A Risk Prediction Model of DNA Methylation Improves Prognosis Evaluation and Indicates Gene Targets in Prostate Cancer

References

• Siegel RL , MillerKD , JemalA. Cancer statistics, 2018. CA Cancer J. Clin.68(1), 7–30 (2018).
   PubMed Web of Science ®Google Scholar
• Eggener SE , CifuAS , NabhanC. Prostate cancer screening. JAMA314(8), 825–826 (2015).
   PubMed Web of Science ®Google Scholar
• Hayes JH , BarryMJ. Screening for prostate cancer with the prostate-specific antigen test: a review of current evidence. JAMA311(11), 1143–1149 (2014).
   PubMed Web of Science ®Google Scholar
• Cooperberg MR , BroeringJM , CarrollPR. Time trends and local variation in primary treatment of localized prostate cancer. J. Clin. Oncol.28(7), 1117–1123 (2010).
   PubMed Web of Science ®Google Scholar
• D’amico AV , WhittingtonR , MalkowiczSBet al. Biochemical outcome after radical prostatectomy, external beam radiation therapy, or interstitial radiation therapy for clinically localized prostate cancer. JAMA280(11), 969–974 (1998).
   PubMed Web of Science ®Google Scholar
• Zumsteg ZS , SprattDE , PeiIet al. A new risk classification system for therapeutic decision making with intermediate-risk prostate cancer patients undergoing dose-escalated external-beam radiation therapy. Eur. Urol.64(6), 895–902 (2013).
   PubMed Web of Science ®Google Scholar
• Kulis M , EstellerM. DNA methylation and cancer. Adv. Genet.70, 27–56 (2010).
   PubMed Web of Science ®Google Scholar
• Moore LD , LeT , FanG. DNA methylation and its basic function. Neuropsychopharmacology38(1), 23–38 (2013).
   PubMed Web of Science ®Google Scholar
• Costa FF , PaixãoVA , CavalherFPet al. SATR-1 hypomethylation is a common and early event in breast cancer. Cancer Genet. Cytogenet.165(2), 135–143 (2006).
   PubMedGoogle Scholar
• Piña IC , GautschiJT , WangGYet al. Psammaplins from the sponge Pseudoceratina purpurea: inhibition of both histone deacetylase and DNA methyltransferase. J. Org. Chem.68(10), 3866–3873 (2003).
   PubMed Web of Science ®Google Scholar
• Klutstein M , NejmanD , GreenfieldR , CedarH. DNA methylation in cancer and aging. Cancer Res.76(12), 3446–3450 (2016).
   PubMed Web of Science ®Google Scholar
• Mikeska T , CraigJM. DNA methylation biomarkers: cancer and beyond. Genes5(3), 821–864 (2014).
   PubMed Web of Science ®Google Scholar
• Crujeiras AB , Diaz-LagaresA , SandovalJet al. DNA methylation map in circulating leukocytes mirrors subcutaneous adipose tissue methylation pattern: a genome-wide analysis from non-obese and obese patients. Sci.Rep.7, 41903 (2017).
   PubMed Web of Science ®Google Scholar
• Williams C , LewseyJD , BriggsAH , MackayDF. Cost-effectiveness analysis in r using a multi-state modeling survival analysis framework: a tutorial. Med. Decis. Making37(4), 340–352 (2017).
   PubMed Web of Science ®Google Scholar
• George B , SealsS , AbanI. Survival analysis and regression models. J. Nucl. Cardiol.21(4), 686–694 (2014).
   PubMed Web of Science ®Google Scholar
• Svane AM , SoerensenM , LundJet al. DNA methylation and all-cause mortality in middle-aged and elderly danish twins. Genes9(2), E72 (2018).
   PubMed Web of Science ®Google Scholar
• Butcher LM , BeckS. Probe Lasso: a novel method to rope in differentially methylated regions with 450K DNA methylation data. Methods72, 21–28 (2015).
   PubMed Web of Science ®Google Scholar
• Song Q , ShangJ , YangZet al. Identification of an immune signature predicting prognosis risk of patients in lung adenocarcinoma. J. Transl. Med.17(1), 70 (2019).
