1
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Nichakawade TD, Ge J, Mog BJ, Lee BS, Pearlman AH, Hwang MS, DiNapoli SR, Wyhs N, Marcou N, Glavaris S, Konig MF, Gabelli SB, Watson E, Sterling C, Wagner-Johnston N, Rozati S, Swinnen L, Fuchs E, Pardoll DM, Gabrielson K, Papadopoulos N, Bettegowda C, Kinzler KW, Zhou S, Sur S, Vogelstein B, Paul S. TRBC1-targeting antibody-drug conjugates for the treatment of T cell cancers. Nature 2024; 628:416-423. [PMID: 38538786 DOI: 10.1038/s41586-024-07233-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 02/16/2024] [Indexed: 04/06/2024]
Abstract
Antibody and chimeric antigen receptor (CAR) T cell-mediated targeted therapies have improved survival in patients with solid and haematologic malignancies1-9. Adults with T cell leukaemias and lymphomas, collectively called T cell cancers, have short survival10,11 and lack such targeted therapies. Thus, T cell cancers particularly warrant the development of CAR T cells and antibodies to improve patient outcomes. Preclinical studies showed that targeting T cell receptor β-chain constant region 1 (TRBC1) can kill cancerous T cells while preserving sufficient healthy T cells to maintain immunity12, making TRBC1 an attractive target to treat T cell cancers. However, the first-in-human clinical trial of anti-TRBC1 CAR T cells reported a low response rate and unexplained loss of anti-TRBC1 CAR T cells13,14. Here we demonstrate that CAR T cells are lost due to killing by the patient's normal T cells, reducing their efficacy. To circumvent this issue, we developed an antibody-drug conjugate that could kill TRBC1+ cancer cells in vitro and cure human T cell cancers in mouse models. The anti-TRBC1 antibody-drug conjugate may provide an optimal format for TRBC1 targeting and produce superior responses in patients with T cell cancers.
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Affiliation(s)
- Tushar D Nichakawade
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Jiaxin Ge
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Brian J Mog
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Bum Seok Lee
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Alexander H Pearlman
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael S Hwang
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Genentech, San Francisco, CA, USA
| | - Sarah R DiNapoli
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Nicolas Wyhs
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Nikita Marcou
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Stephanie Glavaris
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Maximilian F Konig
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
- Division of Rheumatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sandra B Gabelli
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Discovery Chemistry, Merck Research Laboratory, Merck and Co, West Point, PA, USA
| | - Evangeline Watson
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cole Sterling
- Division of Hematologic Malignancies and Bone Marrow Transplantation, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nina Wagner-Johnston
- Division of Hematologic Malignancies and Bone Marrow Transplantation, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sima Rozati
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Lode Swinnen
- Division of Hematologic Malignancies and Bone Marrow Transplantation, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ephraim Fuchs
- Division of Hematologic Malignancies and Bone Marrow Transplantation, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Drew M Pardoll
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kathy Gabrielson
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nickolas Papadopoulos
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chetan Bettegowda
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth W Kinzler
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Shibin Zhou
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Surojit Sur
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Bert Vogelstein
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Suman Paul
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Division of Hematologic Malignancies and Bone Marrow Transplantation, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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2
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Lucero OM, Lee JA, Bowman J, Johnson K, Sapparapu G, Thomas JK, Fan G, Chang BH, Thiel-Klare K, Eide CA, Okada C, Palazzolo M, Lind E, Kosaka Y, Druker BJ, Lydon N, Bowers PM. Patient-Specific Targeting of the T-Cell Receptor Variable Region as a Therapeutic Strategy in Clonal T-Cell Diseases. Clin Cancer Res 2023; 29:4230-4241. [PMID: 37199721 PMCID: PMC10592575 DOI: 10.1158/1078-0432.ccr-22-0906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 01/31/2023] [Accepted: 05/16/2023] [Indexed: 05/19/2023]
Abstract
PURPOSE Targeted therapeutics are a goal of medicine. Methods for targeting T-cell lymphoma lack specificity for the malignant cell, leading to elimination of healthy cells. The T-cell receptor (TCR) is designed for antigen recognition. T-cell malignancies expand from a single clone that expresses one of 48 TCR variable beta (Vβ) genes, providing a distinct therapeutic target. We hypothesized that a mAb that is exclusive to a specific Vβ would eliminate the malignant clone while having minimal effects on healthy T cells. EXPERIMENTAL DESIGN We identified a patient with large granular T-cell leukemia and sequenced his circulating T-cell population, 95% of which expressed Vβ13.3. We developed a panel of anti-Vβ13.3 antibodies to test for binding and elimination of the malignant T-cell clone. RESULTS Therapeutic antibody candidates bound the malignant clone with high affinity. Antibodies killed engineered cell lines expressing the patient TCR Vβ13.3 by antibody-dependent cellular cytotoxicity and TCR-mediated activation-induced cell death, and exhibited specific killing of patient malignant T cells in combination with exogenous natural killer cells. EL4 cells expressing the patient's TCR Vβ13.3 were also killed by antibody administration in an in vivo murine model. CONCLUSIONS This approach serves as an outline for development of therapeutics that can treat clonal T-cell-based malignancies and potentially other T-cell-mediated diseases. See related commentary by Varma and Diefenbach, p. 4024.
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Affiliation(s)
- Olivia M Lucero
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Ji-Ann Lee
- Clinical and Translational Science Institute, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Jenna Bowman
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Kara Johnson
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Gopal Sapparapu
- Clinical and Translational Science Institute, David Geffen School of Medicine, University of California, Los Angeles, California
| | - John K Thomas
- Clinical and Translational Science Institute, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Guang Fan
- Department of Pathology and Clinical Laboratory Medicine, Oregon Health & Science University, Portland, Oregon
| | - Bill H Chang
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Division of Pediatric Hematology and Oncology, Oregon Health & Science University, Portland, Oregon
| | - Karina Thiel-Klare
- Division of Pediatric Hematology and Oncology, Oregon Health & Science University, Portland, Oregon
| | - Christopher A Eide
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Craig Okada
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Mike Palazzolo
- Clinical and Translational Science Institute, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Evan Lind
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Yoko Kosaka
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Division of Pediatric Hematology and Oncology, Oregon Health & Science University, Portland, Oregon
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
- VB Therapeutics LLC, Jackson, Wyoming
| | | | - Peter M Bowers
- Therapeutic Antibody Laboratory, Department of Pulmonology and Critical Care, David Geffen School of Medicine, Los Angeles, California
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3
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Mattila J, Sormunen S, Heikkilä N, Mattila IP, Saramäki J, Arstila TP. Analysis of thymic generation of shared T-cell receptor α repertoire associated with recognition of tumor antigens shows no preference for neoantigens over wild-type antigens. Cancer Med 2023; 12:13486-13496. [PMID: 37114587 PMCID: PMC10315763 DOI: 10.1002/cam4.6002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/06/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND The number of mutations in cancer cells is an important predictor of a positive response to cancer immunotherapy. It has been suggested that the neoantigens produced by these mutations are more immunogenic than nonmutated tumor antigens, which are likely to be protected by immunological tolerance. However, the mechanisms of tolerance as regards tumor antigens are incompletely understood. METHODS Here, we have analyzed the impact of thymic negative selection on shared T-cell receptor (TCR) repertoire associated with the recognition of either mutated or nonmutated tumor antigens by comparing previously known TCR-antigen-pairs to TCR repertoires of 21 immunologically healthy individuals. RESULTS Our results show that TCRα chains associated with either type of tumor antigens are readily generated in the thymus, at a frequency similar to TCRα chains associated with nonself. In the peripheral repertoire, the relative clone size of nonself-associated chains is higher than that of the tumor antigens, but importantly, there is no difference between TCRα chains associated with mutated or nonmutated tumor antigens. CONCLUSION This suggests that the tolerance mechanisms protecting nonmutated tumor antigens are non-deletional and therefore potentially reversible. As unmutated antigens are, unlike mutations, shared by a large number of patients, they may offer advantages in designing immunological approaches to cancer treatment.
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Affiliation(s)
- Joonatan Mattila
- Research Programs Unit, Translational Immunology, Haartmaninkatu 3 (PL 21) 00014, and MedicumUniversity of HelsinkiHelsinkiFinland
| | - Silja Sormunen
- Department of Computer ScienceAalto UniversityEspooFinland
| | - Nelli Heikkilä
- Research Programs Unit, Translational Immunology, Haartmaninkatu 3 (PL 21) 00014, and MedicumUniversity of HelsinkiHelsinkiFinland
- Faculty of Medicine, Center for Vaccinology, Department of Pathology and ImmunologyUniversity of GenevaGenevaSwitzerland
| | - Ilkka P. Mattila
- Department of Pediatric Cardiac and Transplantation SurgeryHospital for Children and Adolescents, Helsinki University Central HospitalHelsinkiFinland
| | - Jari Saramäki
- Department of Computer ScienceAalto UniversityEspooFinland
| | - T. Petteri Arstila
- Research Programs Unit, Translational Immunology, Haartmaninkatu 3 (PL 21) 00014, and MedicumUniversity of HelsinkiHelsinkiFinland
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4
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Wang Y, Tsitsiklis A, Devoe S, Gao W, Chu HH, Zhang Y, Li W, Wong WK, Deane CM, Neau D, Slansky JE, Thomas PG, Robey EA, Dai S. Peptide Centric Vβ Specific Germline Contacts Shape a Specialist T Cell Response. Front Immunol 2022; 13:847092. [PMID: 35967379 PMCID: PMC9372435 DOI: 10.3389/fimmu.2022.847092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 05/31/2022] [Indexed: 11/15/2022] Open
Abstract
Certain CD8 T cell responses are particularly effective at controlling infection, as exemplified by elite control of HIV in individuals harboring HLA-B57. To understand the structural features that contribute to CD8 T cell elite control, we focused on a strongly protective CD8 T cell response directed against a parasite-derived peptide (HF10) presented by an atypical MHC-I molecule, H-2Ld. This response exhibits a focused TCR repertoire dominated by Vβ2, and a representative TCR (TG6) in complex with Ld-HF10 reveals an unusual structure in which both MHC and TCR contribute extensively to peptide specificity, along with a parallel footprint of TCR on its pMHC ligand. The parallel footprint is a common feature of Vβ2-containing TCRs and correlates with an unusual Vα-Vβ interface, CDR loop conformations, and Vβ2-specific germline contacts with peptides. Vβ2 and Ld may represent "specialist" components for antigen recognition that allows for particularly strong and focused T cell responses.
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Affiliation(s)
- Yang Wang
- Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Alexandra Tsitsiklis
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Stephanie Devoe
- Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Wei Gao
- Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States
- Biological Physics Laboratory, College of Science, Beijing Forestry University, Beijing, China
| | - H. Hamlet Chu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Yan Zhang
- Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States
| | - Wei Li
- Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States
| | - Wing Ki Wong
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | | | - David Neau
- Department of Chemistry and Chemical Biology, Northeastern Collaborative Access Team (NE-CAT), Advanced Photon Source, Argonne National Laboratory, Cornell University, Argonne, IL, United States
| | - Jill E. Slansky
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Ellen A. Robey
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Shaodong Dai
- Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
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5
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Towlerton AMH, Ravishankar S, Coffey DG, Puronen CE, Warren EH. Serial Analysis of the T-Cell Receptor β-Chain Repertoire in People Living With HIV Reveals Incomplete Recovery After Long-Term Antiretroviral Therapy. Front Immunol 2022; 13:879190. [PMID: 35585986 PMCID: PMC9108698 DOI: 10.3389/fimmu.2022.879190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Long-term antiretroviral therapy (ART) in people living with HIV (PLHIV) is associated with sustained increases in CD4+ T-cell count, but its effect on the peripheral blood T-cell repertoire has not been comprehensively evaluated. In this study, we performed serial profiling of the composition and diversity of the T-cell receptor β-chain (TRB) repertoire in 30 adults with HIV infection before and after the initiation of ART to define its long-term impact on the TRB repertoire. Serially acquired blood samples from 30 adults with HIV infection collected over a mean of 6 years (range, 1-12) years, with 1-4 samples collected before and 2-8 samples collected after the initiation of ART, were available for analysis. TRB repertoires were characterized via high-throughput sequencing of the TRB variable region performed on genomic DNA extracted from unsorted peripheral blood mononuclear cells. Additional laboratory and clinical metadata including serial measurements of HIV viral load and CD4+ T-cell count were available for all individuals in the cohort. A previously published control group of 189 TRB repertoires from peripheral blood samples of adult bone marrow transplant donors was evaluated for comparison. ART initiation in PLHIV was associated with a sustained reduction in viral load and a significant increase in TRB repertoire diversity. However, repertoire diversity in PLHIV remained significantly lower than in the control group even after long-term ART. The composition of TRB repertoires of PLHIV after ART also remained perturbed compared to the control cohort, as evidenced by large persistent private clonal expansions, reduced efficiency in the generation of TRB CDR3 amino acid sequences, and a narrower range of CDR3 lengths. Network analysis revealed an antigen-experienced structure in the TRB repertoire of PLHIV both before and after ART initiation that was quite distinct from the structure of control repertoires, with a slight shift toward a more naïve structure observed after ART initiation. Though we observe significant improvement in TRB repertoire diversity with durable viral suppression in PLHIV on long-term ART, the composition and structure of these repertoires remain significantly perturbed compared to the control cohort of adult bone marrow transplant donors.
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Affiliation(s)
- Andrea M. H. Towlerton
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Shashidhar Ravishankar
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - David G. Coffey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Division of Medical Oncology, University of Washington, Seattle, WA, United States
- Division of Hematology, University of Miami, Miami, FL, United States
| | - Camille E. Puronen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Division of Medical Oncology, University of Washington, Seattle, WA, United States
| | - Edus H. Warren
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Division of Medical Oncology, University of Washington, Seattle, WA, United States
- *Correspondence: Edus H. Warren,
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Eldershaw SA, Pearce H, Inman CF, Piper KP, Abbotts B, Stephens C, Nicol S, Croft W, Powell R, Begum J, Taylor G, Nunnick J, Walsh D, Sirovica M, Saddique S, Nagra S, Ferguson P, Moss P, Malladi R. DNA and modified vaccinia Ankara prime-boost vaccination generates strong CD8 + T cell responses against minor histocompatibility antigen HA-1. Br J Haematol 2021; 195:433-446. [PMID: 34046897 DOI: 10.1111/bjh.17495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 03/27/2021] [Indexed: 11/29/2022]
Abstract
Allogeneic immune responses underlie the graft-versus-leukaemia effect of stem cell transplantation, but disease relapse occurs in many patients. Minor histocompatibility antigen (mHAg) peptides mediate alloreactive T cell responses and induce graft-versus-leukaemia responses when expressed on patient haematopoietic tissue. We vaccinated nine HA-1-negative donors against HA-1 with a 'prime-boost' protocol of either two or three DNA 'priming' vaccinations prior to 'boost' with modified vaccinia Ankara (MVA). HA-1-specific CD8+ T cell responses were observed in seven donors with magnitude up to 1·5% of total CD8+ T cell repertoire. HA-1-specific responses peaked two weeks post-MVA challenge and were measurable in most donors after 12 months. HA-1-specific T cells demonstrated strong cytotoxic activity and lysed target cells with endogenous HA-1 protein expression. The pattern of T cell receptor (TCR) usage by HA-1-specific T cells revealed strong conservation of T cell receptor beta variable 7-9 (TRBV7-9) usage between donors. These findings describe one of the strongest primary peptide-specific CD8+ T cell responses yet recorded to a DNA-MVA prime-boost regimen and this may reflect the strong immunogenicity of mHAg peptides. Prime-boost vaccination in donors or patients may prove of substantial benefit in boosting graft-versus-leukaemia responses.
