1
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Yu X, Pan M, Ye J, Hathaway CA, Tworoger SS, Lea J, Li B. Quantifiable TCR repertoire changes in prediagnostic blood specimens among patients with high-grade ovarian cancer. Cell Rep Med 2024; 5:101612. [PMID: 38878776 PMCID: PMC11293308 DOI: 10.1016/j.xcrm.2024.101612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/16/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024]
Abstract
High-grade ovarian cancer (HGOC) is a major cause of death in women. Early detection of HGOC usually leads to a cure, yet it remains a clinical challenge with over 90% HGOCs diagnosed at advanced stages. This is mainly because conventional biomarkers are not sensitive enough to detect the microscopic yet metastatic early lesions. In this study, we sequence the blood T cell receptor (TCR) repertoires of 466 patients with ovarian cancer and controls and systematically investigate the immune repertoire signatures in HGOCs. We observe quantifiable changes of selected TCRs in HGOCs that are reproducible in multiple independent cohorts. Importantly, these changes are stronger during stage I. Using pre-diagnostic patient blood samples from the Nurses' Health Study, we confirm that HGOC signals can be detected in the blood TCR repertoire up to 4 years preceding conventional diagnosis. Our findings may provide the basis for future immune-based HGOC early detection criteria.
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Affiliation(s)
- Xuexin Yu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mingyao Pan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jianfeng Ye
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Shelley S Tworoger
- Knight Cancer Institute and Division of Oncological Sciences, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jayanthi Lea
- Department of Gynecology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Bo Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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2
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Maerz MD, Cross DL, Seshadri C. Functional and biological implications of clonotypic diversity among human donor-unrestricted T cells. Immunol Cell Biol 2024; 102:474-486. [PMID: 38659280 PMCID: PMC11236517 DOI: 10.1111/imcb.12751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/04/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024]
Abstract
T cells express a T-cell receptor (TCR) heterodimer that is the product of germline rearrangement and junctional editing resulting in immense clonotypic diversity. The generation of diverse TCR repertoires enables the recognition of pathogen-derived peptide antigens presented by polymorphic major histocompatibility complex (MHC) molecules. However, T cells also recognize nonpeptide antigens through nearly monomorphic antigen-presenting systems, such as cluster of differentiation 1 (CD1), MHC-related protein 1 (MR1) and butyrophilins (BTNs). This potential for shared immune responses across genetically diverse populations led to their designation as donor-unrestricted T cells (DURTs). As might be expected, some CD1-, MR1- and BTN-restricted T cells express a TCR that is conserved across unrelated individuals. However, several recent studies have reported unexpected diversity among DURT TCRs, and increasing evidence suggests that this diversity has functional consequences. Recent reports also challenge the dogma that immune cells are either innate or adaptive and suggest that DURT TCRs may act in both capacities. Here, we review this evidence and propose an expanded view of the role for clonotypic diversity among DURTs in humans, including new perspectives on how DURT TCRs may integrate their adaptive and innate immune functions.
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Affiliation(s)
- Megan D Maerz
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Molecular Medicine and Mechanisms of Disease Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Deborah L Cross
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Chetan Seshadri
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
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3
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Cai Y, Luo M, Yang W, Xu C, Wang P, Xue G, Jin X, Cheng R, Que J, Zhou W, Pang B, Xu S, Li Y, Jiang Q, Xu Z. The Deep Learning Framework iCanTCR Enables Early Cancer Detection Using the T-cell Receptor Repertoire in Peripheral Blood. Cancer Res 2024; 84:1915-1928. [PMID: 38536129 DOI: 10.1158/0008-5472.can-23-0860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/20/2023] [Accepted: 03/19/2024] [Indexed: 06/05/2024]
Abstract
T cells recognize tumor antigens and initiate an anticancer immune response in the very early stages of tumor development, and the antigen specificity of T cells is determined by the T-cell receptor (TCR). Therefore, monitoring changes in the TCR repertoire in peripheral blood may offer a strategy to detect various cancers at a relatively early stage. Here, we developed the deep learning framework iCanTCR to identify patients with cancer based on the TCR repertoire. The iCanTCR framework uses TCRβ sequences from an individual as an input and outputs the predicted cancer probability. The model was trained on over 2,000 publicly available TCR repertoires from 11 types of cancer and healthy controls. Analysis of several additional publicly available datasets validated the ability of iCanTCR to distinguish patients with cancer from noncancer individuals and demonstrated the capability of iCanTCR for the accurate classification of multiple cancers. Importantly, iCanTCR precisely identified individuals with early-stage cancer with an AUC of 86%. Altogether, this work provides a liquid biopsy approach to capture immune signals from peripheral blood for noninvasive cancer diagnosis. SIGNIFICANCE Development of a deep learning-based method for multicancer detection using the TCR repertoire in the peripheral blood establishes the potential of evaluating circulating immune signals for noninvasive early cancer detection.
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Affiliation(s)
- Yideng Cai
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Meng Luo
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Wenyi Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Chang Xu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Pingping Wang
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, China
| | - Guangfu Xue
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Xiyun Jin
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, China
| | - Rui Cheng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jinhao Que
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Wenyang Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Boran Pang
- Center for Difficult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shouping Xu
- Department of Breast Cancer, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yu Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, China
| | - Zhaochun Xu
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, China
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4
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Dou Y, Shan S, Zhang J. UcTCRdb: An unconventional T cell receptor sequence database with online analysis functions. Front Immunol 2023; 14:1158295. [PMID: 36993970 PMCID: PMC10040587 DOI: 10.3389/fimmu.2023.1158295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/02/2023] [Indexed: 03/14/2023] Open
Abstract
Unlike conventional major histocompatibility complex (MHC) class I and II molecules reactive T cells, the unconventional T cell subpopulations recognize various non-polymorphic antigen-presenting molecules and are typically characterized by simplified patterns of T cell receptors (TCRs), rapid effector responses and ‘public’ antigen specificities. Dissecting the recognition patterns of the non-MHC antigens by unconventional TCRs can help us further our understanding of the unconventional T cell immunity. The small size and irregularities of the released unconventional TCR sequences are far from high-quality to support systemic analysis of unconventional TCR repertoire. Here we present UcTCRdb, a database that contains 669,900 unconventional TCRs collected from 34 corresponding studies in humans, mice, and cattle. In UcTCRdb, users can interactively browse TCR features of different unconventional T cell subsets in different species, search and download sequences under different conditions. Additionally, basic and advanced online TCR analysis tools have been integrated into the database, which will facilitate the study of unconventional TCR patterns for users with different backgrounds. UcTCRdb is freely available at http://uctcrdb.cn/.
