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Mudd P, Borcherding N, Kim W, Quinn M, Han F, Zhou J, Sturtz A, Schmitz A, Lei T, Schattgen S, Klebert M, Suessen T, Middleton W, Goss C, Liu C, Crawford J, Thomas P, Teefey S, Presti R, O'Halloran J, Turner J, Ellebedy A. Antigen-specific CD4 + T cells exhibit distinct transcriptional phenotypes in the lymph node and blood following vaccination in humans. RESEARCH SQUARE 2023:rs.3.rs-3304466. [PMID: 37790414 PMCID: PMC10543502 DOI: 10.21203/rs.3.rs-3304466/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
SARS-CoV-2 infection and mRNA vaccination induce robust CD4+ T cell responses that are critical for the development of protective immunity. Here, we evaluated spike-specific CD4+ T cells in the blood and draining lymph node (dLN) of human subjects following BNT162b2 mRNA vaccination using single-cell transcriptomics. We analyze multiple spike-specific CD4+ T cell clonotypes, including novel clonotypes we define here using Trex, a new deep learning-based reverse epitope mapping method integrating single-cell T cell receptor (TCR) sequencing and transcriptomics to predict antigen-specificity. Human dLN spike-specific T follicular helper cells (TFH) exhibited distinct phenotypes, including germinal center (GC)-TFH and IL-10+ TFH, that varied over time during the GC response. Paired TCR clonotype analysis revealed tissue-specific segregation of circulating and dLN clonotypes, despite numerous spike-specific clonotypes in each compartment. Analysis of a separate SARS-CoV-2 infection cohort revealed circulating spike-specific CD4+ T cell profiles distinct from those found following BNT162b2 vaccination. Our findings provide an atlas of human antigen-specific CD4+ T cell transcriptional phenotypes in the dLN and blood following vaccination or infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Charles Goss
- Division of Biostatistics, Washington University in St.Louis
| | - Chang Liu
- Washington University School of Medicine
| | | | | | | | | | - Jane O'Halloran
- Department of Emergency Medicine, Washington University in St.Louis
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Jaiswal S, Nyquist SK, Boyce S, Jivanjee T, Ibrahim S, Bromley JD, Gatter GJ, Gideon H, Patel K, Ganchua SK, Berger B, Fortune SM, Flynn JL, Shalek AK, Behar SM. Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis). BMC Genomics 2022; 23:647. [PMID: 36096729 PMCID: PMC9465142 DOI: 10.1186/s12864-022-08867-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/01/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Cynomolgus macaque (Macaca fascicularis) is an attractive animal model for the study of human disease and is extensively used in biomedical research. Cynomolgus macaques share behavioral, physiological, and genomic traits with humans and recapitulate human disease manifestations not observed in other animal species. To improve the use of the cynomolgus macaque model to investigate immune responses, we defined and characterized the T cell receptor (TCR) repertoire. RESULT We identified and analyzed the alpha (TRA), beta (TRB), gamma (TRG), and delta (TRD) TCR loci of the cynomolgus macaque. The expressed repertoire was determined using 22 unique lung samples from Mycobacterium tuberculosis infected cynomolgus macaques by single cell RNA sequencing. Expressed TCR alpha (TRAV) and beta (TRBV) variable region genes were enriched and identified using gene specific primers, which allowed their functional status to be determined. Analysis of the primers used for cynomolgus macaque TCR variable region gene enrichment showed they could also be used to amplify rhesus macaque (M. mulatta) variable region genes. CONCLUSION The genomic organization of the cynomolgus macaque has great similarity with the rhesus macaque and they shared > 90% sequence similarity with the human TCR repertoire. The identification of the TCR repertoire facilitates analysis of T cell immunity in cynomolgus macaques.
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Affiliation(s)
- Swati Jaiswal
- Department of Microbiology and Physiological Systems, Universityof Massachusetts Chan Medical School, Worcester, MA USA
| | - Sarah K. Nyquist
- grid.116068.80000 0001 2341 2786Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Shayla Boyce
- Department of Microbiology and Physiological Systems, Universityof Massachusetts Chan Medical School, Worcester, MA USA
| | - Tasneem Jivanjee
- grid.116068.80000 0001 2341 2786Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Samira Ibrahim
- grid.116068.80000 0001 2341 2786Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Joshua D. Bromley
- grid.116068.80000 0001 2341 2786Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA USA
| | - G. James Gatter
- grid.116068.80000 0001 2341 2786Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Hannah Gideon
- grid.21925.3d0000 0004 1936 9000Department of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Kush Patel
- grid.21925.3d0000 0004 1936 9000Department of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Sharie Keanne Ganchua
- grid.21925.3d0000 0004 1936 9000Department of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Bonnie Berger
- grid.116068.80000 0001 2341 2786Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Sarah M. Fortune
- grid.38142.3c000000041936754XDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT and Harvard, Boston, MA USA
| | - JoAnne L. Flynn
- grid.21925.3d0000 0004 1936 9000Department of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Alex K. Shalek
- grid.116068.80000 0001 2341 2786Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT and Harvard, Boston, MA USA ,grid.116068.80000 0001 2341 2786Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA USA
| | - Samuel M. Behar
- Department of Microbiology and Physiological Systems, Universityof Massachusetts Chan Medical School, Worcester, MA USA
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