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MESH Headings
- Adult
- Aged
- Allografts
- Antigens, Neoplasm/immunology
- Cytotoxicity, Immunologic
- Epitopes/immunology
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor
- Graft vs Leukemia Effect/immunology
- HLA-A2 Antigen/immunology
- Hematopoietic Stem Cell Transplantation
- Humans
- Immunogenicity, Vaccine
- Immunologic Memory
- Male
- Middle Aged
- Minor Histocompatibility Antigens/immunology
- Oligopeptides/immunology
- Peptides/immunology
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- T-Lymphocytes, Cytotoxic/immunology
- Vaccination
- Vaccines, Attenuated
- Vaccines, DNA/immunology
- Vaccines, DNA/therapeutic use
- Vaccinia virus/immunology
- Viral Vaccines/immunology
- Viral Vaccines/therapeutic use
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Affiliation(s)
- Suzy A Eldershaw
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Birmingham, UK
| | - Hayden Pearce
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Birmingham, UK
| | - Charlotte F Inman
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Birmingham, UK
| | - Karen P Piper
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Birmingham, UK
| | - Ben Abbotts
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Birmingham, UK
| | - Christine Stephens
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Birmingham, UK
| | - Samantha Nicol
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Birmingham, UK
| | - Wayne Croft
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Birmingham, UK
| | - Richard Powell
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Birmingham, UK
| | - Jusnara Begum
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Birmingham, UK
| | - Graham Taylor
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Birmingham, UK
| | - Jane Nunnick
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | - Donna Walsh
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | - Mirjana Sirovica
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | - Shamyla Saddique
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | - Sandeep Nagra
- Department of Haematology, Birmingham Health Partners, Queen Elizabeth Hospital, Birmingham, UK
| | - Paul Ferguson
- Department of Haematology, Birmingham Health Partners, Queen Elizabeth Hospital, Birmingham, UK
| | - Paul Moss
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Birmingham, UK
- Department of Haematology, Birmingham Health Partners, Queen Elizabeth Hospital, Birmingham, UK
| | - Ram Malladi
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Birmingham, UK
- Department of Haematology, Birmingham Health Partners, Queen Elizabeth Hospital, Birmingham, UK
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8
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Liu S, Knochelmann HM, Lomeli SH, Hong A, Richardson M, Yang Z, Lim RJ, Wang Y, Dumitras C, Krysan K, Timmers C, Romeo MJ, Krieg C, O’Quinn EC, Horton JD, Dubinett SM, Paulos CM, Neskey DM, Lo RS. Response and recurrence correlates in individuals treated with neoadjuvant anti-PD-1 therapy for resectable oral cavity squamous cell carcinoma. Cell Rep Med 2021; 2:100411. [PMID: 34755131 PMCID: PMC8561238 DOI: 10.1016/j.xcrm.2021.100411] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/06/2021] [Accepted: 09/20/2021] [Indexed: 01/19/2023]
Abstract
Neoadjuvant PD-1 blockade may be efficacious in some individuals with high-risk, resectable oral cavity head and neck cancer. To explore correlates of response patterns to neoadjuvant nivolumab treatment and post-surgical recurrences, we analyzed longitudinal tumor and blood samples in a cohort of 12 individuals displaying 33% responsiveness. Pretreatment tumor-based detection of FLT4 mutations and PTEN signature enrichment favors response, and high tumor mutational burden improves recurrence-free survival. In contrast, preexisting and/or acquired mutations (in CDKN2A, YAP1, or JAK2) correlate with innate resistance and/or tumor recurrence. Immunologically, tumor response after therapy entails T cell receptor repertoire diversification in peripheral blood and intratumoral expansion of preexisting T cell clones. A high ratio of regulatory T to T helper 17 cells in pretreatment blood predicts low T cell receptor repertoire diversity in pretreatment blood, a low cytolytic T cell signature in pretreatment tumors, and innate resistance. Our study provides a molecular framework to advance neoadjuvant anti-PD-1 therapy for individuals with resectable head and neck cancer.
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MESH Headings
- Antineoplastic Agents, Immunological/therapeutic use
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/immunology
- Carcinoma, Squamous Cell/surgery
- Cyclin-Dependent Kinase Inhibitor p16/genetics
- Cyclin-Dependent Kinase Inhibitor p16/immunology
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Immune Checkpoint Inhibitors/therapeutic use
- Janus Kinase 2/genetics
- Janus Kinase 2/immunology
- Mouth Neoplasms/drug therapy
- Mouth Neoplasms/genetics
- Mouth Neoplasms/immunology
- Mouth Neoplasms/surgery
- Mutation
- Neoadjuvant Therapy/methods
- Neoplasm Recurrence, Local/drug therapy
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/immunology
- Neoplasm Recurrence, Local/surgery
- Nivolumab/therapeutic use
- PTEN Phosphohydrolase/genetics
- PTEN Phosphohydrolase/immunology
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Programmed Cell Death 1 Receptor/genetics
- Programmed Cell Death 1 Receptor/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Survival Analysis
- T-Lymphocytes, Regulatory/drug effects
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/pathology
- Th17 Cells/drug effects
- Th17 Cells/immunology
- Th17 Cells/pathology
- Treatment Outcome
- Vascular Endothelial Growth Factor Receptor-3/genetics
- Vascular Endothelial Growth Factor Receptor-3/immunology
- YAP-Signaling Proteins/genetics
- YAP-Signaling Proteins/immunology
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Affiliation(s)
- Sixue Liu
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hannah M. Knochelmann
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
- Division of Surgical Oncology, Department of Surgery, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shirley H. Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aayoung Hong
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mary Richardson
- Department of Pathology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Zhentao Yang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Raymond J. Lim
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yan Wang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Camelia Dumitras
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kostyantyn Krysan
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Martin J. Romeo
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Carsten Krieg
- Department of Immunology and Microbiology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Elizabeth C. O’Quinn
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Joshua D. Horton
- Department of Otolaryngology – Head and Neck Surgery, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Steve M. Dubinett
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chrystal M. Paulos
- Division of Surgical Oncology, Department of Surgery, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - David M. Neskey
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
- Department of Otolaryngology – Head and Neck Surgery, Medical University of South Carolina, Charleston, SC 29425, USA
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Roger S. Lo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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9
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Verhagen J, van der Meijden ED, Lang V, Kremer AE, Völkl S, Mackensen A, Aigner M, Kremer AN. Human CD4 + T cells specific for dominant epitopes of SARS-CoV-2 Spike and Nucleocapsid proteins with therapeutic potential. Clin Exp Immunol 2021; 205:363-378. [PMID: 34061349 PMCID: PMC8239517 DOI: 10.1111/cei.13627] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 05/21/2021] [Indexed: 12/13/2022] Open
Abstract
Since December 2019, Coronavirus disease-19 (COVID-19) has spread rapidly throughout the world, leading to a global effort to develop vaccines and treatments. Despite extensive progress, there remains a need for treatments to bolster the immune responses in infected immunocompromised individuals, such as cancer patients who recently underwent a haematopoietic stem cell transplantation. Immunological protection against COVID-19 is mediated by both short-lived neutralizing antibodies and long-lasting virus-reactive T cells. Therefore, we propose that T cell therapy may augment efficacy of current treatments. For the greatest efficacy with minimal adverse effects, it is important that any cellular therapy is designed to be as specific and directed as possible. Here, we identify T cells from COVID-19 patients with a potentially protective response to two major antigens of the SARS-CoV-2 virus, Spike and Nucleocapsid protein. By generating clones of highly virus-reactive CD4+ T cells, we were able to confirm a set of nine immunodominant epitopes and characterize T cell responses against these. Accordingly, the sensitivity of T cell clones for their specific epitope, as well as the extent and focus of their cytokine response was examined. Moreover, using an advanced T cell receptor (TCR) sequencing approach, we determined the paired TCR-αβ sequences of clones of interest. While these data on a limited population require further expansion for universal application, the results presented here form a crucial first step towards TCR-transgenic CD4+ T cell therapy of COVID-19.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Amino Acid Sequence
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/virology
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/virology
- COVID-19/immunology
- COVID-19/therapy
- COVID-19/virology
- Clone Cells/immunology
- Clone Cells/virology
- Coronavirus Nucleocapsid Proteins/chemistry
- Coronavirus Nucleocapsid Proteins/genetics
- Coronavirus Nucleocapsid Proteins/immunology
- Cytokines/biosynthesis
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Female
- Humans
- Immunization, Passive
- Immunodominant Epitopes/chemistry
- Immunodominant Epitopes/genetics
- Immunodominant Epitopes/immunology
- Male
- Middle Aged
- Phosphoproteins/chemistry
- Phosphoproteins/genetics
- Phosphoproteins/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- COVID-19 Serotherapy
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Affiliation(s)
- Johan Verhagen
- Department of Medicine 5, Haematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and University Hospital Erlangen, Erlangen, Germany
| | - Edith D van der Meijden
- Department of Medicine 5, Haematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and University Hospital Erlangen, Erlangen, Germany
| | - Vanessa Lang
- Department of Medicine 5, Haematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and University Hospital Erlangen, Erlangen, Germany
| | - Andreas E Kremer
- Department of Medicine 1, Gastroenterology, Pneumology and Endocrinology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and University Hospital Erlangen, Erlangen, Germany
| | - Simon Völkl
- Department of Medicine 5, Haematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and University Hospital Erlangen, Erlangen, Germany
| | - Andreas Mackensen
- Department of Medicine 5, Haematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and University Hospital Erlangen, Erlangen, Germany
| | - Michael Aigner
- Department of Medicine 5, Haematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and University Hospital Erlangen, Erlangen, Germany
| | - Anita N Kremer
- Department of Medicine 5, Haematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and University Hospital Erlangen, Erlangen, Germany
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10
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Moris P, De Pauw J, Postovskaya A, Gielis S, De Neuter N, Bittremieux W, Ogunjimi B, Laukens K, Meysman P. Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification. Brief Bioinform 2021; 22:bbaa318. [PMID: 33346826 PMCID: PMC8294552 DOI: 10.1093/bib/bbaa318] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The prediction of epitope recognition by T-cell receptors (TCRs) has seen many advancements in recent years, with several methods now available that can predict recognition for a specific set of epitopes. However, the generic case of evaluating all possible TCR-epitope pairs remains challenging, mainly due to the high diversity of the interacting sequences and the limited amount of currently available training data. In this work, we provide an overview of the current state of this unsolved problem. First, we examine appropriate validation strategies to accurately assess the generalization performance of generic TCR-epitope recognition models when applied to both seen and unseen epitopes. In addition, we present a novel feature representation approach, which we call ImRex (interaction map recognition). This approach is based on the pairwise combination of physicochemical properties of the individual amino acids in the CDR3 and epitope sequences, which provides a convolutional neural network with the combined representation of both sequences. Lastly, we highlight various challenges that are specific to TCR-epitope data and that can adversely affect model performance. These include the issue of selecting negative data, the imbalanced epitope distribution of curated TCR-epitope datasets and the potential exchangeability of TCR alpha and beta chains. Our results indicate that while extrapolation to unseen epitopes remains a difficult challenge, ImRex makes this feasible for a subset of epitopes that are not too dissimilar from the training data. We show that appropriate feature engineering methods and rigorous benchmark standards are required to create and validate TCR-epitope predictive models.
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MESH Headings
- Animals
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Humans
- Macaca mulatta
- Mice
- Models, Genetic
- Models, Immunological
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pieter Meysman
- Corresponding author: Pieter Meysman, Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, 2020, Belgium. E-mail:
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11
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Brown IK, Dyjack N, Miller MM, Krovi H, Rios C, Woolaver R, Harmacek L, Tu TH, O’Connor BP, Danhorn T, Vestal B, Gapin L, Pinilla C, Seibold MA, Scott-Browne J, Santos RG, Reinhardt RL. Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoire. PLoS Pathog 2021; 17:e1009602. [PMID: 34106992 PMCID: PMC8216541 DOI: 10.1371/journal.ppat.1009602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 06/21/2021] [Accepted: 05/01/2021] [Indexed: 12/30/2022] Open
Abstract
The CD4+ T cell response is critical to host protection against helminth infection. How this response varies across different hosts and tissues remains an important gap in our understanding. Using IL-4-reporter mice to identify responding CD4+ T cells to Nippostrongylus brasiliensis infection, T cell receptor sequencing paired with novel clustering algorithms revealed a broadly reactive and clonally diverse CD4+ T cell response. While the most prevalent clones and clonotypes exhibited some tissue selectivity, most were observed to reside in both the lung and lung-draining lymph nodes. Antigen-reactivity of the broader repertoires was predicted to be shared across both tissues and individual mice. Transcriptome, trajectory, and chromatin accessibility analysis of lung and lymph-node repertoires revealed three unique but related populations of responding IL-4+ CD4+ T cells consistent with T follicular helper, T helper 2, and a transitional population sharing similarity with both populations. The shared antigen reactivity of lymph node and lung repertoires combined with the adoption of tissue-specific gene programs allows for the pairing of cellular and humoral responses critical to the orchestration of anti-helminth immunity. Using various “omic” approaches, the CD4+ T cell receptor (TCR) repertoire was explored after primary helminth infection. Infection generated a broadly reactive and clonally diverse CD4+ T cell response with the most prevalent clonotypes and predicted antigen specificities residing in both the lung and lung-draining lymph nodes. Tissue-specific programming of responding CD4+ T cells directed the establishment of committed Tfh and Th2 cells, both critical for driving distinct hallmarks of type-2 inflammation. These datasets help to explore the diverse yet tissue-specific nature of anti-helminth immunity.
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Affiliation(s)
- Ivy K. Brown
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Nathan Dyjack
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Mindy M. Miller
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Harsha Krovi
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Cydney Rios
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Rachel Woolaver
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Laura Harmacek
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Ting-Hui Tu
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Brian P. O’Connor
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Pediatrics, National Jewish Health, Denver, Colorado, United States of America
| | - Thomas Danhorn
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Brian Vestal
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Laurent Gapin
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Clemencia Pinilla
- Florida International University, Port Saint Lucie, Florida, United States of America
| | - Max A. Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
- Department of Pediatrics, National Jewish Health, Denver, Colorado, United States of America
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - James Scott-Browne
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, United States of America
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Radleigh G. Santos
- Department of Mathematics, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
| | - R. Lee Reinhardt
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- * E-mail:
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12
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Moreews M, Le Gouge K, Khaldi-Plassart S, Pescarmona R, Mathieu AL, Malcus C, Djebali S, Bellomo A, Dauwalder O, Perret M, Villard M, Chopin E, Rouvet I, Vandenesh F, Dupieux C, Pouyau R, Teyssedre S, Guerder M, Louazon T, Moulin-Zinsch A, Duperril M, Patural H, Giovannini-Chami L, Portefaix A, Kassai B, Venet F, Monneret G, Lombard C, Flodrops H, De Guillebon JM, Bajolle F, Launay V, Bastard P, Zhang SY, Dubois V, Thaunat O, Richard JC, Mezidi M, Allatif O, Saker K, Dreux M, Abel L, Casanova JL, Marvel J, Trouillet-Assant S, Klatzmann D, Walzer T, Mariotti-Ferrandiz E, Javouhey E, Belot A. Polyclonal expansion of TCR Vbeta 21.3 + CD4 + and CD8 + T cells is a hallmark of Multisystem Inflammatory Syndrome in Children. Sci Immunol 2021; 6:eabh1516. [PMID: 34035116 PMCID: PMC8815705 DOI: 10.1126/sciimmunol.abh1516] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022]
Abstract
Multiple Inflammatory Syndrome in Children (MIS-C) is a delayed and severe complication of SARS-CoV-2 infection that strikes previously healthy children. As MIS-C combines clinical features of Kawasaki disease and Toxic Shock Syndrome (TSS), we aimed to compare the immunological profile of pediatric patients with these different conditions. We analyzed blood cytokine expression, and the T cell repertoire and phenotype in 36 MIS-C cases, which were compared to 16 KD, 58 TSS, and 42 COVID-19 cases. We observed an increase of serum inflammatory cytokines (IL-6, IL-10, IL-18, TNF-α, IFNγ, CD25s, MCP1, IL-1RA) in MIS-C, TSS and KD, contrasting with low expression of HLA-DR in monocytes. We detected a specific expansion of activated T cells expressing the Vβ21.3 T cell receptor β chain variable region in both CD4 and CD8 subsets in 75% of MIS-C patients and not in any patient with TSS, KD, or acute COVID-19; this correlated with the cytokine storm detected. The T cell repertoire returned to baseline within weeks after MIS-C resolution. Vβ21.3+ T cells from MIS-C patients expressed high levels of HLA-DR, CD38 and CX3CR1 but had weak responses to SARS-CoV-2 peptides in vitro. Consistently, the T cell expansion was not associated with specific classical HLA alleles. Thus, our data suggested that MIS-C is characterized by a polyclonal Vβ21.3 T cell expansion not directed against SARS-CoV-2 antigenic peptides, which is not seen in KD, TSS and acute COVID-19.
