期刊
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
卷 31, 期 1, 页码 132-141出版社
AMER ASSOC CANCER RESEARCH
DOI: 10.1158/1055-9965.EPI-21-0677
关键词
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资金
- Brigham and Women's Hospital: Foundation for Women's Cancer, Reproductive Scientist Development Program
- Honorable Tina Brozman Foundation
- Minnesota Ovarian Cancer Alliance
- Deborah and Robert First Family Foundation
- Saltonstall Foundation
- Potter Foundation
- Brigham Ovarian Cancer Research Fund
- American Cancer Society [SIOP-06-258-01-COUN]
- Mayo Clinic [R21-CA222867, R01-CA248288, P50-CA136393]
- NCI Cancer Center Core Grant [P30-CA008748]
- Cycle for Survival and Breast Cancer Research Foundation grants
- Nicola Murray Foundation
- University of Pittsburgh: NIH SPORE in ovarian cancer [P50 CA228991]
- Penn Medicine Translational Center of Excellence in Ovarian Cancer
- Dr. Miriam and Sheldon G. Adelson Medical Research Foundation
- Tina's Wish Foundation
- Claneil Foundation
- UPMC Hillman Cancer Center and Tissue [P30CA047904]
- Research Pathology/Pitt Biospecimen Core shared resource [P30CA047904]
- National Health and Medical Research Council of Australia [310670, 628903]
- Cancer Institute NSW [12/RIG/1-17, 15/RIG/1-16]
This study investigated the role of DNA methylation in ovarian clear cell carcinoma (OCCC). Two clusters that correlated with clinical features were identified. Tumors in Cluster 1 showed TP53 mutation and abnormal p53 expression, while tumors in Cluster 2 showed aneuploidy and ARID1A/PIK3CA mutation. Differentially expressed genes were enriched for immune-related pathways.
Background: 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 under-stand the role of DNA methylation in clinical and biological subclassification of OCCC. Methods: We interrogated genome-wide methylation using DNA from fresh frozen tumors from 271 cases, applied nonsmooth nonnegative matrix factorization (nsNMF) clustering, and evalu-ated clinical associations and biological pathways. Results: Two approximately equally sized clusters that associated with several clinical features were identified. Compared with Cluster 2 (N = 137), Cluster 1 cases (N = 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 (P < 0.10). Subset analyses of targeted tumor sequencing and IHC data revealed that Cluster 1 tumors showed TP53 mutation and abnormal p53 expression, and Cluster 2 tumors showed aneuploidy and ARID1A/PIK3CA muta-tion (P<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 (N = 369 genes) were differentially expressed across cluster in transcriptomic subset analysis (P < 10(-4)). Differentially expressed genes were enriched for six immune-related pathways, including IFN alpha and IFN gamma responses (P < 10(-6)). Conclusions: DNA methylation clusters in OCCC correlate with disease features and gene expression patterns among immune pathways. Impact: 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.
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