DNA Methylation Profiles of Ovarian Clear Cell Carcinoma

• Published in: Cancer epidemiology, biomarkers & prevention Vol. 31; no. 1; pp. 132 - 141
• Main Authors: Cunningham, Julie M, Winham, Stacey J, Wang, Chen, Weiglt, Britta, Fu, Zhuxuan, Armasu, Sebastian M, McCauley, Bryan M, Brand, Alison H, Chiew, Yoke-Eng, Elishaev, Esther, Gourley, Charlie, Kennedy, Catherine J, Laslavic, Angela, Lester, Jenny, Piskorz, Anna, Sekowska, Magdalena, Brenton, James D, Churchman, Michael, DeFazio, Anna, Drapkin, Ronny, Elias, Kevin M, Huntsman, David G, Karlan, Beth Y, Köbel, Martin, Konner, Jason, Lawrenson, Kate, Papaemmanuil, Elli, Bolton, Kelly L, Modugno, Francesmary, Goode, Ellen L
• Format: Journal Article
• Language: English
• Published: United States 01.01.2022
• Subjects: Adenocarcinoma, Clear Cell - ethnology; Adenocarcinoma, Clear Cell - genetics; Adenocarcinoma, Clear Cell - pathology; Adult; Aged; Aged, 80 and over; Aneuploidy; Class I Phosphatidylinositol 3-Kinases - genetics; CpG Islands - genetics; Disease Progression; DNA Methylation; DNA-Binding Proteins - genetics; Female; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Humans; Middle Aged; Mutation; Neoplasm Staging; Ovarian Neoplasms - ethnology; Ovarian Neoplasms - genetics; Ovarian Neoplasms - pathology; Prognosis; Transcription Factors - genetics; Tumor Suppressor Protein p53 - genetics
• ISSN: 1055-9965; 1538-7755
• DOI: 10.1158/1055-9965.EPI-21-0677

Ovarian clear cell carcinoma (OCCC) is a rare ovarian cancer histotype that tends to be resistant to standard platinum-based chemotherapeutics. We sought to better understand the role of DNA methylation in clinical and biological subclassification of OCCC. We interrogated genome-wide methylation using DNA from fresh frozen tumors from 271 cases, applied nonsmooth nonnegative matrix factorization (nsNMF) clustering, and evaluated clinical associations and biological pathways. Two approximately equally sized clusters that associated with several clinical features were identified. Compared with Cluster 2 ( = 137), Cluster 1 cases ( = 134) presented at a more advanced stage, were less likely to be of Asian ancestry, and tended to have poorer outcomes including macroscopic residual disease following primary debulking surgery ( < 0.10). Subset analyses of targeted tumor sequencing and IHC data revealed that Cluster 1 tumors showed mutation and abnormal p53 expression, and Cluster 2 tumors showed aneuploidy and mutation ( < 0.05). Cluster-defining CpGs included 1,388 CpGs residing within 200 bp of the transcription start sites of 977 genes; 38% of these genes ( = 369 genes) were differentially expressed across cluster in transcriptomic subset analysis ( < 10 ). Differentially expressed genes were enriched for six immune-related pathways, including IFNα and IFNγ responses ( < 10 ). DNA methylation clusters in OCCC correlate with disease features and gene expression patterns among immune pathways. This work serves as a foundation for integrative analyses that better understand the complex biology of OCCC in an effort to improve potential for development of targeted therapeutics.