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Affiliation(s)
- Marion Moreews
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Kenz Le Gouge
- Sorbonne Université, UPMC Univ Paris 06, INSERM UMRS 959, Immunology Immunopathology-Immunotherapy (i3), Paris, France
| | - Samira Khaldi-Plassart
- (RAISE), France; Pediatric Nephrology, Rheumatology, Dermatology Unit, Hôpital Femme Mère Enfant, Hospices Civils de Lyon
- National Referee Centre for Rheumatic and AutoImmune and Systemic diseases in children
| | - Rémi Pescarmona
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- National Referee Centre for Rheumatic and AutoImmune and Systemic diseases in children
- Immunology Laboratory, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite
| | - Anne-Laure Mathieu
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.
| | - Christophe Malcus
- Hospices Civils de Lyon, Edouard Herriot Hospital, Immunology Laboratory, 69437 Lyon, France
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon - bioMérieux), Joint Research Unit HCL-bioMérieux, 69003, Lyon, France
| | - Sophia Djebali
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Alicia Bellomo
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Olivier Dauwalder
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Magali Perret
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Immunology Laboratory, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite
| | - Marine Villard
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Immunology Laboratory, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite
| | - Emilie Chopin
- Cellular Biotechnology Department and Biobank, Hospices Civils de Lyon, Lyon, France
| | - Isabelle Rouvet
- Cellular Biotechnology Department and Biobank, Hospices Civils de Lyon, Lyon, France
| | - Francois Vandenesh
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Céline Dupieux
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Robin Pouyau
- Réanimation Pédiatrique Hôpital Femme-Mère-Enfant Hospices Civils de Lyon, Bron, France
| | - Sonia Teyssedre
- Réanimation Pédiatrique Hôpital Femme-Mère-Enfant Hospices Civils de Lyon, Bron, France
| | - Margaux Guerder
- Réanimation Pédiatrique Hôpital Femme-Mère-Enfant Hospices Civils de Lyon, Bron, France
| | | | - Anne Moulin-Zinsch
- Unité medico-chirurgicale des cardiopathies congénitales, hôpital Louis-Pradel, hospices civils de Lyon, 69677 Bron, France
| | - Marie Duperril
- Pediatric intensive care unit - University hospital of Saint-Étienne, France
| | - Hugues Patural
- Pediatric intensive care unit - University hospital of Saint-Étienne, France
- U1059 INSERM - SAINBIOSE - DVH - Université de Saint-Étienne - 42055, France
| | - Lisa Giovannini-Chami
- Pediatric Pulmonology and Allergology Department, Hôpitaux pédiatriques de Nice CHU-Lenval, Nice, France
- Université Côte d'Azur, France
| | - Aurélie Portefaix
- Center of Clinical Investigation, Lyon University Hospital, Bron, France
| | - Behrouz Kassai
- Center of Clinical Investigation, Lyon University Hospital, Bron, France
| | - Fabienne Venet
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Hospices Civils de Lyon, Edouard Herriot Hospital, Immunology Laboratory, 69437 Lyon, France
| | - Guillaume Monneret
- Hospices Civils de Lyon, Edouard Herriot Hospital, Immunology Laboratory, 69437 Lyon, France
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon - bioMérieux), Joint Research Unit HCL-bioMérieux, 69003, Lyon, France
| | - Christine Lombard
- Immunology Laboratory, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite
| | - Hugues Flodrops
- Service de Pédiatrie, Groupe Hospitalier Sud Réunion, CHU de La Réunion, Saint Pierre, La Réunion, France
| | - Jean-Marie De Guillebon
- Service de Néphrologie, Rhumatologie pédiatrique, Hôpitaux pédiatriques de Nice CHU-Lenval, Nice, France
| | - Fanny Bajolle
- Hôpital Necker Enfants Malades, Centre de référence M3C, AP-HP, Paris, France
| | - Valérie Launay
- Urgences pédiatriques, Hôpital femme Mère Enfant, Hospices Civils de Lyon, Bron, France
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Valérie Dubois
- EFS Auvergne Rhône Alpes, laboratoire Histocompatibilité, 111, rue Elisée-Reclus, 69150 Décines, France
| | - Olivier Thaunat
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- EFS Auvergne Rhône Alpes, laboratoire Histocompatibilité, 111, rue Elisée-Reclus, 69150 Décines, France
- Department of Transplantation, Nephrology and Clinical Immunology, Edouard Herriot University Hospital, Lyon, France
- Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), 8, avenue Rockfeller, 69373, Lyon, France
| | - Jean-Christophe Richard
- Médecine Intensive-Réanimation, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
- Lyon University, France
| | - Mehdi Mezidi
- Médecine Intensive-Réanimation, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
- Lyon University, France
| | - Omran Allatif
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Kahina Saker
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Marlène Dreux
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, NY, USA
| | - Jacqueline Marvel
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Sophie Trouillet-Assant
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - David Klatzmann
- Sorbonne Université, UPMC Univ Paris 06, INSERM UMRS 959, Immunology Immunopathology-Immunotherapy (i3), Paris, France
- Assistance Publique - Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Biotherapy and Département Hospitalo-Universitaire Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
| | - Thierry Walzer
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Université, UPMC Univ Paris 06, INSERM UMRS 959, Immunology Immunopathology-Immunotherapy (i3), Paris, France
- Assistance Publique - Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Biotherapy and Département Hospitalo-Universitaire Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
| | - Etienne Javouhey
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon - bioMérieux), Joint Research Unit HCL-bioMérieux, 69003, Lyon, France
- Réanimation Pédiatrique Hôpital Femme-Mère-Enfant Hospices Civils de Lyon, Bron, France
| | - Alexandre Belot
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.
- Hospices Civils de Lyon, Edouard Herriot Hospital, Immunology Laboratory, 69437 Lyon, France
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13
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Porritt RA, Paschold L, Rivas MN, Cheng MH, Yonker LM, Chandnani H, Lopez M, Simnica D, Schultheiß C, Santiskulvong C, Van Eyk J, McCormick JK, Fasano A, Bahar I, Binder M, Arditi M. HLA class I-associated expansion of TRBV11-2 T cells in multisystem inflammatory syndrome in children. J Clin Invest 2021; 131:146614. [PMID: 33705359 PMCID: PMC8121516 DOI: 10.1172/jci146614] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/04/2021] [Indexed: 12/12/2022] Open
Abstract
Multisystem inflammatory syndrome in children (MIS-C), a hyperinflammatory syndrome associated with SARS-CoV-2 infection, shares clinical features with toxic shock syndrome, which is triggered by bacterial superantigens. Superantigen specificity for different Vβ chains results in Vβ skewing, whereby T cells with specific Vβ chains and diverse antigen specificity are overrepresented in the T cell receptor (TCR) repertoire. Here, we characterized the TCR repertoire of MIS-C patients and found a profound expansion of TCRβ variable gene 11-2 (TRBV11-2), with up to 24% of clonal T cell space occupied by TRBV11-2 T cells, which correlated with MIS-C severity and serum cytokine levels. Analysis of TRBJ gene usage and complementarity-determining region 3 (CDR3) length distribution of MIS-C expanded TRBV11-2 clones revealed extensive junctional diversity. Patients with TRBV11-2 expansion shared HLA class I alleles A02, B35, and C04, indicating what we believe is a novel mechanism for CDR3-independent T cell expansion. In silico modeling indicated that polyacidic residues in the Vβ chain encoded by TRBV11-2 (Vβ21.3) strongly interact with the superantigen-like motif of SARS-CoV-2 spike glycoprotein, suggesting that unprocessed SARS-CoV-2 spike may directly mediate TRBV11-2 expansion. Overall, our data indicate that a CDR3-independent interaction between SARS-CoV-2 spike and TCR leads to T cell expansion and possibly activation, which may account for the clinical presentation of MIS-C.
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Affiliation(s)
- Rebecca A. Porritt
- Departments of Pediatrics, Division of Infectious Diseases and Immunology, Infectious and Immunologic Diseases Research Center (IIDRC) and Department of Biomedical Sciences and
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lisa Paschold
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Magali Noval Rivas
- Departments of Pediatrics, Division of Infectious Diseases and Immunology, Infectious and Immunologic Diseases Research Center (IIDRC) and Department of Biomedical Sciences and
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lael M. Yonker
- Mucosal Immunology and Biology Research Center and Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Harsha Chandnani
- Department of Pediatrics, Loma Linda University Hospital, Loma Linda, California, USA
| | - Merrick Lopez
- Department of Pediatrics, Loma Linda University Hospital, Loma Linda, California, USA
| | - Donjete Simnica
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Christoph Schultheiß
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | | | - Jennifer Van Eyk
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - John K. McCormick
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Alessio Fasano
- Mucosal Immunology and Biology Research Center and Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Moshe Arditi
- Departments of Pediatrics, Division of Infectious Diseases and Immunology, Infectious and Immunologic Diseases Research Center (IIDRC) and Department of Biomedical Sciences and
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
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14
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McCarthy NE, Stagg AJ, Price CL, Mann ER, Gellatly NL, Al-Hassi HO, Knight SC, Panoskaltsis N. Patients with gastrointestinal irritability after TGN1412-induced cytokine storm displayed selective expansion of gut-homing αβ and γδT cells. Cancer Immunol Immunother 2021; 70:1143-1153. [PMID: 33048222 PMCID: PMC7552579 DOI: 10.1007/s00262-020-02723-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/11/2020] [Indexed: 12/17/2022]
Abstract
Following infusion of the anti-CD28 superagonist monoclonal antibody TGN1412, three of six previously healthy, young male recipients developed gastrointestinal irritability associated with increased expression of 'gut-homing' integrin β7 on peripheral blood αβT cells. This subset of patients with intestinal symptoms also displayed a striking and persistent expansion of putative Vδ2+ γδT cells in the circulation which declined over a 2-year period following drug infusion, concordant with subsiding gut symptoms. These data demonstrate that TGN1412-induced gastrointestinal symptoms were associated with dysregulation of the 'gut-homing' pool of blood αβ and γδT cells, induced directly by the antibody and/or arising from the subsequent cytokine storm.
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Affiliation(s)
- Neil E McCarthy
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, London, UK.
- Centre for Immunobiology, The Blizard Institute, Bart's and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Andrew J Stagg
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, London, UK
- Centre for Immunobiology, The Blizard Institute, Bart's and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Claire L Price
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, London, UK
- Lucid Group Communications, Buckinghamshire, UK
| | - Elizabeth R Mann
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, London, UK
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
| | - Nichola L Gellatly
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, London, UK
| | - Hafid O Al-Hassi
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, London, UK
- Research Institute in Healthcare Science, Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, UK
| | - Stella C Knight
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, London, UK
| | - Nicki Panoskaltsis
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, London, UK.
- Department of Haematology, Imperial College London, Northwick Park and St. Mark's Campus, London, UK.
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA.
- BioMedical Systems Engineering Laboratory, Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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15
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Cassotta A, Goldstein JD, Durini G, Jarrossay D, Baggi Menozzi F, Venditti M, Russo A, Falcone M, Lanzavecchia A, Gagliardi MC, Latorre D, Sallusto F. Broadly reactive human CD4 + T cells against Enterobacteriaceae are found in the naïve repertoire and are clonally expanded in the memory repertoire. Eur J Immunol 2021; 51:648-661. [PMID: 33226131 PMCID: PMC7986685 DOI: 10.1002/eji.202048630] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 09/15/2020] [Accepted: 11/19/2020] [Indexed: 12/13/2022]
Abstract
Enterobacteriaceae are a large family of Gram-negative bacteria that includes both commensals and opportunistic pathogens. The latter can cause severe nosocomial infections, with outbreaks of multi-antibiotics resistant strains, thus being a major public health threat. In this study, we report that Enterobacteriaceae-reactive memory Th cells were highly enriched in a CCR6+ CXCR3+ Th1*/17 cell subset and produced IFN-γ, IL-17A, and IL-22. This T cell subset was severely reduced in septic patients with K. pneumoniae bloodstream infection who also selectively lacked circulating K. pneumonie-reactive T cells. By combining heterologous antigenic stimulation, single cell cloning and TCR Vβ sequencing, we demonstrate that a large fraction of memory Th cell clones was broadly cross-reactive to several Enterobacteriaceae species. These cross-reactive Th cell clones were expanded in vivo and a large fraction of them recognized the conserved outer membrane protein A antigen. Interestingly, Enterobacteriaceae broadly cross-reactive T cells were also prominent among in vitro primed naïve T cells. Collectively, these data point to the existence of immunodominant T cell epitopes shared among different Enterobacteriaceae species and targeted by cross-reactive T cells that are readily found in the pre-immune repertoire and are clonally expanded in the memory repertoire.
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Affiliation(s)
- Antonino Cassotta
- Institute for Research in BiomedicineUniversità della Svizzera italianaBellinzonaSwitzerland
- Institute of MicrobiologyETH ZurichSwitzerland
| | - Jérémie D. Goldstein
- Institute for Research in BiomedicineUniversità della Svizzera italianaBellinzonaSwitzerland
| | - Greta Durini
- Institute for Research in BiomedicineUniversità della Svizzera italianaBellinzonaSwitzerland
| | - David Jarrossay
- Institute for Research in BiomedicineUniversità della Svizzera italianaBellinzonaSwitzerland
| | | | - Mario Venditti
- Department of Public Health and Infectious DiseasesSapienza University of RomeRomeItaly
| | - Alessandro Russo
- Department of Clinical and Experimental MedicineUniversity of PisaPisaItaly
| | - Marco Falcone
- Department of Clinical and Experimental MedicineUniversity of PisaPisaItaly
| | - Antonio Lanzavecchia
- Institute for Research in BiomedicineUniversità della Svizzera italianaBellinzonaSwitzerland
| | | | - Daniela Latorre
- Institute for Research in BiomedicineUniversità della Svizzera italianaBellinzonaSwitzerland
- Institute of MicrobiologyETH ZurichSwitzerland
| | - Federica Sallusto
- Institute for Research in BiomedicineUniversità della Svizzera italianaBellinzonaSwitzerland
- Institute of MicrobiologyETH ZurichSwitzerland
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16
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Kovalenko EI, Zvyagin IV, Streltsova MA, Mikelov AI, Erokhina SA, Telford WG, Sapozhnikov AM, Lebedev YB. Surface NKG2C Identifies Differentiated αβT-Cell Clones Expanded in Peripheral Blood. Front Immunol 2021; 11:613882. [PMID: 33664730 PMCID: PMC7921799 DOI: 10.3389/fimmu.2020.613882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/29/2020] [Indexed: 12/24/2022] Open
Abstract
T cells that express CD56 in peripheral blood of healthy humans represent a heterogeneous and poorly studied subset. In this work, we analyzed this subset for NKG2C expression. In both CD56+ and CD56- subsets most of the NKG2C+ T cells had a phenotype of highly differentiated CD8+ TEMRA cells. The CD56+NKG2C+ T cells also expressed a number of NK cell receptors, such as NKG2D, CD16, KIR2DL2/DL3, and maturation marker CD57 more often than the CD56-NKG2C+CD3+ cells. TCR β-chain repertoire of the CD3+CD56+NKG2C+ cell fraction was limited by the prevalence of one or several clonotypes which can be found within the most abundant clonotypes in total or CD8+ T cell fraction TCRβ repertoire. Thus, NKG2C expression in highly differentiated CD56+ T cells was associated with the most expanded αβ T cell clones. NKG2C+ T cells produced almost no IFN-γ in response to stimulation with HCMV pp65-derived peptides. This may be partially due to the high content of CD45RA+CD57+ cells in the fraction. CD3+NKG2C+ cells showed signs of activation, and the frequency of this T-cell subset in HCMV-positive individuals was positively correlated with the frequency of NKG2C+ NK cells that may imply a coordinated in a certain extent development of the NKG2C+ T and NK cell subsets under HCMV infection.
