BIOINFORMATICS CERNA ANALYSIS FOR THE STUDY OF STEM FACTOR SOX2 IN ANAPLASTIC THYROID CANCER.

Abstract

Cancer stem cells (CSC) are believed to play a central role in oncogenesis, but until today their isolation and characterization is still particularly complex. Anaplastic thyroid cancer (ATC) presents several characteristics suggestive of a tumour highly enriched in CSC (high mitotic rate, poor prognosis, high aggressiveness, resistance to treatments, etc). For these reasons ATC represents a good candidate to study CSCs. SOX2 is a key stem transcriptional factor, usually only transiently expressed, that plays a fundamental role in stem cell identity. SOX2 proved to be constitutively expressed in SW1736 cell line, a well established and recognized ATC cell line. The bioinformatics ceRNA analysis permits to discover gene transcripts that may be post-transcriptionally positively co-regulated with the 3’UTR probe. We aimed to perform ceRNA analysis in SW1736 to identify candidate genes that might be involved in SOX2 functional network and in turn in stemness and CSC biogenesis. A competing endogenous RNA (ceRNA) in silico analysis was performed on 3’UTR of SOX2 mRNA. Our analysis harvested several genes involved in the RNA interference mechanism (DICER1, DROSHA, AGO2) and in cell cycle control (TP53, CCND1). To further validate the in silico analysis, in vitro analysis via RT-PCR was performed. Knocking down SOX2 in SW1736 (0.417 expression rate), the interacting ceRNA transcripts were coherently downregulated with significant differences (expression rates from 0.355 to 0.705, p < 0.05). Moreover, a statistical analysis of the ceRNAs in other cell lines and clinical specimens revealed a positive correlation with the expression of TP53, DICER1, DROSHA and AGO2, suggesting the existence of a fine regulatory network.