RNA-Sequencing of Primary Retinoblastoma Tumors Provides New Insights and Challenges Into Tumor Development

Abstract

Retinoblastoma is rare tumor of the retina caused by the homozygous loss of the Retinoblastoma 1 tumor suppressor gene (RB1). Loss of the RB1 protein, pRB, results in de-regulated activity of the E2F transcription factors, chromatin changes and developmental defects leading to tumor development. Extensive microarray profiles of these tumors have enabled the identification of genes sensitive to pRB disruption, however, this technology has a number of limitations in the RNA profiles that they generate. The advent of RNA-sequencing has enabled the global profiling of all of the RNA within the cell including both coding and non-coding features and the detection of aberrant RNA processing events. In this perspective, we focus on discussing how RNA-sequencing of rare Retinoblastoma tumors will build on existing data and open up new area's to improve our understanding of the biology of these tumors. In particular, we discuss how the RB-research field may be to use this data to determine how RB1 loss results in the expression of; non-coding RNAs, causes aberrant RNA processing events and how a deeper analysis of metabolic RNA changes can be utilized to model tumor specific shifts in metabolism. Each section discusses new opportunities and challenges associated with these types of analyses and aims to provide an honest assessment of how understanding these different processes may contribute to the treatment of Retinoblastoma.

Keywords: RB1; RNA-sequencing; Retinoblastoma; metabolic profiling; non-coding RNA (LINC-RNA); tumor.

FIGURE 1

Schematic of the different RNA measurements from Retinoblastoma tumors using conventional microarrays vs. RNA-sequencing.

FIGURE 2

The workflow of RNA-microarray and RNA-sequencing is depicted above. Higher number of targets are detected by RNA-sequencing using which targets of unknown sequence and low abundance targets can both be identified. To detect targets using RNA microarrays, the sequence of the transcripts must be known and expressed in abundance in the cell.