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Affiliation(s)
- Elena I. Kovalenko
- Department of Immunology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ivan V. Zvyagin
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Maria A. Streltsova
- Department of Immunology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Artem I. Mikelov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sofya A. Erokhina
- Department of Immunology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - William G. Telford
- Experimental Transplantation and Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Alexander M. Sapozhnikov
- Department of Immunology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Yury B. Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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17
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Smith AR, Alonso JA, Ayres CM, Singh NK, Hellman LM, Baker BM. Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner. Proc Natl Acad Sci U S A 2021; 118:e2018125118. [PMID: 33468649 PMCID: PMC7848747 DOI: 10.1073/pnas.2018125118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Presentation of peptides by class I MHC proteins underlies T cell immune responses to pathogens and cancer. The association between peptide binding affinity and immunogenicity has led to the engineering of modified peptides with improved MHC binding, with the hope that these peptides would be useful for eliciting cross-reactive immune responses directed toward their weak binding, unmodified counterparts. Increasing evidence, however, indicates that T cell receptors (TCRs) can perceive such anchor-modified peptides differently than wild-type (WT) peptides, although the scope of discrimination is unclear. We show here that even modifications at primary anchors that have no discernible structural impact can lead to substantially stronger or weaker T cell recognition depending on the TCR. Surprisingly, the effect of peptide anchor modification can be sensed by a TCR at regions distant from the site of modification, indicating a through-protein mechanism in which the anchor residue serves as an allosteric modulator for TCR binding. Our findings emphasize caution in the use and interpretation of results from anchor-modified peptides and have implications for how anchor modifications are accounted for in other circumstances, such as predicting the immunogenicity of tumor neoantigens. Our data also highlight an important need to better understand the highly tunable dynamic nature of class I MHC proteins and the impact this has on various forms of immune recognition.
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MESH Headings
- Allosteric Regulation
- Binding Sites
- Cloning, Molecular
- Crystallography, X-Ray
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/genetics
- HLA-A2 Antigen/immunology
- Humans
- Jurkat Cells
- Kinetics
- Models, Molecular
- Peptides/chemistry
- Peptides/genetics
- Peptides/immunology
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Engineering
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Th2 Cells/cytology
- Th2 Cells/immunology
- Thermodynamics
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Affiliation(s)
- Angela R Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Jesus A Alonso
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Nishant K Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Lance M Hellman
- Department of Physical and Life Sciences, Nevada State College, Henderson, NV 89002
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556;
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
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18
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Andreu-Ballester JC, Galindo-Regal L, Hidalgo-Coloma J, Cuéllar C, García-Ballesteros C, Hurtado C, Uribe N, del Carmen Martín M, Jiménez AI, López-Chuliá F, Llombart-Cussac A. Differences in circulating γδ T cells in patients with primary colon cancer and relation with prognostic factors. PLoS One 2020; 15:e0243545. [PMID: 33326443 PMCID: PMC7743935 DOI: 10.1371/journal.pone.0243545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/24/2020] [Indexed: 01/11/2023] Open
Abstract
Downregulation of the T cell system has been proposed as a mechanism to block immunity in colonic cancer (CC). However, little has been studied about circulating αβ and γδ T cells and their immunological status in newly diagnosed patients. The aim of this study was to characterize the αβ and γδ T cell subsets in peripheral blood of patients with CC matched with healthy volunteers. In this prospective case-control study, blood samples were obtained from 96 patients with newly diagnosed treatment-naïve infiltrating colonic adenocarcinoma and 48 healthy volunteers. Pathological report at surgery was obtained from all CC patients. A significant decrease in CD3+ γδ T cells and CD3+CD8+ γδ T cells (p<0.001) were observed in CC patients. Apoptosis was significantly increased in all conventional and both αβ and γδ T cell subsets in patients with CC vs healthy subjects. γδ T cells were decreased in peripheral blood of patients with microscopic infiltration in tissues, history of cancer and synchronous colon cancer (p < 0.05). IFN-γ was significantly reduced in CC patients compared to controls. Cytotoxic effector γδ T cells TEMRA (CD8 and CD56) are the proportionally most abundant T cells in peripheral blood of CC patients. Patients with CC present a deep downregulation in the systemic T-cell immunity. These variations are evident through all tumor stages and suggest that a deficiency in γδ T cell populations could be preventing control of tumor progression. This fact prove the role of immunomodulation on CC carcinogenesis.
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Affiliation(s)
| | | | - Julia Hidalgo-Coloma
- Department of Medical Oncology, Arnau de Vilanova University Hospital, València, Spain
| | - Carmen Cuéllar
- Faculty of Pharmacy, Department of Microbiology and Parasitology, Complutense University, Madrid, Spain
| | | | - Carolina Hurtado
- Faculty of Pharmacy, Laboratory of Parasitology, University San Pablo CEU, Madrid, Spain
| | - Natalia Uribe
- Department of General and Digestive Surgery, Arnau de Vilanova University Hospital, València, Spain
| | - María del Carmen Martín
- Department of General and Digestive Surgery, Arnau de Vilanova University Hospital, València, Spain
| | - Ana Isabel Jiménez
- Pathology Department, Arnau de Vilanova University Hospital, València, Spain
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19
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Smith NL, Nahrendorf W, Sutherland C, Mooney JP, Thompson J, Spence PJ, Cowan GJM. A Conserved TCRβ Signature Dominates a Highly Polyclonal T-Cell Expansion During the Acute Phase of a Murine Malaria Infection. Front Immunol 2020; 11:587756. [PMID: 33329568 PMCID: PMC7719809 DOI: 10.3389/fimmu.2020.587756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/27/2020] [Indexed: 01/31/2023] Open
Abstract
CD4+ αβ T-cells are key mediators of the immune response to a first Plasmodium infection, undergoing extensive activation and splenic expansion during the acute phase of an infection. However, the clonality and clonal composition of this expansion has not previously been described. Using a comparative infection model, we sequenced the splenic CD4+ T-cell receptor repertoires generated over the time-course of a Plasmodium chabaudi infection. We show through repeat replicate experiments, single-cell RNA-seq, and analyses of independent RNA-seq data, that following a first infection - within a highly polyclonal expansion - T-effector repertoires are consistently dominated by TRBV3 gene usage. Clustering by sequence similarity, we find the same dominant clonal signature is expanded across replicates in the acute phase of an infection, revealing a conserved pathogen-specific T-cell response that is consistently a hallmark of a first infection, but not expanded upon re-challenge. Determining the host or parasite factors driving this conserved response may uncover novel immune targets for malaria therapeutic purposes.
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Affiliation(s)
- Natasha L. Smith
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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20
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Poran A, Scherer J, Bushway ME, Besada R, Balogh KN, Wanamaker A, Williams RG, Prabhakara J, Ott PA, Hu-Lieskovan S, Khondker ZS, Gaynor RB, Rooney MS, Srinivasan L. Combined TCR Repertoire Profiles and Blood Cell Phenotypes Predict Melanoma Patient Response to Personalized Neoantigen Therapy plus Anti-PD-1. Cell Rep Med 2020; 1:100141. [PMID: 33294862 PMCID: PMC7691446 DOI: 10.1016/j.xcrm.2020.100141] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/02/2020] [Accepted: 10/22/2020] [Indexed: 01/15/2023]
Abstract
T cells use highly diverse receptors (TCRs) to identify tumor cells presenting neoantigens arising from genetic mutations and establish anti-tumor activity. Immunotherapy harnessing neoantigen-specific T cells to target tumors has emerged as a promising clinical approach. To assess whether a comprehensive peripheral mononuclear blood cell analysis predicts responses to a personalized neoantigen cancer vaccine combined with anti-PD-1 therapy, we characterize the TCR repertoires and T and B cell frequencies in 21 patients with metastatic melanoma who received this regimen. TCR-α/β-chain sequencing reveals that prolonged progression-free survival (PFS) is strongly associated with increased clonal baseline TCR repertoires and longitudinal repertoire stability. Furthermore, the frequencies of antigen-experienced T and B cells in the peripheral blood correlate with repertoire characteristics. Analysis of these baseline immune features enables prediction of PFS following treatment. This method offers a pragmatic clinical approach to assess patients’ immune state and to direct therapeutic decision making. Pre-treatment blood-based factors predict response to immunotherapy TCR repertoire clonality and stability associate with improved clinical outcomes Baseline T and B cell memory phenotypes associate with improved clinical outcomes Combined baseline TCR repertoire and PBMC phenotypes predict immunotherapy response
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Affiliation(s)
- Asaf Poran
- Neon Therapeutics/BioNTech US, Cambridge, MA, USA
- Corresponding author
| | | | | | - Rana Besada
- Neon Therapeutics/BioNTech US, Cambridge, MA, USA
| | | | | | | | | | - Patrick A. Ott
- Dana Farber Cancer Institute, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA, USA
| | - Siwen Hu-Lieskovan
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
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21
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Scharer CD, Fortner KA, Dragon JA, Tighe S, Boss JM, Budd RC. Selective DNA Demethylation Accompanies T Cell Homeostatic Proliferation and Gene Regulation in Lupus-Prone lpr Mice. Immunohorizons 2020; 4:679-687. [PMID: 33097564 PMCID: PMC8141279 DOI: 10.4049/immunohorizons.2000078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/06/2020] [Indexed: 11/19/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is characterized by increased DNA demethylation in T cells, although it is unclear whether this occurs primarily in a subset of SLE T cells. The process driving the DNA demethylation and the consequences on overall gene expression are also poorly understood and whether this represents a secondary consequence of SLE or a primary contributing factor. Lupus-prone lpr mice accumulate large numbers of T cells with age because of a mutation in Fas (CD95). The accumulating T cells include an unusual population of CD4-CD8-TCR-αβ+ (DN) T cells that arise from CD8+ precursors and are also found in human SLE. We have previously observed that T cell accumulation in lpr mice is due to dysregulation of T cell homeostatic proliferation, which parallels an increased expression of numerous genes in the DN subset, including several proinflammatory molecules and checkpoint blockers. We thus determined the DNA methylome in lpr DN T cells compared with their CD8+ precursors. Our findings show that DN T cells manifest discrete sites of extensive demethylation throughout the genome, and these sites correspond to the location of a large proportion of the upregulated genes. Thus, dysregulated homeostatic proliferation in lpr mice and consequent epigenetic alterations may be a contributing factor to lupus pathogenesis.
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Affiliation(s)
- Christopher D Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322;
| | - Karen A Fortner
- Vermont Center for Immunology and Infectious Diseases, Department of Medicine, University of Vermont Larner College of Medicine, Burlington, VT 05405; and
| | - Julie A Dragon
- Vermont Integrative Genomics Resource, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Scott Tighe
- Vermont Integrative Genomics Resource, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Jeremy M Boss
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322
| | - Ralph C Budd
- Vermont Center for Immunology and Infectious Diseases, Department of Medicine, University of Vermont Larner College of Medicine, Burlington, VT 05405; and
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22
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Jaini R, Loya MG, King AT, Thacker S, Sarn NB, Yu Q, Stark GR, Eng C. Germline PTEN mutations are associated with a skewed peripheral immune repertoire in humans and mice. Hum Mol Genet 2020; 29:2353-2364. [PMID: 32588888 PMCID: PMC7424751 DOI: 10.1093/hmg/ddaa118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/08/2020] [Accepted: 06/11/2020] [Indexed: 12/11/2022] Open
Abstract
Individuals with germline mutations in the gene encoding phosphatase and tensin homolog on chromosome ten (PTEN) are diagnosed with PTEN hamartoma tumor syndrome (PHTS) and are at high risk for developing breast, thyroid and other cancers and/or autoimmunity or neurodevelopmental issues including autism spectrum disorders. Although well recognized as a tumor suppressor, involvement of PTEN mutations in mediating such a diverse range of phenotypes indicates a more central involvement for PTEN in immunity than previously recognized. To address this, sequencing of the T-cell receptor variable-region β-chain was performed on peripheral blood from PHTS patients. Based on patient findings, we performed mechanistic studies in two Pten knock-in murine models, distinct from each other in cell compartment-specific predominance of Pten. We found that PTEN mutations in humans and mice are associated with a skewed T- and B-cell gene repertoire, characterized by increased prevalence of high-frequency clones. Immunological characterization showed that Pten mutants have increased B-cell proliferation and a proclivity towards increased T-cell reactivity upon Toll-like-receptor stimulation. Furthermore, decreases in nuclear but not cytoplasmic Pten levels associated with a reduction in expression of the autoimmune regulator (Aire), a critical mediator of central immune tolerance. Mechanistically, we show that nuclear PTEN most likely regulates Aire expression via its emerging role in splicing regulation. We conclude that germline disruption of PTEN, both in human and mouse, results in compromised central immune tolerance processes that may significantly impact individual stress responses and therefore predisposition to autoimmunity and cancer.
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MESH Headings
- Animals
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Cell Proliferation/genetics
- Disease Models, Animal
- Female
- Gene Knock-In Techniques
- Germ-Line Mutation/genetics
- Hamartoma Syndrome, Multiple/blood
- Hamartoma Syndrome, Multiple/genetics
- Hamartoma Syndrome, Multiple/immunology
- Hamartoma Syndrome, Multiple/pathology
- Humans
- Immune Tolerance/genetics
- Male
- Mice
- PTEN Phosphohydrolase/genetics
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- T-Lymphocytes/immunology
- T-Lymphocytes/pathology
- Toll-Like Receptors/genetics
- Toll-Like Receptors/immunology
- Transcription Factors/genetics
- AIRE Protein
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Affiliation(s)
- Ritika Jaini
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Germline High Risk Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Matthew G Loya
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Alexander T King
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Stetson Thacker
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Nicholas B Sarn
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Qi Yu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - George R Stark
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Germline High Risk Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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23
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Abstract
T cell receptor (TCR)-based adoptive T cell therapies (ACT) hold great promise for the treatment of cancer, as TCRs can cover a broad range of target antigens. Here we summarize basic, translational and clinical results that provide insight into the challenges and opportunities of TCR-based ACT. We review the characteristics of target antigens and conventional αβ-TCRs, and provide a summary of published clinical trials with TCR-transgenic T cell therapies. We discuss how synthetic biology and innovative engineering strategies are poised to provide solutions for overcoming current limitations, that include functional avidity, MHC restriction, and most importantly, the tumor microenvironment. We also highlight the impact of precision genome editing on the next iteration of TCR-transgenic T cell therapies, and the discovery of novel immune engineering targets. We are convinced that some of these innovations will enable the field to move TCR gene therapy to the next level.
