Combined megaplex TCR isolation and SMART-based real-time quantitation methods for quantitating antigen-specific T cell clones in mycobacterial infection

Journal of Immunological Methods

Volumn 308, Issue 1-2, 2006, Pages 19-35

  Du, George ^a   Qiu, Liyou ^a   Shen, Ling ^b   Sehgal, Probhat ^c   Shen, Yun ^a   Huang, Dan ^a   Letvin, Norman L ^b   Chen, Zheng W ^a  

^a UNIVERSITY OF ILLINOIS   (United States)

^b BETH ISRAEL DEACONESS MEDICAL CENTER   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Clonal responses of Ag specific T cells; Gene expression; SMART cDNA; T cell receptor repertoires

Indexed keywords

COMPLEMENTARY DNA; GAMMA INTERFERON; MESSENGER RNA; T LYMPHOCYTE RECEPTOR;

ANTIGEN SPECIFICITY; ARTICLE; CELL CLONING; CELL ISOLATION; CONTROLLED STUDY; FLOW CYTOMETRY; GENE AMPLIFICATION; HUMAN; MYCOBACTERIOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PERIPHERAL BLOOD MONONUCLEAR CELL; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION; T LYMPHOCYTE; UNINDEXED SEQUENCE;

ANIMALS; BASE SEQUENCE; DNA; DNA PRIMERS; GENE REARRANGEMENT, BETA-CHAIN T-CELL ANTIGEN RECEPTOR; GENES, T-CELL RECEPTOR BETA; HAPLORHINI; IMMUNOLOGIC TECHNIQUES; RECEPTORS, ANTIGEN, T-CELL; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; T-LYMPHOCYTES; TUBERCULOSIS;

EID: 30844436332     PISSN: 00221759     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jim.2005.09.009     Document Type: Article

References (31)