   PubMed Web of Science ®Google Scholar
• Bertocci MA , BebkoG , VersaceAet al. Reward-related neural activity and structure predict future substance use in dysregulated youth. Psychol. Med.47(8), 1357–1369 (2017).
   PubMed Web of Science ®Google Scholar
• Kuhn M . The caret package. R Foundation for Statistical ComputingVienna, Austria (2012). https://cran.r-project.org/package=caret
   Google Scholar
• Treviño V , Tamez-PenaJ. VALORATE: fast and accurate log-rank test in balanced and unbalanced comparisons of survival curves and cancer genomics. Bioinformatics33(12), 1900–1901 (2017).
   PubMed Web of Science ®Google Scholar
• Uusitalo E , RantanenM , KallionpääRAet al. Distinctive cancer associations in patients with neurofibromatosis type 1. J. Clin. Oncol.34(17), 1978–1986 (2016).
   PubMed Web of Science ®Google Scholar
• Emura T , MatsuiS , ChenHY. compound.Cox: univariate feature selection and compound covariate for predicting survival. Comput. Methods Programs Biomed.168, 21–37 (2019).
   PubMed Web of Science ®Google Scholar
• Cao B , ZhangL , ZouYet al. Survival analysis and prognostic nomogram model for multiple system atrophy. Parkinsonism Relat. Disord.54, 68–73 (2018).
   PubMed Web of Science ®Google Scholar
• Blanche P , DartiguesJF , Jacqmin-GaddaH. Estimating and comparing time-dependent areas under receiver operating characteristic curves for censored event times with competing risks. Stat. Med.32(30), 5381–5397 (2013).
   PubMed Web of Science ®Google Scholar
• Love MI , HuberW , AndersS. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol.15(12), 550 (2014).
   PubMed Web of Science ®Google Scholar
• Langfelder P , HorvathS. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics9, 559 (2008).
   PubMed Web of Science ®Google Scholar
• Maertens A , TranV , KleensangA , HartungTet al. Weighted gene correlation network analysis (WGCNA) reveals novel transcription factors associated with bisphenol a dose-response. Front. Genet.9, 508 (2018).
   PubMed Web of Science ®Google Scholar
• Horvath S , DongJ. Geometric interpretation of gene coexpression network analysis. PLoS Comput. Biol.4(8), e1000117 (2008).
   PubMed Web of Science ®Google Scholar
• Zhou Y , ZhouB , PacheLet al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun.10(1), 1523 (2019).
   PubMed Web of Science ®Google Scholar
• Tang Z , LiC , KangB , GaoG , LiC , ZhangZ. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res.45(W1), W98–W102 (2017).
   PubMed Web of Science ®Google Scholar
• Lonsdale J , ThomasJ , SalvatoreMet al. The Genotype-Tissue Expression (GTEx) project. Nat. Genet.45(6), 580–585 (2013).
   PubMed Web of Science ®Google Scholar
• Human genomics . The genotype-tissue expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science348(6235), 648–660 (2015).
   PubMed Web of Science ®Google Scholar
• Ghosh K , ChatterjeeB , MaheswariU , AthifaM , KanadeSR. 4-Nonylphenol-enhanced EZH2 and RNF2 expression, H3K27me3 and H2AK119ub1 marks resulting in silencing of p21CDKN1A in vitro. Epigenomics11(8), 899–916 (2019).
   PubMed Web of Science ®Google Scholar
• Wang Y , ZengL , LiangCet al. Integrated analysis of transcriptome-wide m6A methylome of osteosarcoma stem cells enriched by chemotherapy. Epigenomics11(15), 1693–1715 (2019).
   PubMed Web of Science ®Google Scholar
• Zhang J , ShiK , HuangWet al. The DNA methylation profile of non-coding RNAs improves prognosis prediction for pancreatic adenocarcinoma. Cancer Cell Int.19, 107 (2019).
   PubMed Web of Science ®Google Scholar
• Royston P , ParmarMK , AltmanDG. Visualizing length of survival in time-to-event studies: a complement to Kaplan-Meier plots. J. Natl Cancer Inst.100(2), 92–97 (2008).
