3,340
Views
53
CrossRef citations to date
0
Altmetric
Original Research

High expression of PD-1 ligands is associated with kataegis mutational signature and APOBEC3 alterations

, &
Article: e1284719 | Received 09 Nov 2016, Accepted 13 Jan 2017, Published online: 15 Mar 2017

References

  • Dudley ME, Wunderlich JR, Robbins PF, Yang JC, Hwu P, Schwartzentruber DJ, Topalian SL, Sherry R, Restifo NP, Hubicki AM et al. Cancer regression and autoimmunity in patients after clonal repopulation with antitumor lymphocytes. Science 2002; 298:850-4; PMID:12242449; http://dx.doi.org/10.1126/science.1076514
  • Pardoll DM. The blockade of immune checkpoints in cancer immunotherapy. Nat Rev Cancer 2012; 12:252-64; PMID:22437870; http://dx.doi.org/10.1038/nrc3239
  • Topalian SL, Sznol M, McDermott DF, Kluger HM, Carvajal RD, Sharfman WH, Brahmer JR, Lawrence DP, Atkins MB, Powderly JD, et al. Survival, durable tumor remission, and long-term safety in patients with advanced melanoma receiving nivolumab. J Clin Oncol 2014; 32:1020-30; PMID:24590637; http://dx.doi.org/10.1200/JCO.2013.53.0105
  • Ansell SM, Lesokhin AM, Borrello I, Halwani A, Scott EC, Gutierrez M, Schuster SJ, Millenson MM, Cattry D, Freeman GJ et al. PD-1 blockade with nivolumab in relapsed or refractory Hodgkin's lymphoma. N Engl J Med 2015; 372:311-9; PMID:25482239; http://dx.doi.org/10.1056/NEJMoa1411087
  • Motzer RJ, Rini BI, McDermott DF, Redman BG, Kuzel TM, Harrison MR, Vaishampayan UN, Drabkin HA, George S, Logan TF et al. Nivolumab for metastatic renal cell carcinoma: results of a randomized phase II trial. J Clin Oncol 2015; 33:1430-7; PMID:25452452; http://dx.doi.org/10.1200/JCO.2014.59.0703
  • Brahmer J, Reckamp KL, Baas P, Crinò L, Eberhardt WEE, Poddubskaya E, Antonia S, Pluzanski A, Vokes EE, Holgado E et al. Nivolumab versus Docetaxel in Advanced Squamous-Cell Non-Small-Cell Lung Cancer. N Engl J Med 2015; 373:123-35; PMID:26028407; http://dx.doi.org/10.1056/NEJMoa1504627
  • Rosenberg JE, Hoffman-Censits J, Powles T, van der Heijden MS, Balar AV, Necchi A, Dawson N, O'Donnell PH, Balmanoukian A,Loriot Y et al. Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial. Lancet 2016; 387:1909-20; PMID:26952546; http://dx.doi.org/10.1016/S0140-6736(16)00561-4
  • Goodman A, Patel SP, Kurzrock R. PD-1-PD-L1 immune-checkpoint blockade in B-cell lymphomas. Nat Rev Clin Oncol 2016; advance online publication; PMID:27805626; http://dx.doi.org/10.1038/nrclinonc.2016.168
  • Ritprajak P, Azuma M. Intrinsic and extrinsic control of expression of the immunoregulatory molecule PD-L1 in epithelial cells and squamous cell carcinoma. Oral Oncol 2015; 51:221-8; PMID:25500094; http://dx.doi.org/10.1016/j.oraloncology.2014.11.014
  • Twa DDW, Chan FC, Ben-Neriah S, Woolcock BW, Mottok A, Tan KL, Slack GW, Gunawardana J, Lim RS, McPherson AW et al. Genomic rearrangements involving programmed death ligands are recurrent in primary mediastinal large B-cell lymphoma. Blood 2014; 123:2062-5; PMID:24497532; http://dx.doi.org/10.1182/blood-2013-10-535443
