Global impact of the DNA/RNA helicase DHX9 on the processing of coding and noncoding transcripts in Ewing sarcoma pathogenesis

Maria Paola Paronetto, PhD,  IRCCS Santa Lucia Foundation
Recipient of the: Pittsburgh Cure Sarcoma Research Award

Ewing Sarcomas (ES) are biologically aggressive tumors of bone and soft tissues, characterized by in frame chromosomal translocation leading to the expression of the EWS-FLI1 oncogene. They affect mainly children and adolescents. A combination of surgery and radiation therapy, followed by chemotherapy is the only treatment up to date. Unfortunately, radiation and the drugs used in chemotherapy damage normal cells as well as cancer cells, and in the long term can have deleterious effects on the other organs of children affected.
The DNA/RNA helicase DHX9 has been identified as a molecular partner of the oncoprotein EWS-FLI1. DHX9 interacts with EWS-FLI1 and stimulates the transcriptional activity of EWS-FLI1-regulated promoters. Consequently, DHX9 binding to EWS-FLI1 is important for its oncogenic function and for the accomplishment of neoplastic transformation. Notably, knockdown of DHX9 expression critically reduced ES cell viability and sensitivity to imposed genotoxic stress.
Since formation of the EWS-FLI1-DHX9 complex enhances EWS-FLI1 oncogenic activity and tumor maintenance, the possibility to modulate, or even inhibit, this interaction could have enormous therapeutic value in ES. Recently, it has been shown that small molecule inhibitors of the interaction between DHX9 and EWS-FLI1 inhibit ES cell growth by inducing apoptosis, while enhancing DHX9 helicase activity, open the possibility of new valuable therapeutic tools.
The advent of whole-genome next generation RNA-sequencing techniques has revealed an unexpected complexity in the gene expression programs of human cells. A large portion of the human transcripts is represented by long non-coding RNAs (lncRNAs). In the very last years, it has become apparent that thousands of genes produce highly conserved and stable circular RNAs (circRNAs) with gene-regulatory potential. The expression of distinct circRNAs is often disease specific or predictive of outcome. Notably, DHX9 helicase plays a direct role in circRNAs biogenesis, and its ablation increases the number of unresolved circRNAs.
In this context, our project aims at taking advantage of high-throughput sequencing to identify coding and noncoding transcripts affected by DHX9 or by DHX9/EWS-FLI1 interaction.
The project will be focused on two specific aims:

AIM1: Transcriptome profiling of DHX9-deficient and YK-4-279-treated ES cells
AIM2: Modulation of circRNA biogenesis by DHX9 depletion and YK-4-279 treatment in ES cells

The results obtainable with our studies may open the path for the development of tools, such as antisense oligonucleotides or RNA molecules, which can drive downregulation of dangerous transcripts activated by DHX9-EWS-FLI1.