Breakpoint Analysis of Transcriptional and Genomic Profiles Uncovers Novel Gene Fusions Spanning Multiple Human Cancer Types
Figure 5
Discovery and characterization of EWSR1/CREM in melanoma.
(A) Array CGH heatmap displaying intragenic EWSR1 breakpoints identified in the SH-4 and CHL-1 melanoma cell lines. (B) Paired-end RNA-seq identification of EWSR1/CREM in CHL-1. Paired-end reads supporting the rearrangement are depicted along with the predicted gene fusion structure. CREM contributes a basic leucine zipper motif (ZIP), while EWSR1 contributes the EWS Activation Domain (EAD). (C) RT-PCR verification of EWSR1/CREM in CHL-1. (D) Quantitative RT-PCR using primers flanking the gene fusion junction verifies EWSR1/CREM knockdown following transfection of an siRNA pool targeting the 3′ end of CREM. (E, F, G) Transfection of CHL-1 with CREM-targeting siRNA pool results in (E) decreased cell proliferation, (F) decreased invasion, and (G) a higher fraction of senescent cells, compared to non-targeting control (NTC). **P<0.01 (two-sided Student's t-test).