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Valdemar-Aguilar CM, Manisekaran R, Acosta-Torres LS, López-Marín LM. Spotlight on mycobacterial lipid exploitation using nanotechnology for diagnosis, vaccines, and treatments. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2023; 48:102653. [PMID: 36646193 PMCID: PMC9839462 DOI: 10.1016/j.nano.2023.102653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/24/2022] [Accepted: 01/07/2023] [Indexed: 01/15/2023]
Abstract
Tuberculosis (TB), historically the most significant cause of human morbidity and mortality, has returned as the top infectious disease worldwide, under circumstances worsened by the COVID-19 pandemic's devastating effects on public health. Although Mycobacterium tuberculosis, the causal agent, has been known of for more than a century, the development of tools to control it has been largely neglected. With the advancement of nanotechnology, the possibility of engineering tools at the nanoscale creates unique opportunities to exploit any molecular type. However, little attention has been paid to one of the major attributes of the pathogen, represented by the atypical coat and its abundant lipids. In this review, an overview of the lipids encountered in M. tuberculosis and interest in exploiting them for the development of TB control tools are presented. Then, the amalgamation of nanotechnology with mycobacterial lipids from both reported and future works are discussed.
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Affiliation(s)
- Carlos M. Valdemar-Aguilar
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Campus Juriquilla, 76230 Querétaro, Mexico,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico
| | - Ravichandran Manisekaran
- Interdisciplinary Research Laboratory (LII), Nanostructures and Biomaterials Area, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Predio el Saucillo y el Potrero, Comunidad de los Tepetates, 37689 León, Mexico.
| | - Laura S. Acosta-Torres
- Interdisciplinary Research Laboratory (LII), Nanostructures and Biomaterials Area, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Predio el Saucillo y el Potrero, Comunidad de los Tepetates, 37689 León, Mexico
| | - Luz M. López-Marín
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Campus Juriquilla, 76230 Querétaro, Mexico,Corresponding authors
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6
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Johnson AC, Silva JAF, Kim SC, Larsen CP. Progress in kidney transplantation: The role for systems immunology. Front Med (Lausanne) 2022; 9:1070385. [PMID: 36590970 PMCID: PMC9800623 DOI: 10.3389/fmed.2022.1070385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
The development of systems biology represents an immense breakthrough in our ability to perform translational research and deliver personalized and precision medicine. A multidisciplinary approach in combination with use of novel techniques allows for the extraction and analysis of vast quantities of data even from the volume and source limited samples that can be obtained from human subjects. Continued advances in microfluidics, scalability and affordability of sequencing technologies, and development of data analysis tools have made the application of a multi-omics, or systems, approach more accessible for use outside of specialized centers. The study of alloimmune and protective immune responses after solid organ transplant offers innumerable opportunities for a multi-omics approach, however, transplant immunology labs are only just beginning to adopt the systems methodology. In this review, we focus on advances in biological techniques and how they are improving our understanding of the immune system and its interactions, highlighting potential applications in transplant immunology. First, we describe the techniques that are available, with emphasis on major advances that allow for increased scalability. Then, we review initial applications in the field of transplantation with a focus on topics that are nearing clinical integration. Finally, we examine major barriers to adapting these methods and discuss potential future developments.
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Deng L, Harms A, Ravens S, Prinz I, Tan L. Systematic pattern analyses of Vδ2+ TCRs reveal that shared “public” Vδ2+ γδ T cell clones are a consequence of rearrangement bias and a higher expansion status. Front Immunol 2022; 13:960920. [DOI: 10.3389/fimmu.2022.960920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundVγ9Vδ2+ T cells are a major innate T cell subset in human peripheral blood. Their Vδ2+ VDJ-rearrangements are short and simple in the fetal thymus and gradually increase in diversity and CDR3 length along with development. So-called “public” versions of Vδ2+ TCRs are shared among individuals of all ages. However, it is unclear whether such frequently occurring “public” Vγ9Vδ2+ T cell clones are derived from the fetal thymus and whether they are fitter to proliferate and persist than infrequent “private” clones.MethodsShared “public” Vδ2+ TCRs were identified from Vδ2+ TCR-repertoires collected from 89 individuals, including newborns (cord blood), infants, and adults (peripheral blood). Distance matrices of Vδ2+ CDR3 were generated by TCRdist3 and then embedded into a UMAP for visualizing the heterogeneity of Vδ2+ TCRs.ResultsVδ2+ CDR3 distance matrix embedded by UMAP revealed that the heterogeneity of Vδ2+ TCRs is primarily determined by the J-usage and CDR3aa length, while age or publicity-specific motifs were not found. The most prevalent public Vδ2+ TCRs showed germline-like rearrangement with low N-insertions. Age-related features were also identified. Public Vδ2+TRDJ1 TCRs from cord blood showed higher N-insertions and longer CDR3 lengths. Synonymous codons resulting from VDJ rearrangement also contribute to the generation of public Vδ2+ TCRs. Each public TCR was always produced by multiple different transcripts, even with different D gene usage, and the publicity of Vδ2+ TCRs was positively associated with expansion status.ConclusionTo conclude, the heterogeneity of Vδ2+ TCRs is mainly determined by TRDJ-usage and the length of CDR3aa sequences. Public Vδ2+ TCRs result from germline-like rearrangement and synonymous codons, associated with a higher expansion status.
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8
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James CA, Yu KKQ, Mayer-Blackwell K, Fiore-Gartland A, Smith MT, Layton ED, Johnson JL, Hanekom WA, Scriba TJ, Seshadri C. Durable Expansion of TCR-δ Meta-Clonotypes After BCG Revaccination in Humans. Front Immunol 2022; 13:834757. [PMID: 35432299 PMCID: PMC9005636 DOI: 10.3389/fimmu.2022.834757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium bovis bacille Calmette-Guérin (BCG) has been used for 100 years and prevents disseminated tuberculosis and death in young children. However, it shows only partial efficacy against pulmonary tuberculosis (TB) in adults, so new vaccines are urgently needed. The protective efficacy of BCG depends on T cells, which are typically activated by pathogen-derived protein antigens that bind to highly polymorphic major histocompatibility complex (MHC) molecules. Some T cells recognize non-protein antigens via antigen presenting systems that are independent of genetic background, leading to their designation as donor-unrestricted T (DURT) cells. Whether live whole cell vaccines, like BCG, can induce durable expansions of DURT cells in humans is not known. We used combinatorial tetramer staining, multi-parameter flow cytometry, and immunosequencing to comprehensively characterize the effect of BCG on activation and expansion of DURT cell subsets. We examined peripheral blood mononuclear cells (PBMC) derived from a Phase I study of South African adults in which samples were archived at baseline, 3 weeks, and 52 weeks post-BCG revaccination. We did not observe a change in the frequency of total mucosal-associated invariant T (MAIT) cells, invariant natural killer T (iNKT) cells, germline encoded mycolyl-reactive (GEM) T cells, or γδ T cells at 52 weeks post-BCG. However, immunosequencing revealed a set of TCR-δ clonotypes that were expanded at 52 weeks post-BCG revaccination. These expanded clones expressed the Vδ2 gene segment and could be further defined on the basis of biochemical similarity into several 'meta-clonotypes' that likely recognize similar epitopes. Our data reveal that BCG vaccination leads to durable expansion of DURT cell clonotypes despite a limited effect on total circulating frequencies in the blood and have implications for defining the immunogenicity of candidate whole cell TB vaccines.
