High-throughput RNAi screen in Ewing sarcoma cells identifies leucine rich repeats and WD repeat domain containing 1 (LRWD1) as a regulator of EWS-FLI1 driven cell viability

Gene. 2017 Jan 5:596:137-146. doi: 10.1016/j.gene.2016.10.021. Epub 2016 Oct 17.

Abstract

A translocation leading to the formation of an oncogenic EWS-ETS fusion protein defines Ewing sarcoma. The most frequent gene fusion, present in 85 percent of Ewing sarcomas, is EWS-FLI1. Here, a high-throughput RNA interference screen was performed to identify genes whose function is critical for EWS-FLI1 driven cell viability. In total, 6781 genes were targeted by siRNA molecules and the screen was performed both in presence and absence of doxycycline-inducible expression of the EWS-FLI1 shRNA in A673/TR/shEF Ewing sarcoma cells. The Leucine rich repeats and WD repeat Domain containing 1 (LRWD1) targeting siRNA pool was the strongest hit reducing cell viability only in EWS-FLI1 expressing Ewing sarcoma cells. LRWD1 had been previously described as a testis specific gene with only limited information on its function. Analysis of LRWD1 mRNA levels in patient samples indicated that high expression associated with poor overall survival in Ewing sarcoma. Gene ontology analysis of LRWD1 co-expressed genes in Ewing tumors revealed association with DNA replication and analysis of differentially expressed genes in LRWD1 depleted Ewing sarcoma cells indicated a role in connective tissue development and cellular morphogenesis. Moreover, EWS-FLI1 repressed genes with repressive H3K27me3 chromatin marks were highly enriched among LRWD1 target genes in A673/TR/shEF Ewing sarcoma cells, suggesting that LRWD1 contributes to EWS-FLI1 driven transcriptional regulation. Taken together, we have identified LRWD1 as a novel regulator of EWS-FLI1 driven cell viability in A673/TR/shEF Ewing sarcoma cells, shown association between high LRWD1 mRNA expression and aggressive disease and identified processes by which LRWD1 may promote oncogenesis in Ewing sarcoma.

Keywords: DNA replication; EWS-FLI1; Ewing sarcoma; LRWD1; RNA interference; WD repeat.

MeSH terms

  • Bone Neoplasms / genetics*
  • Bone Neoplasms / mortality
  • Bone Neoplasms / pathology
  • Cell Cycle / genetics
  • Cell Line, Tumor
  • Cell Survival / genetics
  • Doxycycline / pharmacology
  • Female
  • Gene Expression Regulation, Neoplastic / drug effects
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Kaplan-Meier Estimate
  • Male
  • Microtubule Proteins / genetics*
  • Microtubule Proteins / metabolism
  • Oncogene Proteins, Fusion / genetics*
  • Oncogene Proteins, Fusion / metabolism
  • Proto-Oncogene Protein c-fli-1 / genetics*
  • Proto-Oncogene Protein c-fli-1 / metabolism
  • RNA Interference
  • RNA-Binding Protein EWS / genetics*
  • RNA-Binding Protein EWS / metabolism
  • Sarcoma, Ewing / genetics*
  • Sarcoma, Ewing / mortality
  • Sarcoma, Ewing / pathology
  • WD40 Repeats

Substances

  • EWS-FLI fusion protein
  • LRWD1 protein, human
  • Microtubule Proteins
  • Oncogene Proteins, Fusion
  • Proto-Oncogene Protein c-fli-1
  • RNA-Binding Protein EWS
  • Doxycycline