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tel-00827710, version 1 - 29 May 2013 5. References 1. Arens R, Schoenberger SP (2010) Plasticity in programming of effector and memory CD8 T-cell formation. Immunol Rev 235 (1):190-205. doi:10.1111/j.0105-2896.2010.00899.x 2. Schumacher TNM, Gerlach C, Heijst JWJv (2010) Mapping the life histories of T cells. Nature Publishing Group 10 (9):621-631. doi:10.1038/nri2822 3. Coulie PG, Karanikas V, Lurquin C, Colau D, Connerotte T, Hanagiri T, Van Pel A, Lucas S, Godelaine D, Lonchay C, Marchand M, Van Baren N, Boon T (2002) Cytolytic T-cell responses of cancer patients vaccinated with a MAGE antigen. Immunol Rev 188:33-42 4. Lamoreaux L, Roederer M, Koup R (2006) Intracellular cytokine optimization and standard operating procedure. Nat Protoc 1 (3):1507-1516. doi:10.1038/nprot.2006.268 5. Sun Y, Iglesias E, Samri A, Kamkamidze G, Decoville T, Carcelain G, Autran B (2003) A systematic comparison of methods to measure HIV-1 specific CD8 T cells. J Immunol Methods 272 (1-2):23-34 6. Altman JD, Moss PA, Goulder PJ, Barouch DH, McHeyzer-Williams MG, Bell JI, McMichael AJ, Davis MM (1996) Phenotypic analysis of antigen-specific T lymphocytes. Science 274 (5284):94-96 7. Altman JD, Davis MM (2003) MHC-peptide tetramers to visualize antigen-specific T cells. Curr Protoc Immunol Chapter 17:Unit 17.13. doi:10.1002/0471142735.im1703s53 8. Davis MM, Altman JD, Newell EW (2011) Interrogating the repertoire: broadening the scope of peptide–MHC multimer analysis. Nature Reviews Immunology 11 (8):551-558. doi:10.1038/nri3020 9. Klenerman P, Cerundolo V, Dunbar PR (2002) TRACKING T CELLS WITH TETRAMERS: NEW TALES FROM NEW TOOLS. Nature Reviews Immunology 2 (4):263-272. doi:10.1038/nri777 10. Romero P, Valmori D, Pittet MJ, Zippelius A, Rimoldi D, Lévy F, Dutoit V, Ayyoub M, Rubio-Godoy V, Michielin O, Guillaume P, Batard P, Luescher IF, Lejeune F, Liénard D, Rufer N, Dietrich P-Y, Speiser DE, Cerottini J-C (2002) Antigenicity and immunogenicity of Melan-A/MART-1 derived peptides as targets for tumor reactive CTL in human melanoma. Immunol Rev 188:81-96 224

tel-00827710, version 1 - 29 May 2013 11. Baitsch L, Baumgaertner P, Devevre E, Raghav SK, Legat A, Barba L, Wieckowski S, Bouzourene H, Deplancke B, Romero P, Rufer N, Speiser DE (2011) Exhaustion of tumor-specific CD8+ T cells in metastases from melanoma patients. The Journal of clinical investigation 121 (6):2350-2360. doi:10.1172/JCI46102 12. Kanodia S, Wieder E, Lu S, Talpaz M, Alatrash G, Clise-Dwyer K, Molldrem JJ (2010) PR1-specific T cells are associated with unmaintained cytogenetic remission of chronic myelogenous leukemia after interferon withdrawal. PLoS ONE 5 (7):e11770. doi:10.1371/journal.pone.0011770 13. Rosenberg SA, Dudley ME, Restifo NP (2008) Cancer immunotherapy. N Engl J Med 359 (10):1072. doi:10.1056/NEJMc081511 14. Appay V, Douek DC, Price DA (2008) CD8+ T cell efficacy in vaccination and disease. Nat Med 14 (6):623-628. doi:10.1038/nm.f.1774 15. Ma Q, Wang C, Jones D, Quintanilla KE, Li D, Wang Y, Wieder ED, Clise-Dwyer K, Alatrash G, Mj Y, Munsell MF, Lu S, Qazilbash MH, Molldrem JJ (2010) Adoptive transfer of PR1 cytotoxic T lymphocytes associated with reduced leukemia burden in a mouse acute myeloid leukemia xenograft model. Cytotherapy 12 (8):1056-1062. doi:10.3109/14653249.2010.506506 16. Wooldridge L, Lissina A, Cole DK, Berg HAvd, Price DA, Sewell AK (2009) Tricks with tetramers: how to get the most from multimeric peptide-MHC. Immunology 126 (2):147- 164. doi:10.1111/j.1365-2567.2008.02848.x 17. Bakker AH, Schumacher TNM (2005) MHC multimer technology: current status and future prospects. Curr Opin Immunol 17 (4):428-433. doi:10.1016/j.coi.2005.06.008 18. Toebes M, Coccoris M, Bins A, Rodenko B, Gomez R, Nieuwkoop NJ, Van De Kasteele W, Rimmelzwaan GF, Haanen JBAG, Ovaa H, Schumacher TNM (2006) Design and use of conditional MHC class I ligands. Nat Med 12 (2):246-251. doi:10.1038/nm1360 19. Hadrup SR, Toebes M, Rodenko B, Bakker AH, Egan DA, Ovaa H, Schumacher TNM (2009) High-throughput T-cell epitope discovery through MHC peptide exchange. Methods Mol Biol 524:383-405. doi:10.1007/978-1-59745-450-6_28 20. Newell EW, Klein LO, Yu W, Davis MM (2009) Simultaneous detection of many T-cell specificities using combinatorial tetramer staining. Nature Publishing Group 6 (7):497- 499. doi:10.1038/nmeth.1344 Page 225 of 256