  • Kataoka K, Shiraishi Y, Takeda Y, Sakata S, Matsumoto M, Nagano S, Maeda T, Nagata Y, Kitanaka A, Mizuno S et al. Aberrant PD-L1 expression through 3′-UTR disruption in multiple cancers. Nature 2016; 534:402-6; PMID:27281199; http://dx.doi.org/10.1038/nature18294
  • Patel SP, Kurzrock R. PD-L1 expression as a predictive biomarker in cancer immunotherapy. Mol Cancer Ther 2015; 14:847-56; PMID:25695955; http://dx.doi.org/10.1158/1535-7163.MCT-14-0983
  • Taube JM, Klein A, Brahmer JR, Xu H, Pan X, Kim JH, Chen L, Pardoll DM, Topalian SL, Anders RA. Association of PD-1, PD-1 ligands, and other features of the tumor immune microenvironment with response to anti-PD-1 therapy. Clin Cancer Res 2014; 20:5064-74; PMID:24714771; http://dx.doi.org/10.11581078-0432.CCR-13-3271
  • Roemer MGM, Advani RH, Ligon AH, Natkunam Y, Redd RA, Homer H, Connelly CF, Sun HH, Daadi SE, Freeman GJ et al. PD-L1and PD-L2 genetic alterations define classical hodgkin lymphoma and predict outcome. J Clin Oncol 2016; 34:2690-7; PMID:27069084; http://dx.doi.org/10.1200/JCO.2016.66.4482
  • Le DT, Uram JN, Wang H, Bartlett BR, Kemberling H, Eyring AD, Skora AD, Luber BS, Azad NS, Laheru D et al. PD-1 blockade in tumors with mismatch-repair deficiency. N Engl J Med 2015; 372:2509-20; PMID:26028255; http://dx.doi.org/10.1056/NEJMoa1500596
  • Lal N, Beggs AD, Willcox BE, Middleton GW. An immunogenomic stratification of colorectal cancer: implications for development of targeted immunotherapy. Oncoimmunology 2015; 4(3):e976052; PMID:25949894; http://dx.doi.org/10.4161/2162402X.2014.976052
  • Madore J, Strbenac D, Vilain R, Menzies AM, Yang JYH, Thompson JF, Long GV, Mann GJ, Scolyer RA, Wilmott JS. PD-L1 negative status is associated with lower mutation burden, differential expression of immune-related genes, and worse survival in stage III melanoma. Clin Cancer Res 2016; 22:3915-23; PMID:26960397; http://dx.doi.org/10.1158/1078-0432.CCR-15-1714
  • Rizvi NA, Hellmann MD, Snyder A, Kvistborg P, Makarov V, Havel JJ, Lee W, Yuan J, Wong P, Ho TS et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 2015; 348:124-8; PMID:25765070; http://dx.doi.org/10.1126/science.aaa1348
  • Howitt BE, Shukla SA, Sholl LM, Ritterhouse LL, Watkins JC, Rodig S, Stover E, Strickland KC, D'Andrea AD, Wu CJ et al. Association of polymerase e-mutated and microsatellite-instable endometrial cancers with neoantigen load, number of tumor-infiltrating lymphocytes, and expression of PD-1 and PD-L1. JAMA Oncol 2015; 1:1319-23; PMID:26181000; http://dx.doi.org/10.1001/jamaoncol.2015.2151
  • Mullane SA, Werner L, Rosenberg J, Signoretti S, Callea M, Choueiri TK, Freeman GJ, Bellmunt J. Correlation of Apobec Mrna expression with overall survival and pd-l1 pxpression in urothelial carcinoma. Sci Rep 2016; 6:27702; PMID:27283319; http://dx.doi.org/10.1038/srep27702
  • Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SAJR, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Børresen-Dale A-L et al. Signatures of mutational processes in human cancer. Nature 2013; 500:415-21; PMID:23945592; http://dx.doi.org/10.1038/nature12477