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Affiliation(s)
- Charlotte A. James
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Krystle K. Q. Yu
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Malisa T. Smith
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Erik D. Layton
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - John L. Johnson
- Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Willem A. Hanekom
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Chetan Seshadri
- Department of Medicine, University of Washington, Seattle, WA, United States
- Tuberculosis Research and Training Center, University of Washington, Seattle, WA, United States
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9
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James CA, Xu Y, Aguilar MS, Jing L, Layton ED, Gilleron M, Minnaard AJ, Scriba TJ, Day CL, Warren EH, Koelle DM, Seshadri C. CD4 and CD8 co-receptors modulate functional avidity of CD1b-restricted T cells. Nat Commun 2022; 13:78. [PMID: 35013257 PMCID: PMC8748927 DOI: 10.1038/s41467-021-27764-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/10/2021] [Indexed: 12/13/2022] Open
Abstract
T cells recognize mycobacterial glycolipid (mycolipid) antigens presented by CD1b molecules, but the role of CD4 and CD8 co-receptors in mycolipid recognition is unknown. Here we show CD1b-mycolipid tetramers reveal a hierarchy in which circulating T cells expressing CD4 or CD8 co-receptor stain with a higher tetramer mean fluorescence intensity than CD4-CD8- T cells. CD4+ primary T cells transduced with mycolipid-specific T cell receptors bind CD1b-mycolipid tetramer with a higher fluorescence intensity than CD8+ primary T cells. The presence of either CD4 or CD8 also decreases the threshold for interferon-γ secretion. Co-receptor expression increases surface expression of CD3ε, suggesting a mechanism for increased tetramer binding and activation. Targeted transcriptional profiling of mycolipid-specific T cells from individuals with active tuberculosis reveals canonical markers associated with cytotoxicity among CD8+ compared to CD4+ T cells. Thus, expression of co-receptors modulates T cell receptor avidity for mycobacterial lipids, leading to in vivo functional diversity during tuberculosis disease.
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Affiliation(s)
- Charlotte A James
- Molecular Medicine and Mechanisms of Disease PhD Program (M3D), Department of Pathology, University of Washington, Seattle, WA, USA
| | - Yuexin Xu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Erik D Layton
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Martine Gilleron
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077, Toulouse, France
| | - Adriaan J Minnaard
- Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Cheryl L Day
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Edus H Warren
- Molecular Medicine and Mechanisms of Disease PhD Program (M3D), Department of Pathology, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David M Koelle
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Benaroya Research Institute, Seattle, WA, USA
| | - Chetan Seshadri
- Department of Medicine, University of Washington, Seattle, WA, USA.
- Tuberculosis Research and Training Center, Seattle, WA, USA.
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10
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Zhou AX, Scriba TJ, Day CL, Hagge DA, Seshadri C. A simple assay to quantify mycobacterial lipid antigen-specific T cell receptors in human tissues and blood. PLoS Negl Trop Dis 2021; 15:e0010018. [PMID: 34914694 PMCID: PMC8717985 DOI: 10.1371/journal.pntd.0010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/30/2021] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
T cell receptors (TCRs) encode the history of antigenic challenge within an individual and have the potential to serve as molecular markers of infection. In addition to peptide antigens bound to highly polymorphic MHC molecules, T cells have also evolved to recognize bacterial lipids when bound to non-polymorphic CD1 molecules. One such subset, germline-encoded, mycolyl lipid-reactive (GEM) T cells, recognizes mycobacterial cell wall lipids and expresses a conserved TCR-ɑ chain that is shared among genetically unrelated individuals. We developed a quantitative PCR assay to determine expression of the GEM TCR-ɑ nucleotide sequence in human tissues and blood. This assay was validated on plasmids and T cell lines. We tested blood samples from South African subjects with or without tuberculin reactivity or with active tuberculosis disease. We were able to detect GEM TCR-ɑ above the limit of detection in 92% of donors but found no difference in GEM TCR-ɑ expression among the three groups after normalizing for total TCR-ɑ expression. In a cohort of leprosy patients from Nepal, we successfully detected GEM TCR-ɑ in 100% of skin biopsies with histologically confirmed tuberculoid and lepromatous leprosy. Thus, GEM T cells constitute part of the T cell repertoire in the skin. However, GEM TCR-ɑ expression was not different between leprosy patients and control subjects after normalization. Further, these results reveal the feasibility of developing a simple, field deployable molecular diagnostic based on mycobacterial lipid antigen-specific TCR sequences that are readily detectable in human tissues and blood independent of genetic background.
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MESH Headings
- Antigens, CD1/genetics
- Antigens, CD1/immunology
- Cell Wall/genetics
- Cell Wall/immunology
- Cohort Studies
- Humans
- Leprosy/blood
- Leprosy/diagnosis
- Leprosy/immunology
- Leprosy/microbiology
- Lipids/immunology
- Molecular Diagnostic Techniques/methods
- Mycobacterium/genetics
- Mycobacterium/immunology
- Mycobacterium/isolation & purification
- Nepal
- Polymerase Chain Reaction
- Receptors, Antigen, T-Cell, alpha-beta/blood
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- South Africa
- T-Lymphocytes/immunology
- T-Lymphocytes/microbiology
- Tuberculosis/blood
- Tuberculosis/diagnosis
- Tuberculosis/immunology
- Tuberculosis/microbiology
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Affiliation(s)
- Angela X. Zhou
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Tuberculosis Research and Training Center, University of Washington, Seattle, Washington, United States of America
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Cheryl L. Day
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Deanna A. Hagge
- Mycobacterial Research Laboratories, Anandaban Hospital, Kathmandu, Nepal
| | - Chetan Seshadri
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Tuberculosis Research and Training Center, University of Washington, Seattle, Washington, United States of America
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11
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GIANA allows computationally-efficient TCR clustering and multi-disease repertoire classification by isometric transformation. Nat Commun 2021; 12:4699. [PMID: 34349111 PMCID: PMC8339063 DOI: 10.1038/s41467-021-25006-7] [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: 02/26/2021] [Accepted: 07/19/2021] [Indexed: 01/18/2023] Open
Abstract
Similarity in T-cell receptor (TCR) sequences implies shared antigen specificity between receptors, and could be used to discover novel therapeutic targets. However, existing methods that cluster T-cell receptor sequences by similarity are computationally inefficient, making them impractical to use on the ever-expanding datasets of the immune repertoire. Here, we developed GIANA (Geometric Isometry-based TCR AligNment Algorithm) a computationally efficient tool for this task that provides the same level of clustering specificity as TCRdist at 600 times its speed, and without sacrificing accuracy. GIANA also allows the rapid query of large reference cohorts within minutes. Using GIANA to cluster large-scale TCR datasets provides candidate disease-specific receptors, and provides a new solution to repertoire classification. Querying unseen TCR-seq samples against an existing reference differentiates samples from patients across various cohorts associated with cancer, infectious and autoimmune disease. Our results demonstrate how GIANA could be used as the basis for a TCR-based non-invasive multi-disease diagnostic platform. Grouping T-cell receptors (TCRs) by sequence similarity could lead to new immunological insights. Here, the authors propose a tool that allows the rapid clustering of millions of TCR sequences, identifying TCRs potentially associated with the response to cancer, infectious and autoimmune diseases.
