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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
Genome-wide DNA methylation analysis of KRAS mutant cell lines
Ben Yi Tew1, Joel K Durand2, Kirsten L Bryant2
1Department of Translational Genomics, University of Southern California, Los Angeles, CA, 90033, USA.
Abstract:
Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 differentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in differentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream effector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer.
Insights
Oncogenic KRAS mutations drive cancer through DNA methylation changes. These epigenetic alterations appear stochastic, offering new therapeutic targets for KRAS-driven cancers.
Area of Science:
- Cancer biology
- Epigenetics
- Genomics
Background:
- Oncogenic RAS mutations are hallmarks of many cancers, linked to altered DNA methylation.
- The precise mechanisms driving aberrant DNA methylation in RAS-driven cancers are debated, with theories including stochastic events versus specific signaling pathways.
- Understanding KRAS-associated DNA methylation is crucial for developing targeted therapies.
Purpose of the Study:
- To investigate the patterns and drivers of DNA methylation changes associated with oncogenic KRAS.
- To determine if KRAS-mediated DNA methylation is stochastic or driven by canonical downstream signaling pathways.
- To identify potential therapeutic targets within KRAS-driven cancers based on epigenetic alterations.
Main Methods:
- Analysis of basal CpG methylation in 11 KRAS-mutant pancreatic cancer cell lines.
- KRAS knockdown experiments in pancreatic cancer cell lines and assessment of differentially methylated CpGs (DM CpGs).
- Treatment of KRAS-mutant cells with an ERK1/2 inhibitor and evaluation of DM CpGs.
- KRAS G12V overexpression in an isogenic lung model to assess DM CpGs.
- Gene ontology analysis of differentially methylated promoter regions.
Main Results:
- Strikingly similar basal methylation patterns were observed across KRAS-mutant pancreatic cancer cell lines.
- KRAS knockdown induced unique methylation changes in each cell line, with limited overlap.
- ERK1/2 inhibition showed minimal impact on DNA methylation compared to KRAS knockdown.
- KRAS G12V overexpression in a lung model resulted in extensive DM CpGs (>50,600).
- Gene ontology analysis revealed enrichment for differentiation and development genes in DM promoter regions.
Conclusions:
- KRAS-mediated DNA methylation changes are largely stochastic and independent of canonical downstream effector signaling like ERK1/2.
- Epigenetically altered genes driven by KRAS expression represent potential therapeutic targets in KRAS-driven cancers.
- The findings provide a deeper understanding of the epigenetic landscape in KRAS-mutant cancers.