  • Burns MB, Temiz NA, Harris RS. Evidence for APOBEC3B mutagenesis in multiple human cancers. Nat Genet 2013; 45:977-83; PMID:23852168; http://dx.doi.org/10.1038/ng.2701
  • Chen SH, Habib G, Yang CY, Gu ZW, Lee BR, Weng SA, Silberman SR, Cai SJ, Deslypere JP, Rosseneu M et al. Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon. Science 1987; 238:363-6; PMID:3659919; http://dx.doi.org/10.1126/science.3659919
  • Ramiro A, San-Martin BR, McBride K, Jankovic M, Barreto V, Nussenzweig A, Nussenzweig MC. The role of activation-induced deaminase in antibody diversification and chromosome translocations. Adv Immunol. 2007; 94:75-107; PMID:17560272; http://dx.doi.org/10.1016/S0065-2776(06)94003-6
  • Cullen BR. Role and mechanism of action of the APOBEC3 family of antiretroviral resistance factors. J Virol 2006; 80:1067-76; PMID:16414984; http://dx.doi.org/10.1128/JVI.80.3.1067-1076.2006
  • Smith HC, Bennett RP, Kizilyer A, McDougall WM, Prohaska KM. Functions and regulation of the APOBEC family of proteins. Semin Cell Dev Biol 2012; 23:258-68; PMID:22001110; http://dx.doi.org/10.1016/j.semcdb.2011.10.004
  • McFadden D, others. Conditional logit analysis of qualitative choice behavior. 1973 [ cited 2016 Sep 3]; Available from: https://elsa.berkeley.edu/reprints/mcfadden/zarembka.pdf
  • Koller D, Friedman N. Probabilistic Graphical Models: Principles and Techniques. Cambridge, MA: MIT Press; 2009.
  • Brahmer JR, Tykodi SS, Chow LQM, Hwu W-J, Topalian SL, Hwu P, Drake CG, Camacho LH, Kauh J, Odunsi K et al. Safety and activity of anti-PD-L1 antibody in patients with advanced cancer. N Engl J Med 2012; 366:2455-65; PMID:22658128; http://dx.doi.org/10.1056/NEJMoa1200694
  • Argyris EG, Acheampong E, Wang F, Huang J, Chen K, Mukhtar M, Zhang H. The interferon-induced expression of APOBEC3G in human blood-brain barrier exerts a potent intrinsic immunity to block HIV-1 entry to central nervous system. Virology 2007; 367:440-51; PMID:17631933; http://dx.doi.org/10.1016/j.virol.2007.06.010
  • Hofmeyer KA, Jeon H, Zang X. The PD-1/PD-L1 (B7-H1) pathway in chronic infection-induced cytotoxic T lymphocyte exhaustion. J Biomed Biotechnol 2011; 2011:451694; PMID:21960736; http://dx.doi.org/10.1155/2011/451694
  • Waeckerle-Men Y, Starke A, Wuthrich RP. PD-L1 partially protects renal tubular epithelial cells from the attack of CD8+ cytotoxic T cells. Nephrol Dial Transplant 2007; 22:1527-36; PMID:17339272; http://dx.doi.org/10.1093/ndt/gfl818
  • Wang C-J, Chou F-C, Chu C-H, Wu J-C, Lin S-H, Chang D-M, Sytwu H-K. Protective role of programmed death 1 ligand 1 (PD-L1)in nonobese diabetic mice: the paradox in transgenic models. Diabetes 2008; 57:1861-9; PMID:18420489; http://dx.doi.org/10.2337/db07-1260
  • Madsen P, Anant S, Rasmussen HH, Gromov P, Vorum H, Dumanski JP, Tommerup N, Collins JE, Wright CL, Dunham I et al. Psoriasis upregulated phorbolin-1 shares structural but not functional similarity to the mRNA-editing protein apobec-1. J Invest Dermatol 1999; 113:162-9; PMID:10469298; http://dx.doi.org/10.1046/j.1523-1747.1999.00682.x