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MESH Headings
- Biomedical Engineering
- Cell Engineering
- Cell- and Tissue-Based Therapy/adverse effects
- Cell- and Tissue-Based Therapy/methods
- Cell- and Tissue-Based Therapy/trends
- Gene Editing
- Genetic Therapy
- Humans
- Immunotherapy, Adoptive/adverse effects
- Immunotherapy, Adoptive/methods
- Immunotherapy, Adoptive/trends
- Lymphocyte Activation
- Molecular Targeted Therapy
- Neoplasms/genetics
- Neoplasms/immunology
- Neoplasms/therapy
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Safety
- Synthetic Biology
- T-Lymphocytes/immunology
- T-Lymphocytes/transplantation
- Translational Research, Biomedical
- Tumor Microenvironment/genetics
- Tumor Microenvironment/immunology
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Affiliation(s)
| | - Caroline Arber
- Department of oncology UNIL CHUV, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, 1015 Lausanne, Switzerland;
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24
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Li G, Li J, Zhang H, Zhang Y, Liu D, Hao Y, Han J, Du J, Zhu L, Zeng Y, Li B, Li R, Song C, Zhang F, Chen C, Zhao H, Zeng H. Partial recovery of disturbed V-J pairing profiles of T-cell receptor in people living with HIV receiving long-term antiretroviral therapy. Sci China Life Sci 2020; 64:152-161. [PMID: 32567004 PMCID: PMC7306449 DOI: 10.1007/s11427-020-1718-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/16/2020] [Indexed: 02/07/2023]
Abstract
Chronic human immunodeficiency virus (HIV) infection not only causes a gradual loss of CD4+ T cells but also leads to a disturbance of the T cell receptor (TCR) repertoire. In people living with HIV (PLWH), monitoring TCR repertoire is challenged by the inconsistency of complementarity determining region 3 (CDR3) and limited cell numbers in clinical samples. Thus, a quantitative method is necessary for monitoring the TCR repertoire in PLWH. We characterized the TCR V-J pairing profile of naïve and memory CD4+ T cells in healthy donors, HIV-infected antiretroviral therapy (ART)-naïve patients and long-term (over 5 years) ART-experienced patients by performing TCR sequencing. We developed a V-J index with 18 parameters which were subdivided into five categories (expression coverage, cumulative percentage of the top tenth percentile, diversity, intra-individual similarity and inter-individual similarity). In ART-naïve patients, 14 of the 18 parameters were significantly altered. Long-term ART recovered ten parameters. The four unrecovered parameters were related to inter-individual similarity. Therefore, these findings indicate that long-term ART could only partially recover TCR V-J pairs and introduce newly impacted V-J pairs. Moreover, these results provide new insights into the V-J pairing of the TCR and into the disturbance of TCR repertoire in HIV infection.
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MESH Headings
- Adult
- Anti-Retroviral Agents/therapeutic use
- CD4 Lymphocyte Count
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
- Female
- HIV Infections/drug therapy
- HIV Infections/genetics
- HIV Infections/immunology
- Humans
- Immunoglobulin Joining Region/genetics
- Immunoglobulin Joining Region/immunology
- Immunoglobulin Variable Region/genetics
- Immunoglobulin Variable Region/immunology
- Immunologic Memory/immunology
- Male
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Time Factors
- Young Adult
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Affiliation(s)
- Guoli Li
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Jiarui Li
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Henghui Zhang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Yu Zhang
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Di Liu
- Computational Virology Group, Center for Bacteria and Virus Resources and Application, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yu Hao
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Junyan Han
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Juan Du
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Liuluan Zhu
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Yongqin Zeng
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Bei Li
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Rui Li
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Chuan Song
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Fujie Zhang
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Chen Chen
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China.
| | - Hongxin Zhao
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
| | - Hui Zeng
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China.
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25
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Mayadev J, Zamarin D, Deng W, Lankes H, O'Cearbhaill R, Aghajanian CA, Schilder R. Anti-PD-L1 (atezolizumab) as an immune primer and concurrently with extended-field chemoradiotherapy for node-positive locally advanced cervical cancer. Int J Gynecol Cancer 2020; 30:701-704. [PMID: 31871115 PMCID: PMC7310564 DOI: 10.1136/ijgc-2019-001012] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND There is a lack of data exploring the use and optimal timing of immunotherapy and chemoradiation therapy (CRT) in node-positive cervical cancer. Further translational research into mechanisms of response and resistance to immunotherapy in advanced cervical cancer is warranted. PRIMARY OBJECTIVES To determine if sequencing of atezolizumab and CRT result in differential immune activation, as determined by clonal expansion of T cell receptor beta (TCRB) repertoires in peripheral blood on day 21. STUDY HYPOTHESIS There is a difference for clonal expansion of T cell receptor beta repertoires in the peripheral blood at day 21 between the priming and concurrent atezolizumab and CRT in Arm A vs the concurrent atezolizumab and CRT in Arm B. TRIAL DESIGN Locally advanced cervical cancer patients with lymph node-positive disease will be randomized on this open-label, randomized trial with two experimental arms. Arm A will get one dose of atezolizumab prior to cisplatin CRT, and then two subsequent doses of atezolizumab during the CRT, and Arm B will get three doses during CRT. Patients will be followed for 2 years to assess outcomes. MAJOR INCLUSION/EXCLUSION CRITERIA Patients must have histologically confirmed, newly diagnosed advanced cervical cancer (squamous cell carcinoma, adenocarcinoma, and adenosquamous cell carcinoma): FIGO 2009 clinical stages IB2/IIA with positive para-aortic nodes, or FIGO 2009 clinical stages IIB/IIIB/IVA with positive pelvic or para-aortic lymph nodes. Exclusion criteria include those who had a prior hysterectomy or lymph node dissection. PRIMARY ENDPOINTS Clonal expansion of TCRB) repertoires in peripheral blood on day 21. SAMPLE SIZE The sample size will be 40 patients. ESTIMATED DATES FOR COMPLETING ACCRUAL AND PRESENTING RESULTS We estimate accrual to finish by the summer of 2020 with presentation of results to follow in 2021. TRIAL REGISTRATION NCT03738228.
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Affiliation(s)
- Jyoti Mayadev
- Department of Radiation Medicine and Applied Sciences, University of California San Diego Medical Center, La Jolla, California, USA
| | - Dmitriy Zamarin
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Wei Deng
- Department of Biostatistics and Bioinformatics, NRG Oncology, Clinical Trial Development Division, Buffalo, New York, USA
| | - Heather Lankes
- Biopathology Center, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Roisin O'Cearbhaill
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Carol A Aghajanian
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Russell Schilder
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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26
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Gil A, Kamga L, Chirravuri-Venkata R, Aslan N, Clark F, Ghersi D, Luzuriaga K, Selin LK. Epstein-Barr Virus Epitope-Major Histocompatibility Complex Interaction Combined with Convergent Recombination Drives Selection of Diverse T Cell Receptor α and β Repertoires. mBio 2020; 11:e00250-20. [PMID: 32184241 PMCID: PMC7078470 DOI: 10.1128/mbio.00250-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 02/11/2020] [Indexed: 01/07/2023] Open
Abstract
Recognition modes of individual T cell receptors (TCRs) are well studied, but factors driving the selection of TCR repertoires from primary through persistent human virus infections are less well understood. Using deep sequencing, we demonstrate a high degree of diversity of Epstein-Barr virus (EBV)-specific clonotypes in acute infectious mononucleosis (AIM). Only 9% of unique clonotypes detected in AIM persisted into convalescence; the majority (91%) of unique clonotypes detected in AIM were not detected in convalescence and were seeming replaced by equally diverse "de novo" clonotypes. The persistent clonotypes had a greater probability of being generated than nonpersistent clonotypes due to convergence recombination of multiple nucleotide sequences to encode the same amino acid sequence, as well as the use of shorter complementarity-determining regions 3 (CDR3s) with fewer nucleotide additions (i.e., sequences closer to germ line). Moreover, the two most immunodominant HLA-A2-restricted EBV epitopes, BRLF1109 and BMLF1280, show highly distinct antigen-specific public (i.e., shared between individuals) features. In fact, TCRα CDR3 motifs played a dominant role, while TCRβ played a minimal role, in the selection of TCR repertoire to an immunodominant EBV epitope, BRLF1. This contrasts with the majority of previously reported repertoires, which appear to be selected either on TCRβ CDR3 interactions with peptide/major histocompatibility complex (MHC) or in combination with TCRα CDR3. Understanding of how TCR-peptide-MHC complex interactions drive repertoire selection can be used to develop optimal strategies for vaccine design or generation of appropriate adoptive immunotherapies for viral infections in transplant settings or for cancer.IMPORTANCE Several lines of evidence suggest that TCRα and TCRβ repertoires play a role in disease outcomes and treatment strategies during viral infections in transplant patients and in cancer and autoimmune disease therapy. Our data suggest that it is essential that we understand the basic principles of how to drive optimum repertoires for both TCR chains, α and β. We address this important issue by characterizing the CD8 TCR repertoire to a common persistent human viral infection (EBV), which is controlled by appropriate CD8 T cell responses. The ultimate goal would be to determine if the individuals who are infected asymptomatically develop a different TCR repertoire than those that develop the immunopathology of AIM. Here, we begin by doing an in-depth characterization of both CD8 T cell TCRα and TCRβ repertoires to two immunodominant EBV epitopes over the course of AIM, identifying potential factors that may be driving their selection.
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Affiliation(s)
- Anna Gil
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Larisa Kamga
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Nuray Aslan
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Fransenio Clark
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Dario Ghersi
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Katherine Luzuriaga
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Liisa K Selin
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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27
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Singh NK, Abualrous ET, Ayres CM, Noé F, Gowthaman R, Pierce BG, Baker BM. Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen. Proteins 2020; 88:503-513. [PMID: 31589793 PMCID: PMC6982585 DOI: 10.1002/prot.25829] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/08/2019] [Accepted: 09/17/2019] [Indexed: 11/11/2022]
Abstract
Recognition of antigenic peptides bound to major histocompatibility complex (MHC) proteins by αβ T cell receptors (TCRs) is a hallmark of T cell mediated immunity. Recent data suggest that variations in TCR binding geometry may influence T cell signaling, which could help explain outliers in relationships between physical parameters such as TCR-pMHC binding affinity and T cell function. Traditionally, TCR binding geometry has been described with simple descriptors such as the crossing angle, which quantifies what has become known as the TCR's diagonal binding mode. However, these descriptors often fail to reveal distinctions in binding geometry that are apparent through visual inspection. To provide a better framework for relating TCR structure to T cell function, we developed a comprehensive system for quantifying the geometries of how TCRs bind peptide/MHC complexes. We show that our system can discern differences not clearly revealed by more common methods. As an example of its potential to impact biology, we used it to reveal differences in how TCRs bind class I and class II peptide/MHC complexes, which we show allow the TCR to maximize access to and "read out" the peptide antigen. We anticipate our system will be of use in not only exploring these and other details of TCR-peptide/MHC binding interactions, but also addressing questions about how TCR binding geometry relates to T cell function, as well as modeling structural properties of class I and class II TCR-peptide/MHC complexes from sequence information. The system is available at https://tcr3d.ibbr.umd.edu/tcr_com or for download as a script.
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MESH Headings
- Binding Sites
- Crystallography, X-Ray
- Histocompatibility Antigens Class I/chemistry
- Histocompatibility Antigens Class I/immunology
- Histocompatibility Antigens Class I/metabolism
- Histocompatibility Antigens Class II/chemistry
- Histocompatibility Antigens Class II/immunology
- Histocompatibility Antigens Class II/metabolism
- Humans
- Models, Molecular
- Principal Component Analysis
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocytes/chemistry
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Thermodynamics
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Affiliation(s)
- Nishant K. Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Esam T. Abualrous
- Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Frank Noé
- Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Ragul Gowthaman
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Brian G. Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
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28
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Hahn AM, Winkler TH. Resolving the mystery-How TCR transgenic mouse models shed light on the elusive case of gamma delta T cells. J Leukoc Biol 2020; 107:993-1007. [PMID: 32068302 DOI: 10.1002/jlb.1mr0120-237r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/08/2020] [Accepted: 01/20/2020] [Indexed: 12/22/2022] Open
Abstract
Cutting-edge questions in αβ T cell biology were addressed by investigating a range of different genetically modified mouse models. In comparison, the γδ T cell field lacks behind on the availability of such models. Nevertheless, transgenic mouse models proved useful for the investigation of γδ T cell biology and their stepwise development in the thymus. In general, animal models and especially mouse models give access to a wide range of opportunities of modulating γδ T cells, which is unachievable in human beings. Because of their complex biology and specific tissue tropism, it is especially challenging to investigate γδ T cells in in vitro experiments since they might not reliably reflect their behavior and phenotype under physiologic conditions. This review aims to provide a comprehensive historical overview about how different transgenic mouse models contributed in regards of the understanding of γδ T cell biology, whereby a special focus is set on studies including the elusive role of the γδTCR. Furthermore, evolutionary and translational remarks are discussed under the aspect of future implications for the field. The ultimate full understanding of γδ T cells will pave the way for their usage as a powerful new tool in immunotherapy.
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MESH Headings
- Animals
- Cell Differentiation
- Cell Lineage/genetics
- Cell Lineage/immunology
- Cell Movement
- Founder Effect
- Gene Expression
- Humans
- Immunotherapy/methods
- Mice
- Mice, Transgenic/genetics
- Mice, Transgenic/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Signal Transduction
- Species Specificity
- T-Lymphocytes/classification
- T-Lymphocytes/cytology
- T-Lymphocytes/immunology
- Thymus Gland/cytology
- Thymus Gland/immunology
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Affiliation(s)
- Anne M Hahn
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen, Germany
| | - Thomas H Winkler
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen, Germany
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29
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Ruiter B, Smith NP, Monian B, Tu AA, Fleming E, Virkud YV, Patil SU, Whittaker CA, Love JC, Shreffler WG. Expansion of the CD4 + effector T-cell repertoire characterizes peanut-allergic patients with heightened clinical sensitivity. J Allergy Clin Immunol 2020; 145:270-282. [PMID: 31654649 PMCID: PMC6949413 DOI: 10.1016/j.jaci.2019.09.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/06/2019] [Accepted: 09/06/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Individuals with peanut allergy range in clinical sensitivity: some can consume grams of peanut before experiencing any symptoms, whereas others suffer systemic reactions to 10 mg or less. Current diagnostic testing only partially predicts this clinical heterogeneity. OBJECTIVE We sought to identify characteristics of the peanut-specific CD4+ T-cell response in peanut-allergic patients that correlate with high clinical sensitivity. METHODS We studied the T-cell receptor β-chain (TCRβ) usage and phenotypes of peanut-activated, CD154+ CD4+ memory T cells using fluorescence-activated cell sorting, TCRβ sequencing, and RNA-Seq, in reactive and hyporeactive patients who were stratified by clinical sensitivity. RESULTS TCRβ analysis of the CD154+ and CD154- fractions revealed more than 6000 complementarity determining region 3 sequences and motifs that were significantly enriched in the activated cells and 17% of the sequences were shared between peanut-allergic individuals, suggesting strong convergent selection of peanut-specific clones. These clones were more numerous among the reactive patients, and this expansion was identified within effector, but not regulatory T-cell populations. The transcriptional profile of CD154+ T cells in the reactive group skewed toward a polarized TH2 effector phenotype, and expression of TH2 cytokines strongly correlated with peanut-specific IgE levels. There were, however, also non-TH2-related differences in phenotype. Furthermore, the ratio of peanut-specific clones in the effector versus regulatory T-cell compartment, which distinguished the clinical groups, was independent of specific IgE concentration. CONCLUSIONS Expansion of the peanut-specific effector T-cell repertoire is correlated with clinical sensitivity, and this observation may be useful to inform our assessment of disease phenotype and to monitor disease longitudinally.
