Non-coding and Coding Transcriptional Profiles Are Significantly Altered in Pediatric Retinoblastoma Tumors

Discussion Inactivation of the RB/E2F pathway is a common feature of cancer (22). In this analysis, we sought to understand how the homozygous deletion of the RB1 gene changed the transcriptional profile of both coding and non-coding genes in the rare pediatric tumor, Retinoblastoma. To do this, we compared the gene expression of Retinoblastoma tumors with that from normal retinal tissue using RNA-sequencing. This represents the first time that such an approach has been used to generate a complete transcriptional profile of these tumors and builds upon previous coding RNA studies (23–25, 33). Our work expands our coverage of the genome for Retinoblastoma and includes the expression from non-coding regions of the genome, including long non-coding RNAs (LNC-RNAs), anti-sense RNAs, and transposable elements. This new in-depth analysis of RNA changes, coupled with our recent proteomic profiling of this cohort of Retinoblastoma (34), provides a new resource for the Retinoblastoma and RB-loss research community. In agreement with previous microarray based studies (23–25, 33), we find very strong transcriptional upregulation of E2F target genes involved in cell cycle progression and apoptosis. In contrast, p53 and MYC target genes are only mildly affected. Most of the down regulated genes are associated with retina cell differentiation and ocular development. These results are consistent with retinal cells when they abnormally differentiate and cause lineage specif...
Source: Frontiers in Oncology - Category: Cancer & Oncology Source Type: research