NotI Microarrays: Novel Epigenetic Markers for Early Detection and Prognosis of High Grade Serous Ovarian Cancer

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.

Novel tumor suppressor candidates on chromosome 3 revealed by NotI-microarrays in cervical cancer

“…These results, and our recent data obtained for lung and ovarian cancers using NotI-microarrays, 7,8 suggest that methylation of promoter regions is the important mechanism leading to inactivation of TSG and TSG-candidates on chromosome 3.…”

“…Many of these genes (LOC285205, FGD5, RPL32, ROPN1, CGGBP1, NBEAL2, LOC285375 and others) were not shown to be involved in cervical carcinogenesis previously, but according to our recent data many of them were involved in the development of non-small cell lung and ovarian cancer. 7,8 These findings suggest that genetic and epigenetic destabilization of genes at chromosome 3 is common mechanisms of epithelial tumors development. According literature data, the protein products of newly identified genes belong to pathways affected during development and progression of different cancer types (Table S2): in WNT signaling pathway (E3 ubiquitin-protein ligase, PDZRN3), in the regulation of cellular polarity and invasion (PRICKLE2), in regulation of the actin cytoskeleton (FGD5), in MAP kinase signaling pathway (FGF12) and others.…”

“…This methodology has been described in detail earlier. 8,10 Briefly, the essence of this method consists of the ability of the NotI restriction enzyme to recognize and digest only the unmethylated CG-rich motif GCGGCCGC often found in CpG islands associated with regulatory region of many genes (Fig. 1).…”

PPM1M and PRICKLE2 are potential tumor suppressor genes in human clear-cell renal cell carcinoma

“…PRICKLE2 is involved in the WNT/ planar cell polarity (PCP) signaling pathway that controls tissue polarity and cell movement [4]. These genes are tumor suppressor candidates in cervical cancer, non-small cell lung cancer and ovarian cancer [5][6][7]. It is possible, that these two genes might be potential tumor-suppressor genes in ccRCC as well.…”

Promising markers of CIMP+ colon tumors identified on the basis of TCGA data analysis

“…Впервые фенотип CIMP+ был обнаружен при раке толстой кишки (Toyota et al, 1999), но в последние годы данный термин все чаще используют для описания интенсивного гиперметилирования промоторов генов и в других видах рака, включая рак легкого, молоч-ной железы, мочевого пузыря, матки, желудка, яичника, поджелудочной железы, почек и предстательной железы (Suzuki et al, 2014). Проведенные нами ранее исследова-ния нарушений паттернов метилирования генов хромосо-мы 3 с применением NotI-микрочипов позволили также предположить существование опухолей CIMP+ (20-30 % опухолей) при раке легкого, яичника, шейки матки и почки (Dmitriev et al, 2012(Dmitriev et al, , 2014Kashuba et al, 2012;Senchenko et al, 2013). Молекулярные и клинико-патологические особенности этого типа опухолей позволяют считать, что возникновение различных CIMP+ опухолей обусловлено единым молекулярным механизмом (Suzuki et al, 2014).…”