   PubMedGoogle Scholar
• Liu X , HuAX , ZhaoJL , ChenFL. Identification of key gene modules in human osteosarcoma by co-expression analysis weighted gene co-expression network analysis (WGCNA). J. Cell. Biochem.118(11), 3953–3959 (2017).
   PubMed Web of Science ®Google Scholar
• Ravasz E , SomeraAL , MongruDA , OltvaiZN , BarabásiAL. Hierarchical organization of modularity in metabolic networks. Science297(5586), 1551–1555 (2002).
   PubMed Web of Science ®Google Scholar
• Yip AM , HorvathS. Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics8, 22 (2007).
   PubMed Web of Science ®Google Scholar
• Aleksic T , GrayN , WuXet al. Nuclear IGF1R interacts with regulatory regions of chromatin to promote RNA polymerase II recruitment and gene expression associated with advanced tumor stage. Cancer Res.78(13), 3497–3509 (2018).
   PubMed Web of Science ®Google Scholar
• Jia X , ChenJ , SunSet al. Detection of aggressive prostate cancer associated glycoproteins in urine using glycoproteomics and mass spectrometry. Proteomics16(23), 2989–2996 (2016).
   PubMed Web of Science ®Google Scholar
• Komoroski RA , HolderJC , PappasAA , FinkbeinerAE. 31P NMR of phospholipid metabolites in prostate cancer and benign prostatic hyperplasia. Magn. Reson. Med.65(4), 911–913 (2011).
   PubMed Web of Science ®Google Scholar
• Fahrenholtz CD , GreeneAM , BeltranPJ , BurnsteinKL. A novel calcium-dependent mechanism of acquired resistance to IGF-1 receptor inhibition in prostate cancer cells. Oncotarget5(19), 9007–9021 (2014).
   PubMedGoogle Scholar
• Aly A , MullinsCD , HussainA. Understanding heterogeneity of treatment effect in prostate cancer. Curr. Opin. Oncol.27(3), 209–216 (2015).
   PubMed Web of Science ®Google Scholar
• Wang X , WangD , ZhangH , FengM , WuX. Genome-wide analysis of DNA methylation identifies two CpG sites for the early screening of colorectal cancer. Epigenomics12(1), 37–52 (2019)
   PubMed Web of Science ®Google Scholar
• Murphy K , MurphyBT , BoyceSet al. Integrating biomarkers across omic platforms: an approach to improve stratification of patients with indolent and aggressive prostate cancer. Mol. Oncol.12(9), 1513–1525 (2018).
   PubMed Web of Science ®Google Scholar
• Jeyapala R , KamdarS , Olkhov-MitselEet al. An integrative DNA methylation model for improved prognostication of postsurgery recurrence and therapy in prostate cancer patients. Urol. Oncol.38(2), 39.e1–39.e9 (2019).
   PubMed Web of Science ®Google Scholar
• Vainio P , GuptaS , KetolaKet al. Arachidonic acid pathway members PLA2G7, HPGD, EPHX2, and CYP4F8 identified as putative novel therapeutic targets in prostate cancer. Am. J. Pathol.178(2), 525–536 (2011).
   PubMed Web of Science ®Google Scholar
• Vainio P , LehtinenL , MirttiTet al. Phospholipase PLA2G7, associated with aggressive prostate cancer, promotes prostate cancer cell migration and invasion and is inhibited by statins. Oncotarget2(12), 1176–1190 (2011).
   PubMedGoogle Scholar
• Christian PA , FiandaloMV , SchwarzeSR. Possible role of death receptor-mediated apoptosis by the E3 ubiquitin ligases Siah2 and POSH. Mol. Cancer10, 57 (2011).
   PubMed Web of Science ®Google Scholar
• Van Der Heul-Nieuwenhuijsen L , DitsNF , JensterG. Gene expression of forkhead transcription factors in the normal and diseased human prostate. BJU Int.103(11), 1574–1580 (2009).
   PubMed Web of Science ®Google Scholar
• Xin Z , ZhangY , JiangZet al. Insulinoma-associated protein 1 is a novel sensitive and specific marker for small cell carcinoma of the prostate. Hum. Pathol.79, 151–159 (2018).
   PubMed Web of Science ®Google Scholar