Novel transcription-induced fusion RNAs in prostate cancer

Abstract

Prostate cancer is a clinically and pathologically heterogeneous disease with a broad spectrum of molecular abnormalities in the genome and transcriptome. One key feature is the involvement of chromosomal rearrangements creating fusion genes. Recent RNA-sequencing technology has uncovered that fusions which are not caused by chromosomal rearrangements, but rather meditated at transcription level, are common in both healthy and diseased cells. Such fusion transcripts have been proven highly associated with prostate cancer development and progression. To discover novel fusion transcripts, we analyzed RNA sequencing data from 44 primary prostate tumors and matched benign tissues from The Cancer Genome Atlas. Twenty-one high-confident candidates were significantly enriched in malignant vs. benign samples. Thirteen of the candidates have not previously been described in prostate cancer, and among them, five long intergenic non-coding RNAs are involved as fusion partners. Their expressions were validated in 50 additional prostate tumor samples and seven prostate cancer cell lines. For four fusion transcripts, we found a positive correlation between their expression and the expression of the 3' partner gene. Among these, differential exon usage and qRT-PCR analyses in particular support that SLC45A3-ELK4 is mediated by an RNA polymerase read-through mechanism.

Keywords: RNA sequencing; expression profile; fusion transcript; prostate cancer.

Figure 1. Flowchart of fusion transcript filtering

The identified fusion transcripts were filtered in a successive manner, following the initial analysis of 44 paired tumor and benign prostate samples by deFuse software.

Figure 2. The TMEM219-TAOK2 fusion transcript

(A) The fusion transcript was detected from the VCaP, DU145, PC3, 22Rv1, NCI-H660 and LNCaP cell lines (see Supplementary Table 2), and the specific breakpoint was verified by Sanger sequencing. (B) Example data from the TCGA prostate tumor “TCGA-HC-7211-01A-11R-2118-07” shows seven split reads spanning the chimeric transcript breakpoint, from exon 5 of TMEM219 (ENST00000414689) to exon 2 of TAOK2 (ENST00000279394). The fusion transcript is predicted to include an in-frame open reading frame encoding a chimeric protein with the combination of transmembrane and serine/threonine kinase domains. The genomic view of the fusion event is from the top showing annotated exons of the fusion partner genes and the number of split reads supporting breakpoint (curved line), the RNA expression levels (read counts), and genomic coordinates for the fusion transcript in mega base pairs from the p-telomere of chromosome 16.

Figure 3. Differential expression of 3′ fusion partner genes

(A) and (B) show the expression of the 3′ partner genes, B3GNT6 and ELK4, of the fusions ACER3-B3GNT6 and SLC45A3-ELK4 in 44 pairs of tumor and benign prostate samples. (C) and (D) show the expression of 3′ partner genes B3GNT6 and ELK4 in 50 additional prostate tumors. (E) and (F) show the correlation between the expression of ACER3-B3GNT6 and SLC45A3-ELK4 and their respective 3′ partner genes, B3GNT6 and ELK4. X and Y axes represent log2 transformed expression values (FPKM, fragments per kilobase of transcript per million mapped reads; RPKM, reads per kilobase of transcript per million mapped reads).