Genome-wide profiling at methylated promoters in pancreatic adenocarcinoma

Abstract

Many genes undergo aberrant methylation in human cancers, and microarray platforms enable more comprehensive profiling of aberrant DNA methylation patterns.Results: 1,010 of 87,922 probes on the 88 K promoter array (606 genes) had a higher signal (log 2 > 2) in the pancreatic cancer line, Panc-1 compared to the non-neoplastic pancreatic duct line, HPDE. Using this cut-off, bisulfite sequencing and/ or MSP confirmed differential methylation of all 27 genes (66 probes) predicted to be methylated by the MCA array. More than half of the genes aberrantly hypermethylated in Panc-1 were not expressed in the pancreatic duct (HPDE) by expression array analysis. Using the 244 K CpG island array, 1,968 CpG islands were differentially methylated in MiaPaca2 compared to normal pancreas. The MCA method was more likely to identify hypermethylation within CpG islands than a cocktail of methylation sensitive restriction enzymes. DNA methylation profiles using 10 ng of DNA were highly correlated with those obtained using 5 mg of DNA (R2 = 0.98). Analysis of 57 pancreatic cancers and 34 normal pancreata using MSP identified MDFI, hsa-miR-9-1, ZNF415, CNTNAP2 and ELOVL4 as methylated in 96%, 89%, 86%, 82% and 68% of the cancers vs. 9%, 15%, 6%, 3% and 9% of normal pancreata, respectively. Methods: We used methylated CpG island amplification (MCA) and Agilent promoter and CpG island microarrays to identify differential DNA methylation patterns in pancreatic cancer vs. normal pancreas. We examined MCA array reproducibility, compared it to methylation profiles obtained using a cocktail of methylation-sensitive restriction enzymes and examined gene expression of methylated genes.Conclusion: Promoter and CpG island array analysis finds aberrant methylation of hundreds of promoters and CpG islands in pancreatic cancer cells.

Hsa-miR-9 methylation status is associated with cancer development and metastatic recurrence in patients with clear cell renal cell carcinoma

“…Previous studies have shown extensive epigenetic silencing of one or several of the miR-9 genes in cancer (Lehmann et al, 2008;Lujambio et al, 2008;Omura et al, 2008;Bandres et al, 2009;Hsu et al, 2009). This silencing was common in tumor tissue, whereas nearly absent in normal tissue.…”

“…This silencing was common in tumor tissue, whereas nearly absent in normal tissue. For example, in pancreatic adenocarcinoma, miR-9-1 was found to be methylated Hsa-miR-9 methylation and renal cell carcinoma MAT Hildebrandt et al in 89% of the tumor samples, but only 15% of the normal tissues (Omura et al, 2008). Furthermore, methylation of lysine residues 9 and 27 of histone H3, hallmarks of epigenetic gene silencing, was associated with miR-9-3 when gene expression was suppressed in breast cancer (Hsu et al, 2009).…”

“…The mature hsa-miR-9 transcript is produced by three independent genes: miR-9-1, miR-9-2 and miR-9-3, located on chromosomes 1, 5 and 15, respectively. Previous studies have shown that these microRNA genes are commonly hypermethylated in tumor tissue (Lehmann et al, 2008;Lujambio et al, 2008;Omura et al, 2008;Bandres et al, 2009;Hsu et al, 2009). Furthermore, hsa-miR-9 methylation was shown to be associated with the development of metastasis (Lujambio et al, 2008;Bandres et al, 2009).…”

Epigenetic regulation of microRNA expression in colorectal cancer

“…Hsa-miR-9 has been described as a putative tumor suppressor gene in recurrent ovarian cancer 31 and genome-wide profiling of methylated promoters identified hsa-miR-9-1 as a miRNA frequently hypermethylated in pancreatic adenocarcinoma. 32 Lehmann et al 33 showed differential methylation of hsa-miR-9-1 in a large series of primary human breast cancer specimens. In agreement with our results a good correlation between hypermethylation of the hsa-miR-9-1 gene and downregulation of expression in tumor tissue was found.…”

Serum miR-9 as a prognostic biomarker in patients with osteosarcoma

“…[19][20][21] Altered miR-9 expression is associated with the development and progression of cancers, [22][23][24][25] Kaplan-Meier analysis of overall survival in patients with osteosarcoma, stratified according to median serum microRNA-9 (miR-9) concentration (expression). The colour version of this figure is available at: http://imr.sagepub.com nonsmall-cell lung cancer 16 ) highly expressed miR-9 promotes cancer-cell growth and/or metastasis.…”