Identifying specificity groups in the T cell receptor repertoire

Nature

Volumn 547, Issue 7661, 2017, Pages 94-98

  Glanville, Jacob ^a   Huang, Huang ^a   Nau, Allison ^a   Hatton, Olivia ^a,e   Wagar, Lisa E ^a   Rubelt, Florian ^a   Ji, Xuhuai ^a   Han, Arnold ^a,f   Krams, Sheri M ^a   Pettus, Christina ^b   Haas, Nikhil ^b   Arlehamn, Cecilia S Lindestam ^c   Sette, Alessandro ^c   Boyd, Scott D ^a   Scriba, Thomas J ^d   Martinez, Olivia M ^a   Davis, Mark M ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF SAN FRANCISCO   (United States)

^c LA JOLLA INSTITUTE FOR ALLERGY AND IMMUNOLOGY   (United States)

^d UNIVERSITY OF CAPE TOWN   (South Africa)

^e Department of Psychology   (United States)

^f Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HLA DRB1 ANTIGEN; T LYMPHOCYTE RECEPTOR; EPITOPE; HLA ANTIGEN; LIGAND; LYMPHOCYTE ANTIGEN RECEPTOR;

ALGORITHM; ALLELE; ANTIGEN; BACTERIUM; CELLS AND CELL COMPONENTS; GENETIC ANALYSIS; MAJOR HISTOCOMPATIBILITY COMPLEX; PEPTIDE; PROTEIN; TUBERCULOSIS;

ANTIGEN RECOGNITION; ANTIGEN SPECIFICITY; ARTICLE; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; COMPLEMENTARITY DETERMINING REGION; CYTOMEGALOVIRUS; EPSTEIN BARR VIRUS; HIGH THROUGHPUT SEQUENCING; HLA SYSTEM; HUMAN; INFLUENZA VIRUS; MAJOR HISTOCOMPATIBILITY COMPLEX; NONHUMAN; PREDICTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TUBERCULOSIS; ADOLESCENT; ALGORITHM; AMINO ACID SEQUENCE; CHEMISTRY; ENZYME SPECIFICITY; IMMUNOLOGY; MOLECULAR MODEL; MYCOBACTERIUM TUBERCULOSIS; X RAY CRYSTALLOGRAPHY;

MYCOBACTERIUM TUBERCULOSIS;

ADOLESCENT; ALGORITHMS; AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; EPITOPES, T-LYMPHOCYTE; HLA ANTIGENS; HUMANS; LIGANDS; MODELS, MOLECULAR; MYCOBACTERIUM TUBERCULOSIS; RECEPTORS, ANTIGEN, T-CELL; SUBSTRATE SPECIFICITY;

EID: 85022229481     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature22976     Document Type: Article

References (23)

1. Arstila, T. P. et al. A direct estimate of the human T cell receptor diversity. Science 286, 958-961 (1999).
2. Davis, M. M. & Bjorkman, P. J. T-cell antigen receptor genes and T-cell recognition. Nature 334, 395-402 (1988).
3. Qi, Q. et al. Diversity and clonal selection in the human T-cell repertoire. Proc. Natl Acad. Sci. USA 111, 13139-13144 (2014).
4. Shortman, K., Egerton, M., Spangrude, G. J. & Scollay, R. The generation and fate of thymocytes. Semin. Immunol. 2, 3-12 (1990).
5. Rudolph, M. G., Stanfield, R. L. & Wilson, I. A. How TCRs bind MHCs, peptides, and coreceptors. Annu. Rev. Immunol. 24, 419-466 (2006).
6. Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000).
7. Warren, R. L. et al. Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Res. 21, 790-797 (2011).
8. Rubelt, F. et al. Individual heritable differences result in unique cell lymphocyte receptor repertoires of naive and antigen-experienced cells. Nat. Commun. 7, 11112 (2016).
9. Li, W. & Godzik, A. CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659 (2006).
10. Song, I. et al. Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope. Nat. Struct. Mol. Biol. 24, 395-406 (2017).
11. Chattopadhyay, P. K., Yu, J. & Roederer, M. A live-cell assay to detect antigen-specific CD4+ T cells with diverse cytokine profiles. Nat. Med. 11, 1113-1117 (2005).
12. Frentsch, M. et al. Direct access to CD4+ T cells specific for defined antigens according to CD154 expression. Nat. Med. 11, 1118-1124 (2005).
13. Lindestam Arlehamn, C. S. et al. A quantitative analysis of complexity of human pathogen-specific CD4 T cell responses in healthy M. tuberculosis-infected South Africans. PLoS Pathog. 12, e1005760 (2016).
14. Han, A., Glanville, J., Hansmann, L. & Davis, M. M. Linking T-cell receptor sequence to functional phenotype at the single-cell level. Nat. Biotechnol. 32, 684-692 (2014).
15. Lindestam Arlehamn, C. S. et al. Memory T cells in latent Mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ TH1 subset. PLoS Pathog. 9, e1003130 (2013).
16. Sallusto, F. Heterogeneity of human CD4+ T cells against microbes. Annu. Rev. Immunol. 34, 317-334 (2016).
17. Sharma, G. & Holt, R. A. T-cell epitope discovery technologies. Hum. Immunol. 75, 514-519 (2014).
18. Wang, P. et al. Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics 11, 568 (2010).
19. Mahomed, H. et al. Predictive factors for latent tuberculosis infection among adolescents in a high-burden area in South Africa. Int. J. Tuberc. Lung Dis. 15, 331-336 (2011).
20. Han, A. et al. Dietary gluten triggers concomitant activation of CD4+ and CD8+ T cells and T cells in celiac disease. Proc. Natl Acad. Sci. USA 110, 13073-13078 (2013).
21. Glanville, J. et al. Naive antibody gene-segment frequencies are heritable and unaltered by chronic lymphocyte ablation. Proc. Natl Acad. Sci. USA 108, 20066-20071 (2011).
22. Glanville, J. et al. Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire. Proc. Natl Acad. Sci. USA 106, 20216-20221 (2009).
23. Hathaway, N. A. et al. Dynamics and memory of heterochromatin in living cells. Cell 149, 1447-1460 (2012).