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Updated: May 17, 2026
Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
DNA methylation biomarkers and their utility for solid cancer diagnostics
Karen A Heichman1, Jorja D Warren
1ARUP Laboratories, Inc., Salt Lake City, UT, USA. karen.heichman@aruplab.com
Abstract:
Cellular DNA undergoes profound changes in methylation during cancer development, with hypermethylation occurring in specific gene promoters, amidst a backdrop of generalized hypomethylation. DNA methylation in cancer often causes the silencing of tumor suppressors and other genes important for cellular growth, regulation and differentiation. Over the past two decades, there have been thousands of publications describing the methylation status of hundreds of genes in cancer, with numerous associations with clinical states, disease outcomes and therapeutic responses being reported. New methods for DNA methylation fingerprinting have emerged, allowing for the exponential growth of "epigenomic" information. Despite this wealth of data, only a handful of methylated genes are utilized as cancer biomarkers in the clinical laboratory. A literature review centered on DNA methylation in six solid cancers was performed, including colorectal, pancreatic, prostate, bladder, breast and ovarian. Commonly methylated genes in the six cancer types were identified and catalogued, and could serve in the future as tissue-based biomarkers or as part of cancer-specific panels. Perhaps more importantly, this endeavor has also focused on methylated genes that appear to be unique to particular cancers. These genes may be more versatile for clinical use, with blood or urine-based cancer screening becoming a reality.
Insights
Cancer DNA methylation patterns, specifically gene promoter hypermethylation, are crucial for tumor development. Identifying commonly and uniquely methylated genes across six solid cancers offers potential for novel diagnostic biomarkers.
Area of Science:
- Oncology
- Epigenetics
- Molecular Biology
Background:
- Cellular DNA methylation undergoes significant alterations during cancer development, characterized by gene promoter hypermethylation and global hypomethylation.
- Aberrant DNA methylation in cancer frequently leads to the silencing of critical genes involved in tumor suppression, cellular growth, regulation, and differentiation.
- Thousands of studies have documented gene methylation in cancer, linking it to clinical status, outcomes, and treatment responses, with emerging epigenomic data.
Purpose of the Study:
- To review and catalogue commonly methylated genes across six major solid cancers: colorectal, pancreatic, prostate, bladder, breast, and ovarian.
- To identify cancer-specific methylated genes that could serve as more versatile biomarkers.
- To explore the potential of these methylated genes for developing novel cancer diagnostic tools.
Main Methods:
- A comprehensive literature review was conducted focusing on DNA methylation studies in six specific solid cancers.
- Analysis centered on identifying frequently methylated genes within these cancer types.
- Particular attention was given to cataloguing genes methylated uniquely in specific cancers.
Main Results:
- Commonly methylated genes were identified across the six studied solid cancers, providing a catalogue for potential tissue-based biomarker development.
- A subset of methylated genes uniquely associated with particular cancers was highlighted.
- The findings suggest that these unique methylated genes may be more suitable for developing accessible screening methods.
Conclusions:
- The identified commonly and uniquely methylated genes represent promising candidates for future cancer biomarker panels.
- Unique methylated genes hold potential for advancing non-invasive cancer screening through blood or urine tests.
- This research consolidates epigenomic information to guide the development of next-generation cancer diagnostics.
