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Updated: Apr 23, 2026
Methyl-binding DNA capture Sequencing for Patient Tissues
Published on: October 31, 2016
High-frequency aberrantly methylated targets in pancreatic adenocarcinoma identified via global DNA methylation
Yangxing Zhao1, Jinfeng Sun2, Hongyu Zhang3
1State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, LN 2200/25, Xietu Road, Shanghai 200032, China.
Background:
Extensive reprogramming and dysregulation of DNA methylation is an important characteristic of pancreatic cancer (PC). Our study aimed to characterize the genomic methylation patterns in various genomic contexts of PC. The methyl capture sequencing (methylCap-seq) method was used to map differently methylated regions (DMRs) in pooled samples from ten PC tissues and ten adjacent non-tumor (PN) tissues. A selection of DMRs was validated in an independent set of PC and PN samples using methylation-specific PCR (MSP), bisulfite sequencing PCR (BSP), and methylation sensitive restriction enzyme-based qPCR (MSRE-qPCR). The mRNA and expressed sequence tag (EST) expression of the corresponding genes was investigated using RT-qPCR.
Results:
A total of 1,131 PC-specific and 727 PN-specific hypermethylated DMRs were identified in association with CpG islands (CGIs), including gene-associated CGIs and orphan CGIs; 2,955 PC-specific and 2,386 PN-specific hypermethylated DMRs were associated with gene promoters, including promoters containing or lacking CGIs. Moreover, 1,744 PC-specific and 1,488 PN-specific hypermethylated DMRs were found to be associated with CGIs or CGI shores. These results suggested that aberrant hypermethylation in PC typically occurs in regions surrounding the transcription start site (TSS). The BSP, MSP, MSRE-qPCR, and RT-qPCR data indicated that the aberrant DNA methylation in PC tissue and in PC cell lines was associated with gene (or corresponding EST) expression.
Conclusions:
Our study characterized the genome-wide DNA methylation patterns in PC and identified DMRs that were distributed among various genomic contexts that might influence the expression of corresponding genes or transcripts to promote PC. These DMRs might serve as diagnostic biomarkers or therapeutic targets for PC.
Insights
Extensive DNA methylation changes characterize pancreatic cancer (PC). This study identified specific hypermethylated regions in PC tissues, linking aberrant methylation to gene expression and suggesting potential diagnostic biomarkers or therapeutic targets for PC.
Area of Science:
- Oncology
- Epigenetics
- Genomics
Background:
- Pancreatic cancer (PC) exhibits significant DNA methylation reprogramming and dysregulation.
- Understanding genomic methylation patterns is crucial for PC characterization.
Purpose of the Study:
- To characterize genome-wide DNA methylation patterns in pancreatic cancer.
- To identify differentially methylated regions (DMRs) in various genomic contexts within PC.
Main Methods:
- Methyl capture sequencing (methylCap-seq) was employed to map DMRs in PC and adjacent non-tumor (PN) tissues.
- Validation of selected DMRs was performed using methylation-specific PCR (MSP), bisulfite sequencing PCR (BSP), and MSRE-qPCR.
- Gene and expressed sequence tag (EST) expression levels were assessed via RT-qPCR.
Main Results:
- Identified numerous PC-specific and PN-specific hypermethylated DMRs associated with CpG islands (CGIs), gene promoters, and CGI shores.
- Aberrant hypermethylation in PC predominantly occurs near transcription start sites (TSS).
- Aberrant DNA methylation in PC tissues and cell lines correlated with altered gene (or EST) expression.
Conclusions:
- Genome-wide DNA methylation patterns in PC were characterized, revealing DMRs across diverse genomic contexts.
- Identified DMRs may influence gene expression, potentially driving PC development.
- These DMRs hold promise as diagnostic biomarkers or therapeutic targets for pancreatic cancer.