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12
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Wanjalla CN, McDonnell WJ, Ram R, Chopra A, Gangula R, Leary S, Mashayekhi M, Simmons JD, Warren CM, Bailin S, Gabriel CL, Guo L, Furch BD, Lima MC, Woodward BO, Hannah L, Pilkinton MA, Fuller DT, Kawai K, Virmani R, Finn AV, Hasty AH, Mallal SA, Kalams SA, Koethe JR. Single-cell analysis shows that adipose tissue of persons with both HIV and diabetes is enriched for clonal, cytotoxic, and CMV-specific CD4+ T cells. CELL REPORTS MEDICINE 2021; 2:100205. [PMID: 33665640 PMCID: PMC7897802 DOI: 10.1016/j.xcrm.2021.100205] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 09/22/2020] [Accepted: 01/21/2021] [Indexed: 12/11/2022]
Abstract
Persons with HIV are at increased risk for diabetes mellitus compared with individuals without HIV. Adipose tissue is an important regulator of glucose and lipid metabolism, and adipose tissue T cells modulate local inflammatory responses and, by extension, adipocyte function. Persons with HIV and diabetes have a high proportion of CX3CR1+ GPR56+ CD57+ (C-G-C+) CD4+ T cells in adipose tissue, a subset of which are cytomegalovirus specific, whereas individuals with diabetes but without HIV have predominantly CD69+ CD4+ T cells. Adipose tissue CD69+ and C-G-C+ CD4+ T cell subsets demonstrate higher receptor clonality compared with the same cells in blood, potentially reflecting antigen-driven expansion, but C-G-C+ CD4+ T cells have a more inflammatory and cytotoxic RNA transcriptome. Future studies will explore whether viral antigens have a role in recruitment and proliferation of pro-inflammatory C-G-C+ CD4+ T cells in adipose tissue of persons with HIV.
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Affiliation(s)
- Celestine N Wanjalla
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Translational Immunology and Infectious Disease, Vanderbilt University Medical Center, Nashville, TN, USA.,Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wyatt J McDonnell
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Translational Immunology and Infectious Disease, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, USA.,10x Genomics, Pleasanton, CA, USA
| | - Ramesh Ram
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
| | - Rama Gangula
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
| | - Mona Mashayekhi
- Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua D Simmons
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christian M Warren
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Samuel Bailin
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Curtis L Gabriel
- Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University, Nashville, TN, USA
| | - Liang Guo
- CVPath Institute, Gaithersburg, MD, USA
| | - Briana D Furch
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Morgan C Lima
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Beverly O Woodward
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - LaToya Hannah
- Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mark A Pilkinton
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Translational Immunology and Infectious Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | | | - Alyssa H Hasty
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Simon A Mallal
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Translational Immunology and Infectious Disease, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, USA.,Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, USA.,VANTAGE, Vanderbilt University Medical Center, Nashville, TN, USA.,Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
| | - Spyros A Kalams
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Translational Immunology and Infectious Disease, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, USA.,Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John R Koethe
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Translational Immunology and Infectious Disease, Vanderbilt University Medical Center, Nashville, TN, USA.,Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, USA.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
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13
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Layton ED, Barman S, Wilburn DB, Yu KKQ, Smith MT, Altman JD, Scriba TJ, Tahiri N, Minnaard AJ, Roederer M, Seder RA, Darrah PA, Seshadri C. T Cells Specific for a Mycobacterial Glycolipid Expand after Intravenous Bacillus Calmette-Guérin Vaccination. THE JOURNAL OF IMMUNOLOGY 2021; 206:1240-1250. [PMID: 33536255 DOI: 10.4049/jimmunol.2001065] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/01/2021] [Indexed: 12/12/2022]
Abstract
Intradermal vaccination with Mycobacterium bovis bacillus Calmette-Guérin (BCG) protects infants from disseminated tuberculosis, and i.v. BCG protects nonhuman primates (NHP) against pulmonary and extrapulmonary tuberculosis. In humans and NHP, protection is thought to be mediated by T cells, which typically recognize bacterial peptide Ags bound to MHC proteins. However, during vertebrate evolution, T cells acquired the capacity to recognize lipid Ags bound to CD1a, CD1b, and CD1c proteins expressed on APCs. It is unknown whether BCG induces T cell immunity to mycobacterial lipids and whether CD1-restricted T cells are resident in the lung. In this study, we developed and validated Macaca mulatta (Mamu) CD1b and CD1c tetramers to probe ex vivo phenotypes and functions of T cells specific for glucose monomycolate (GMM), an immunodominant mycobacterial lipid Ag. We discovered that CD1b and CD1c present GMM to T cells in both humans and NHP. We show that GMM-specific T cells are expanded in rhesus macaque blood 4 wk after i.v. BCG, which has been shown to protect NHP with near-sterilizing efficacy upon M. tuberculosis challenge. After vaccination, these T cells are detected at high frequency within bronchoalveolar fluid and express CD69 and CD103, markers associated with resident memory T cells. Thus, our data expand the repertoire of T cells known to be induced by whole cell mycobacterial vaccines, such as BCG, and show that lipid Ag-specific T cells are resident in the lungs, where they may contribute to protective immunity.
