Chimeric RNA landscape in the Chinese population and the role of <i>SFT2D2-TBX19</i> in prostate cancer progression.

406 Background: Specific gene fusions and their fusion products (chimeric transcripts and proteins) have served as ideal diagnostic markers and therapeutic targets for cancer. However, few systematic studies for chimeric transcriptome have been conducted in prostate cancer (PCa), and none in the Chinese populations. Methods: We analyzed raw RNA-seq data from PCa patients in the Chinese Prostate Cancer Genome Epigenome Atlas (CPGEA) to predict chimeric RNAs using the Eriscript. Fluorescence-activated cell sorting (FACS) was employed to isolate tumor cells, cancer-associated fibroblasts (CAFs), tumor-associated macrophages (TAMs), and T cells from fresh clinical specimens. Cellular functional assays, western blotting, FISH, electron microscopy, RNA pull-down, and immunofluorescence were employed to elucidate the underlying mechanisms by which the chimeric SFT2D2-TBX19 regulates prostate cancer progression. Results: Over 100,000 chimeric RNAs have been predicted in CPGEA. After several rounds of screening, we identified 301 of them with differential expression between cancerous and adjacent normal tissues, and 101 out of them were validated in clinical samples. About 20% showed prognosis correlation, indicating their potential biomarker values. Further experiments found differential expression of those chimeras among cancer epithelial cells, CAFs, TAMs, and T cells. We further examined the effect of these chimeric RNAs, and found examples of chimeric RNAs directly regulates the growth and motility of tumor cells, and regulate communications between tumor cells and their microenvironment, which jointly facilitate tumor progression. An important chimeric RNA, SFT2D2-TBX19 , was identified as encoding the TBX19-202 protein. Both TBX19-202 and its parental TBX19, which share homologous amino acid sequences, enhance prostate cancer cell proliferation, migration and invasion. Additionally, SFT2D2-TBX19 also can work as a lncRNA which could interact with the ATP synthase F1 subunit ATP5F1A, increasing ATP5F1A phosphorylation, which stabilizes the interaction between ATP5F1A and ATP5F1B. The region spanning 1801-2400bp of SFT2D2-TBX19 and the intermediate structural domain of ATP5F1A are crucial functional areas. This stabilization of ATP5F1A and ATP5F1B enhances mitochondrial ATP synthase activity and ATP production, thus maintaining prostate cancer cell proliferation. Conclusions: These findings established the atlas of chimeric transcriptome in PCa from the Chinese populations, and provided a large list of validated chimeric RNAs that have the potentials of becoming novel biomarkers and/or treatment targets. Our research provides comprehensive evidence that the SFT2D2-TBX19 promotes prostate cancer progression by encoding the TBX19-202 protein and stabilizing mitochondrial ATP synthase through ATP5F1A phosphorylation.