tel-00827710, version 1 - 29 May 2013<br />

11. Baitsch L, Baumgaertner P, Devevre E, Raghav SK, Legat A, Barba L, Wieckowski S,<br />

Bouzourene H, Deplancke B, Romero P, Rufer N, Speiser DE (2011) Exhaustion of<br />

tumor-specific CD8+ T cells in m<strong>et</strong>astases from melanoma patients. The Journal of<br />

clinical investigation 121 (6):2350-2360. doi:10.1172/JCI46102<br />

12. Kanodia S, Wie<strong>de</strong>r E, Lu S, Talpaz M, Alatrash G, Clise-Dwyer K, Molldrem JJ (2010)<br />

PR1-specific T cells are associated with unmaintained cytogen<strong>et</strong>ic remission of chronic<br />

myelogenous leukemia after interferon withdrawal. PLoS ONE 5 (7):e11770.<br />

doi:10.1371/journal.pone.0011770<br />

13. Rosenberg SA, Dudley ME, Restifo NP (2008) Cancer immunotherapy. N Engl J Med<br />

359 (10):1072. doi:10.1056/NEJMc081511<br />

14. Appay V, Douek DC, Price DA (2008) CD8+ T cell efficacy in vaccination and disease.<br />

Nat Med 14 (6):623-628. doi:10.1038/nm.f.1774<br />

15. Ma Q, Wang C, Jones D, Quintanilla KE, Li D, Wang Y, Wie<strong>de</strong>r ED, Clise-Dwyer K,<br />

Alatrash G, Mj Y, Munsell MF, Lu S, Qazilbash MH, Molldrem JJ (2010) Adoptive<br />

transfer of PR1 cytotoxic T lymphocytes associated with reduced leukemia bur<strong>de</strong>n in a<br />

mouse acute myeloid leukemia xenograft mo<strong>de</strong>l. Cytotherapy 12 (8):1056-1062.<br />

doi:10.3109/14653249.2010.506506<br />

16. Wooldridge L, Lissina A, Cole DK, Berg HAvd, Price DA, Sewell AK (2009) Tricks with<br />

t<strong>et</strong>ramers: how to g<strong>et</strong> the most from multimeric pepti<strong>de</strong>-MHC. Immunology 126 (2):147-<br />

164. doi:10.1111/j.1365-2567.2008.02848.x<br />

17. Bakker AH, Schumacher TNM (2005) MHC multimer technology: current status and<br />

future prospects. Curr Opin Immunol 17 (4):428-433. doi:10.1016/j.coi.2005.06.008<br />

18. Toebes M, Coccoris M, Bins A, Ro<strong>de</strong>nko B, Gomez R, Nieuwkoop NJ, Van De Kasteele<br />

W, Rimmelzwaan GF, Haanen JBAG, Ovaa H, Schumacher TNM (2006) Design and use<br />

of conditional MHC class I ligands. Nat Med 12 (2):246-251. doi:10.1038/nm1360<br />

19. Hadrup SR, Toebes M, Ro<strong>de</strong>nko B, Bakker AH, Egan DA, Ovaa H, Schumacher TNM<br />

(2009) High-throughput T-cell epitope discovery through MHC pepti<strong>de</strong> exchange.<br />

M<strong>et</strong>hods Mol Biol 524:383-405. doi:10.1007/978-1-59745-450-6_28<br />

20. Newell EW, Klein LO, Yu W, Davis MM (2009) Simultaneous d<strong>et</strong>ection of many T-cell<br />

specificities using combinatorial t<strong>et</strong>ramer staining. Nature Publishing Group 6 (7):497-<br />

499. doi:10.1038/nm<strong>et</strong>h.1344<br />

Page 225 of 256

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