Cancer testis antigens in myelodysplastic syndromes revisited: a targeted RNA-seq approach

References

• Arber DA, Orazi A, Hasserjian R, Thiele J, Borowitz MJ, Le Beau MM, Bloomfield CD, Cazzola M, Vardiman JW. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016 May;127(20):2391–9. doi:10.1182/blood-2016-03-643544.
   PubMed Web of Science ®Google Scholar
• Platzbecker U. Treatment of MDS. Blood. 2019 Mar;133(10):1096–1107. doi:10.1182/blood-2018-10-844696.
   PubMed Web of Science ®Google Scholar
• Bart J, Groen HJM, van der Graaf WTA, Hollema H, Hendrikse NH, Vaalburg W, Sleijfer DT, de Vries EG. An oncological view on the blood-testis barrier. Lancet Oncol. 2002 Jun;3(6):357–363. doi:10.1016/S1470-2045(02)00776-3.
   PubMed Web of Science ®Google Scholar
• Nishikawa H, Maeda Y, Ishida T, Gnjatic S, Sato E, Mori F, Sugiyama D, Ito A, Fukumori Y, Utsunomiya A, et al. Cancer/testis antigens are novel targets of immunotherapy for adult T-cell leukemia/lymphoma. Blood. 2012 Mar;119(13):3097–3104. doi:10.1182/blood-2011-09-379982.
   PubMed Web of Science ®Google Scholar
• Rezvani K, Yong ASM, Tawab A, Jafarpour B, Eniafe R, Mielke S, Savani BN, Keyvanfar K, Li Y, Kurlander R, et al. Ex vivo characterization of polyclonal memory CD8+ T-cell responses to PRAME-specific peptides in patients with acute lymphoblastic leukemia and acute and chronic myeloid leukemia. Blood. 2009 Mar;113(10):2245–2255. doi:10.1182/blood-2008-03-144071.
   PubMed Web of Science ®Google Scholar
• Goodyear O, Piper K, Khan N, Starczynski J, Mahendra P, Pratt G, Moss P. CD8+T cells specific for cancer germline gene antigens are found in many patients with multiple myeloma, and their frequency correlates with disease burden. Blood. 2005 Dec;106(13):4217–4224. doi:10.1182/blood-2005-02-0563.
   PubMed Web of Science ®Google Scholar
• Wang C, Gu Y, Zhang K, Xie K, Zhu M, Dai N, Jiang Y, Guo X, Liu M, Dai J, et al. Systematic identification of genes with a cancer-testis expression pattern in 19 cancer types. Nat Commun. 2016 Jan;7(1):10499. doi:10.1038/ncomms10499.
   PubMedGoogle Scholar
• Jungbluth AA, Chen Y-T, Stockert E, Busam KJ, Kolb D, Iversen K, Coplan K, Williamson B, Altorki N, Old LJ, et al. Immunohistochemical analysis of NY-ESO-1 antigen expression in normal and malignant human tissues. Int J Cancer. 2001 Jun;92(6):856–860. doi:10.1002/ijc.1282.
   PubMed Web of Science ®Google Scholar
• Mercer TR, Clark MB, Crawford J, Brunck ME, Gerhardt DJ, Taft RJ, Nielsen LK, Dinger ME, Mattick JS. Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. Nat Protoc. 2014 May;9(5):989–1009. doi:10.1038/nprot.2014.058.
   PubMed Web of Science ®Google Scholar
• Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009 Jan;10(1):57–63. NIH Public Access. doi:10.1038/nrg2484.
   PubMed Web of Science ®Google Scholar
• Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol. 2012 Jan;30(1):99–104. Nature Publishing Group. doi:10.1038/nbt.2024.
   Web of Science ®Google Scholar
• Hart T, Komori H, LaMere S, Podshivalova K, Salomon DR. Finding the active genes in deep RNA-seq gene expression studies. BMC Genomics. 2013 Nov;14(1):778. doi:10.1186/1471-2164-14-778.
   PubMedGoogle Scholar
• Fenaux P, Mufti GJ, Hellstrom-Lindberg E, Santini V, Finelli C, Giagounidis A, Schoch R, Gattermann N, Sanz G, List A, et al. Efficacy of azacitidine compared with that of conventional care regimens in the treatment of higher-risk myelodysplastic syndromes: a randomised, open-label, phase III study. Lancet Oncol. 2009 Mar;10(3):223–232. doi:10.1016/S1470-2045(09)70003-8.
