Functional Genomic Screening Reveals Splicing of the EWS-FLI1 Fusion Transcript as a Vulnerability in Ewing Sarcoma

Cell Rep. 2016 Jan 26;14(3):598-610. doi: 10.1016/j.celrep.2015.12.063. Epub 2016 Jan 14.

Abstract

Ewing sarcoma cells depend on the EWS-FLI1 fusion transcription factor for cell survival. Using an assay of EWS-FLI1 activity and genome-wide RNAi screening, we have identified proteins required for the processing of the EWS-FLI1 pre-mRNA. We show that Ewing sarcoma cells harboring a genomic breakpoint that retains exon 8 of EWSR1 require the RNA-binding protein HNRNPH1 to express in-frame EWS-FLI1. We also demonstrate the sensitivity of EWS-FLI1 fusion transcripts to the loss of function of the U2 snRNP component, SF3B1. Disrupted splicing of the EWS-FLI1 transcript alters EWS-FLI1 protein expression and EWS-FLI1-driven expression. Our results show that the processing of the EWS-FLI1 fusion RNA is a potentially targetable vulnerability in Ewing sarcoma cells.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • Calmodulin-Binding Proteins / antagonists & inhibitors
  • Calmodulin-Binding Proteins / genetics
  • Calmodulin-Binding Proteins / metabolism
  • Cell Line, Tumor
  • Cell Survival
  • Exons
  • Gene Expression Regulation, Neoplastic
  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H / antagonists & inhibitors
  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H / genetics
  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H / metabolism
  • Humans
  • Microfilament Proteins / antagonists & inhibitors
  • Microfilament Proteins / genetics
  • Microfilament Proteins / metabolism
  • Oncogene Proteins, Fusion / antagonists & inhibitors
  • Oncogene Proteins, Fusion / genetics
  • Oncogene Proteins, Fusion / metabolism*
  • Phosphoproteins / antagonists & inhibitors
  • Phosphoproteins / genetics
  • Phosphoproteins / metabolism
  • Proto-Oncogene Protein c-fli-1 / antagonists & inhibitors
  • Proto-Oncogene Protein c-fli-1 / genetics
  • Proto-Oncogene Protein c-fli-1 / metabolism*
  • RNA Interference
  • RNA Precursors / metabolism
  • RNA Splicing
  • RNA Splicing Factors
  • RNA, Small Interfering / metabolism
  • RNA-Binding Protein EWS / antagonists & inhibitors
  • RNA-Binding Protein EWS / genetics
  • RNA-Binding Protein EWS / metabolism*
  • RNA-Binding Proteins / antagonists & inhibitors
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Receptors, Cytoplasmic and Nuclear / antagonists & inhibitors
  • Receptors, Cytoplasmic and Nuclear / genetics
  • Receptors, Cytoplasmic and Nuclear / metabolism
  • Ribonucleoprotein, U2 Small Nuclear / antagonists & inhibitors
  • Ribonucleoprotein, U2 Small Nuclear / genetics
  • Ribonucleoprotein, U2 Small Nuclear / metabolism
  • Sarcoma, Ewing / pathology
  • Trans-Activators
  • Transcription Factors / antagonists & inhibitors
  • Transcription Factors / genetics
  • Transcription Factors / metabolism

Substances

  • Calmodulin-Binding Proteins
  • EWS-FLI fusion protein
  • EWSR1 protein, human
  • FLII protein, human
  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H
  • Microfilament Proteins
  • Oncogene Proteins, Fusion
  • Phosphoproteins
  • Proto-Oncogene Protein c-fli-1
  • RNA Precursors
  • RNA Splicing Factors
  • RNA, Small Interfering
  • RNA-Binding Protein EWS
  • RNA-Binding Proteins
  • Receptors, Cytoplasmic and Nuclear
  • Ribonucleoprotein, U2 Small Nuclear
  • SF3B1 protein, human
  • SUPT6H protein, human
  • Trans-Activators
  • Transcription Factors