. Because of the effect of age on dendritic cell function, T cell-mediated immune suppression, reduced proliferative capacity of T cells, and other immune responses, the efficacy of vaccines often wanes with advanced age. This article summarizes the discussion and proceedings of a workshop organized by the Association of Specialty Professors, the Infectious Diseases Society of America, the American Geriatrics Society, the National Institute on Aging, and the National Institute of Allergy and Infectious Diseases. Leading researchers and clinicians in the fields of immunology, epidemiology, infectious diseases, geriatrics, and gerontology reviewed the current status of vaccines in older adults, identified knowledge gaps, and suggest priority areas for future research. The goal of the workshop was to identify what is known about immunizations (efficacy, effect, and current schedule) in older adults and to recommend priorities for future research. Investigation in the areas identified has the potential to enhance understanding of the immune process in aging individuals, inform vaccine development, and lead to more-effective strategies to reduce the risk of vaccine-preventable illness in older adults.
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Affiliation(s)
- Kevin P High
- Division of Infectious Diseases, Department of Internal Medicine, School of Medicine, Wake Forest University, Winston-Salem, North Carolina 27157, USA.
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Abstract
A workshop group developed the concept of a "polyspecific" TCR/BCR in the framework of today's consensus model. They argue that the individual TCR/BCR combining site is composed of a packet of specificities randomly plucked from the repertoire, hence it is "polyspecific." This essay analyzes the conclusions of the workshop and suggests an alternative. "Polyspecificity" must be dissected into its two component parts, specificity and degeneracy. The TCR and the BCR must be treated differently because the TCR recognizes allele-specifically the MHC-encoded restricting element (R) that serves as the platform presenting peptide (P). Only the anti-P paratope of the TCR behaves analogously to the BCR paratope. The two paratopes are selected to recognize a shape-determinant referred to as an epitope or ligand. The paratope is functionally unispecific in recognition, not polyspecific, with respect to shape; it is degenerate in recognition with respect to chemistry. The recognized shape-determinant can be the product of many chemically different substances, peptide, carbohydrate, lipid, steroid, nucleic acid, etc. Such a degenerate set is functionally treated by the paratope as one shape/epitope/ligand and, in no sense, can a paratope recognizing such a degenerate set be described as "polyspecific." Degeneracy and specificity are concepts that must be distinguished. The two positions are analyzed in this essay, the experiments used to support the view that the paratope of the TCR/BCR is polyspecific, are reinterpreted, and an alternative framework with its accompanying nomenclature, is presented.
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MESH Headings
- Animals
- Antigens/immunology
- Binding Sites/immunology
- Binding Sites, Antibody/immunology
- Cross Reactions
- Epitopes/immunology
- Humans
- Ligands
- Models, Immunological
- Receptors, Antigen, B-Cell/chemistry
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- Self Tolerance
- T-Lymphocytes/immunology
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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