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Affiliation(s)
- Erik D Layton
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109
| | - Soumik Barman
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109
| | - Damien B Wilburn
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
| | - Krystle K Q Yu
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109
| | - Malisa T Smith
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109
| | - John D Altman
- National Institutes of Health Tetramer Core Facility, Emory University, Atlanta, GA 30329
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 9747, South Africa
| | - Nabil Tahiri
- Stratingh Institute for Chemistry, University of Groningen 7925, Groningen, the Netherlands
| | - Adriaan J Minnaard
- Stratingh Institute for Chemistry, University of Groningen 7925, Groningen, the Netherlands
| | - Mario Roederer
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892; and
| | - Robert A Seder
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892; and
| | - Patricia A Darrah
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892; and
| | - Chetan Seshadri
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109; .,Tuberculosis Research and Training Center, University of Washington, Seattle, WA 98109
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14
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Morgun E, Cao L, Wang CR. Role of Group 1 CD1-Restricted T Cells in Host Defense and Inflammatory Diseases. Crit Rev Immunol 2021; 41:1-21. [PMID: 35381140 PMCID: PMC10128144 DOI: 10.1615/critrevimmunol.2021040089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Group 1 CD1-restricted T cells are members of the unconventional T cell family that recognize lipid antigens presented by CD1a, CD1b, and CD1c molecules. Although they developmentally mirror invariant natural killer T cells, they have diverse antigen specificity and functional capacity, with both anti-microbial and autoreactive targets. The role of group 1 CD1-restricted T cells has been best established in Mycobacterium tuberculosis (Mtb) infection in which a wide variety of lipid antigens have been identified and their ability to confer protection against Mtb infection in a CD1 transgenic mouse model has been shown. Group 1 CD1-restricted T cells have also been implicated in other infections, inflammatory conditions, and malignancies. In particular, autoreactive group 1 CD1-restricted T cells have been shown to play a role in several skin inflammatory conditions. The prevalence of group 1 CD1 autoreactive T cells in healthy individuals suggests the presence of regulatory mechanisms to suppress autoreactivity in homeostasis. The more recent use of group 1 CD1 tetramers and mouse models has allowed for better characterization of their phenotype, functional capacity, and underlying mechanisms of antigen-specific and autoreactive activation. These discoveries may pave the way for the development of novel vaccines and immunotherapies that target group 1 CD1-restricted T cells.
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Affiliation(s)
- Eva Morgun
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Liang Cao
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Chyung-Ru Wang
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
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15
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de Lima Moreira M, Souter MNT, Chen Z, Loh L, McCluskey J, Pellicci DG, Eckle SBG. Hypersensitivities following allergen antigen recognition by unconventional T cells. Allergy 2020; 75:2477-2490. [PMID: 32181878 PMCID: PMC11056244 DOI: 10.1111/all.14279] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/24/2020] [Accepted: 03/09/2020] [Indexed: 02/06/2023]
Abstract
Conventional T cells recognise protein-derived antigens in the context of major histocompatibility complex (MHC) class Ia and class II molecules and provide anti-microbial and anti-tumour immunity. Conventional T cells have also been implicated in type IV (also termed delayed-type or T cell-mediated) hypersensitivity reactions in response to protein-derived allergen antigens. In addition to conventional T cells, subsets of unconventional T cells exist, which recognise non-protein antigens in the context of monomorphic MHC class I-like molecules. These include T cells that are restricted to the cluster of differentiation 1 (CD1) family members, known as CD1-restricted T cells, and mucosal-associated invariant T cells (MAIT cells) that are restricted to the MHC-related protein 1 (MR1). Compared with conventional T cells, much less is known about the immune functions of unconventional T cells and their role in hypersensitivities. Here, we review allergen antigen presentation by MHC-I-like molecules, their recognition by unconventional T cells, and the potential role of unconventional T cells in hypersensitivities. We also speculate on possible scenarios of allergen antigen presentation by MHC-I-like molecules to unconventional T cells, the hallmarks of such responses, and the expected frequencies of hypersensitivities within the human population.
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Affiliation(s)
- Marcela de Lima Moreira
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic., Australia
| | - Michael N. T. Souter
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic., Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Vic., Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic., Australia
| | - Liyen Loh
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic., Australia
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic., Australia
| | | | - Sidonia B. G. Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic., Australia
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16
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Beshnova D, Ye J, Onabolu O, Moon B, Zheng W, Fu YX, Brugarolas J, Lea J, Li B. De novo prediction of cancer-associated T cell receptors for noninvasive cancer detection. Sci Transl Med 2020; 12:eaaz3738. [PMID: 32817363 PMCID: PMC7887928 DOI: 10.1126/scitranslmed.aaz3738] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 03/05/2020] [Accepted: 07/21/2020] [Indexed: 01/21/2023]
Abstract
The adaptive immune system recognizes tumor antigens at an early stage to eradicate cancer cells. This process is accompanied by systemic proliferation of the tumor antigen-specific T lymphocytes. While detection of asymptomatic early-stage cancers is challenging due to small tumor size and limited somatic alterations, tracking peripheral T cell repertoire changes may provide an attractive solution to cancer diagnosis. Here, we developed a deep learning method called DeepCAT to enable de novo prediction of cancer-associated T cell receptors (TCRs). We validated DeepCAT using cancer-specific or non-cancer TCRs obtained from multiple major histocompatibility complex I (MHC-I) multimer-sorting experiments and demonstrated its prediction power for TCRs specific to cancer antigens. We blindly applied DeepCAT to distinguish over 250 patients with cancer from over 600 healthy individuals using blood TCR sequences and observed high prediction accuracy, with area under the curve (AUC) ≥ 0.95 for multiple early-stage cancers. This work sets the stage for using the peripheral blood TCR repertoire for noninvasive cancer detection.
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Affiliation(s)
- Daria Beshnova
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jianfeng Ye
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Oreoluwa Onabolu
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benjamin Moon
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenxin Zheng
- Department of Obstetrics and Gynecology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang-Xin Fu
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - James Brugarolas
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jayanthi Lea
- Department of Obstetrics and Gynecology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bo Li
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA.
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
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17
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Ogongo P, Steyn AJ, Karim F, Dullabh KJ, Awala I, Madansein R, Leslie A, Behar SM. Differential skewing of donor-unrestricted and γδ T cell repertoires in tuberculosis-infected human lungs. J Clin Invest 2020; 130:214-230. [PMID: 31763997 PMCID: PMC6934215 DOI: 10.1172/jci130711] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/25/2019] [Indexed: 12/12/2022] Open
Abstract
Unconventional T cells that recognize mycobacterial antigens are of great interest as potential vaccine targets against tuberculosis (TB). This includes donor-unrestricted T cells (DURTs), such as mucosa-associated invariant T cells (MAITs), CD1-restricted T cells, and γδ T cells. We exploited the distinctive nature of DURTs and γδ T cell receptors (TCRs) to investigate the involvement of these T cells during TB in the human lung by global TCR sequencing. Making use of surgical lung resections, we investigated the distribution, frequency, and characteristics of TCRs in lung tissue and matched blood from individuals infected with TB. Despite depletion of MAITs and certain CD1-restricted T cells from the blood, we found that the DURT repertoire was well preserved in the lungs, irrespective of disease status or HIV coinfection. The TCRδ repertoire, in contrast, was highly skewed in the lungs, where it was dominated by Vδ1 and distinguished by highly localized clonal expansions, consistent with the nonrecirculating lung-resident γδ T cell population. These data show that repertoire sequencing is a powerful tool for tracking T cell subsets during disease.
