Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling

Frontiers in Immunology

Volumn 4, Issue DEC, 2013, Pages

  Mamedov, Ilgar Z ^a,b   Britanova, Olga V ^a   Zvyagin, Ivan V ^a,b   Turchaninova, Maria A ^a   Bolotin, Dmitriy A ^a   Putintseva, Ekaterina V ^a   Lebedev, Yuriy B ^a   Chudakov, Dmitriy M ^a,b  

^a SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^b MASARYK UNIVERSITY   (Czech Republic)

Author keywords

BCR repertoires; CDNA libraries; IG repertoires; MiTCR; NGS applications; T cell receptor; T cell receptor repertoire; TCR repertoires

Indexed keywords

EID: 84892159495     PISSN: None     EISSN: 16643224     Source Type: Journal    
DOI: 10.3389/fimmu.2013.00456     Document Type: Article

References (30)

1. Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res (2009) 19:1817-24. doi:10.1101/gr.092924.109
2. 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. doi:10.1182/blood-2009-04-217604
3. Ravn U, Gueneau F, Baerlocher L, Osteras M, Desmurs M, Malinge P, et al. By-passing in vitro screening-next generation sequencing technologies applied to antibody display and in silico candidate selection. Nucleic Acids Res (2010) 38:e193. doi:10.1093/nar/gkq789
4. Reddy ST, Ge X, Miklos AE, Hughes RA, Kang SH, Hoi KH, et al. Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells. Nat Biotechnol (2010) 28:965-9. doi:10.1038/nbt.1673
5. Robins HS, Srivastava SK, Campregher PV, Turtle CJ, Andriesen J, Riddell SR, et al. Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci Transl Med (2010) 2:47ra64. doi:10.1126/scitranslmed.3001442
6. Wang C, Sanders CM, Yang Q, Schroeder HW Jr, Wang E, Babrzadeh F, et al. High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proc Natl Acad Sci U S A (2010) 107:1518-23. doi:10.1073/pnas.0913939107
7. Nguyen P, Ma J, Pei D, Obert C, Cheng C, Geiger TL. Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire. BMC Genomics (2011) 12:106. doi:10.1186/1471-2164-12-106
8. 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. doi:10.1101/gr.115428.110
9. Baum PD, Venturi V, Price DA. Wrestling with the repertoire: the promise and perils of next generation sequencing for antigen receptors. Eur J Immunol (2012) 42:2834-9. doi:10.1002/eji.201242999
10. Bolotin DA, Mamedov IZ, Britanova OV, Zvyagin IV, Shagin D, Ustyugova SV, et al. Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms. Eur J Immunol (2012) 42:3073-83. doi:10.1002/eji.201242517
11. Klarenbeek PL, Remmerswaal EB, Ten Berge IJ, Doorenspleet ME, Van Schaik BD, Esveldt RE, et al. Deep sequencing of antiviral T-cell responses to HCMV and EBV in humans reveals a stable repertoire that is maintained for many years. PLoS Pathog (2012) 8:e1002889. doi:10.1371/journal.ppat.1002889
12. 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) 19:1534-41. doi:10.1038/nm.3359
13. Turchaninova MA, Britanova OV, Bolotin DA, Shugay M, Putintseva EV, Staroverov DB, et al. Pairing of T-cell receptor chains via emulsion PCR. Eur J Immunol (2013) 43:2507-15. doi:10.1002/eji.201343453
14. Mamedov IZ, Britanova OV, Chkalina AV, Staroverov DB, Amosova AL, Mishin AS, et al. Individual characterization of stably expanded T cell clones in ankylosing spondylitis patients. Autoimmunity (2009) 42:525-36. doi:10.1080/08916930902960362
15. Britanova OV, Staroverov DB, Chkalina AV, Kotlobay AA, Zvezdova ES, Bochkova AG, et al. Single high-dose treatment with glucosaminyl-muramyl dipeptide is ineffective in treating ankylosing spondylitis. Rheumatol Int (2011) 31:1101-3. doi:10.1007/s00296-010-1663-3
16. Mamedov IZ, Britanova OV, Bolotin DA, Chkalina AV, Staroverov DB, Zvyagin IV, et al. Quantitative tracking of T cell clones after haematopoietic stem cell transplantation. EMBO Mol Med (2011) 3:201-7. doi:10.1002/emmm.201100129
17. Britanova OV, Bochkova AG, Staroverov DB, Fedorenko DA, Bolotin DA, Mamedov IZ, et al. First autologous hematopoietic SCT for ankylosing spondylitis: a case report and clues to understanding the therapy. Bone Marrow Transplant (2012) 47:1479-81. doi:10.1038/bmt.2012.44
18. Luk'ianov SA, Gurskaia NG, Luk'ianov KA, Tarabykin VS, Sverdlov ED. Highly-effective subtractive hybridization of cDNA. Bioorg Khim (1994) 20: 701-4.
19. Porter-Jordan K, Rosenberg EI, Keiser JF, Gross JD, Ross AM, Nasim S, et al. Nested polymerase chain reaction assay for the detection of Cytomegalovirus overcomes false positives caused by contamination with fragmented DNA. J Med Virol (1990) 30:85-91. doi:10.1002/jmv.1890300202
20. Matz M, Shagin D, Bogdanova E, Britanova O, Lukyanov S, Diatchenko L, et al. Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res (1999) 27:1558-60. doi:10.1093/nar/27.6.1558
21. Douek DC, Betts MR, Brenchley JM, Hill BJ, Ambrozak DR, Ngai KL, et al. A novel approach to the analysis of specificity, clonality, and frequency of HIV-specific T cell responses reveals a potential mechanism for control of viral escape. J Immunol (2002) 168:3099-104.
22. Elnifro EM, Ashshi AM, Cooper RJ, Klapper PE. Multiplex PCR: optimization and application in diagnostic virology. Clin Microbiol Rev (2000) 13:559-70. doi:10.1128/CMR.13.4.559-570.2000
23. Markoulatos P, Siafakas N, Moncany M. Multiplex polymerase chain reaction: a practical approach. J Clin Lab Anal (2002) 16:47-51. doi:10.1002/jcla.2058
24. Paillard F, Sterkers G, Vaquero C. Transcriptional and post-transcriptional regulation of TcR, CD4 and CD8 gene expression during activation of normal human T lymphocytes. EMBO J (1990) 9:1867-72.
25. Doskow JR, Wilkinson MF. CD3-gamma,-delta,-epsilon,-zeta, T-cell receptor-alpha and-beta transcripts are independently regulated during thymocyte ontogeny and T-cell activation. Immunology (1992) 77:465-8.
26. Andersen RS, Kvistborg P, Frosig TM, Pedersen NW, Lyngaa R, Bakker AH, et al. Parallel detection of antigen-specific T cell responses by combinatorial encoding of MHC multimers. Nat Protoc (2012) 7:891-902. doi:10.1038/nprot.2012.037
27. Franz B, May KF Jr, Dranoff G, Wucherpfennig K. Ex vivo characterization and isolation of rare memory B cells with antigen tetramers. Blood (2011) 118:348-57. doi:10.1182/blood-2011-03-341917
28. Thomas N, Heather J, Ndifon W, Shawe-Taylor J, Chain B. Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. Bioinformatics (2013) 29:542-50. doi:10.1093/bioinformatics/btt004
29. 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. doi:10.1038/nmeth.2555
30. Kivioja T, Vaharautio A, Karlsson K, Bonke M, Enge M, Linnarsson S, et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods (2012) 9:72-4. doi:10.1038/nmeth.1778