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Updated: Jun 12, 2026
Testing Targeted Therapies in Cancer using Structural DNA Alteration Analysis and Patient-Derived Xenografts
Published on: July 25, 2020
High-definition DNA methylation profiles from breast and ovarian carcinoma cell lines with differing doxorubicin
Michael Boettcher1, Frank Kischkel, Jörg D Hoheisel
1Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany. m.boettcher@dkfz.de
Abstract:
Acquired drug resistance represents a frequent obstacle which hampers efficient chemotherapy of cancers. The contribution of aberrant DNA methylation to the development of drug resistant tumor cells has gained increasing attention over the past decades. Hence, the objective of the presented study was to characterize DNA methylation changes which arise from treatment of tumor cells with the chemotherapeutic drug doxorubicin. DNA methylation levels from CpG islands (CGIs) linked to twenty-eight genes, whose expression levels had previously been shown to contribute to resistance against DNA double strand break inducing drugs or tumor progression in different cancer types were analyzed. High-definition DNA methylation profiles which consisted of methylation levels from 800 CpG sites mapping to CGIs around the transcription start sites of the selected genes were determined. In order to investigate the influence of CGI methylation on the expression of associated genes, their mRNA levels were investigated via qRT-PCR. It was shown that the employed method is suitable for providing highly accurate methylation profiles, comparable to those obtained via clone sequencing, the gold standard for high-definition DNA methylation studies. In breast carcinoma cells with acquired resistance against the double strand break inducing drug doxorubicin, changes in methylation of specific cytosines from CGIs linked to thirteen genes were detected. Moreover, similarities between methylation profiles obtained from breast and ovarian carcinoma cell lines with acquired doxorubicin resistance were found. The expression levels of a subset of analyzed genes were shown to be linked to the methylation levels of the analyzed CGIs. Our results provide detailed DNA methylation information from two separate model systems for acquired doxorubicin resistance and suggest the occurrence of similar methylation changes in both systems upon exposure to the drug.
Insights
Acquired drug resistance in cancer is a major challenge. This study reveals specific DNA methylation changes in tumor cells treated with doxorubicin, offering insights into cancer drug resistance mechanisms.
Area of Science:
- Oncology
- Epigenetics
- Molecular Biology
Background:
- Acquired drug resistance is a significant hurdle in cancer chemotherapy.
- Aberrant DNA methylation is increasingly recognized for its role in developing drug-resistant tumor cells.
Purpose of the Study:
- To characterize DNA methylation alterations in tumor cells following doxorubicin treatment.
- To investigate the relationship between CpG island (CGI) methylation and gene expression in acquired doxorubicin resistance.
Main Methods:
- Analysis of DNA methylation profiles at 800 CpG sites within CGIs of 28 selected genes.
- Quantitative reverse transcription polymerase chain reaction (qRT-PCR) to assess mRNA levels.
- Comparison of methylation profiling accuracy against clone sequencing.
Main Results:
- Developed a method for high-definition DNA methylation profiling with high accuracy.
- Identified methylation changes in CGIs linked to 13 genes in doxorubicin-resistant breast carcinoma cells.
- Observed similarities in methylation profiles between resistant breast and ovarian carcinoma cell lines.
- Found correlations between CGI methylation levels and the expression of a subset of genes.
Conclusions:
- The study provides detailed DNA methylation data from two distinct models of acquired doxorubicin resistance.
- Similar DNA methylation changes occur in both breast and ovarian cancer cells upon doxorubicin exposure.
- These findings contribute to understanding the epigenetic basis of chemotherapy resistance.