   PubMed Web of Science ®Google Scholar
• Almstedt M, Blagitko-Dorfs N, Duque-Afonso J, Karbach J, Pfeifer D, Jäger E, Lübbert M. The DNA demethylating agent 5-aza-2′-deoxycytidine induces expression of NY-ESO-1 and other cancer/testis antigens in myeloid leukemia cells. Leuk Res. 2010 Jul;34(7):899–905. doi:10.1016/j.leukres.2010.02.004.
   PubMed Web of Science ®Google Scholar
• Goodyear O, Agathanggelou A, Novitzky-Basso I, Siddique S, McSkeane T, Ryan G, Vyas P, Cavenagh J, Stankovic T, Moss P, et al. Induction of a CD8+ T-cell response to the MAGE cancer testis antigen by combined treatment with azacitidine and sodium valproate in patients with acute myeloid leukemia and myelodysplasia. Blood. 2010 Sep;116(11):1908–1918. doi:10.1182/blood-2009-11-249474.
   PubMed Web of Science ®Google Scholar
• Vardiman JW, Thiele J, Arber DA, Brunning RD, Borowitz MJ, Porwit A, Harris NL, Le Beau MM, Hellström-Lindberg E, Tefferi A, et al. The 2008 revision of the World Health Organization (WHO) classification of myeloid neoplasms and acute leukemia: rationale and important changes. Blood. 2009 Jul;114(5), 937–951.
   PubMed Web of Science ®Google Scholar
• Arber DA, Orazi A, Hasserjian R, Thiele J, Borowitz MJ, Le Beau MM, Bloomfield CD, Cazzola M, Vardiman JW. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016 May;127(20), 2391–2405.
   PubMed Web of Science ®Google Scholar
• GESMD. Guías españolas de diagnóstico y tratamiento de los síndromes mielodisplásicos y la leucemia mielomonocítica crónica Grupo Español de Síndromes Mielodisplásicos (GESMD). Haematologica. 2012;97(Suppl. 5).
   Google Scholar
• Cheson BD, Greenberg PL, Bennett JM, Lowenberg B, Wijermans PW, Nimer SD, Pinto A, Beran M, de Witte TM, Stone RM, et al. Clinical application and proposal for modification of the International Working Group (IWG) response criteria in myelodysplasia. Blood. 2006 Jul;108(2):419–425. doi:10.1182/blood-2005-10-4149.
   PubMed Web of Science ®Google Scholar
• Moutaftsi M, Peters B, Pasquetto V, Tscharke DC, Sidney J, Bui -H-H, Grey H, Sette A. A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus. Nat Biotechnol. 2006 Jul;24(7):817–819. doi:10.1038/nbt1215.
   PubMed Web of Science ®Google Scholar
• Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society: Series B (Methodological). 1995;57(1):289–300. WileyRoyal Statistical Society. doi:10.1111/j.2517-6161.1995.tb02031.x.
   Web of Science ®Google Scholar
• Simpson AJG, Caballero OL, Jungbluth A, Chen YT, Old LJ. Cancer/testis antigens, gametogenesis and cancer. Nat Rev Cancer. 2005;5(8):615–625. doi:10.1038/nrc1669.
   PubMed Web of Science ®Google Scholar
• Hofmann O, Caballero OL, Stevenson BJ, Chen Y-T, Cohen T, Chua R, Maher CA, Panji S, Schaefer U, Kruger A, et al. Genome-wide analysis of cancer/testis gene expression. Proc Natl Acad Sci. 2008 Dec;105(51), 20422–20427.
   PubMed Web of Science ®Google Scholar
• Loriot A, Boon T, De Smet C. Five new human cancer-germline genes identified among 12 genes expressed in spermatogonia. Int J Cancer. 2003 Jun;105(3):371–376. doi:10.1002/ijc.11104.
   PubMed Web of Science ®Google Scholar
• Grunwald C, Koslowski M, Arsiray T, Dhaene K, Praet M, Victor A, Morresi-Hauf A, Lindner M, Passlick B, Lehr H-A, et al. Expression of multiple epigenetically regulated cancer/germline genes in nonsmall cell lung cancer. Int J Cancer. 2006 May;118(10):2522–2528. doi:10.1002/ijc.21669.
   PubMed Web of Science ®Google Scholar
• Gkountela S, Castro-Giner F, Szczerba BM, Vetter M, Landin J, Scherrer R, Krol I, Scheidmann MC, Beisel C, Stirnimann CU, et al. Circulating tumor cell clustering shapes DNA methylation to enable metastasis seeding. Cell. 2019;176(1–2):98–112.e14. doi:10.1016/j.cell.2018.11.046.
