Neary B, Lin S, Qiu P. Methylation of CpG Sites as Biomarkers Predictive of Drug-Specific
Patient Survival in Cancer.
Cancer Inform 2022;
21:11769351221131124. [PMID:
36340286 PMCID:
PMC9634212 DOI:
10.1177/11769351221131124]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 09/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background:
Though the development of targeted cancer drugs continues to accelerate,
doctors still lack reliable methods for predicting patient response to
standard-of-care therapies for most cancers. DNA methylation has been
implicated in tumor drug response and is a promising source of predictive
biomarkers of drug efficacy, yet the relationship between drug efficacy and
DNA methylation remains largely unexplored.
Method:
In this analysis, we performed log-rank survival analyses on patients grouped
by cancer and drug exposure to find CpG sites where binary methylation
status is associated with differential survival in patients treated with a
specific drug but not in patients with the same cancer who were not exposed
to that drug. We also clustered these drug-specific CpG sites based on
co-methylation among patients to identify broader methylation patterns that
may be related to drug efficacy, which we investigated for transcription
factor binding site enrichment using gene set enrichment analysis.
Results:
We identified CpG sites that were drug-specific predictors of survival in 38
cancer-drug patient groups across 15 cancers and 20 drugs. These included 11
CpG sites with similar drug-specific survival effects in multiple cancers.
We also identified 76 clusters of CpG sites with stronger associations with
patient drug response, many of which contained CpG sites in gene promoters
containing transcription factor binding sites.
Conclusion:
These findings are promising biomarkers of drug response for a variety of
drugs and contribute to our understanding of drug-methylation interactions
in cancer. Investigation and validation of these results could lead to the
development of targeted co-therapies aimed at manipulating methylation in
order to improve efficacy of commonly used therapies and could improve
patient survival and quality of life by furthering the effort toward drug
response prediction.
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