1. Y. Akatsuka, E.G. Martin, A. Madonik, A.A. Barsoukov, and J.A. Hansen Rapid screening of T-cell receptor (TCR) variable gene usage by multiplex PCR: application for assessment of clonal composition Tissue Antigens 53 1999 122
2. J.D. Altman, P.A. Moss, P.J. Goulder, D.H. Barouch, M.G. McHeyzer-Williams, J.I. Bell, A.J. McMichael, and M.M. Davis Phenotypic analysis of antigen-specific T lymphocytes Science 274 1996 94
3. Z.W. Chen, Z.C. Kou, C. Lekutis, L. Shen, D. Zhou, M. Halloran, J. Li, J. Sodroski, D. Lee-Parritz, and N.L. Letvin T cell receptor V beta repertoire in an acute infection of rhesus monkeys with simian immunodeficiency viruses and a chimeric simian-human immunodeficiency virus J. Exp. Med. 182 1995 21
4. Z.W. Chen, L. Shen, J.D. Regan, Z. Kou, S.H. Ghim, and N.L. Letvin The T cell receptor gene usage by simian immunodeficiency virus gag-specific cytotoxic T lymphocytes in rhesus monkeys J. Immunol. 156 1996 1469
5. + T lymphocyte population J. Immunol. 166 2001 4525
6. R. Cheynier, S. Gratton, M. Halloran, I. Stahmer, N.L. Letvin, and S. Wain-Hobson Antigenic stimulation by BCG vaccine as an in vivo driving force for SIV replication and dissemination Nat. Med. 4 1998 421
7. G.B. Cohen, S.A. Islam, M.S. Noble, C. Lau, C. Brander, M.A. Altfeld, E.S. Rosenberg, J.E. Schmitz, T.O. Cameron, and S.A. Kalams Clonotype tracking of TCR repertoires during chronic virus infections Virology 304 2002 474
8. D.C. Douek, M.R. Betts, J.M. Brenchley, B.J. Hill, D.R. Ambrozak, K.L. Ngai, N.J. Karandikar, J.P. Casazza, and R.A. Koup 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. 168 2002 3099
9. R.B. Gallagher, B.Y. Yeap, W. Bi, K.J. Livak, N. Beaubier, S. Rao, C.D. Bloomfield, F.R. Appelbaum, M.S. Tallman, J.L. Slack, and C.L. Willman Quantitative real-time RT-PCR analysis of PML-RAR alpha mRNA in acute promyelocytic leukemia: assessment of prognostic significance in adult patients from intergroup protocol 0129 Blood 101 2003 2521
10. A. Gallard, G. Foucras, C. Coureau, and J.C. Guery Tracking T cell clonotypes in complex T lymphocyte populations by real-time quantitative PCR using fluorogenic complementarity-determining region-3-specific probes J. Immunol. Methods 270 2002 269
11. S. Gustincich, M. Contini, M. Gariboldi, M. Puopolo, K. Kadota, H. Bono, J. LeMieux, P. Walsh, P. Carninci, Y. Hayashizaki, Y. Okazaki, and E. Raviola Gene discovery in genetically labeled single dopaminergic neurons of the retina Proc. Natl. Acad. Sci. U. S. A. 101 2004 5069
12. M. Herrler Use of SMART-generated cDNA for differential gene expression studies J. Mol. Med. 78 2000 B23
13. P. Klenerman, V. Cerundolo, and P.R. Dunbar Tracking T cells with tetramers: new tales from new tools Nat. Rev., Immunol. 2 2002 263
14. Z.C. Kou, M. Halloran, D. Lee-Parritz, L. Shen, M. Simon, P.K. Sehgal, Y. Shen, and Z.W. Chen In vivo effects of a bacterial superantigen on macaque TCR repertoires J. Immunol. 160 1998 5170
15. M.J. Kuroda, J.E. Schmitz, D.H. Barouch, A. Craiu, T.M. Allen, A. Sette, D.I. Watkins, M.A. Forman, and N.L. Letvin Analysis of gag-specific cytotoxic T lymphocytes in simian immunodeficiency virus-infected rhesus monkeys by cell staining with a tetrameric major histocompatibility complex class I-peptide complex J. Exp. Med. 187 1998 1373
16. M. Larsson, X. Jin, B. Ramratnam, G.S. Ogg, J. Engelmayer, M.A. Demoitie, A.J. McMichael, W.I. Cox, R.M. Steinman, D. Nixon, and N. Bhardwaj A recombinant vaccinia virus based ELISPOT assay detects high frequencies of Pol-specific CD8 T cells in HIV-1-positive individuals Aids 13 1999 767
17. + T cell immune responses J. Immunol. Methods 261 2002 177
18. K.J. Livak, and T.D. Schmittgen Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method Methods 25 2001 402
19. K. Maslanka, T. Piatek, J. Gorski, and M. Yassai Molecular analysis of T cell repertoires. Spectratypes generated by multiplex polymerase chain reaction and evaluated by radioactivity or fluorescence Hum. Immunol. 44 1995 28
20. D. Meyer-Olson, N.H. Shoukry, K.W. Brady, H. Kim, D.P. Olson, K. Hartman, A.K. Shintani, C.M. Walker, and S.A. Kalams Limited T cell receptor diversity of HCV-specific T cell responses is associated with CTL escape J. Exp. Med. 200 2004 307
21. + T cells are detectable in most individuals with active HIV-1 infection, but decline with prolonged viral suppression Nat. Med. 5 1999 518
22. M. Rihl, D. Baeten, N. Seta, J. Gu, F. De Keyser, E.M. Veys, J.G. Kuipers, H. Zeidler, and D.T. Yu Technical validation of cDNA based microarray as screening technique to identify candidate genes in synovial tissue biopsy specimens from patients with spondyloarthropathy Ann. Rheum. Dis. 63 2004 498
23. C.P. Semighini, M. Marins, M.H. Goldman, and G.H. Goldman Quantitative analysis of the relative transcript levels of ABC transporter Atr genes in Aspergillus nidulans by real-time reverse transcription-PCR assay Appl. Environ. Microbiol. 68 2002 1351
24. D. Seth, M.D. Gorrell, P.H. McGuinness, M.A. Leo, C.S. Lieber, G.W. McCaughan, and P.S. Haber SMART amplification maintains representation of relative gene expression: quantitative validation by real time PCR and application to studies of alcoholic liver disease in primates J. Biochem. Biophys. Methods 55 2003 53
25. Y. Shen, D. Zhou, L. Qiu, X. Lai, M. Simon, L. Shen, Z. Kou, Q. Wang, L. Jiang, J. Estep, R. Hunt, M. Clagett, P.K. Sehgal, Y. Li, X. Zeng, C.T. Morita, M.B. Brenner, N.L. Letvin, and Z.W. Chen Adaptive immune response of V gamma2Vdelta2+ T cells during mycobacterial infections Science 295 2002 2255
26. J.J. van Dongen, A.W. Langerak, M. Bruggemann, P.A. Evans, M. Hummel, F.L. Lavender, E. Delabesse, F. Davi, E. Schuuring, R. Garcia-Sanz, J.H. van Krieken, J. Droese, D. Gonzalez, C. Bastard, H.E. White, M. Spaargaren, M. Gonzalez, A. Parreira, J.L. Smith, G.J. Morgan, M. Kneba, and E.A. Macintyre Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936 Leukemia 17 2003 2257
27. J. Wang, L. Hu, S.R. Hamilton, K.R. Coombes, and W. Zhang RNA amplification strategies for cDNA microarray experiments Biotechniques 34 2003 394
28. R. Wellenreuther, I. Schupp, A. Poustka, and S. Wiemann SMART amplification combined with cDNA size fractionation in order to obtain large full-length clones BMC Genomics 5 2004 36
29. D. Zhou, Y. Shen, L. Chalifoux, D. Lee-Parritz, M. Simon, P.K. Sehgal, L. Zheng, M. Halloran, and Z.W. Chen Mycobacterium bovis bacille Calmette-Guérin enhances pathogenicity of simian immunodeficiency virus infection and accelerates progression to AIDS in macaques: a role of persistent T cell activation in AIDS pathogenesis J. Immunol. 162 1999 2204
30. B. Zhumabayeva, L. Diatchenko, A. Chenchik, and P.D. Siebert Use of SMART-generated cDNA for gene expression studies in multiple human tumors Biotechniques 30 2001 158
31. B. Zhumabayeva, A. Chenchik, P.D. Siebert, and M. Herrler Disease profiling arrays: reverse format cDNA arrays complimentary to microarrays Adv. Biochem. Eng. Biotechnol. 86 2004 191