DNA methylation changes in ovarian cancer are cumulative with disease progression and identify tumor stage.

TitleDNA methylation changes in ovarian cancer are cumulative with disease progression and identify tumor stage.
Publication TypeJournal Article
Year of Publication2008
AuthorsWatts GS, Futscher BW, Holtan N, Degeest K, Domann FE, Rose SL
JournalBMC Med Genomics
Volume1
Pagination47
Date Published2008 Sep 30
ISSN1755-8794
Abstract

BACKGROUND: Hypermethylation of promoter CpG islands with associated loss of gene expression, and hypomethylation of CpG-rich repetitive elements that may destabilize the genome are common events in most, if not all, epithelial cancers.

METHODS: The methylation of 6,502 CpG-rich sequences spanning the genome was analyzed in 137 ovarian samples (ten normal, 23 low malignant potential, 18 stage I, 16 stage II, 54 stage III, and 16 stage IV) ranging from normal tissue through to stage IV cancer using a sequence-validated human CpG island microarray. The microarray contained 5' promoter-associated CpG islands as well as CpG-rich satellite and Alu repetitive elements.

RESULTS: Results showed a progressive de-evolution of normal CpG methylation patterns with disease progression; 659 CpG islands showed significant loss or gain of methylation. Satellite and Alu sequences were primarily associated with loss of methylation, while promoter CpG islands composed the majority of sequences with gains in methylation. Since the majority of ovarian tumors are late stage when diagnosed, we tested whether DNA methylation profiles could differentiate between normal and low malignant potential (LMP) compared to stage III ovarian samples. We developed a class predictor consisting of three CpG-rich sequences that was 100% sensitive and 89% specific when used to predict an independent set of normal and LMP samples versus stage III samples. Bisulfite sequencing confirmed the NKX-2-3 promoter CpG island was hypermethylated with disease progression. In addition, 5-aza-2'-deoxycytidine treatment of the ES2 and OVCAR ovarian cancer cell lines re-expressed NKX-2-3. Finally, we merged our CpG methylation results with previously published ovarian expression microarray data and identified correlated expression changes.

CONCLUSION: Our results show that changes in CpG methylation are cumulative with ovarian cancer progression in a sequence-type dependent manner, and that CpG island microarrays can rapidly discover novel genes affected by CpG methylation in clinical samples of ovarian cancer.

DOI10.1186/1755-8794-1-47
Alternate JournalBMC Med Genomics
PubMed ID18826610
PubMed Central IDPMC2566571
Grant ListP30 CA023074 / CA / NCI NIH HHS / United States
P30 ES006694 / ES / NIEHS NIH HHS / United States
R01 CA073612 / CA / NCI NIH HHS / United States
R33 CA091351 / CA / NCI NIH HHS / United States
Faculty Member Reference: 
George Watts, Ph.D.