Profiling tissue-resident T cell repertoires by RNA sequencing

Genome Medicine

Volumn 7, Issue 1, 2015, Pages

  Brown, Scott D ^a,b   Raeburn, Lisa A ^a,c   Holt, Robert A ^a,b,c  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c SIMON FRASER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CD3 ANTIGEN; T LYMPHOCYTE RECEPTOR; LYMPHOCYTE ANTIGEN RECEPTOR;

ARTICLE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; GENE EXPRESSION; LYMPHOCYTE COUNT; LYMPHOCYTE FUNCTION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE ANALYSIS; T LYMPHOCYTE; TUMOR MICROENVIRONMENT; GENETICS; HUMAN; IMMUNOLOGY; NEOPLASM;

HUMANS; NEOPLASMS; RECEPTORS, ANTIGEN, T-CELL; SEQUENCE ANALYSIS, RNA; T-LYMPHOCYTES;

EID: 84948737706     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-015-0248-x     Document Type: Article

References (31)

1. Woodsworth DJ, Castellarin M, Holt RA. Sequence analysis of T-cell repertoires in health and disease. Genome Med. 2013;5:98.
2. Freeman JD, Warren L, Webb JR, Nelson BH, Holt RA. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res. 2009;19:1817-24.
3. Robins HS, Campregher PV, Srivastava SK, Wacher A, Turtle CJ, Kahsai O, et al. Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood. 2009;114:4099-107.
4. Clemente CG, Mihm MC, Bufalino R, Zurrida S, Collini P, Cascinelli N. Prognostic value of tumor infiltrating lymphocytes in the vertical growth phase of primary cutaneous melanoma. Cancer. 1996;77:1303-10.
5. Sato E, Olson SH, Ahn J, Bundy B, Nishikawa H, Qian F, et al. Intraepithelial CD8+ tumor-infiltrating lymphocytes and a high CD8+/regulatory T cell ratio are associated with favorable prognosis in ovarian cancer. Proc Natl Acad Sci U S A. 2005;102:18538-43.
6. Cantaert T, Brouard S, Thurlings RM, Pallier A, Salinas GF, Braud C, et al. Alterations of the synovial T cell repertoire in anti-citrullinated protein antibody-positive rheumatoid arthritis. Arthritis Rheum. 2009;60:1944-56.
7. Jonasson L, Holm J, Skalli O, Bondjers G, Hansson GK. Regional accumulations of T cells, macrophages, and smooth muscle cells in the human atherosclerotic plaque. Arterioscler Thromb Vasc Biol. 1986;6:131-8.
8. Traugott U, Reinherz E, Raine C. Multiple sclerosis: distribution of T cell subsets within active chronic lesions. Science. 1983;219:308-10.
9. Matloubian M, Concepcion RJ, Ahmed R. CD4+ T cells are required to sustain CD8+ cytotoxic T-cell responses during chronic viral infection. J Virol. 1994;68:8056-63.
10. Moon JJ, Chu HH, Pepper M, McSorley SJ, Jameson SC, Kedl RM, et al. Naive CD4(+) T cell frequency varies for different epitopes and predicts repertoire diversity and response magnitude. Immunity. 2007;27:203-13.
11. Parrott DM V, Tait C, MacKenzie S, Mowat AM, Davies MDJ, Micklem HS. Analysis of the effector functions of different populations of mucosal lymphocytes. Ann N Y Acad Sci. 1983;409(1 The Secretory):307-20.
12. Warren RL, Freeman JD, Zeng T, Choe G, Munro S, Moore R, 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. 2011;21:790-7.
13. Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, et al. Derivation of HLA types from shotgun sequence datasets. Genome Med. 2012;4:95.
14. Boegel S, Löwer M, Schäfer M, Bukur T, De GJ, Boisguérin V, et al. HLA typing from RNA-Seq sequence reads. Genome Med. 2012;4:102.
15. Warren RL, Freeman DJ, Pleasance S, Watson P, Moore RA, Cochrane K, et al. Co-occurrence of anaerobic bacteria in colorectal carcinomas. Microbiome. 2013;1:16.
16. Bolotin DA, Shugay M, Mamedov IZ, Putintseva EV, Turchaninova MA, Zvyagin IV, et al. MiTCR: software for T-cell receptor sequencing data analysis. Nat Methods. 2013;10:813-4.
17. Lefranc M-P. IMGT, the International ImMunoGeneTics Information System. Cold Spring Harb Protoc. 2011;2011:595-603.
18. Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57-74.
19. Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigó R, et al. Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res. 2012;40:10073-83.
20. Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, et al. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 2010;38:e178.
21. Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323.
22. Brown SD, Warren RL, Gibb EA, Martin SD, Spinelli JJ, Nelson BH, et al. Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival. Genome Res. 2014;24:743-50.
23. Li W, Jaroszewski L, Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics. 2001;17:282-3.
24. Li W, Jaroszewski L, Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics. 2002;18:77-82.
25. R Core Team. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2013.
26. Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res. 2012;22:299-306.
27. Wu D, Sherwood A, Fromm JR, Winter SS, Dunsmore KP, Loh ML, et al. High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia. Sci Transl Med. 2012;4:134ra63.
28. Schumacher T, Bunse L, Pusch S, Sahm F, Wiestler B, Quandt J, et al. A vaccine targeting mutant IDH1 induces antitumour immunity. Nature. 2014;512:324-7.
29. Kreiter S, Vormehr M, van de Roemer N, Diken M, Löwer M, Diekmann J, et al. Mutant MHC class II epitopes drive therapeutic immune responses to cancer. Nature. 2015;520:692-6.
30. Tran E, Turcotte S, Gros A, Robbins PF, Lu Y-C, Dudley ME, et al. Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer. Science. 2014;344:641-5.
31. Lossius A, Johansen JN, Vartdal F, Robins H, Jurate Šaltyte B, Holmøy T, et al. High-throughput sequencing of TCR repertoires in multiple sclerosis reveals intrathecal enrichment of EBV-reactive CD8+ T cells. Eur J Immunol. 2014;44:3439-52.