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Hypermethylation of multiple genes in pancreatic adenocarcinoma
1Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21205, USA.
Abstract:
Hypermethylation of CpG islands is a common mechanism by which tumor suppressor genes are inactivated. We studied 45 pancreatic carcinomas and 14 normal pancreata for aberrant DNA methylation of CpG islands of multiple genes and clones using methylation-specific PCR (MSP) and bisulfite-modified sequencing. Using MSP, we detected aberrant methylation of at least one locus in 60% of carcinomas. The genes analyzed included RARbeta (methylated in 20%), p16 (18%), CACNA1G (16%), TIMP-3 (11%), E-cad (7%), THBS1 (7%), hMLH1 (4%), DAP kinase (2%), and MGMT (0%). In addition, aberrant methylation was found in three CpG islands (MINT31, -1, and -2) in 38, 38, and 14% of carcinomas, respectively. Hypermethylation was largely confined to the carcinomas with only three loci (E-cad, DAP kinase, and MINT2) harboring methylation in some normal pancreata (36, 21, and 14%, respectively). Simultaneous methylation of at least four loci was observed in 5 of 36 (14%) pancreatic adenocarcinomas. We defined this subgroup of pancreatic adenocarcinomas as "CpG island-methylator-phenotype positive (CIMP+)." Two of four carcinomas with microsatellite instability harbored promoter hypermethylation of hMLH1, and both cases were CIMP+. Thus, we conclude that many pancreatic carcinomas hypermethylate a small percentage of genes, whereas a subset displays a CIMP+ phenotype.
Insights
Many pancreatic cancers show abnormal DNA methylation in tumor suppressor genes. A subset of these cancers exhibits a CpG island-methylator-phenotype (CIMP+), indicating widespread gene silencing.
Area of Science:
- Molecular Oncology
- Epigenetics
- Cancer Genomics
Background:
- Hypermethylation of CpG islands is a key mechanism for inactivating tumor suppressor genes in cancer.
- Understanding aberrant DNA methylation patterns in pancreatic cancer is crucial for identifying potential therapeutic targets and diagnostic markers.
Purpose of the Study:
- To investigate aberrant DNA methylation of CpG islands in multiple genes and clones in pancreatic carcinomas.
- To identify a potential subset of pancreatic adenocarcinomas with a distinct methylation phenotype.
Main Methods:
- Analysis of 45 pancreatic carcinomas and 14 normal pancreata.
- Utilized methylation-specific PCR (MSP) and bisulfite-modified sequencing to detect aberrant DNA methylation.
- Examined methylation status of genes including RARbeta, p16, CACNA1G, TIMP-3, E-cad, THBS1, hMLH1, DAP kinase, MGMT, and CpG islands MINT31, -1, and -2.
Main Results:
- Aberrant methylation was detected in at least one locus in 60% of pancreatic carcinomas.
- Specific genes showed varying methylation frequencies: RARbeta (20%), p16 (18%), CACNA1G (16%), TIMP-3 (11%), E-cad (7%), THBS1 (7%), hMLH1 (4%), DAP kinase (2%), MGMT (0%).
- CpG islands MINT31, -1, and -2 were methylated in 38%, 38%, and 14% of carcinomas, respectively.
- Simultaneous methylation of at least four loci (CpG island-methylator-phenotype positive or CIMP+) was observed in 14% of pancreatic adenocarcinomas.
- Two of four microsatellite instability-positive carcinomas showed hMLH1 promoter hypermethylation and were CIMP+.
Conclusions:
- Many pancreatic carcinomas exhibit hypermethylation of a small subset of genes.
- A distinct subgroup of pancreatic adenocarcinomas displays a CpG island-methylator-phenotype (CIMP+).
- The CIMP+ phenotype may be associated with microsatellite instability and hMLH1 promoter hypermethylation.