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Background  The epigenetics of ovarian carcinogenesis remains poorly described. We have in the present study investigated the promoter methylation status of 13 genes in primary ovarian carcinomas (n = 52) and their  in vitro  models (n = 4; ES-2, OV-90, OVCAR-3, and SKOV-3) by methylation-specific polymerase chain reaction (MSP). Direct bisulphite sequencing analysis was used to confirm the methylation status of individual genes. The MSP results were compared with clinico- pathological features.    Results  Eight out of the 13 genes were hypermethylated among the ovarian carcinomas, and altogether 40 of 52 tumours were methylated in one or more genes. Promoter hypermethylation of  HOXA9 ,  RASSF1A ,  APC ,  CDH13 ,  HOXB5 ,  SCGB3A1 (HIN-1) ,  CRABP1 , and  MLH1  was found in 51% (26/51), 49% (23/47), 24% (12/51), 20% (10/51), 12% (6/52), 10% (5/52), 4% (2/48), and 2% (1/51) of the carcinomas, respectively, whereas  ADAMTS1 ,  MGMT ,  NR3C1 ,  p14   ARF  , and  p16   INK 4 a   were unmethylated in all samples. The methylation frequencies of  HOXA9  and  SCGB3A1  were higher among relatively early-stage carcinomas (FIGO I-II) than among carcinomas of later stages (FIGO III-IV;  P  = 0.002,  P  = 0.020, respectively). The majority of the early-stage carcinomas were of the endometrioid histotype. Additionally,  HOXA9  hypermethylation was more common in tumours from patients older than 60 years of age (15/21) than among those of younger age (11/30;  P  = 0.023). Finally, there was a significant difference in  HOXA9  methylation frequency among the histological types ( P  = 0.007).    Conclusion  DNA hypermethylation of tumour suppressor genes seems to play an important role in ovarian carcinogenesis and  HOXA9 ,  HOXB5 ,  SCGB3A1 , and  CRABP1  are identified as novel hypermethylated target genes in this tumour type.

DNA methylation profiling of ovarian carcinomas and their in vitro models identifies HOXA9, HOXB5, SCGB3A1, and CRABP1 as novel targets