Methylation Signature Implicated in Immuno-Suppressive Activities in Tubo-Ovarian High-Grade Serous Carcinoma. Methylation Signature Implicated in Immuno-Suppressive Activities in Tubo-Ovarian High-Grade Serous Carcinoma

Background: Better understanding of prognostic factors in tubo-ovarian high-grade serous carcinoma (HGSC) is critical, as diagnosis confers an aggressive disease course. Variation in tumor DNA methylation shows promise predicting outcome, yet prior studies were largely platform-specific and unable to evaluate multiple molecular features. Methods: We analyzed genome-wide DNA methylation in 1,040 frozen HGSC, including 325 previously reported upon, seeking a multi-platform quantitative methylation signature which we evaluated in relation to clinical features, tumor characteristics, time to recurrence/death, extent of CD8+ tumor-infiltrating lymphocytes (TILs), gene expression molecular subtypes, and gene expression of the ATP-binding cassette transporter TAP1. Results: Methylation signature was associated with shorter time to recurrence, independent of clinical factors (N=715 new set, HR 1.65, 95% CI 1.10-2.46, p=0.015; N=325 published set HR 2.87, 95% CI 2.17-3.81, p=2.2 x 10-13) and remained prognostic after adjustment for gene expression molecular subtype and TAP1 expression (N=599, HR 2.22, 95% CI 1.66-2.95, p=4.1 x 10-8). Methylation signature was inversely related to CD8+ TIL levels (p=2.4 x 10-7) and TAP1 expression (p=0.0011) and was associated with gene expression molecular subtype (p=5.9 x 10-4) in covariate-adjusted analysis. Conclusions: Multi-center analysis identified a novel quantitative tumor methylation signature of HGSC applicable to numerous commercially available platforms indicative of shorter time to recurrence/death, adjusting for other factors. Along with immune cell composition analysis, these results suggest a role for DNA methylation in the immunosuppressive microenvironment. Impact: This work aids in identification of targetable epigenome processes and stratification of patients for whom tailored treatment may be most beneficial. Overall design: Bisulphite converted DNA from 36 samples were hybridised to the Illumina Infinium Methylation EPIC and 325 samples were hybridised to the Illumina InfiniumHumanMethylation 450 BeadChip. Data for 4 samples are not included in GEO submission (3 samples due to consent and 1 sample as a potential sample mix-up). All the other samples were previously made publicly available, as follows: TCGA methylation data are available via the cBioPortal for Cancer Genomics (https://www.cbioportal.org/; RRID:SCR_014555); other data are available on Gene Expression Omnibus (GEO; RRID:SCR_005012) under the following accession numbers: GSE65820, GSE211686, GSE72021, and GSE1333556.