Transcription-mediated chimeric RNAs in prostate cancer: time to revisit old hypothesis?

Abstract

Chromosomal rearrangements and fusion genes play important roles in tumor development and progression. Four high-frequency prostate cancer-specific fusion genes were recently reported in Chinese cases. We attempted to confirm one of the fusion genes, USP9Y-TTTY15, by reverse transcription PCR, but detected the presence of the USP9Y-TTTY15 fusion transcript in cancer samples, nonmalignant prostate tissues, and normal tissues from other organs, demonstrating that it is a transcription-induced chimeric RNA, which is commonly produced in normal tissues. In 105 prostate cancer samples and case-matched adjacent nonmalignant tissues, we determined the expression level of USP9Y-TTTY15 and a previously reported transcription-induced chimeric RNA, SLC45A3-ELK4. The expression levels of both chimeric RNAs vary greatly in cancer and normal cells. USP9Y-TTTY15 expression is neither higher in cancer than adjacent normal tissues, nor correlated with features of advanced prostate cancer. Although the expression level of SLC45A3-ELK4 is higher in cancer than normal cells, and a dramatic increase in its expression from normal to cancer cells is correlated with advanced disease, its expression level in cancer samples alone is not correlated with any clinical parameters. These data show that both chimeric RNAs contribute less to prostate carcinogenesis than previously reported.

FIG. 1.

Detection of the USP9Y-TTTY15 fusion transcript in prostate cancer and adjacent nonmalignant prostate tissue. (A) Examples of the RT-PCR products of the USP9Y-TTTY15 fusion transcript at 232 bp in prostate cancer (lanes 1–5) and case-matched adjacent normal tissue (lanes 6–10) samples along with a negative control without input cDNA template (lane 11). Marker: 1 Kb plus (Life Technology) DNA size marker. (B) Schematic presentation of the alignment of TTTY15 and USP9Y on the Y chromosome and the fusion transcripts based on the sequencing data of the fusion at the end of USP9Y exon 3 and the beginning of TTTY15 exon 3. The bottom panel is a representative image of the fusion sequence from a clinical sample. The position of the nucleotide fusion site is indicated by the black arrows.

FIG. 2.

Detection of the USP9Y-TTTY15 fusion transcript by RT-PCR in normal lung, gall bladder, and kidney tissues. Gel image showing the USP9Y-TTTY15 fusion transcript detected at the expected size of 232 bp. A positive control using a prostate cancer cDNA sample and a negative control without cDNA template were also included. Marker: 1 Kb plus (Life Technology) DNA size marker.

FIG. 3.

USP9Y-TTTY15 expression in UK prostate samples. (A) Examples of the RT-PCR products of the USP9Y-TTTY15 fusion transcript at 232 bp in two BPHs, one prostate cancer sample (WX33T), together with its adjacent normal tissue (WX33N) from an UK patient and two prostate cell lines (PNT2 and LNCaP). (B) USP9Y-TTTY15 expression level measured by qRT-PCR in UK samples was presented in N fold change relative to sample P80BPH (setting the expression level at 1). Light blue, BPH samples; purple, normal prostate tissue; green, PIN samples; brown, cancer samples; dark blue, prostate cell lines. BPH, benign prostatic hyperplasia; N, normal; PIN, prostate intraepithelial neoplasia; T, tumor.

FIG. 4.

Distribution of the transcription-mediated chimera expression. (A) The distribution of USP9Y-TTTY15 expression level in the Chinese prostate cancer and adjacent nonmalignant tissues overall and in different clinical subgroups. (B) The distribution of SLC45A3-ELK4 expression level in the Chinese prostate cancer and adjacent nonmalignant tissues, split into different groups based on clinical parameters. The expression level of USP9Y-TTTY15 and SLC45A3-ELK4 (y axis) was presented in n fold change relative to sample 31C (setting the expression level at 1). Age, age of the patient at diagnosis; GS, Gleason score; PSA, prostate specific antigen.