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Affiliation(s)
- Bert Ruiter
- Center for Immunology & Inflammatory Diseases, Massachusetts General Hospital, Boston, Mass; Harvard Medical School, Boston, Mass.
| | - Neal P Smith
- Center for Immunology & Inflammatory Diseases, Massachusetts General Hospital, Boston, Mass
| | - Brinda Monian
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Mass
| | - Ang A Tu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Mass
| | - Elizabeth Fleming
- Center for Immunology & Inflammatory Diseases, Massachusetts General Hospital, Boston, Mass
| | - Yamini V Virkud
- Center for Immunology & Inflammatory Diseases, Massachusetts General Hospital, Boston, Mass; Harvard Medical School, Boston, Mass; Food Allergy Center, Massachusetts General Hospital, Boston, Mass
| | - Sarita U Patil
- Center for Immunology & Inflammatory Diseases, Massachusetts General Hospital, Boston, Mass; Harvard Medical School, Boston, Mass; Food Allergy Center, Massachusetts General Hospital, Boston, Mass
| | - Charles A Whittaker
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Mass; The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility in the Swanson Biotechnology Center, Massachusetts Institute of Technology, Cambridge, Mass
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Mass
| | - Wayne G Shreffler
- Center for Immunology & Inflammatory Diseases, Massachusetts General Hospital, Boston, Mass; Harvard Medical School, Boston, Mass; Food Allergy Center, Massachusetts General Hospital, Boston, Mass
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30
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Kamga L, Gil A, Song I, Brody R, Ghersi D, Aslan N, Stern LJ, Selin LK, Luzuriaga K. CDR3α drives selection of the immunodominant Epstein Barr virus (EBV) BRLF1-specific CD8 T cell receptor repertoire in primary infection. PLoS Pathog 2019; 15:e1008122. [PMID: 31765434 PMCID: PMC6901265 DOI: 10.1371/journal.ppat.1008122] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/09/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
The T cell receptor (TCR) repertoire is an essential component of the CD8 T-cell immune response. Here, we seek to investigate factors that drive selection of TCR repertoires specific to the HLA-A2-restricted immunodominant epitope BRLF1109-117 (YVLDHLIVV) over the course of primary Epstein Barr virus (EBV) infection. Using single-cell paired TCRαβ sequencing of tetramer sorted CD8 T cells ex vivo, we show at the clonal level that recognition of the HLA-A2-restricted BRLF1 (YVL-BR, BRLF-1109) epitope is mainly driven by the TCRα chain. For the first time, we identify a CDR3α (complementarity determining region 3 α) motif, KDTDKL, resulting from an obligate AV8.1-AJ34 pairing that was shared by all four individuals studied. This observation coupled with the fact that this public AV8.1-KDTDKL-AJ34 TCR pairs with multiple different TCRβ chains within the same donor (median 4; range: 1–9), suggests that there are some unique structural features of the interaction between the YVL-BR/MHC and the AV8.1-KDTDKL-AJ34 TCR that leads to this high level of selection. Newly developed TCR motif algorithms identified a lysine at position 1 of the CDR3α motif that is highly conserved and likely important for antigen recognition. Crystal structure analysis of the YVL-BR/HLA-A2 complex revealed that the MHC-bound peptide bulges at position 4, exposing a negatively charged aspartic acid that may interact with the positively charged lysine of CDR3α. TCR cloning and site-directed mutagenesis of the CDR3α lysine ablated YVL-BR-tetramer staining and substantially reduced CD69 upregulation on TCR mutant-transduced cells following antigen-specific stimulation. Reduced activation of T cells expressing this CDR3 motif was also observed following exposure to mutated (D4A) peptide. In summary, we show that a highly public TCR repertoire to an immunodominant epitope of a common human virus is almost completely selected on the basis of CDR3α and provide a likely structural basis for the selection. These studies emphasize the importance of examining TCRα, as well as TCRβ, in understanding the CD8 T cell receptor repertoire. EBV is a ubiquitous human virus that has been linked to several diseases, including cancers and post-transplant lymphoproliferative disorders. CD8 T cells are important for controlling EBV replication. Generation and maintenance of virus-specific CD8 T cells is dependent on specific interaction between MHC-peptide complexes on the infected cell and the TCR. In this study, we performed single cell sequencing of paired TCR α and β chains from EBV-specific CD8 T cells isolated at two time points (primary infection and convalescence) from four individuals undergoing acute EBV infection. We describe a TCRα sequence that was shared by all four individuals and identify conserved residues within this sequence that likely contribute to viral recognition. Examination of the crystal structure of the peptide-MHC complex and subsequent experimental data suggest that a specific interaction between a negatively charged aspartic acid at position 4 of the peptide and a positively charged lysine in the TCR may be particularly important. These findings are highly relevant to current efforts to understand how the TCR repertoire may contribute to or protect against disease, the development of TCR diagnostics for diseases, and at improving the efficacy of T cell based therapies.
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MESH Headings
- Amino Acid Sequence
- CD8-Positive T-Lymphocytes/immunology
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
- Complementarity Determining Regions/metabolism
- Epitopes, T-Lymphocyte/immunology
- Epstein-Barr Virus Infections/immunology
- Epstein-Barr Virus Infections/virology
- HLA-A2 Antigen/immunology
- Herpesvirus 4, Human/immunology
- Humans
- Immediate-Early Proteins/genetics
- Immediate-Early Proteins/immunology
- Immediate-Early Proteins/metabolism
- Immunodominant Epitopes/immunology
- Peptide Fragments/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocytes, Cytotoxic/immunology
- Trans-Activators/genetics
- Trans-Activators/immunology
- Trans-Activators/metabolism
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Affiliation(s)
- Larisa Kamga
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Anna Gil
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Inyoung Song
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Robin Brody
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Dario Ghersi
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Nebraska, United States of America
| | - Nuray Aslan
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Lawrence J. Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Liisa K. Selin
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (LKS); (KL)
| | - Katherine Luzuriaga
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (LKS); (KL)
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31
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Flores C, Wildes T, Dean BD, Moore G, Drake J, Abraham R, Gil J, Yegorov O, Yang C, Dean J, Moneypenny C, Shin D, Pham C, Krauser J, King J, Grant G, Driscoll T, Kurtzberg J, McLendon R, Gururangan S, Mitchell D. Massive clonal expansion of medulloblastoma-specific T cells during adoptive cellular therapy. Sci Adv 2019; 5:eaav9879. [PMID: 31807694 PMCID: PMC6881165 DOI: 10.1126/sciadv.aav9879] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 09/17/2019] [Indexed: 05/04/2023]
Abstract
In both human and murine systems, we have developed an adoptive cellular therapy platform against medulloblastoma and glioblastoma that uses dendritic cells pulsed with a tumor RNA transcriptome to expand polyclonal tumor-reactive T cells against a plurality of antigens within heterogeneous brain tumors. We demonstrate that peripheral TCR Vβ repertoire analysis after adoptive cellular therapy reveals that effective response to adoptive cellular therapy is concordant with massive in vivo expansion and persistence of tumor-specific T cell clones within the peripheral blood. In preclinical models of medulloblastoma and glioblastoma, and in a patient with relapsed medulloblastoma receiving adoptive cellular therapy, an early and massive expansion of tumor-reactive lymphocytes, coupled with prolonged persistence in the peripheral blood, is observed during effective therapeutic response to immunotherapy treatment.
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Affiliation(s)
- C. Flores
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - T. Wildes
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - B. DiVita Dean
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - G. Moore
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - J. Drake
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - R. Abraham
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - J. Gil
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - O. Yegorov
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - C. Yang
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - J. Dean
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - C. Moneypenny
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - D. Shin
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
- U.S. Army, 1600 Spearhead Division Ave., Fort Knox, KY, USA
| | - C. Pham
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - J. Krauser
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - J. King
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - G. Grant
- Department of Neurosurgery, Stanford University Medical Center, Palo Alto, CA, USA
| | - T. Driscoll
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - J. Kurtzberg
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - R. McLendon
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - S. Gururangan
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
- Department of Pediatrics, University of Florida, Gainesville, FL, USA
| | - D. Mitchell
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
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32
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Dembic Z. On integrity in immunity during ontogeny or how thymic regulatory T cells work. Scand J Immunol 2019; 90:e12806. [PMID: 31276223 DOI: 10.1111/sji.12806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 12/14/2022]
Abstract
The Standard model of T cell recognition asserts that T cell receptor (TCR) specificities are positively and negatively selected during ontogeny in the thymus and that peripheral T cell repertoire has mild self-major histocompatibility complex (MHC) reactivity, known as MHC restriction of foreign antigen. Thus, the TCR must bind both a restrictive molecule (MHC allele) and a peptide reclining in its groove (pMHC ligand) in order to transmit signal into a T cell. The Standard and Cohn's Tritope models suggest contradictory roles for complementarity-determining regions (CDRs) of the TCRs. Here, I discuss both concepts and propose a different solution to ontogenetic mechanism for TCR-MHC-conserved interaction. I suggest that double (CD4+ CD8+ )-positive (DP) developing thymocytes compete with their αβTCRs for binding to self-pMHC on cortical thymic epithelial cells (cTECs) that present a selected set of tissue-restricted antigens. The competition between DPs involves TCR editing and secondary rearrangements, similar to germinal-centre B cell somatic hypermutation. These processes would generate cells with higher TCR affinity for self-pMHC, facilitating sufficiently long binding to cTECs to become thymic T regulatory cells (tTregs). Furthermore, CD4+ Foxp3+ tTregs can be generated by mTECs via Aire-dependent and Aire-independent pathways, and additionally on thymic bone marrow-derived APCs including thymic Aire-expressing B cells. Thymic Tregs differ from the induced peripheral Tregs, which comprise the negative feedback loop to restrain immune responses. The implication of thymocytes' competition for the highest binding to self-pMHC is the co-evolution of species-specific αβTCR V regions with MHC alleles.
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Affiliation(s)
- Zlatko Dembic
- Department of Oral Biology, University of Oslo, Oslo, Norway
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33
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Cebula A, Kuczma M, Szurek E, Pietrzak M, Savage N, Elhefnawy WR, Rempala G, Kraj P, Ignatowicz L. Dormant pathogenic CD4 + T cells are prevalent in the peripheral repertoire of healthy mice. Nat Commun 2019; 10:4882. [PMID: 31653839 PMCID: PMC6814812 DOI: 10.1038/s41467-019-12820-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/25/2019] [Indexed: 01/09/2023] Open
Abstract
Thymic central tolerance eliminates most immature T cells with autoreactive T cell receptors (TCR) that recognize self MHC/peptide complexes. Regardless, an unknown number of autoreactive CD4+Foxp3- T cells escape negative selection and in the periphery require continuous suppression by CD4+Foxp3+ regulatory cells (Tregs). Here, we compare immune repertoires of Treg-deficient and Treg-sufficient mice to find Tregs continuously constraining one-third of mature CD4+Foxp3- cells from converting to pathogenic effectors in healthy mice. These dormant pathogenic clones frequently express TCRs activatable by ubiquitous autoantigens presented by class II MHCs on conventional dendritic cells, including self-peptides that select them in the thymus. Our data thus suggest that identification of most potentially autoreactive CD4+ T cells in the peripheral repertoire is critical to harness or redirect these cells for therapeutic advantage.
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Affiliation(s)
- Anna Cebula
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Michal Kuczma
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Edyta Szurek
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Maciej Pietrzak
- Mathematical Biosciences Institute, Ohio State University, Columbus, OH, USA
| | - Natasha Savage
- Department of Pathology, Augusta University, Augusta, GA, USA
| | - Wessam R Elhefnawy
- Department of Computer Science, Old Dominion University, Norfolk, VA, USA
| | - Grzegorz Rempala
- Mathematical Biosciences Institute, Ohio State University, Columbus, OH, USA
| | - Piotr Kraj
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | - Leszek Ignatowicz
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
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34
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Abstract
Modulating unconventional antigen presentation could treat infections and cancer
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Affiliation(s)
- Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands.
| | - Simone A Joosten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
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35
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Aris M, Bravo AI, Garcia Alvarez HM, Carri I, Podaza E, Blanco PA, Rotondaro C, Bentivegna S, Nielsen M, Barrio MM, Mordoh J. Immunization With the CSF-470 Vaccine Plus BCG and rhGM-CSF Induced in a Cutaneous Melanoma Patient a TCRβ Repertoire Found at Vaccination Site and Tumor Infiltrating Lymphocytes That Persisted in Blood. Front Immunol 2019; 10:2213. [PMID: 31620131 PMCID: PMC6759869 DOI: 10.3389/fimmu.2019.02213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 09/02/2019] [Indexed: 12/31/2022] Open
Abstract
The CSF-470 cellular vaccine plus BCG and rhGM-CSF increased distant metastases-free survival in cutaneous melanoma patients stages IIB-IIC-III relative to medium dose IFN-α2b (CASVAC-0401 study). Patient-045 developed a mature vaccination site (VAC-SITE) and a regional cutaneous metastasis (C-MTS), which were excised during the protocol, remaining disease-free 36 months from vaccination start. CDR3-TCRβ repertoire sequencing in PBMC and tissue samples, along with skin-DTH score and IFN-γ ELISPOT assay, were performed to analyze the T-cell immune response dynamics throughout the immunization protocol. Histopathological analysis of the VAC-SITE revealed a highly-inflamed granulomatous structure encircled by CD11c+ nested-clusters, brisk CD8+ and scarce FOXP3+, lymphocytes with numerous Langhans multinucleated-giant-cells and macrophages. A large tumor-regression area fulfilled the C-MTS with brisk lymphocyte infiltration, mainly composed of CD8+PD1+ T-cells, CD20+ B-cells, and scarce FOXP3+ cells. Increasing DTH score and IFN-γ ELISPOT assay signal against the CSF-470 vaccine-lysate was evidenced throughout immunization. TCRβ repertoire analysis revealed for the first time the presence of common clonotypes between a VAC-SITE and a C-MTS; most of them persisted in blood by the end of the immunization protocol. In vitro boost with vaccine-lysate revealed the expansion of persistent clones that infiltrated the VAC-SITE and/or the C-MTS; other persistent clones expanded in the patient's blood as well. We propose that expansion of such persistent clonotypes might derive from two different although complementary mechanisms: the proliferation of specific clones as well as the expansion of redundant clones, which increased the number of nucleotide rearrangements per clonotype, suggesting a functional antigenic selection. In this patient, immunization with the CSF-470 vaccine plus BCG and rhGM-CSF induced a T-cell repertoire at the VAC-SITE that was able to infiltrate an emerging C-MTS, which resulted in the expansion of a T-cell repertoire that persisted in blood by the end of the 2-year treatment.
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Affiliation(s)
- Mariana Aris
- Centro de Investigaciones Oncológicas-Fundación Cáncer, Buenos Aires, Argentina
| | - Alicia Inés Bravo
- Unidad de Inmunopatología, Hospital Interzonal General de Agudos Eva Perón, Buenos Aires, Argentina
| | | | | | - Enrique Podaza
- Centro de Investigaciones Oncológicas-Fundación Cáncer, Buenos Aires, Argentina
| | | | | | - Sofia Bentivegna
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Morten Nielsen
- IIBIO-UNSAM, Buenos Aires, Argentina
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | - José Mordoh
- Centro de Investigaciones Oncológicas-Fundación Cáncer, Buenos Aires, Argentina
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
- Instituto Alexander Fleming, Buenos Aires, Argentina
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36
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Kudo Y, Haymaker C, Zhang J, Reuben A, Duose DY, Fujimoto J, Roy-Chowdhuri S, Solis Soto LM, Dejima H, Parra ER, Mino B, Abraham R, Ikeda N, Vaporcyan A, Gibbons D, Zhang J, Lang FF, Luthra R, Lee JJ, Moran C, Huse JT, Kadara H, Wistuba II. Suppressed immune microenvironment and repertoire in brain metastases from patients with resected non-small-cell lung cancer. Ann Oncol 2019; 30:1521-1530. [PMID: 31282941 PMCID: PMC6771224 DOI: 10.1093/annonc/mdz207] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The tumor immune microenvironment (TIME) of lung cancer brain metastasis is largely unexplored. We carried out immune profiling and sequencing analysis of paired resected primary tumors and brain metastases of non-small-cell lung carcinoma (NSCLC). PATIENTS AND METHODS TIME profiling of archival formalin-fixed and paraffin-embedded specimens of paired primary tumors and brain metastases from 39 patients with surgically resected NSCLCs was carried out using a 770 immune gene expression panel and by T-cell receptor beta repertoire (TCRβ) sequencing. Immunohistochemistry was carried out for validation. Targeted sequencing was carried out to catalog hot spot mutations in cancer genes. RESULTS Somatic hot spot mutations were mostly shared between both tumor sites (28/39 patients; 71%). We identified 161 differentially expressed genes, indicating inhibition of dendritic cell maturation, Th1, and leukocyte extravasation signaling pathways, in brain metastases compared with primary tumors (P < 0.01). The proinflammatory cell adhesion molecule vascular cell adhesion protein 1 was significantly suppressed in brain metastases compared with primary tumors. Brain metastases exhibited lower T cell and elevated macrophage infiltration compared with primary tumors (P < 0.001). T-cell clones were expanded in 64% of brain metastases compared with their corresponding primary tumors. Furthermore, while TCR repertoires were largely shared between paired brain metastases and primary tumors, T-cell densities were sparse in the metastases. CONCLUSION We present findings that suggest that the TIME in brain metastases from NSCLC is immunosuppressed and comprises immune phenotypes (e.g. immunosuppressive tumor-associated macrophages) that may help guide immunotherapeutic strategies for NSCLC brain metastases.