   PubMed Web of Science ®Google Scholar
• Wang Y, Han KJ, Pang XW, Vaughan HA, Qu W, Dong XY, Peng J-R, Zhao H-T, Rui J-A, Leng X-S, et al. Large scale identification of human hepatocellular carcinoma-associated antigens by autoantibodies. J Immunol. 2002;169(2):1102–1109. doi:10.4049/jimmunol.169.2.1102.
   PubMed Web of Science ®Google Scholar
• Ma Y, Xin Y, Li R, Wang Z, Yue Q, Xiao F, Hao X. TFDP3 was expressed in coordination with E2F1 to inhibit E2F1-mediated apoptosis in prostate cancer. Gene. 2014;537(2):253–259. doi:10.1016/j.gene.2013.12.051.
   PubMed Web of Science ®Google Scholar
• Yin K, Liu Y, Chu M, Wang Y. TFDP3 regulates epithelial-mesenchymal transition in breast cancer. PLoS One. 2017;12(1):e0170573. doi:10.1371/journal.pone.0170573.
   Web of Science ®Google Scholar
• Ingram L, Munro S, Coutts AS, La Thangue NB. E2F-1 regulation by an unusual DNA damage-responsive DP partner subunit. Cell Death Differ. 2011;18(1):122–132. doi:10.1038/cdd.2010.70.
   PubMed Web of Science ®Google Scholar
• Cho B, Lim Y, Lee DY, Park SY, Lee H, Jeoung D Il, Yang H, Bang Y-J, Jeoung D-I. Identification and characterization of a novel cancer/testis antigen gene CAGE. Biochem Biophys Res Commun. 2002;292(3):715–726. doi:10.1006/bbrc.2002.6701.
   PubMed Web of Science ®Google Scholar
• Kim Y, Park D, Kim H, Choi M, Lee H, Lee YS, Choe J, Kim YM, Jeoung D. MiR-200b and cancer/testis antigen cage form a feedback loop to regulate the invasion and tumorigenic and angiogenic responses of a cancer cell line to microtubule-Targeting drugs. J Biol Chem. 2013;288(51):36502–36518. doi:10.1074/jbc.M113.502047.
   PubMed Web of Science ®Google Scholar
• Baumgaertner P, Rufer N, Devevre E, Derre L, Rimoldi D, Geldhof C, Voelter V, Liénard D, Romero P, Speiser DE, et al. Ex vivo detectable human CD8 T-cell responses to cancer-testis antigens. Cancer Res. 2006;66(4):1912–1918. doi:10.1158/0008-5472.CAN-05-3793.
   PubMed Web of Science ®Google Scholar
• Griffiths EA, Srivastava P, Matsuzaki J, Brumberger Z, Wang ES, Kocent J, Miller A, Roloff GW, Wong HY, Paluch BE, et al. NY-ESO-1 vaccination in combination with decitabine induces antigen-specific T-lymphocyte responses in patients with myelodysplastic syndrome. Clin Cancer Res. 2018;24(5):1019–1029. NIH Public Access.
   PubMed Web of Science ®Google Scholar
• Thomas R, Al-Khadairi G, Roelands J, Hendrickx W, Dermime S, Bedognetti D, Decock J. NY-ESO-1 based immunotherapy of cancer: current perspectives. Front Immunol. 2018;9. doi:10.3389/fimmu.2018.00947.
   Web of Science ®Google Scholar
• Sabado RL, Bhardwaj N. Cancer immunotherapy: dendritic-cell vaccines on the move. Nature. 2015;519(7543):300–301. doi:10.1038/nature14211.
   PubMed Web of Science ®Google Scholar
• Robbins PF, Morgan RA, Feldman SA, Yang JC, Sherry RM, Dudley ME, Wunderlich JR, Nahvi AV, Helman LJ, Mackall CL, et al. Tumor regression in patients with metastatic synovial cell sarcoma and melanoma using genetically engineered lymphocytes reactive with NY-ESO-1. J Clin Oncol. 2011;29(7):917–924. doi:10.1200/JCO.2010.32.2537.
   PubMed Web of Science ®Google Scholar
• Robbins PF, Kassim SH, Tran TLN, Crystal JS, Morgan RA, Feldman SA, Yang JC, Dudley ME, Wunderlich JR, Sherry RM, et al. A pilot trial using lymphocytes genetically engineered with an NY-ESO-1-reactive T-cell receptor: long-term follow-up and correlates with response. Clin Cancer Res. 2015;21(5):1019–1027. doi:10.1158/1078-0432.CCR-14-2708.
   PubMed Web of Science ®Google Scholar