Abstract
Chromosome 3-specific NotI microarray (NMA) containing 180 clones with 188 genes was used in the study to analyze 18 high grade serous ovarian cancer (HGSOC) samples and 7 benign ovarian tumors. We aimed to find novel methylation-dependent biomarkers for early detection and prognosis of HGSOC. Thirty five NotI markers showed frequency of methylation/deletion more or equal to 17%. To check the results of NMA hybridizations several samples for four genes (LRRC3B, THRB, ITGA9 and RBSP3 (CTDSPL)) were bisulfite sequenced and confirmed the results of NMA hybridization. A set of eight biomarkers: NKIRAS1/RPL15, THRB, RBPS3 (CTDSPL), IQSEC1, NBEAL2, ZIC4, LOC285205 and FOXP1, was identified as the most prominent set capable to detect both early and late stages of ovarian cancer. Sensitivity of this set is equal to (72 ± 11)% and specificity (94 ± 5)%. Early stages represented the most complicated cases for detection. To distinguish between Stages I + II and Stages III + IV of ovarian cancer the most perspective set of biomarkers would include LOC285205, CGGBP1, EPHB1 and NKIRAS1/RPL15. The sensitivity of the set is equal to (80 ± 13)% and the specificity is (88 ± 12)%. Using this technique we plan to validate this panel with new epithelial ovarian cancer samples and add markers from other chromosomes.
Highlights
Epithelial ovarian cancer (EOC) remains a highly lethal malignancy
DNA; (B) digestion with methyl-specific rare-cutter enzyme NotI; (C) ligation of fragments with NotI-linker containing biotin; (D) digestion with 4-base pair recognizing restriction enzyme Sau3AI; (E) conjugation to microbeads containing streptavidin; washing; (F) amplification of DNA sequences that has been attached to microbeads
25 ovarian samples (18 EOC and 7 benign ovarian adenomas (BOA)); (B) Vertically, 35 NotI sites arranged by methylation/deletion frequency
Summary
Epithelial ovarian cancer (EOC) remains a highly lethal malignancy. It is the fifth leading cause of cancer deaths among women in the United States (22,000 new cases and 16,000 deaths annually) and causes more than 140,000 deaths annually in women worldwide. The epithelium is the tissue where most ovarian cancers arise [2]. Ovarian cancer is classified into several stages according to the American Joint Committee on Cancer/Tumor Node Metastasis (AJCC/TNM) and International Federation of Gynecology and Obstetrics (FIGO) staging systems which are based on how far the cancer has spread. In Stages I and II, the tumor is confined to the ovaries, while there is local metastasis (usually lymph) in Stage III and there is distal organ metastases in Stage IV [3]
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