publication . Article . Other literature type . 2017

Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state.

Leo Swadling; Shaked Afik; Eleanor Barnes;
Open Access English
  • Published: 19 Sep 2017 Journal: Nucleic Acids Research, volume 45, issue 16 (issn: 0305-1048, eissn: 1362-4962, Copyright policy)
Abstract
ABSTRACT The T cell compartment must contain diversity in both TCR repertoire and cell state to provide effective immunity against pathogens 1,2 . However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state at the single cell level because most analysis of the TCR repertoire has, to date, aggregated information from populations of cells. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current protocols to directly sequence the TCR require the use of long sequencing reads, increasing the cost and decreasing the number of ...
Subjects
free text keywords: Methods Online, RNA characterisation and manipulation, Computational Methods, Massively Parallel (Deep) Sequencing, Genetics
Funded by
NIH| Systems Biological Analysis of Innate and Adaptive Responses to Vaccination
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1U19AI090023-01
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
59 references, page 1 of 4

1. Appay,V., Dunbar,P.R., Callan,M., Klenerman,P., Gillespie,G.M.A., Papagno,L., Ogg,G.S., King,A., Lechner,F., Spina,C.A. et al. (2002) Memory CD8+ T cells vary in differentiation phenotype in different persistent virus infections. Nat. Med., 8, 379-385. [OpenAIRE]

2. Newell,E.W., Sigal,N., Bendall,S.C., Nolan,G.P. and Davis,M.M. (2012) Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. Immunity, 36, 142-152.

3. Chattopadhyay,P.K. and Roederer,M. (2015) A mine is a terrible thing to waste: high content, single cell technologies for comprehensive immune analysis. Am. J. Transplant, 15, 1155-1161.

4. Fuertes Marraco,S.A., Soneson,C., Cagnon,L., Gannon,P.O., Allard,M., Maillard,S.A., Montandon,N., Rufer,N., Waldvogel,S., Delorenzi,M. et al. (2015) Long-lasting stem cell like memory CD8 T cells with a na¨ıve-like profile upon yellow fever vaccination. Sci. Transl. Med., 7, 282ra48.

5. Pulko,V., Davies,J.S., Martinez,C., Lanteri,M.C., Busch,M.P., Diamond,M.S., Knox,K., Bush,E.C., Sims,P.A., Sinari,S. et al. (2016) Human memory T cells with a naive phenotype accumulate with aging and respond to persistent viruses. Nat. Immunol., 17, 966-975. [OpenAIRE]

6. Swadling,L., Capone,S., Antrobus,R.D., Brown,A., Richardson,R., Newell,E.W., Halliday,J., Kelly,C., Bowen,D., Fergusson,J. et al. (2014) A human vaccine strategy based on chimpanzee adenoviral and MVA vectors that primes, boosts, and sustains functional HCV-specific T cell memory. Sci. Transl. Med., 6, 261ra153.

7. Venturi,V., Quigley,M.F., Greenaway,H.Y., Ng,P.C., Ende,Z.S., McIntosh,T., Asher,T.E., Almeida,J.R., Levy,S., Price,D.A. et al. (2011) A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. J. Immunol., 186, 4285-4294.

8. Robins,H.S., Srivastava,S.K., Campregher,P.V., Turtle,C.J., Andriesen,J., Riddell,S.R., Carlson,C.S. and Warren,E.H. (2010) Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci. Transl. Med., 2, 47ra64.

9. Venturi,V., Price,D.A., Douek,D.C. and Davenport,M.P. (2008) The molecular basis for public T-cell responses? Nat. Rev. Immunol., 8, 231-238.

10. Venturi,V., Kedzierska,K., Price,D.A., Doherty,P.C., Douek,D.C., Turner,S.J. and Davenport,M.P. (2006) Sharing of T cell receptors in antigen-specific responses is driven by convergent recombination. Proc. Natl. Acad. Sci. U.S.A., 103, 18691-18696. [OpenAIRE]

11. Ji,X., Lyu,S.-C., Spindler,M., Bacchetta,R., Goncharov,I., Han,A., Glanville,J., Wang,W., Roncarolo,M., Meyer,E. et al. (2015) Deep profiling of single T cell receptor repertoire and phenotype with targeted RNA-seq (TECH2P. 927). J. Immunol., 194, 206-237.

12. Li,B., Li,T., Pignon,J.-C., Wang,B., Wang,J., Shukla,S.A., Dou,R., Chen,Q., Hodi,F.S., Choueiri,T.K. et al. (2016) Landscape of tumor-infiltrating T cell repertoire of human cancers. Nat. Genet., 48, 725-732. [OpenAIRE]

13. Han,A., Glanville,J., Hansmann,L. and Davis,M.M. (2014) Linking T-cell receptor sequence to functional phenotype at the single-cell level. Nat. Biotechnol., 32, 684-692.

