DNA methylation profiling of ovarian carcinomas and their in vitro models identifies HOXA9, HOXB5, SCGB3A1, and CRABP1 as novel targets.
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, p14ARF, and p16INK4a 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).


CONCLUSIONS
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.
Wu
Qinghua
Q
Department of Pathology, Rikshospitalet-Radiumhospitalet Medical Center, Oslo, Norway. qinghuaw@labmed.uio.no
Lothe
Ragnhild A
RA
Ahlquist
Terje
T
Silins
Ilvars
I
Tropé
Claes G
CG
Micci
Francesca
F
Nesland
Jahn M
JM
Suo
Zhenhe
Z
Lind
Guro E
GE
D001483:Base Sequence; D016207:Cytokines / Q000235:genetics*; D019175:DNA Methylation; D004273:DNA, Neoplasm; D005260:Female; D020869:Gene Expression Profiling; D042822:Genomic Instability; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D066298:In Vitro Techniques; D018895:Microsatellite Repeats / Q000235:genetics; D008875:Middle Aged; D008954:Models, Biological; D008969:Molecular Sequence Data; D010051:Ovarian Neoplasms / Q000235:genetics*; D011401:Promoter Regions, Genetic; D018168:Receptors, Retinoic Acid / Q000235:genetics*; D025521:Tumor Suppressor Proteins / Q000235:genetics*
D016207:Cytokines; D004273:DNA, Neoplasm; C489126:HOXB5 protein, human; D018398:Homeodomain Proteins; D018168:Receptors, Retinoic Acid; C434732:SCGB3A1 protein, human; D025521:Tumor Suppressor Proteins; C097899:homeobox protein HOXA9; C082927:retinoic acid binding protein I, cellular