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MESH Headings
- Adult
- Aged
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/immunology
- Brain Neoplasms/immunology
- Brain Neoplasms/pathology
- Brain Neoplasms/secondary
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/surgery
- Dendritic Cells/immunology
- Female
- Gene Expression Regulation, Neoplastic/immunology
- Humans
- Immunohistochemistry
- Male
- Middle Aged
- Mutation/genetics
- Neoplasm Proteins/genetics
- Neoplasm Proteins/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Tumor Microenvironment/genetics
- Tumor Microenvironment/immunology
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Affiliation(s)
- Y Kudo
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Surgery, Tokyo Medical University, Tokyo, Japan
| | - C Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Zhang
- Departments of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Reuben
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - D Y Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Roy-Chowdhuri
- Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - L M Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H Dejima
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - E R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - B Mino
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Abraham
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - N Ikeda
- Department of Surgery, Tokyo Medical University, Tokyo, Japan
| | - A Vaporcyan
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - D Gibbons
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Zhang
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - F F Lang
- Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Luthra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA; Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J J Lee
- Departments of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C Moran
- Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J T Huse
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA; Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - I I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA; Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
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37
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Kisielow P. How does the immune system learn to distinguish between good and evil? The first definitive studies of T cell central tolerance and positive selection. Immunogenetics 2019; 71:513-518. [PMID: 31418051 PMCID: PMC6790186 DOI: 10.1007/s00251-019-01127-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/03/2019] [Indexed: 12/12/2022]
Abstract
Demonstration that immature CD4 + 8+ thymocytes contain T cell precursors that are subjected to positive and negative selection was the major step towards understanding how the adaptive immune system acquires the ability to distinguish foreign or abnormal (mutated or infected) self-cells from normal (healthy) cells. In the present review, the roles of TCR, CD4, CD8, and MHC molecules in intrathymic selection and some of the crucial experiments that contributed to the solution of the great immunological puzzle of self/nonself discrimination are described in an historical perspective. Recently, these experiments were highlighted by the immunological community by awarding the 2016 Novartis Prize for Immunology to Philippa Marrack, John Kappler, and Harald von Boehmer.
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Affiliation(s)
- Paweł Kisielow
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl St. 12, 53-114, Wroclaw, Poland.
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38
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Carter JA, Preall JB, Grigaityte K, Goldfless SJ, Jeffery E, Briggs AW, Vigneault F, Atwal GS. Single T Cell Sequencing Demonstrates the Functional Role of αβ TCR Pairing in Cell Lineage and Antigen Specificity. Front Immunol 2019; 10:1516. [PMID: 31417541 PMCID: PMC6684766 DOI: 10.3389/fimmu.2019.01516] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/18/2019] [Indexed: 12/13/2022] Open
Abstract
Although structural studies of individual T cell receptors (TCRs) have revealed important roles for both the α and β chain in directing MHC and antigen recognition, repertoire-level immunogenomic analyses have historically examined the β chain alone. To determine the amount of useful information about TCR repertoire function encoded within αβ pairings, we analyzed paired TCR sequences from nearly 100,000 unique CD4+ and CD8+ T cells captured using two different high-throughput, single-cell sequencing approaches. Our results demonstrate little overlap in the healthy CD4+ and CD8+ repertoires, with shared TCR sequences possessing significantly shorter CDR3 sequences corresponding to higher generation probabilities. We further utilized tools from information theory and machine learning to show that while α and β chains are only weakly associated with lineage, αβ pairings appear to synergistically drive TCR-MHC interactions. Vαβ gene pairings were found to be the TCR feature most informative of T cell lineage, supporting the existence of germline-encoded paired αβ TCR-MHC interaction motifs. Finally, annotating our TCR pairs using a database of sequences with known antigen specificities, we demonstrate that approximately a third of the T cells possess α and β chains that each recognize different known antigens, suggesting that αβ pairing is critical for the accurate inference of repertoire functionality. Together, these findings provide biological insight into the functional implications of αβ pairing and highlight the utility of single-cell sequencing in immunogenomics.
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Affiliation(s)
- Jason A. Carter
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | | | - Kristina Grigaityte
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | | | | | | | | | - Gurinder S. Atwal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
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39
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Lu S, White JV, Judy RI, Merritt LL, Lin WL, Zhang X, Solomides C, Nwaneshiudu I, Gaughan J, Monos DS, Oleszak EL, Platsoucas CD. Clonally expanded alpha-chain T-cell receptor (TCR) transcripts are present in aneurysmal lesions of patients with Abdominal Aortic Aneurysm (AAA). PLoS One 2019; 14:e0218990. [PMID: 31310631 PMCID: PMC6634378 DOI: 10.1371/journal.pone.0218990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 06/14/2019] [Indexed: 01/25/2023] Open
Abstract
Abdominal aortic aneurysm (AAA) is a life-threatening immunological disease responsible for 1 to 2% of all deaths in 65 year old or older individuals. Although mononuclear cell infiltrates have been demonstrated in AAA lesions and autoimmunity may be responsible for the initiation and account for the propagation of the disease, the information available about the pathogenesis of AAA is limited. To examine whether AAA lesions from patients with AAA contain clonally expanded α-chain TCR transcripts, we amplified by the non-palindromic adaptor-PCR (NPA-PCR)/Vα-specific PCR and/or the Vα-specific PCR these α-chain TCR transcripts. The amplified transcripts were cloned and sequenced. Substantial proportions of identical α-chain TCR transcripts were identified in AAA lesions of 4 of 5 patients, demonstrating that clonally expanded T cells are present in these AAA lesions. These results were statistically significant by the bimodal distribution. Three of 5 of these patients were typed by DNA-based HLA-typing and all three expressed DRB1 alleles containing the DRβGln70 amino acid residue that has been demonstrated to be associated with AAA. All three patients exhibited clonally expanded T cells in AAA lesions. Four of the 5 patients with AAA who exhibited clonal expansions of α-chain TCR transcripts, also exhibited clonal expansions of β-chain TCR transcripts in AAA lesions, as we have demonstrated previously (J Immunol 192:4897, 2014). αβ TCR-expressing T cells infiltrating AAA lesions contain T-cell clones which have undergone proliferation and clonal expansion in vivo in response to as yet unidentified specific antigens that may be self or nonself. These results provide additional evidence supporting the hypothesis that AAA is a specific antigen-driven T-cell autoimmune disease.
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MESH Headings
- Aged
- Aged, 80 and over
- Amino Acid Sequence/genetics
- Antigens/genetics
- Antigens/immunology
- Aortic Aneurysm, Abdominal/genetics
- Aortic Aneurysm, Abdominal/immunology
- Aortic Aneurysm, Abdominal/pathology
- Cells, Cultured
- Clone Cells/immunology
- Humans
- Male
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Sequence Analysis, RNA
- T-Lymphocytes/immunology
- T-Lymphocytes/pathology
- Transcription, Genetic
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Affiliation(s)
- Song Lu
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - John V. White
- Department of Surgery, Advocate Lutheran General Hospital and University of Illinois School of Medicine, Park Ridge, IL, United States of America
| | - Raquel I. Judy
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States of America
| | - Lisa L. Merritt
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States of America
| | - Wan Lu Lin
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - Xiaoying Zhang
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - Charalambos Solomides
- Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - Ifeyinwa Nwaneshiudu
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - John Gaughan
- Biostatistics Consulting Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - Dimitri S. Monos
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Emilia L. Oleszak
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States of America
- Department of Anatomy and Cell Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
- Center for Molecular Medicine, Old Dominion University, Norfolk, VA, United States of America
| | - Chris D. Platsoucas
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States of America
- Center for Molecular Medicine, Old Dominion University, Norfolk, VA, United States of America
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40
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Pedromonico Arrym M, Martins Alves PC, Virginello Castelhano M, Nitsch Mazzola T, Muller Banzato Pinto de Lemos R, Zaccariotto TR, Levy CE, Guimarães F, Nolasco da Silva MT. Preservation of cytotoxic granule production in response to mycobacterial antigens by T-lymphocytes from vertically HIV-infected Brazilian youth on effective combined antiretroviral therapy. Braz J Infect Dis 2019; 23:151-159. [PMID: 31271732 PMCID: PMC9428219 DOI: 10.1016/j.bjid.2019.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 05/30/2019] [Accepted: 06/12/2019] [Indexed: 11/19/2022] Open
Abstract
Background HIV infection harms adaptive cellular immunity mechanisms. Long-term virological control by combined antiretroviral therapy (cART) reduces the risk of mycobacterial infections. Thus, we aimed to study cellular responses to mycobacterial antigens in 20 HIV-infected adolescents with at least one year of virological control (HIV-RNA <40 copies/mL) and 20 healthy adolescents. Methods We evaluated CD8 and γδ T-cell degranulation by measurement of CD107a membrane expression after stimulation with lysates from BCG (10 μg/mL) and H37RA Mycobacterium tuberculosis (Mtb, 10 μg/mL). Immune activation and antigen-presenting ability were also assessed by determination of HLA-DR, CD80, and CD86 markers. Results TCR γδ T-cell CD107a expression was similar between groups in response to mycobacterial antigens, and lower in the HIV-infected group in response to mitogen. Higher baseline HLA-DR expression and lower mycobacterial-stimulated expression was found within the HIV-infected group. Conclusions Similar degranulation in stimulated CD8+ and TCR γδ T-cells from HIV-infected adolescents, when compared to healthy controls suggests long-term immunological preservation with immune reconstitution under successful cART. However, differences in HLA-DR expression may represent ongoing inflammation and lower specific responses in HIV-infected youth. These features may be relevant in the context of the precocity and severity of vertically acquired HIV infection.
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Affiliation(s)
- Mauro Pedromonico Arrym
- State University of Campinas, Faculty of Medical Sciences, Laboratory of Translational Research in Child and Adolescent Health, Center for Investigation in Pediatrics, Campinas, SP, Brazil
| | - Paulo César Martins Alves
- State University of Campinas, Faculty of Medical Sciences, Laboratory of Translational Research in Child and Adolescent Health, Center for Investigation in Pediatrics, Campinas, SP, Brazil
| | - Mariana Virginello Castelhano
- State University of Campinas, Faculty of Medical Sciences, Laboratory of Translational Research in Child and Adolescent Health, Center for Investigation in Pediatrics, Campinas, SP, Brazil
| | - Taís Nitsch Mazzola
- State University of Campinas, Center for Molecular Biology and Genetical Engineering, Campinas, SP, Brazil
| | | | - Tânia Regina Zaccariotto
- State University of Campinas Clinics Hospital, Clinical Pathology Laboratory, Campinas, SP, Brazil
| | - Carlos Emilio Levy
- State University of Campinas Clinics Hospital, Clinical Pathology Laboratory, Campinas, SP, Brazil
| | - Fernando Guimarães
- State University of Campinas, Center for Integral Attention to Women's Health, SP, Brazil
| | - Marcos Tadeu Nolasco da Silva
- State University of Campinas, Faculty of Medical Sciences, Laboratory of Translational Research in Child and Adolescent Health, Center for Investigation in Pediatrics, Campinas, SP, Brazil.
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41
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Fehrenkamp BD, Miller RD. γδ T cells are the predominant T cell type in opossum mammaries during lactation. Dev Comp Immunol 2019; 95:96-100. [PMID: 30768943 PMCID: PMC7278272 DOI: 10.1016/j.dci.2019.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 05/27/2023]
Abstract
Milk provides mammalian neonates with nutritional support and passive immunity. This is particularly true in marsupials where young are born highly altricial and lacking many components of a fully functional adaptive immune system. Here we investigated the T cell populations in the mammaries of a lactating marsupial, the gray short-tailed opossum Monodelphis domestica. Immunohistochemistry confirmed the presence of T cells within the opossum mammaries throughout lactation. Results of quantifying transcript abundance for lymphocyte markers are consistent with γδ T cells being the most common T cell type within lactating mammaries. Numbers of γδ T cells appear to peak early during the first postnatal week, and then decline throughout lactation until weaning. In contrast, numbers of αβ T cells and γμ T cells appear to be low to non-existent in the lactating mammaries. The results support an ancient and conserved role of immune cells in the evolution and function of mammalian mammary tissue.
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MESH Headings
- Adaptive Immunity/genetics
- Adaptive Immunity/immunology
- Animals
- Female
- Gene Expression Regulation, Developmental/immunology
- Lactation/immunology
- Mammary Glands, Animal/cytology
- Mammary Glands, Animal/growth & development
- Mammary Glands, Animal/immunology
- Mammary Glands, Animal/metabolism
- Monodelphis/immunology
- Monodelphis/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
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Affiliation(s)
- Bethaney D Fehrenkamp
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, 1 University of New Mexico, MSC03-2020, Albuquerque, NM, 87131-1091, USA
| | - Robert D Miller
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, 1 University of New Mexico, MSC03-2020, Albuquerque, NM, 87131-1091, USA.
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42
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Spidale NA, Frascoli M, Kang J. γδTCR-independent origin of neonatal γδ T cells prewired for IL-17 production. Curr Opin Immunol 2019; 58:60-67. [PMID: 31128446 PMCID: PMC7147991 DOI: 10.1016/j.coi.2019.04.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/19/2019] [Indexed: 12/20/2022]
Abstract
A classical view of T cell lineages consists of two major clades of T cells expressing either the αβ or γδ T cell receptor (TCR). However, genome-wide assessments indicate molecular clusters segregating T cell subsets that are preprogrammed for effector function (innate) from those that mediate conventional adaptive response, regardless of the TCR types. Within this paradigm, γδ T cells remain the prototypic innate-like lymphocytes, many subsets of which are programmed during intrathymic development for committed peripheral tissue localization and effector responses. Emerging evidence for innate γδ T cell lineage choice dictated by developmental gene programs rather than the sensory TCR is discussed in this review.
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MESH Headings
- Adaptive Immunity/immunology
- Animals
- Cell Differentiation/immunology
- Cell Lineage/immunology
- Humans
- Immunity, Innate/immunology
- Interleukin-17/immunology
- Interleukin-17/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
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Affiliation(s)
- Nicholas A Spidale
- University of Massachusetts Medical School, Department of Pathology, Worcester, MA, United States
| | - Michela Frascoli
- University of Massachusetts Medical School, Department of Pathology, Worcester, MA, United States
| | - Joonsoo Kang
- University of Massachusetts Medical School, Department of Pathology, Worcester, MA, United States.
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43
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Zeng J, Tang SY, Wang S. Derivation of mimetic γδ T cells endowed with cancer recognition receptors from reprogrammed γδ T cell. PLoS One 2019; 14:e0216815. [PMID: 31071196 PMCID: PMC6508724 DOI: 10.1371/journal.pone.0216815] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/23/2019] [Indexed: 01/13/2023] Open
Abstract
Using induced pluripotent stem cells (iPSCs) to derive chimeric antigen receptor-modified T (CAR-T) cells has great industrial potential. A previous study used αβ T cell-derived CAR-modified iPSCs to produce CAR-T cells. However, these αβ T cells are restricted to autologous use and only recognize single cancer antigen. To make CAR-T alternative for allogeneic use, we reprogrammed γδ T cell into iPSCs (γδ T-iPSCs) to circumvent the risk of graft-versus-host disease. To target multiple cancer-associated antigens, we used an "NK cell-promoting" protocol to differentiate γδ T-iPSCs and to induce expression of natural killer receptors (NKRs). Through such two-step strategy, mimetic γδ T cells endowed with an array of NKRs and thus designated as "γδ natural killer T (γδ NKT) cells" were derived. With no/low-level expression of inhibitory killer cell immunoglobulin-like receptors (KIRs) and immune checkpoint receptors, γδ NKT cells may provide a potent "off-the-shelf" cytotoxic cell source to recognize multiple ubiquitous antigens in a broad spectrum of cancers.
