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- Title
COMPLEX NETWORK GENE NETWORK ANALYSIS OF GENOME WIDE METHYLATION DATA OF ORAL CQARCINOMA FORMALIN FIXED TISSUE.
- Authors
MOATAR, ALEXANDRA; CHIS, AIMEE; MIOK, VIKTORIAN; SAMOILA, CORINA; SECLAMAN, EDWARD; ANGHEL, ANDREI; SIRBU, IOAN-OVIDIU; MARIAN, CATALIN
- Abstract
Oral scuamocellular cancer (OSCC) is the sixth most common malignancy and the fourth cause of death due to cancer in men worldwide, due to its’ (usually) late diagnostic. Recent work has involved multiple epigenetic mechanisms in the pathogenesis of OSCC, the most common of which are specific DNA methylation profiles and changes in microRNA expression, both at tissue and biological fluids level. The aim of our study was to identify the methylation profile of OSCC tissues with a potential impact on microRNA expression. We have used the Infinium array-basedMethylation Assay to quantitatively assessthe genome wide methylation status at single-CpG-site level using DNA purified from formalin fixed OSCC pooled samples from the University of Medicine archive. After quality control, filtering out poor performing probes and normalization of data (using the preprocessQuantile method, to minimize the unwanted variation within and between samples), we performed PCA analysis and generated MultiDimensional Scaling (MDS) plots to visualize and explore the differences between OSCC and normal tissue samples. Following the identification of the differentially methylatedmicroRNA loci, we performed qRT-PCR analysis of microRNA expression to validate the predicted effect of DNA methylation upon miR expression. Complex network analysis of prediction data and OSCC GEO data sets reveal the impact of DNA methylation and microRNA changes upon OSCC transcriptome. Our data depict a complex image of the intertwining between the two major epigenetic mechanisms and contribute to a better understanding of OSCC pathogeny.
- Subjects
GENE regulatory networks; EPIGENOMICS; METHYLATION; DNA methylation; FORMALDEHYDE; MULTIDIMENSIONAL scaling
- Publication
Journal of Experimental & Molecular Biology, 2019, Vol 20, Issue 3, p71
- ISSN
2601-6974
- Publication type
Article