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Affiliation(s)
- Paul Ogongo
- Africa Health Research Institute and.,School of Laboratory Medicine, Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | | | | | - Kaylesh J Dullabh
- Department of Cardiothoracic Surgery, Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ismael Awala
- Department of Cardiothoracic Surgery, Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Rajhmun Madansein
- Department of Cardiothoracic Surgery, Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Alasdair Leslie
- Africa Health Research Institute and.,Department of Infection and Immunity, University College London, London, United Kingdom
| | - Samuel M Behar
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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18
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Teraguchi S, Saputri DS, Llamas-Covarrubias MA, Davila A, Diez D, Nazlica SA, Rozewicki J, Ismanto HS, Wilamowski J, Xie J, Xu Z, Loza-Lopez MDJ, van Eerden FJ, Li S, Standley DM. Methods for sequence and structural analysis of B and T cell receptor repertoires. Comput Struct Biotechnol J 2020; 18:2000-2011. [PMID: 32802272 PMCID: PMC7366105 DOI: 10.1016/j.csbj.2020.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 02/07/2023] Open
Abstract
B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of defense molecules that, collectively, can distinguish self from non-self and facilitate destruction of antigen-bearing cells such as pathogens or tumors. The analysis of BCR and TCR repertoires plays an important role in both basic immunology as well as in biotechnology. Because the repertoires are highly diverse, specialized software methods are needed to extract meaningful information from BCR and TCR sequence data. Here, we review recent developments in bioinformatics tools for analysis of BCR and TCR repertoires, with an emphasis on those that incorporate structural features. After describing the recent sequencing technologies for immune receptor repertoires, we survey structural modeling methods for BCR and TCRs, along with methods for clustering such models. We review downstream analyses, including BCR and TCR epitope prediction, antibody-antigen docking and TCR-peptide-MHC Modeling. We also briefly discuss molecular dynamics in this context.
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Affiliation(s)
- Shunsuke Teraguchi
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Dianita S. Saputri
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Mara Anais Llamas-Covarrubias
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Mexico
| | - Ana Davila
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Diego Diez
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Sedat Aybars Nazlica
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - John Rozewicki
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Hendra S. Ismanto
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Jan Wilamowski
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Jiaqi Xie
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Zichang Xu
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | | | - Floris J. van Eerden
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Songling Li
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Daron M. Standley
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
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19
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James CA, Seshadri C. T Cell Responses to Mycobacterial Glycolipids: On the Spectrum of "Innateness". Front Immunol 2020; 11:170. [PMID: 32117300 PMCID: PMC7026021 DOI: 10.3389/fimmu.2020.00170] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/22/2020] [Indexed: 12/12/2022] Open
Abstract
Diseases due to mycobacteria, including tuberculosis, leprosy, and Buruli ulcer, rank among the top causes of death and disability worldwide. Animal studies have revealed the importance of T cells in controlling these infections. However, the specific antigens recognized by T cells that confer protective immunity and their associated functions remain to be definitively established. T cells that respond to mycobacterial peptide antigens exhibit classical features of adaptive immunity and have been well-studied in humans and animal models. Recently, innate-like T cells that recognize lipid and metabolite antigens have also been implicated. Specifically, T cells that recognize mycobacterial glycolipid antigens (mycolipids) have been shown to confer protection to tuberculosis in animal models and share some biological characteristics with adaptive and innate-like T cells. Here, we review the existing data suggesting that mycolipid-specific T cells exist on a spectrum of “innateness,” which will influence how they can be leveraged to develop new diagnostics and vaccines for mycobacterial diseases.
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Affiliation(s)
- Charlotte A James
- Molecular Medicine and Mechanisms of Disease (M3D) PhD Program, Department of Pathology, School of Medicine, University of Washington, Seattle, WA, United States
| | - Chetan Seshadri
- Department of Medicine, School of Medicine, University of Washington, Seattle, WA, United States.,Tuberculosis Research and Training Center, School of Medicine, University of Washington, Seattle, WA, United States
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20
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Reinink P, Shahine A, Gras S, Cheng TY, Farquhar R, Lopez K, Suliman SA, Reijneveld JF, Le Nours J, Tan LL, León SR, Jimenez J, Calderon R, Lecca L, Murray MB, Rossjohn J, Moody DB, Van Rhijn I. A TCR β-Chain Motif Biases toward Recognition of Human CD1 Proteins. THE JOURNAL OF IMMUNOLOGY 2019; 203:3395-3406. [PMID: 31694911 DOI: 10.4049/jimmunol.1900872] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/09/2019] [Indexed: 12/30/2022]
Abstract
High-throughput TCR sequencing allows interrogation of the human TCR repertoire, potentially connecting TCR sequences to antigenic targets. Unlike the highly polymorphic MHC proteins, monomorphic Ag-presenting molecules such as MR1, CD1d, and CD1b present Ags to T cells with species-wide TCR motifs. CD1b tetramer studies and a survey of the 27 published CD1b-restricted TCRs demonstrated a TCR motif in humans defined by the TCR β-chain variable gene 4-1 (TRBV4-1) region. Unexpectedly, TRBV4-1 was involved in recognition of CD1b regardless of the chemical class of the carried lipid. Crystal structures of two CD1b-specific TRBV4-1+ TCRs show that germline-encoded residues in CDR1 and CDR3 regions of TRBV4-1-encoded sequences interact with each other and consolidate the surface of the TCR. Mutational studies identified a key positively charged residue in TRBV4-1 and a key negatively charged residue in CD1b that is shared with CD1c, which is also recognized by TRBV4-1 TCRs. These data show that one TCR V region can mediate a mechanism of recognition of two related monomorphic Ag-presenting molecules that does not rely on a defined lipid Ag.
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Affiliation(s)
- Peter Reinink
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584CL Utrecht, the Netherlands.,Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Adam Shahine
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Stephanie Gras
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Tan-Yun Cheng
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Rachel Farquhar
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Kattya Lopez
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115.,Socios en Salud Sucursal Peru, 15001 Lima, Peru
| | - Sara A Suliman
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Josephine F Reijneveld
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584CL Utrecht, the Netherlands.,Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115.,Stratingh Institute for Chemistry, University of Groningen, 9747AG Groningen, the Netherlands
| | - Jérôme Le Nours
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Li Lynn Tan
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | | | | | | | | | - Megan B Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA 02115.,Division of Global Health Equity, Brigham and Women's Hospital, Boston, MA 02115.,Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115; and
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,Institute of Infection and Immunity, School of Medicine, Cardiff University, CF14 4XN Cardiff, United Kingdom
| | - D Branch Moody
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Ildiko Van Rhijn
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584CL Utrecht, the Netherlands; .,Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
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21
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Davidsen K, Olson BJ, DeWitt WS, Feng J, Harkins E, Bradley P, Matsen FA. Deep generative models for T cell receptor protein sequences. eLife 2019; 8:e46935. [PMID: 31487240 PMCID: PMC6728137 DOI: 10.7554/elife.46935] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023] Open
Abstract
Probabilistic models of adaptive immune repertoire sequence distributions can be used to infer the expansion of immune cells in response to stimulus, differentiate genetic from environmental factors that determine repertoire sharing, and evaluate the suitability of various target immune sequences for stimulation via vaccination. Classically, these models are defined in terms of a probabilistic V(D)J recombination model which is sometimes combined with a selection model. In this paper we take a different approach, fitting variational autoencoder (VAE) models parameterized by deep neural networks to T cell receptor (TCR) repertoires. We show that simple VAE models can perform accurate cohort frequency estimation, learn the rules of VDJ recombination, and generalize well to unseen sequences. Further, we demonstrate that VAE-like models can distinguish between real sequences and sequences generated according to a recombination-selection model, and that many characteristics of VAE-generated sequences are similar to those of real sequences.