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MESH Headings
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- HCT116 Cells
- Hep G2 Cells
- Humans
- Induced Pluripotent Stem Cells/immunology
- Induced Pluripotent Stem Cells/pathology
- K562 Cells
- MCF-7 Cells
- Natural Killer T-Cells/immunology
- Natural Killer T-Cells/pathology
- Neoplasms/genetics
- Neoplasms/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/immunology
- THP-1 Cells
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Affiliation(s)
- Jieming Zeng
- Institute of Bioengineering and Nanotechnology, Singapore
- * E-mail: , (JZ); (SW)
| | - Shin Yi Tang
- Institute of Bioengineering and Nanotechnology, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Shu Wang
- Institute of Bioengineering and Nanotechnology, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- * E-mail: , (JZ); (SW)
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44
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Shimizu K, Sato Y, Kawamura M, Nakazato H, Watanabe T, Ohara O, Fujii SI. Eomes transcription factor is required for the development and differentiation of invariant NKT cells. Commun Biol 2019; 2:150. [PMID: 31044175 PMCID: PMC6488575 DOI: 10.1038/s42003-019-0389-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 03/18/2019] [Indexed: 12/27/2022] Open
Abstract
Eomes regulates the differentiation of CD8+ T cells into effector and memory phases. However, its role in invariant (i)NKT cells remains unknown. Here, we show the impact of Eomes on iNKT cells in the thymus and peripheral tissue using conditional knockout (Eomes-cKO) mice. In the thymus, CD1d-tetramer+CD24+CD44-NK1.1-CD69+stage 0 iNKT cells express higher levels of Eomes than the other iNKT stages. We also found that Eomes regulates NKT1 cell differentiation predominantly. Interestingly, the expression of Eomes in the steady state is low, but can be upregulated after TCR stimulation. We also showed epigenetic changes in the Eomes locus after activation. In addition, vaccination of C57BL/6, but not Eomes-cKO mice with iNKT ligand-loaded dendritic cells generated KLRG1+iNKT cells in lung, characterized as effector memory phenotype by transcriptome profiling. Thus, Eomes regulates not only the differentiation of NKT1 cells in the thymus, but also their differentiation into memory-like KLRG1+iNKT cells in the periphery.
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MESH Headings
- Animals
- Antigens, CD/genetics
- Antigens, CD/immunology
- CD8-Positive T-Lymphocytes/cytology
- CD8-Positive T-Lymphocytes/immunology
- Cell Differentiation
- Cell Lineage/genetics
- Cell Lineage/immunology
- Cell Proliferation
- Dendritic Cells/cytology
- Dendritic Cells/immunology
- Gene Expression Profiling
- Gene Expression Regulation/immunology
- Immunologic Memory/genetics
- Lectins, C-Type/genetics
- Lectins, C-Type/immunology
- Lung/cytology
- Lung/immunology
- Lymphocyte Activation
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Natural Killer T-Cells/cytology
- Natural Killer T-Cells/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- Signal Transduction
- T-Box Domain Proteins/deficiency
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/immunology
- Thymus Gland/cytology
- Thymus Gland/immunology
- Transcriptome/immunology
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Affiliation(s)
- Kanako Shimizu
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
| | - Yusuke Sato
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
| | - Masami Kawamura
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
| | - Hiroshi Nakazato
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
| | - Takashi Watanabe
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
| | - Shin-ichiro Fujii
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
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45
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Rabiger FV, Bismarck D, Protschka M, Köhler G, Moore PF, Büttner M, von Buttlar H, Alber G, Eschke M. Canine tissue-associated CD4+CD8α+ double-positive T cells are an activated T cell subpopulation with heterogeneous functional potential. PLoS One 2019; 14:e0213597. [PMID: 30865691 PMCID: PMC6415905 DOI: 10.1371/journal.pone.0213597] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/25/2019] [Indexed: 12/28/2022] Open
Abstract
Canine CD4+CD8α+ double-positive (dp) T cells of peripheral blood are a unique effector memory T cell subpopulation characterized by an increased expression of activation markers in comparison with conventional CD4+ or CD8α+ single-positive (sp) T cells. In this study, we investigated CD4+CD8α+ dp T cells in secondary lymphatic organs (i.e. mesenteric and tracheobronchial lymph nodes, spleen, Peyer’s patches) and non-lymphatic tissues (i.e. lung and epithelium of the small intestine) within a homogeneous group of healthy Beagle dogs by multi-color flow cytometry. The aim of this systematic analysis was to identify the tissue-specific localization and characteristics of this distinct T cell subpopulation. Our results revealed a mature extrathymic CD1a-CD4+CD8α+ dp T cell population in all analyzed organs, with highest frequencies within Peyer’s patches. Constitutive expression of the activation marker CD25 is a feature of many CD4+CD8α+ dp T cells independent of their localization and points to an effector phenotype. A proportion of lymph node CD4+CD8α+ dp T cells is FoxP3+ indicating regulatory potential. Within the intestinal environment, the cytotoxic marker granzyme B is expressed by CD4+CD8α+ dp intraepithelial lymphocytes. In addition, a fraction of CD4+CD8α+ dp intraepithelial lymphocytes and of mesenteric lymph node CD4+CD8α+ dp T cells is TCRγδ+. However, the main T cell receptor of all tissue-associated CD4+CD8α+ dp T cells could be identified as TCRαβ. Interestingly, the majority of the CD4+CD8α+ dp T cell subpopulation expresses the unconventional CD8αα homodimer, in contrast to CD8α+ sp T cells, and CD4+CD8α+ dp thymocytes which are mainly CD8αβ+. The presented data provide the basis for a functional analysis of tissue-specific CD4+CD8α+ dp T cells to elucidate their role in health and disease of dogs.
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Affiliation(s)
- Friederike V. Rabiger
- Institute of Immunology/Molecular Pathogenesis, Center for Biotechnology and Biomedicine, College of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | - Doris Bismarck
- Institute of Immunology/Molecular Pathogenesis, Center for Biotechnology and Biomedicine, College of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | - Martina Protschka
- Institute of Immunology/Molecular Pathogenesis, Center for Biotechnology and Biomedicine, College of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | | | - Peter F. Moore
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, United States
| | - Mathias Büttner
- Institute of Immunology/Molecular Pathogenesis, Center for Biotechnology and Biomedicine, College of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | - Heiner von Buttlar
- Institute of Immunology/Molecular Pathogenesis, Center for Biotechnology and Biomedicine, College of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | - Gottfried Alber
- Institute of Immunology/Molecular Pathogenesis, Center for Biotechnology and Biomedicine, College of Veterinary Medicine, University of Leipzig, Leipzig, Germany
- * E-mail:
| | - Maria Eschke
- Institute of Immunology/Molecular Pathogenesis, Center for Biotechnology and Biomedicine, College of Veterinary Medicine, University of Leipzig, Leipzig, Germany
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46
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Abstract
The T-cell (TCR) repertoire relies on the diversity of receptors composed of two chains, called α and β, to recognize pathogens. Using results of high throughput sequencing and computational chain-pairing experiments of human TCR repertoires, we quantitively characterize the αβ generation process. We estimate the probabilities of a rescue recombination of the β chain on the second chromosome upon failure or success on the first chromosome. Unlike β chains, α chains recombine simultaneously on both chromosomes, resulting in correlated statistics of the two genes which we predict using a mechanistic model. We find that ∼35% of cells express both α chains. Altogether, our statistical analysis gives a complete quantitative mechanistic picture that results in the observed correlations in the generative process. We learn that the probability to generate any TCRαβ is lower than 10(-12) and estimate the generation diversity and sharing properties of the αβ TCR repertoire.
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MESH Headings
- Chromosomes, Human
- Humans
- Probability
- Receptors, Antigen, T-Cell, alpha-beta/biosynthesis
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombination, Genetic
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Affiliation(s)
- Thomas Dupic
- Laboratoire de physique théorique et hautes énergies, CNRS and Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
| | - Quentin Marcou
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
- * E-mail: (AMW); (TM)
| | - Thierry Mora
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
- * E-mail: (AMW); (TM)
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47
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Shinkai Y, Koyasu S, Nakayama KI, Murphy KM, Loh DY, Reinherz EL, Alt FW. Pillars Article: Restoration of T Cell Development in RAG-2-Deficient Mice by Functional TCR Transgenes. Science. 1993. 259: 822-825. J Immunol 2019; 202:1317-1320. [PMID: 30782850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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48
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Zhu Y, Zhang S, Li Z, Wang H, Li Z, Hu Y, Chen H, Zhang X, Cui L, Zhang J, He W. miR-125b-5p and miR-99a-5p downregulate human γδ T-cell activation and cytotoxicity. Cell Mol Immunol 2019; 16:112-125. [PMID: 29429995 PMCID: PMC6355834 DOI: 10.1038/cmi.2017.164] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 12/04/2017] [Accepted: 12/04/2017] [Indexed: 01/02/2023] Open
Abstract
As an important component of innate immunity, human circulating γδ T cells function in rapid responses to infections and tumorigenesis. MicroRNAs (miRNAs) play a critical regulatory role in multiple biological processes and diseases. Therefore, how the functions of circulating human γδ T cells are regulated by miRNAs merits investigation. In this study, we profiled the miRNA expression patterns in human peripheral γδ T cells from 21 healthy donors and identified 14 miRNAs that were differentially expressed between peripheral αβ T cells and γδ T cells. Of the 14 identified genes, 7 miRNAs were downregulated, including miR-150-5p, miR-450a-5p, miR-193b-3p, miR-365a-3p, miR-31-5p, miR-125b-5p and miR-99a-5p, whereas the other 7 miRNAs were upregulated, including miR-34a-5p, miR-16-5p, miR-15b-5p, miR-24-3p, miR-22-3p, miR-22-5p and miR-9-5p, in γδ T cells compared with αβ T cells. In subsequent functional studies, we found that both miR-125b-5p and miR-99a-5p downregulated γδ T cell activation and cytotoxicity to tumor cells. Overexpression of miR-125b-5p or miR-99a-5p in γδ T cells inhibited γδ T cell activation and promoted γδ T cell apoptosis. Additionally, miR-125b-5p knockdown facilitated the cytotoxicity of γδ T cells toward tumor cells in vitro by increasing degranulation and secretion of IFN-γ and TNF-α. Our findings improve the understanding of the regulatory functions of miRNAs in γδ T cell activation and cytotoxicity, which has implications for interventional approaches to γδ T cell-mediated cancer therapy.
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MESH Headings
- Apoptosis
- Cell Proliferation
- Cells, Cultured
- Down-Regulation
- Gene Expression Regulation, Neoplastic
- Humans
- Lymphocyte Activation/immunology
- MicroRNAs/genetics
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- T-Lymphocytes/pathology
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Affiliation(s)
- Yuli Zhu
- Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, 100005, Beijing, China
- Institute of blood transfusion, Qingdao Blood Center, 266071, Qingdao, China
| | - Siya Zhang
- Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, 100005, Beijing, China
| | - Zinan Li
- Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, 100005, Beijing, China
| | - Huaishan Wang
- Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, 100005, Beijing, China
| | - Zhen Li
- Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, 100005, Beijing, China
| | - Yu Hu
- Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, 100005, Beijing, China
| | - Hui Chen
- Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, 100005, Beijing, China
| | - Xuan Zhang
- Department of Rheumatology & Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Lianxian Cui
- Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, 100005, Beijing, China
| | - Jianmin Zhang
- Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, 100005, Beijing, China.
| | - Wei He
- Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, 100005, Beijing, China.
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49
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Massari S, Bellini M, Ciccarese S, Antonacci R. Overview of the Germline and Expressed Repertoires of the TRB Genes in Sus scrofa. Front Immunol 2018; 9:2526. [PMID: 30455691 PMCID: PMC6230588 DOI: 10.3389/fimmu.2018.02526] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/12/2018] [Indexed: 11/19/2022] Open
Abstract
The α/β T cell receptor (TR) is a complex heterodimer that recognizes antigenic peptides and binds to major histocompatibility complex (MH) molecules. Both α and β chains are encoded by different genes localized on two distinct chromosomal loci: TRA and TRB. The present study employed the recent release of the swine genome assembly to define the genomic organization of the TRB locus. According to the sequencing data, the pig TRB locus spans approximately 400 kb of genomic DNA and consists of 38 TRBV genes belonging to 24 subgroups located upstream of three in tandem TRBD-J-C clusters, which are followed by a TRBV gene in an inverted transcriptional orientation. Comparative analysis confirms that the general organization of the TRB locus is similar among mammalian species, but the number of germline TRBV genes varies greatly even between species belonging to the same order, determining the diversity and specificity of the immune response. However, sequence analysis of the TRB locus also suggests the presence of blocks of conserved homology in the genomic region across mammals. Furthermore, by analysing a public cDNA collection, we identified the usage pattern of the TRBV, TRBD, and TRBJ genes in the adult pig TRB repertoire, and we noted that the expressed TRBV repertoire seems to be broader and more diverse than the germline repertoire, in line with the presence of a high level of TRBV gene polymorphisms. Because the nucleotide differences seems to be principally concentrated in the CDR2 region, it is reasonable to presume that most T cell β-chain diversity can be related to polymorphisms in pig MH molecules. Domestic pigs represent a valuable animal model as they are even more anatomically, genetically and physiologically similar to humans than are mice. Therefore, present knowledge on the genomic organization of the pig TRB locus allows the collection of increased information on the basic aspects of the porcine immune system and contributes to filling the gaps left by rodent models.
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Affiliation(s)
- Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, Lecce, Italy
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50
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Gan Y, Wang C, Fang Y, Yao Y, Tu X, Wang J, Huang X, Tan Y, Chen T, Zhang K, Shen Y, Zhou L, Liu J, Lai X. Mycobacterium tuberculosis peptide E7/HLA-DRB1 tetramers with different HLA-DR alleles bound CD4 + T cells might share identical CDR3 region. Sci Rep 2018; 8:9903. [PMID: 29967390 PMCID: PMC6028479 DOI: 10.1038/s41598-018-28344-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/21/2018] [Indexed: 12/02/2022] Open
Abstract
Human CD4+ T cells play an important role in the immune response to Mycobacterium tuberculosis (MTB). However, little is known about the spectratyping characteristics of the CD4+ T-cell receptor (TCR) α- and β-chains CDR3 region in tuberculosis (TB) patients. We sorted MTB peptide E7-bound CD4+ T cells by using E7/HLA-DR tetramers constructed with different HLA-DRB1 alleles and extracted the CDR3 amino-acid sequences of TCR α- and β-chains. The results showed that the CDR3 sequences of E7-bound CD4+ T cells were completely or partially identical in a single patient. The sequences of MTB peptide C5-bound CD4+ T cells shared another, and non-peptide bound CD4+ T cells, as well as unbound CD4+ T cells with tetramers were different from each other. Specifically, diverse CDR3 sequences of E7-bound CD4+ T cells displayed similar protein tertiary structure in one TB patient. In summary, the TCR α- and β-chains of CDR3 lineage of CD4+ T cells in TB patients apparently drifted, and the predominant CDR3 sequences of TCR α- and β-chains that recognized the MTB antigen exhibited peptide specificity, and certain HLA-DR restriction was also established. This study elucidates the possible causes and mechanisms of peptide-specific CD4+ T-cell-related presentation against MTB.
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Affiliation(s)
- Yichuan Gan
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Cong Wang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Yimin Fang
- State Key Laboratory of Respiratory Disease of China, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou, 510095, China
| | - Yanan Yao
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Xiaoxin Tu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Jiao Wang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Xi Huang
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease of China, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou, 510095, China
| | - Tao Chen
- Tuberculosis Control Center of Guangdong Province, 485 West Huangpu Avenue, Guangzhou, 510630, China
| | - Kouxing Zhang
- Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou, 510630, China
| | - Yanming Shen
- State Key Laboratory of Respiratory Disease of China, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou, 510095, China
| | - Lin Zhou
- Tuberculosis Control Center of Guangdong Province, 485 West Huangpu Avenue, Guangzhou, 510630, China.
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease of China, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou, 510095, China.
| | - Xiaomin Lai
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China.
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China.
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China.
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