title: A global profile of gene promoter methylation in treatment-naïve urothelial cancer.
abstract: The epigenetic alteration of aberrant hypermethylation in the promoter CpG island of a gene is associated with repression of transcription. In neoplastic cells, aberrant hypermethylation is well described as a mechanism of allele inactivation of particular genes with a tumor suppressor function. To investigate the role of aberrant hypermethylation in the biology and progression of urothelial cancer, we examined 101 urothelial (transitional cell) carcinomas (UC), broadly representative of the disease at presentation, with no prior immunotherapy, chemotherapy or radiotherapy, by Infinium HM27 containing 14,495 genes. The genome-wide signature of aberrant promoter hypermethylation in UC consisted of 729 genes significant by a Wilcoxon test, hypermethylated in a CpG island within 1 kb of the transcriptional start site and unmethylated in normal urothelium from aged individuals. We examined differences in gene methylation between the two main groups of UC: the 75% that are superficial, which often recur but rarely progress, and the 25% with muscle invasion and poor prognosis. We further examined pairwise comparisons of the pathologic subgroups of high or low grade, invasive or non-invasive (pTa), and high grade superficial or low grade superficial UC. Pathways analysis indicated over-representation of genes involved in cell adhesion or metabolism in muscle-invasive UC. Notably, the TET2 epigenetic regulator was one of only two genes more frequently methylated in superficial tumors and the sole gene in low grade UC. Other chromatin remodeling genes, MLL3 and ACTL6B, also showed aberrant hypermethylation. The Infinium methylation value for representative genes was verified by pyrosequencing. An available mRNA expression data set indicated many of the hypermethylated genes of interest to be downregulated in UC. Unsupervised clustering of the most differentially methylated genes distinguished muscle invasive from superficial UC. After filtering, cluster analysis showed a CpG Island Methylator Phenotype (CIMP)-like pattern of widespread methylation in 11 (11%) tumors. Nine of these 11 tumors had hypermethylation of TET2. Our analysis provides a basis for further studies of hypermethylation in the development and progression of UC.
authors: Cancer Epigenetics Program; Fox Chase Cancer Center; Philadelphia PA, USA.
authors: Ilsiya
authors: I
authors: Ibragimova
authors: Department of Pathology; Fox Chase Cancer Center; Philadelphia PA, USA.
authors: Essel
authors: E
authors: Dulaimi
authors: Department of Biostatistics and Bioinformatics; Fox Chase Cancer Center; Philadelphia PA, USA.
authors: Michael J
authors: MJ
authors: Slifker
authors: Department of Urology; Fox Chase Cancer Center; Philadelphia PA, USA.
authors: David Y
authors: DY
authors: Chen
authors: Department of Urology; Fox Chase Cancer Center; Philadelphia PA, USA.
authors: Robert G
authors: RG
authors: Uzzo
authors: Cancer Epigenetics Program; Fox Chase Cancer Center; Philadelphia PA, USA.
authors: Paul
authors: P
authors: Cairns
mesh_terms: D000199:Actins / Q000235:genetics / Q000378:metabolism; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002295:Carcinoma, Transitional Cell / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism; D018899:CpG Islands; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D049308:Dioxygenases; D044127:Epigenesis, Genetic; D005260:Female; D015894:Genome, Human; D006801:Humans; D008297:Male; D008875:Middle Aged; D017354:Point Mutation; D011401:Promoter Regions, Genetic; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000378:metabolism; D014571:Urologic Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D019459:Urothelium / Q000378:metabolism* / Q000473:pathology
chemical_list: C467332:ACTL6B protein, human; D000199:Actins; D002868:Chromosomal Proteins, Non-Histone; D004268:DNA-Binding Proteins; C452979:KMT2C protein, human; D011518:Proto-Oncogene Proteins; D049308:Dioxygenases; C541081:TET2 protein, human
keywords: CIMP; MLL3; TET2; bladder cancer; hypermethylation; methylome; transitional cell carcinoma; urothelial carcinoma