14. Li,B. and Dewey,C.N. (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 323.

15. Stubbington,M.J.T., L o¨nnberg,T., Proserpio,V., Clare,S., Speak,A.O., Dougan,G. and Teichmann,S.A. (2016) T cell fate and clonality inference from single-cell transcriptomes. Nat. Methods, 13, 329-332. [OpenAIRE]

59 references, page 1 of 4
Abstract
ABSTRACT The T cell compartment must contain diversity in both TCR repertoire and cell state to provide effective immunity against pathogens 1,2 . However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state at the single cell level because most analysis of the TCR repertoire has, to date, aggregated information from populations of cells. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current protocols to directly sequence the TCR require the use of long sequencing reads, increasing the cost and decreasing the number of ...
Subjects
free text keywords: Methods Online, RNA characterisation and manipulation, Computational Methods, Massively Parallel (Deep) Sequencing, Genetics
Funded by
NIH| Systems Biological Analysis of Innate and Adaptive Responses to Vaccination
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1U19AI090023-01
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
59 references, page 1 of 4

1. Appay,V., Dunbar,P.R., Callan,M., Klenerman,P., Gillespie,G.M.A., Papagno,L., Ogg,G.S., King,A., Lechner,F., Spina,C.A. et al. (2002) Memory CD8+ T cells vary in differentiation phenotype in different persistent virus infections. Nat. Med., 8, 379-385. [OpenAIRE]

2. Newell,E.W., Sigal,N., Bendall,S.C., Nolan,G.P. and Davis,M.M. (2012) Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. Immunity, 36, 142-152.

3. Chattopadhyay,P.K. and Roederer,M. (2015) A mine is a terrible thing to waste: high content, single cell technologies for comprehensive immune analysis. Am. J. Transplant, 15, 1155-1161.

4. Fuertes Marraco,S.A., Soneson,C., Cagnon,L., Gannon,P.O., Allard,M., Maillard,S.A., Montandon,N., Rufer,N., Waldvogel,S., Delorenzi,M. et al. (2015) Long-lasting stem cell like memory CD8 T cells with a na¨ıve-like profile upon yellow fever vaccination. Sci. Transl. Med., 7, 282ra48.

5. Pulko,V., Davies,J.S., Martinez,C., Lanteri,M.C., Busch,M.P., Diamond,M.S., Knox,K., Bush,E.C., Sims,P.A., Sinari,S. et al. (2016) Human memory T cells with a naive phenotype accumulate with aging and respond to persistent viruses. Nat. Immunol., 17, 966-975. [OpenAIRE]

6. Swadling,L., Capone,S., Antrobus,R.D., Brown,A., Richardson,R., Newell,E.W., Halliday,J., Kelly,C., Bowen,D., Fergusson,J. et al. (2014) A human vaccine strategy based on chimpanzee adenoviral and MVA vectors that primes, boosts, and sustains functional HCV-specific T cell memory. Sci. Transl. Med., 6, 261ra153.

7. Venturi,V., Quigley,M.F., Greenaway,H.Y., Ng,P.C., Ende,Z.S., McIntosh,T., Asher,T.E., Almeida,J.R., Levy,S., Price,D.A. et al. (2011) A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. J. Immunol., 186, 4285-4294.

8. Robins,H.S., Srivastava,S.K., Campregher,P.V., Turtle,C.J., Andriesen,J., Riddell,S.R., Carlson,C.S. and Warren,E.H. (2010) Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci. Transl. Med., 2, 47ra64.

9. Venturi,V., Price,D.A., Douek,D.C. and Davenport,M.P. (2008) The molecular basis for public T-cell responses? Nat. Rev. Immunol., 8, 231-238.

10. Venturi,V., Kedzierska,K., Price,D.A., Doherty,P.C., Douek,D.C., Turner,S.J. and Davenport,M.P. (2006) Sharing of T cell receptors in antigen-specific responses is driven by convergent recombination. Proc. Natl. Acad. Sci. U.S.A., 103, 18691-18696. [OpenAIRE]

11. Ji,X., Lyu,S.-C., Spindler,M., Bacchetta,R., Goncharov,I., Han,A., Glanville,J., Wang,W., Roncarolo,M., Meyer,E. et al. (2015) Deep profiling of single T cell receptor repertoire and phenotype with targeted RNA-seq (TECH2P. 927). J. Immunol., 194, 206-237.

12. Li,B., Li,T., Pignon,J.-C., Wang,B., Wang,J., Shukla,S.A., Dou,R., Chen,Q., Hodi,F.S., Choueiri,T.K. et al. (2016) Landscape of tumor-infiltrating T cell repertoire of human cancers. Nat. Genet., 48, 725-732. [OpenAIRE]

13. Han,A., Glanville,J., Hansmann,L. and Davis,M.M. (2014) Linking T-cell receptor sequence to functional phenotype at the single-cell level. Nat. Biotechnol., 32, 684-692.

14. Li,B. and Dewey,C.N. (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 323.

15. Stubbington,M.J.T., L o¨nnberg,T., Proserpio,V., Clare,S., Speak,A.O., Dougan,G. and Teichmann,S.A. (2016) T cell fate and clonality inference from single-cell transcriptomes. Nat. Methods, 13, 329-332. [OpenAIRE]

59 references, page 1 of 4
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