title: Diagnostic and prognostic utility of a DNA hypermethylated gene signature in prostate cancer.
abstract: We aimed to identify a prostate cancer DNA hypermethylation microarray signature (denoted as PHYMA) that differentiates prostate cancer from benign prostate hyperplasia (BPH), high from low-grade and lethal from non-lethal cancers. This is a non-randomized retrospective study in 111 local Asian men (87 prostate cancers and 24 BPH) treated from 1995 to 2009 in our institution. Archival prostate epithelia were laser-capture microdissected and genomic DNA extracted and bisulfite-converted. Samples were profiled using Illumina GoldenGate Methylation microarray, with raw data processed by GenomeStudio. A classification model was generated using support vector machine, consisting of a 55-probe DNA methylation signature of 46 genes. The model was independently validated on an internal testing dataset which yielded cancer detection sensitivity and specificity of 95.3% and 100% respectively, with overall accuracy of 96.4%. Second validation on another independent western cohort yielded 89.8% sensitivity and 66.7% specificity, with overall accuracy of 88.7%. A PHYMA score was developed for each sample based on the state of methylation in the PHYMA signature. Increasing PHYMA score was significantly associated with higher Gleason score and Gleason primary grade. Men with higher PHYMA scores have poorer survival on univariate (p = 0.0038, HR = 3.89) and multivariate analyses when controlled for (i) clinical stage (p = 0.055, HR = 2.57), and (ii) clinical stage and Gleason score (p = 0.043, HR = 2.61). We further performed bisulfite genomic sequencing on 2 relatively unknown genes to demonstrate robustness of the assay results. PHYMA is thus a signature with high sensitivity and specificity for discriminating tumors from BPH, and has a potential role in early detection and in predicting survival.
authors.affiliation: Centre for Quantitative Medicine, Duke-National University of Singapore Graduate Medical School, Singapore, Singapore, Singapore; Cancer & Stem Cell Biology, Duke-National University of Singapore Graduate Medical School, Singapore, Singapore, Singapore.
authors.forename: Liang Kee
authors.initials: LK
authors.lastname: Goh
authors.affiliation: Cancer Science Institute, National University of Singapore, Singapore, Singapore, Singapore.
authors.forename: Natalia
authors.initials: N
authors.lastname: Liem
authors.affiliation: Centre for Quantitative Medicine, Duke-National University of Singapore Graduate Medical School, Singapore, Singapore, Singapore.
authors.forename: Aadhitthya
authors.initials: A
authors.lastname: Vijayaraghavan
authors.affiliation: Cancer & Stem Cell Biology, Duke-National University of Singapore Graduate Medical School, Singapore, Singapore, Singapore.
authors.forename: Gengbo
authors.initials: G
authors.lastname: Chen
authors.affiliation: Cancer Science Institute, National University of Singapore, Singapore, Singapore, Singapore.
authors.forename: Pei Li
authors.initials: PL
authors.lastname: Lim
authors.affiliation: Department of Urology, Singapore General Hospital, Singapore, Singapore, Singapore.
authors.forename: Kae-Jack
authors.initials: KJ
authors.lastname: Tay
authors.affiliation: Department of Urology, Singapore General Hospital, Singapore, Singapore, Singapore.
authors.forename: Michelle
authors.initials: M
authors.lastname: Chang
authors.affiliation: Cancer Science Institute, National University of Singapore, Singapore, Singapore, Singapore.
authors.forename: John Soon Wah
authors.initials: JS
authors.lastname: Low
authors.affiliation: Department of Urology, Singapore General Hospital, Singapore, Singapore, Singapore.
authors.forename: Adita
authors.initials: A
authors.lastname: Joshi
authors.affiliation: Department of Urology, Singapore General Hospital, Singapore, Singapore, Singapore.
authors.forename: Hong Hong
authors.initials: HH
authors.lastname: Huang
authors.affiliation: Department of Pathology, Singapore General Hospital, Singapore, Singapore, Singapore.
authors.forename: Emarene
authors.initials: E
authors.lastname: Kalaw
authors.affiliation: Department of Pathology, Singapore General Hospital, Singapore, Singapore, Singapore.
authors.forename: Puay Hoon
authors.initials: PH
authors.lastname: Tan
authors.affiliation: Cancer Science Institute, National University of Singapore, Singapore, Singapore, Singapore.
authors.forename: Wen-Son
authors.initials: WS
authors.lastname: Hsieh
authors.affiliation: Cancer Science Institute, National University of Singapore, Singapore, Singapore, Singapore.
authors.forename: Wei Peng
authors.initials: WP
authors.lastname: Yong
authors.affiliation: Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America.
authors.forename: Joshi
authors.initials: J
authors.lastname: Alumkal
authors.affiliation: Department of Urology, Singapore General Hospital, Singapore, Singapore, Singapore.
authors.forename: Hong Gee
authors.initials: HG
authors.lastname: Sim
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D044466:Asian People; D002454:Cell Differentiation; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D008875:Middle Aged; D015999:Multivariate Analysis; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D016016:Proportional Hazards Models; D011470:Prostatic Hyperplasia / Q000175:diagnosis / Q000473:pathology; D011471:Prostatic Neoplasms / Q000175:diagnosis / Q000208:ethnology / Q000235:genetics*; D015203:Reproducibility of Results; D012189:Retrospective Studies; D012680:Sensitivity and Specificity