Quantitative genome-wide methylation analysis of high-grade non-muscle invasive bladder cancer

Abstract

High-grade non-muscle invasive bladder cancer (HG-NMIBC) is a clinically unpredictable disease with greater risks of recurrence and progression relative to their low-intermediate-grade counterparts. The molecular events, including those affecting the epigenome, that characterize this disease entity in the context of tumor development, recurrence, and progression, are incompletely understood. We therefore interrogated genome-wide DNA methylation using HumanMethylation450 BeadChip arrays in 21 primary HG-NMIBC tumors relative to normal bladder controls. Using strict inclusion-exclusion criteria we identified 1,057 hypermethylated CpGs within gene promoter-associated CpG islands, representing 256 genes. We validated the array data by bisulphite pyrosequencing and examined 25 array-identified candidate genes in an independent cohort of 30 HG-NMIBC and 18 low-intermediate-grade NMIBC. These analyses revealed significantly higher methylation frequencies in high-grade tumors relative to low-intermediate-grade tumors for the ATP5G2, IRX1 and VAX2 genes (P<0.05), and similarly significant increases in mean levels of methylation in high-grade tumors for the ATP5G2, VAX2, INSRR, PRDM14, VSX1, TFAP2b, PRRX1, and HIST1H4F genes (P<0.05). Although inappropriate promoter methylation was not invariantly associated with reduced transcript expression, a significant association was apparent for the ARHGEF4, PON3, STAT5a, and VAX2 gene transcripts (P<0.05). Herein, we present the first genome-wide DNA methylation analysis in a unique HG-NMIBC cohort, showing extensive and discrete methylation changes relative to normal bladder and low-intermediate-grade tumors. The genes we identified hold significant potential as targets for novel therapeutic intervention either alone, or in combination, with more conventional therapeutic options in the treatment of this clinically unpredictable disease.

Epigenome-Wide DNA Methylation Profiling Identifies Differential Methylation Biomarkers in High-Grade Bladder Cancer

“…Several methylation markers previously shown to be associated with grade in bladder cancer are CD99 , CDH13 , RARB , RASSF1A , SFRP5 , and TMEFF2 [33] , [34] , [35] , [36] . A number of other markers of BC grade have also been shown specifically in NMIBC including ACTL5B , ATP5G2 , BCL2 , BRCA1 , CIDEA , DAPK , FRZB , HOXB2 , ITPKB , IRX1 , KRT13 , MGMT , MLL3 , RASSF1A , RUNX3 , TERT , TET2 , TRPA1 , VAX2 , and VHL [37] , [38] , [39] , [40] , [41] , [42] , [43] . Of these markers, several have been implicated across multiple studies, including BRCA1 , CDH13 , RASSF1A , and TMEFF2 , whereas other novel markers have emerged from only single studies thus far [24] , [33] , [35] , [37] , [39] , [44] , [45] , [46] .…”

Paraoxonase 3 is involved in the multi-drug resistance of esophageal cancer

“…Previous studies also showed that PON3 is hypermethylated in colorectal cancer [ 9 ] and chordomas [ 21 ]. Notably, the genome-wide DNA methylation analysis identified that several genes, including PON3, are aberrantly methylated in the high-grade non-muscle invasive bladder cancer [ 22 ]. These findings suggest that epigenetic modifications are usually associated with the development and/or progression of different type of tumors [ 13 , 23 ].…”

Gene modules and non-coding RNAs involved in pancreatic tumorigenesis through acinar ductal metaplasia

“…Crosstalk genes including H2AFZ (synonym of H2A.Z) were annotated in ADM-PanIN-PDAC. Histones are found to be associated with the cancer-predisposing in ammation or even trans-differentiation [31]. Histone H3 has the potential to be a biomarker for evaluating the severity of acute pancreatitis due to caerulein triggered extensive pancreatic acinar cell death in animal model [32].…”