Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells

Immunology and Cell Biology

Volumn 94, Issue 6, 2016, Pages 604-611

  Eltahla, Auda A ^a   Rizzetto, Simone ^a   Pirozyan, Mehdi R ^a   Betz Stablein, Brigid D ^a   Venturi, Vanessa ^b   Kedzierska, Katherine ^c   Lloyd, Andrew R ^a   Bull, Rowena A ^a   Luciani, Fabio ^a  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

^c UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; T LYMPHOCYTE RECEPTOR; T LYMPHOCYTE RECEPTOR ALPHA CHAIN; T LYMPHOCYTE RECEPTOR BETA CHAIN; TRANSCRIPTOME; EPITOPE; LYMPHOCYTE ANTIGEN RECEPTOR;

ANTIGEN SPECIFICITY; ARTICLE; CASE REPORT; CELL ISOLATION; CONTROLLED STUDY; GENE EXPRESSION PROFILING; HEPATITIS C; HUMAN; HUMAN CELL; LYMPHOCYTE SUBPOPULATION; POLYMERASE CHAIN REACTION; RNA SEQUENCE; SINGLE CELL ANALYSIS; STANDARD; T LYMPHOCYTE; GENE EXPRESSION REGULATION; GENETICS; IMMUNOLOGY; METABOLISM; PROCEDURES; SEQUENCE ANALYSIS; VDJ RECOMBINATION;

EPITOPES; EPITOPES, T-LYMPHOCYTE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; RECEPTORS, ANTIGEN, T-CELL; RECEPTORS, ANTIGEN, T-CELL, ALPHA-BETA; SEQUENCE ANALYSIS, RNA; SINGLE-CELL ANALYSIS; T-LYMPHOCYTES; TRANSCRIPTOME; V(D)J RECOMBINATION;

EID: 84960155048     PISSN: 08189641     EISSN: 14401711     Source Type: Journal    
DOI: 10.1038/icb.2016.16     Document Type: Article

References (33)

1. Kaech SM, Cui W. Transcriptional control of effector, and memory CD8+ T cell differentiation. Nat Rev Immunol 2012; 12: 749-761
2. Kaech SM, Wherry EJ. Heterogeneity, and cell-fate decisions in effector, and memory CD8+ T cell differentiation during viral infection. Immunity 2007; 27: 393-405
3. Newell EW, Davis MM. Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells. Nat Biotechnol 2014; 32: 149-157
4. Bull RA, Leung P, Gaudieri S, Deshpande P, Cameron B, Walker M, et al. Transmitted/Founder Viruses Rapidly Escape from CD8+ T Cell Responses in Acute Hepatitis C Virus Infection. Journal of virology 2015; 89: 5478-5490
5. Turner SJ, La Gruta NL, Kedzierska K, Thomas PG, Doherty PC. Functional implications of T cell receptor diversity. Curr Opin Immunol 2009; 21: 286-290
6. Chattopadhyay PK, Gierahn TM, Roederer M, Love JC. Single-cell technologies for monitoring immune systems. Nature immunology 2014; 15: 128-135
7. Buchholz VR, Flossdorf M, Hensel I, Kretschmer L, Weissbrich B, Graf P, et al. Disparate individual fates compose robust CD8+ T cell immunity. Science 2013; 340: 630-635
8. Gerlach C, Rohr JC, Perie L, Van Rooij N, Van Heijst JW, Velds A, et al. Heterogeneous differentiation patterns of individual CD8+ T cells. Science 2013; 340: 635-639
9. Fan HC, Fu GK, Fodor SP. Expression profiling. Combinatorial labeling of single cells for gene expression cytometry. Science 2015; 347: 1258367
10. Dash P, Wang GC, Thomas PG. Single-Cell Analysis of T-Cell Receptor alphabeta Repertoire. Methods Mol Biol 2015; 1343: 181-197
11. Linnemann C, Heemskerk B, Kvistborg P, Kluin RJ, Bolotin DA, Chen X, et al. High-throughput identification of antigen-specific TCRs by TCR gene capture. Nat Med 2013; 19: 1534-1541
12. Han A, Glanville J, Hansmann L, Davis MM. Linking T-cell receptor sequence to functional phenotype at the single-cell level. Nat Biotechnol 2014; 32: 684-692
13. Picelli S, Faridani OR, Björklund AK, Winberg G, Sagasser S, Sandberg R. Full-length RNA-seq from single cells using Smart-seq2. Nature protocols 2014; 9: 171-181
14. Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nature biotechnology 2015; 33: 155-160
15. Stegle O, Teichmann SA, Marioni JC. Computational, and analytical challenges in single-cell transcriptomics. Nat Rev Genet 2015; 16: 133-145
16. Brennecke P, Anders S, Kim JK, Kolodziejczyk AA, Zhang X, Proserpio V, et al. Accounting for technical noise in single-cell RNA-seq experiments. Nature methods 2013; 10: 1093-1095
17. Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, et al. The dynamics, and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol 2014; 32: 381-386
18. Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008; 9: 559
19. Stubbington MJT, Lönnberg T, Proserpio V, Clare S, Speak AO, Dougan G, et al. Simultaneously inferring T cell fate, and clonality from single cell transcriptomes. bioRxiv (e-pub ahead of print 28 August 2015; doi: http: //dx.doi.org/10.1101/025676
20. Grun D, Van Oudenaarden A. Design, and Analysis of Single-Cell Sequencing Experiments. Cell 2015; 163: 799-810
21. Nikolich-Zugich J, Slifka MK, Messaoudi I. The many important facets of T-cell repertoire diversity. Nat Rev Immunol 2004; 4: 123-132
22. Attaf M, Huseby E, Sewell AK. Alphabeta T cell receptors as predictors of health, and disease. Cell Mol Immunol 2015; 12: 391-399
23. Miles JJ, Douek DC, Price DA. Bias in the alphabeta T-cell repertoire: implications for disease pathogenesis, and vaccination. Immunol Cell Biol 2011; 89: 375-387
24. Luciani F, Bretana NA, Teutsch S, Amin J, Topp L, Dore GJ, et al. A prospective study of hepatitis C incidence in Australian prisoners. Addiction 2014; 109: 1695-1706
25. Picelli S, Björklund ÅKK, Faridani OR, Sagasser S, Winberg G, Sandberg R. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nature methods 2013; 10: 1096-1098
26. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30: 2114-2120
27. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions, and gene fusions. Genome biology 2013; 14: R36
28. Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z. GOrilla: a tool for discovery, and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 2009; 10: 48
29. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011; 29: 644-652
30. Ye J, Ma N, Madden TL, Ostell JM. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res 2013; 41 (Web Server issue): W34-W40
31. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature methods 2012; 9: 357-359
32. Wang GC, Dash P, McCullers JA, Doherty PC, Thomas PG. T cell receptor alphabeta diversity inversely correlates with pathogen-specific antibody levels in human cytomegalovirus infection. Sci Transl Med 2012; 4: 128ra42
33. Nguyen TH, Rowntree LC, Pellicci DG, Bird NL, Handel A, Kjer-Nielsen L, et al. Recognition of distinct cross-reactive virus-specific CD8+ T cells reveals a unique TCR signature in a clinical setting. J Immunol 2014; 192: 5039-5049