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Affiliation(s)
- Kristian Davidsen
- University of WashingtonSeattleUnited States
- Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Branden J Olson
- University of WashingtonSeattleUnited States
- Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - William S DeWitt
- University of WashingtonSeattleUnited States
- Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Jean Feng
- University of WashingtonSeattleUnited States
- Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Elias Harkins
- University of WashingtonSeattleUnited States
- Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Philip Bradley
- University of WashingtonSeattleUnited States
- Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Frederick A Matsen
- University of WashingtonSeattleUnited States
- Fred Hutchinson Cancer Research CenterSeattleUnited States
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22
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Boonyaratanakornkit J, Taylor JJ. Techniques to Study Antigen-Specific B Cell Responses. Front Immunol 2019; 10:1694. [PMID: 31396218 PMCID: PMC6667631 DOI: 10.3389/fimmu.2019.01694] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022] Open
Abstract
Antibodies against foreign antigens are a critical component of the overall immune response and can facilitate pathogen clearance during a primary infection and also protect against subsequent infections. Dysregulation of the antibody response can lead to an autoimmune disease, malignancy, or enhanced infection. Since the experimental delineation of a distinct B cell lineage in 1965, various methods have been developed to understand antigen-specific B cell responses in the context of autoimmune diseases, primary immunodeficiencies, infection, and vaccination. In this review, we summarize the established techniques and discuss new and emerging technologies for probing the B cell response in vitro and in vivo by taking advantage of the specificity of B cell receptor (BCR)-associated and secreted antibodies. These include ELISPOT, flow cytometry, mass cytometry, and fluorescence microscopy to identify and/or isolate primary antigen-specific B cells. We also present our approach to identify rare antigen-specific B cells using magnetic enrichment followed by flow cytometry. Once these cells are isolated, in vitro proliferation assays and adoptive transfer experiments in mice can be used to further characterize antigen-specific B cell activation, function, and fate. Transgenic mouse models of B cells targeting model antigens and of B cell signaling have also significantly advanced our understanding of antigen-specific B cell responses in vivo.
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Affiliation(s)
- Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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23
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Pereira CS, Pérez-Cabezas B, Ribeiro H, Maia ML, Cardoso MT, Dias AF, Azevedo O, Ferreira MF, Garcia P, Rodrigues E, Castro-Chaves P, Martins E, Aguiar P, Pineda M, Amraoui Y, Fecarotta S, Leão-Teles E, Deng S, Savage PB, Macedo MF. Lipid Antigen Presentation by CD1b and CD1d in Lysosomal Storage Disease Patients. Front Immunol 2019; 10:1264. [PMID: 31214199 PMCID: PMC6558002 DOI: 10.3389/fimmu.2019.01264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 05/17/2019] [Indexed: 12/29/2022] Open
Abstract
The lysosome has a key role in the presentation of lipid antigens by CD1 molecules. While defects in lipid antigen presentation and in invariant Natural Killer T (iNKT) cell response were detected in several mouse models of lysosomal storage diseases (LSD), the impact of lysosomal engorgement in human lipid antigen presentation is poorly characterized. Here, we analyzed the capacity of monocyte-derived dendritic cells (Mo-DCs) from Fabry, Gaucher, Niemann Pick type C and Mucopolysaccharidosis type VI disease patients to present exogenous antigens to lipid-specific T cells. The CD1b- and CD1d-restricted presentation of lipid antigens by Mo-DCs revealed an ability of LSD patients to induce CD1-restricted T cell responses within the control range. Similarly, freshly isolated monocytes from Fabry and Gaucher disease patients had a normal ability to present α-Galactosylceramide (α-GalCer) antigen by CD1d. Gaucher disease patients' monocytes had an increased capacity to present α-Gal-(1-2)-αGalCer, an antigen that needs internalization and processing to become antigenic. In summary, our results show that Fabry, Gaucher, Niemann Pick type C, and Mucopolysaccharidosis type VI disease patients do not present a decreased capacity to present CD1d-restricted lipid antigens. These observations are in contrast to what was observed in mouse models of LSD. The percentage of total iNKT cells in the peripheral blood of these patients is also similar to control individuals. In addition, we show that the presentation of exogenous lipids that directly bind CD1b, the human CD1 isoform with an intracellular trafficking to the lysosome, is normal in these patients.
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Affiliation(s)
- Catia S Pereira
- CAGE, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.,CAGE, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Begoña Pérez-Cabezas
- CAGE, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.,CAGE, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Helena Ribeiro
- CAGE, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.,CAGE, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Departamento de Química, Universidade de Aveiro, Aveiro, Portugal
| | - M Luz Maia
- UniLipe, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - M Teresa Cardoso
- Centro de Referência de Doenças Hereditárias do Metabolismo (DHM), Centro Hospitalar de São João, Medicina Interna, Porto, Portugal
| | - Ana F Dias
- UniLipe, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Olga Azevedo
- Centro de Referência de Doenças Lisossomais de Sobrecarga, Hospital da Senhora da Oliveira, Guimarães, Portugal
| | - M Fatima Ferreira
- Centro de Referência de Doenças Hereditárias do Metabolismo (DHM), Hematologia Clínica, Centro Hospitalar de São João, Porto, Portugal
| | - Paula Garcia
- Centro de Referência de Doenças Hereditárias do Metabolismo (DHM), Centro Hospitalar e Universitário de Coimbra, Centro de Desenvolvimento da Criança, Coimbra, Portugal
| | - Esmeralda Rodrigues
- Centro de Referência de Doenças Hereditárias do Metabolismo (DHM), Pediatria, Centro Hospitalar de São João, Porto, Portugal
| | - Paulo Castro-Chaves
- Centro de Referência de Doenças Hereditárias do Metabolismo (DHM), Centro Hospitalar de São João, Medicina Interna, Porto, Portugal
| | - Esmeralda Martins
- Centro de Referência de Doenças Hereditárias do Metabolismo (DHM), Pediatria, Centro Hospitalar do Porto, Porto, Portugal
| | - Patricio Aguiar
- Centro de Referência de Doenças Hereditárias do Metabolismo (DHM), Medicina, Centro Hospitalar Lisboa Norte (CHLN), Lisbon, Portugal
| | - Mercè Pineda
- Centre de Recerca e Investigació, Fundacio Hospital Sant Joan de Déu, Barcelona, Spain
| | - Yasmina Amraoui
- Department of Pediatrics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Simona Fecarotta
- Department of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Elisa Leão-Teles
- Centro de Referência de Doenças Hereditárias do Metabolismo (DHM), Pediatria, Centro Hospitalar de São João, Porto, Portugal
| | - Shenglou Deng
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, United States
| | - Paul B Savage
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, United States
| | - M Fatima Macedo
