Intratumor DNA Methylation Heterogeneity Reflects Clonal Evolution in Aggressive Prostate Cancer

• Published in: Cell reports (Cambridge) Vol. 8; no. 3; pp. 798 - 806
• Main Authors: Brocks, David, Assenov, Yassen, Minner, Sarah, Bogatyrova, Olga, Simon, Ronald, Koop, Christina, Oakes, Christopher, Zucknick, Manuela, Lipka, Daniel Bernhard, Weischenfeldt, Joachim, Feuerbach, Lars, Cowper-Sal·lari, Richard, Lupien, Mathieu, Brors, Benedikt, Korbel, Jan, Schlomm, Thorsten, Tanay, Amos, Sauter, Guido, Gerhäuser, Clarissa, Plass, Christoph
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 07.08.2014; Elsevier
• Subjects: Adenocarcinoma - genetics; Adenocarcinoma - pathology; Clonal Evolution; DNA Copy Number Variations; DNA Methylation; Epigenesis, Genetic; Genetic Heterogeneity; Humans; Lymphatic Metastasis; Male; Middle Aged; Prostatic Neoplasms - genetics; Prostatic Neoplasms - pathology
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2014.06.053

Despite much evidence on epigenetic abnormalities in cancer, it is currently unclear to what extent epigenetic alterations can be associated with tumors’ clonal genetic origins. Here, we show that the prostate intratumor heterogeneity in DNA methylation and copy-number patterns can be explained by a unified evolutionary process. By assaying multiple topographically distinct tumor sites, premalignant lesions, and lymph node metastases within five cases of prostate cancer, we demonstrate that both DNA methylation and copy-number heterogeneity consistently reflect the life history of the tumors. Furthermore, we show cases of genetic or epigenetic convergent evolution and highlight the diversity in the evolutionary origins and aberration spectrum between tumor and metastatic subclones. Importantly, DNA methylation can complement genetic data by serving as a proxy for activity at regulatory domains, as we show through identification of high epigenetic heterogeneity at androgen-receptor-bound enhancers. Epigenome variation thereby expands on the current genome-centric view on tumor heterogeneity. [Display omitted] •Epigenetic intratumor heterogeneity reflects prostate tumors’ clonal genetic origins•Tumor and metastatic subclones exhibit diverse evolutionary origins•Distinct tumor lineages show convergent evolution of methylation patterns•Degree of methylation variability at a locus depends on genetic and epigenetic context Several recent studies have examined the clonal origins of tumor populations on the basis of genetic variability. Brocks et al. now show that subclonal lineages also differ in their DNA methylation patterns and that methylation heterogeneity is consistent with the tumors’ genetic history. Furthermore, high methylation variability at enhancers bound by androgen receptor, which are known to play a role in prostate tumorigenesis, suggests that DNA methylation data can serve as a proxy for the functional state of tumor subclones.