  • Jang B-C, Park Y-K, Choi I-H, Kim S-P, Hwang J-B, Baek W-K, Suh M-H, Mun K-C, Suh S-I. 12-O-tetradecanoyl phorbol 13-acetate induces the expression of B7-DC, -H1, -H2, and -H3 in K562 cells. Int J Oncol 2007; 31:1439-47; PMID:17982670; http://dx.doi.org/10.3892/ijo.31.6.1439
  • Emerit I, Cerutti PA. Tumour promoter phorbol-12-myristate-13-acetate induces chromosomal damage via indirect action. Nature 1981; 293:144-6; PMID:7266668; http://dx.doi.org/10.1038/293144a0
  • Andor N, Graham TA, Jansen M, Xia LC, Aktipis CA, Petritsch C, Ji HP, Maley CC. Pan-cancer analysis of the extent and consequences of intratumor heterogeneity. Nat Med 2016; 22:105-13; PMID:26618723; http://dx.doi.org/10.1038/nm.3984
  • Greaves M, Maley CC. Clonal evolution in cancer. Nature 2012; 481:306-13; PMID:22258609; http://dx.doi.org/10.1038/nature10762
  • Swanton C, McGranahan N, Starrett GJ, Harris RS. APOBEC Enzymes: mutagenic fuel for cancer evolution and heterogeneity. Cancer Discov 2015; 5:704-12; PMID:26091828; http://dx.doi.org/10.1158/2159-8290.CD-15-0344
  • Middlebrooks CD, Banday AR, Matsuda K, Udquim K-I, Onabajo OO, Paquin A, Figueroa JD, Zhu B, Koutros S, Kubo M et al. Association of germline variants in the APOBEC3 region with cancer risk and enrichment with APOBEC-signature mutations in tumors. Nat Genet 2016; 48:1330-8; PMID:27643540; http://dx.doi.org/10.1038/ng.3670
  • Briggs S, Tomlinson I. Germline and somatic polymerase ϵ and δ mutations define a new class of hypermutated colorectal and endometrial cancers. J Pathol 2013; 230:148-53; PMID:23447401; http://dx.doi.org/10.1002/path.4185
  • Khagi Y, Kurzrock R, Patel SP. Next generation predictive biomarkers for immune checkpoint inhibition. Cancer Metastasis Rev 2016; pp 1-12; PMID:27873079; http://dx.doi.org/10.1007/s10555-016-9652-y
  • Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 2013; 499:214-8; PMID:23770567; http://dx.doi.org/10.1038/nature12213
  • Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, Linhart D, Vivanco I, Lee JC, Huang JH, Alexander S et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci USA 2007; 104:20007-12; PMID:18077431; http://dx.doi.org/10.1073/pnas.0710052104
  • Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform 2011; 12:323; PMID:21816040; http://dx.doi.org/10.1186/1471-2105-12-323
  • Roberts SA, Lawrence MS, Klimczak LJ, Grimm SA, Fargo D, Stojanov P, Kiezun A, Kryukov GV, Carter SL, Saksena G et al. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat Genet 2013; 45:970-6; PMID:23852170; http://dx.doi.org/10.1038/ng.2702
  • Wang X. Firth logistic regression for rare variant association tests. Front Genet 2014; 5:187; PMID:24995013; http://dx.doi.org/10.3389/fgene.2014.00187
  • Heinze G, Puhr R. Bias-reduced and separation-proof conditional logistic regression with small or sparse data sets. Stat Med 2010; 29:770-7; PMID:20213709; http://dx.doi.org/10.1002/sim.3794
  • Steyerberg EW, Harrell FE, Borsboom GJ, Eijkemans MJ, Vergouwe Y, Habbema JD. Internal validation of predictive models: efficiency of some procedures for logistic regression analysis. J Clin Epidemiol 2001; 54:774-81; PMID:11470385; http://dx.doi.org/10.1016/S0895-4356(01)00341-9