- CAGE, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.,CAGE, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Departamento de Ciências Médicas, Universidade de Aveiro, Aveiro, Portugal
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24
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Joosten SA, Ottenhoff TH, Lewinsohn DM, Hoft DF, Moody DB, Seshadri C. Harnessing donor unrestricted T-cells for new vaccines against tuberculosis. Vaccine 2019; 37:3022-3030. [PMID: 31040086 PMCID: PMC6525272 DOI: 10.1016/j.vaccine.2019.04.050] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/02/2019] [Accepted: 04/13/2019] [Indexed: 01/14/2023]
Abstract
Mycobacterium bovis bacille Calmette-Guérin (BCG) prevents extrapulmonary tuberculosis (TB) and death among infants but fails to consistently and sufficiently prevent pulmonary TB in adults. Thus, TB remains the leading infectious cause of death worldwide, and new vaccine approaches are urgently needed. T-cells are important for protective immunity to Mycobacterium tuberculosis (Mtb), but the optimal T-cell antigens to be included in new vaccines are not established. T-cells are often thought of as responding mainly to peptide antigens presented by polymorphic major histocompatibility complex (MHC) I and II molecules. Over the past two decades, the number of non-peptidic Mtb derived antigens for αβ and γδ T-cells has expanded rapidly, creating broader perspectives about the types of molecules that could be targeted by T-cell-based vaccines against TB. Many of these non-peptide responsive T-cell subsets in humans are activated in a manner that is unrestricted by classical MHC-dependent antigen-presenting systems, but instead require essentially nonpolymorphic presentation systems. These systems are Cluster of differentiation 1 (CD1), MHC related protein 1 (MR1), butyrophilin 3A1, as well as the nonclassical MHC class Ib family member HLA-E. Thus, the resulting T-cell responses can be shared among a genetically diverse population, creating the concept of donor-unrestricted T-cells (DURTs). Here, we review evidence that DURTs are an abundant component of the human immune system and recognize many antigens expressed by Mtb, including antigens that are expressed in BCG and other candidate whole cell vaccines. Further, DURTs exhibit functional diversity and demonstrate the ability to control microbial infection in small animal models. Finally, we outline specific knowledge gaps and research priorities that must be addressed to realize the full potential of DURTs as part of new TB vaccines approaches.
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Affiliation(s)
- Simone A. Joosten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Tom H.M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - David M. Lewinsohn
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, Oregon Health Sciences University, Portland, USA
| | - Daniel F. Hoft
- Department of Internal Medicine, Saint Louis University, Doisy Research Center, 8th floor, 1100 S. Grand Blvd., St. Louis, MO 63104, USA
| | - D. Branch Moody
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham & Women’s Hospital, Boston, Harvard Medical School, USA
| | - Chetan Seshadri
- Department of Medicine, Division of Infectious Diseases, University of Washington, Seattle, USA,Tuberculosis Research & Training Center, University of Washington, Seattle, USA,Corresponding author at: University of Washington Medical Center, 750 Republican Street, Room E663, Seattle, WA 98109, USA.
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25
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Taheri M, Danesh H, Bizhani F, Bahari G, Naderi M, Hashemi M. Association between genetic variants in CD1A and CD1D genes and pulmonary tuberculosis in an Iranian population. Biomed Rep 2019; 10:259-265. [PMID: 30972222 DOI: 10.3892/br.2019.1201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/12/2019] [Indexed: 11/06/2022] Open
Abstract
Cluster of differentiation (CD)1 molecules are a highly conserved family of MCH-like transmembrane glycoproteins that bind lipid and glycolipid antigens and present a diverse range of microbial and self-glycolipids to antigen-specific T cells. The current study aimed to find out the impact of CD1A and CD1D polymorphisms on pulmonary tuberculosis (PTB). This case-control study encompassed 172 PTB patients and 180 healthy subjects. Genotyping of CD1A and CD1D variants was achieved using the polymerase chain reaction restriction fragment length polymorphism method. The results revealed that CD1A rs411089 variant significantly increased the risk of PTB in recessive model [odds ratio (OR)=2.71, 95% confidence interval (CI)=1.38-5.57, CC vs. TT+TC, P=0.005]. CD1D rs859009 polymorphism significantly reduced the risk of PTB in heterozygous codominant (OR=0.50, 95% CI=0.29-0.86, P=0.011, GC vs. GG) and dominant (OR=0.53, 95% CI=0.31-0.88, P=0.019, GC+CC vs. GG) inheritance model. The CD1A rs366316, CD1D rs973742 and CD1D rs859010 were not associated with the risk/protection from PTB (P>0.05). The results of the present study suggest that CD1A rs411089 and CD1D rs859009 but not CD1A rs366316, CD1D rs973742 and CD1D rs859010 polymorphisms are associated with PTB in a sample of the Iranian population. Further investigation with different ethnicities and larger sample sizes are necessary to certify the findings of the present study.
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Affiliation(s)
- Mohsen Taheri
- Genetics of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan 98167-4318, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-4318, Iran
| | - Hiva Danesh
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-4318, Iran
| | - Fatemeh Bizhani
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-4318, Iran
| | - Gholamreza Bahari
- Children and Adolescent Health Research Center, Zahedan University of Medical Sciences, Zahedan 98167-4318, Iran
| | - Mohammad Naderi
- Infectious Diseases and Tropical Medicine Research Center, Zahedan University of Medical Sciences, Zahedan 98167-4318, Iran
| | - Mohammad Hashemi
- Genetics of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan 98167-4318, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-4318, Iran
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26
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Bradley P, Thomas PG. Using T Cell Receptor Repertoires to Understand the Principles of Adaptive Immune Recognition. Annu Rev Immunol 2019; 37:547-570. [PMID: 30699000 DOI: 10.1146/annurev-immunol-042718-041757] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Adaptive immune recognition is mediated by antigen receptors on B and T cells generated by somatic recombination during lineage development. The high level of diversity resulting from this process posed technical limitations that previously limited the comprehensive analysis of adaptive immune recognition. Advances over the last ten years have produced data and approaches allowing insights into how T cells develop, evolutionary signatures of recombination and selection, and the features of T cell receptors that mediate epitope-specific binding and T cell activation. The size and complexity of these data have necessitated the generation of novel computational and analytical approaches, which are transforming how T cell immunology is conducted. Here we review the development and application of novel biological, theoretical, and computational methods for understanding T cell recognition and discuss the potential for improved models of receptor:antigen interactions.
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Affiliation(s)
- Philip Bradley
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; .,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA;
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