5,666
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Multi-Omics Analysis Based on Integrated Genomics, Epigenomics and Transcriptomics in Pancreatic Cancer

, , , , & ORCID Icon
Pages 507-524 | Received 09 Dec 2019, Accepted 23 Jan 2020, Published online: 12 Feb 2020

References

  • Siegel RL , MillerKD , JemalA. Cancer statistics, 2019. CA Cancer J. Clin.69(1), 7–34 (2019).
  • Mcguigan A , KellyP , TurkingtonRC , JonesC , ColemanHG , MccainRS. Pancreatic cancer: a review of clinical diagnosis, epidemiology, treatment and outcomes. World J. Gastroenterol.24(43), 4846–4861 (2018).
  • Hidalgo M . Pancreatic cancer. N. Engl. J. Med.362(17), 1605–1617 (2010).
  • Garrido-Laguna I , HidalgoM. Pancreatic cancer: from state-of-the-art treatments to promising novel therapies. Nat. Rev. Clin. Oncol.12(6), 319–334 (2015).
  • Mo Q , ShenR , GuoC , VannucciM , ChanKS , HilsenbeckSG. A fully Bayesian latent variable model for integrative clustering analysis of multi-type omics data. Biostatistics19(1), 71–86 (2018).
  • Waddell N , PajicM , PatchAMet al. Whole genomes redefine the mutational landscape of pancreatic cancer. Nature518(7540), 495–501 (2015).
  • Girirajan S , CampbellCD , EichlerEE. Human copy number variation and complex genetic disease. Annu. Rev. Genet.45, 203–226 (2011).
  • Huang L , YuD , WuCet al. Copy number variation at 6q13 functions as a long-range regulator and is associated with pancreatic cancer risk. Carcinogenesis33(1), 94–100 (2012).
  • Lee JH , GiovannettiE , HwangJHet al. Loss of 18q22.3 involving the carboxypeptidase of glutamate-like gene is associated with poor prognosis in resected pancreatic cancer. Clin. Cancer. Res.18(2), 524–533 (2012).
  • Witkiewicz AK , McmillanEA , BalajiUet al. Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets. Nat. Commun.6, 6744 (2015).
  • Hung YH , HsuMC , ChenLT , HungWC , PanMR. Alteration of epigenetic modifiers in pancreatic cancer and its clinical implication. J. Clin. Med.8(6), 903 (2019).
  • Sharma S , KellyTK , JonesPA. Epigenetics in cancer. Carcinogenesis31(1), 27–36 (2010).
  • Lomberk G , BlumY , NicolleRet al. Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes. Nat. Commun.9(1), 1978 (2018).
  • Zucman-Rossi J , VillanuevaA , NaultJC , LlovetJM. Genetic landscape and biomarkers of hepatocellular carcinoma. Gastroenterology149(5), 1226–1239, e1224 (2015).
  • Silverman BR , ShiJ. Alterations of epigenetic regulators in pancreatic cancer and their clinical implications. Int. J. Mol. Sci.17(12), 2138 (2016).
  • Eissa MaL , LernerL , AbdelfatahEet al. Promoter methylation of ADAMTS1 and BNC1 as potential biomarkers for early detection of pancreatic cancer in blood. Clin. Epigenetics11(1), 59 (2019).
  • Shen R , OlshenAB , LadanyiM. Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics25(22), 2906–2912 (2009).
  • Li T , FanJ , WangBet al. TIMER: a web server for comprehensive analysis of tumor-infiltrating immune cells. Cancer Res.77(21), e108–e110 (2017).
  • Li B , SeversonE , PignonJCet al. Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome Biol.17(1), 174 (2016).
  • Gaujoux R , SeoigheC. A flexible R package for nonnegative matrix factorization. BMC Bioinformatics11, 367 (2010).
  • Woo HG , ChoiJH , YoonSet al. Integrative analysis of genomic and epigenomic regulation of the transcriptome in liver cancer. Nat. Commun.8(1), 839 (2017).
  • Zheng M , HuY , GouRet al. Integrated multi-omics analysis of genomics, epigenomics, and transcriptomics in ovarian carcinoma. Aging (Albany NY)11(12), 4198–4215 (2019).
  • Cancer Genome Atlas Research Network (Electronic address: [email protected]) . Integrated genomic characterization of pancreatic ductal adenocarcinoma. Cancer Cell32(2), 185–203, e113 (2017).
  • Barrett T , WilhiteSE , LedouxPet al. NCBI GEO: archive for functional genomics data sets – update. Nucleic Acids Res.41(Database issue), D991–D995 (2013).
  • Stratford JK , BentremDJ , AndersonJMet al. A six-gene signature predicts survival of patients with localized pancreatic ductal adenocarcinoma. PLoS Med.7(7), e1000307 (2010).
  • Moffitt RA , MarayatiR , FlateELet al. Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma. Nat. Genet.47(10), 1168–1178 (2015).
  • Chang TW , ChenCC , ChenKY , SuJH , ChangJH , ChangMC. Ribosomal phosphoprotein P0 interacts with GCIP and overexpression of P0 is associated with cellular proliferation in breast and liver carcinoma cells. Oncogene27(3), 332–338 (2008).
  • Chen KY , ChenCC , TsengYL , ChangYC , ChangMC. GCIP functions as a tumor suppressor in non-small cell lung cancer by suppressing Id1-mediated tumor promotion. Oncotarget5(13), 5017–5028 (2014).
  • Ma W , StaffordLJ , LiDet al. GCIP/CCNDBP1, a helix-loop-helix protein, suppresses tumorigenesis. J. Cell. Biochem.100(6), 1376–1386 (2007).
  • Shen W , XieJ , ZhaoSet al. ICAM3 mediates inflammatory signaling to promote cancer cell stemness. Cancer Lett.422, 29–43 (2018).
  • Shen W , ZhangX , DuRet al. ICAM3 mediates tumor metastasis via a LFA-1-ICAM3-ERM dependent manner. Biochim. Biophys. Acta. Mol. Basis. Dis.1864(8), 2566–2578 (2018).
  • Zhang W , CuiQ , QuW , DingX , JiangD , LiuH. TRIM58/cg26157385 methylation is associated with eight prognostic genes in lung squamous cell carcinoma. Oncol. Rep.40(1), 206–216 (2018).
  • Kamisawa T , WoodLD , ItoiT , TakaoriK. Pancreatic cancer. Lancet388(10039), 73–85 (2016).
  • Bailey P , ChangDK , NonesKet al. Genomic analyses identify molecular subtypes of pancreatic cancer. Nature531(7592), 47–52 (2016).
  • Collisson EA , SadanandamA , OlsonPet al. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat. Med.17(4), 500–503 (2011).