vtRNA2-1/nc886 Produces a Small RNA That Contributes to Its Tumor Suppression Action through the microRNA Pathway in Prostate Cancer

Abstract

vtRNA2-1 is a vault RNA initially classified as microRNA precursor hsa-mir-886 and recently proposed as “nc886”, a new type of non-coding RNA involved in cancer progression acting as an oncogene and tumor suppressor gene in different tissues. We have shown that vtRNA2-1/nc886 is epigenetically repressed in neoplastic cells, increasing cell proliferation and invasion in prostate tissue. Here we investigate the ability of vtRNA2-1/nc886 to produce small-RNAs and their biological effect in prostate cells. The interrogation of public small-RNA transcriptomes of prostate and other tissues uncovered two small RNAs, snc886-3p and snc886-5p, derived from vtRNA2-1/nc886 (previously hsa-miR-886-3p and hsa-miR-886-5p). Re-analysis of PAR-CLIP and knockout of microRNA biogenesis enzymes data showed that these small RNAs are products of DICER, independent of DROSHA, and associate with Argonaute proteins, satisfying microRNA attributes. In addition, the overexpression of snc886-3p provokes the downregulation of mRNAs bearing sequences complementary to its “seed” in their 3′-UTRs. Microarray and in vitro functional assays in DU145, LNCaP and PC3 cell lines revealed that snc886-3p reduced cell cycle progression and increases apoptosis, like its precursor vtRNA2-1/nc886. Finally, we found a list of direct candidate targets genes of snc886-3p upregulated and associated with disease condition and progression in PRAD-TCGA data. Overall, our findings suggest that vtRNA2-1/nc886 and its processed product snc886-3p are synthesized in prostate cells, exerting a tumor suppressor action.

Pan-Cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology

“…It is also important to mention that gene expression interpretations based solely on chromatin accessibility are blind to post-transcriptional regulatory events such as processing, localization, and stability of the RNA transcript. Nevertheless, since the chromatin status of the different vtRNA promoters has been positively correlated with the abundance of their transcripts (Ahn et al, 2018;Fort et al, 2018;Helbo et al, 2015;Lee et al, 2014aLee et al, , 2014bPark et al, 2017;Sallustio et al, 2016;Treppendahl et al, 2012), ATAC-seq is likely a good surrogate of vtRNA expression.…”

“…Moreover, vtRNA2-1 was proposed as a new type of ncRNA functioning as a tumor suppressor gene (TSG) that inhibits PKR, and was consequently renamed as "nc886" (Golec et al, 2019;Jeon et al, 2012aJeon et al, , 2012bLee et al, 2011). Then, its anti-proliferative and TSG function was described in prostate (Aakula et al, 2015;Fort et al, 2018;Ma et al, 2020), skin (Lee et al, 2019a), gastric (Lee et al, 2014b) and esophageal (Im et al, 2020;Lee et al, 2014a) and cholangiocarcinoma cells (Kunkeaw et al, 2012). Conversely, a pro-proliferative and anti-apoptotic oncogenic role was proposed for vtRNA2-1 in renal (Lei et al, 2017), ovarian (Ahn et al, 2018), thyroid (Lee et al, 2016), cervical (Li et al, 2017) and endometrial (Hu et al, 2017) tissues.…”

“…Indeed, small RNAs with microRNA like function were demonstrated to derive from vtRNA1-1 (svRNAs) and to repress the expression CYP3A4, a key enzyme of drug metabolism (Meng et al, 2016;Persson et al, 2009). VtRNA2-1 has also been shown to act as a microRNA precursor in different tissues, serving both as TSG in prostate (Aakula et al, 2015;Fendler et al, 2011;Fort et al, 2020), bladder (Nordentoft et al, 2012), breast (Tahiri et al, 2014), colon (Yu et al, 2011), lung (Bi et al, 2014;Cao et al, 2013;Gao et al, 2011;Shen et al, 2018) and thyroid cancers (Dettmer et al, 2014;Xiong et al, 2011) and as oncogene (OG) in renal (Yu et al, 2014), colorectal (Schou et al, 2014) and esophagus cancer (Okumura et al, 2016) through the repression of specific mRNA transcripts in human cancer.…”

“…The vtRNAs transcription is controlled by promoter DNA methylation. Different lines of evidence revealed that the epigenetic control of vtRNA2-1 is complex and owns clinical relevance in several tissues solid tumors including breast, lung, colon, bladder, prostate, esophagus, hepatic and stomach cancer (Cao et al, 2013;Fort et al, 2018;Lee et al, 2014aLee et al, , 2014bRomanelli et al, 2014;Treppendahl et al, 2012;Yu et al, 2020). Intriguing aspects of the epigenetic regulation of vtRNA2-1 locus comprise its dependence on the parental origin of the allele (Joo et al, 2018;Paliwal et al, 2013), and its sensitivity to the periconceptional environment ((Silver et al, 2015) and subsequent independent studies (van Dijk et al, 2018;Richmond et al, 2018)).…”

“…Nonetheless, since chromatin accessibility plays a critical role in the regulation of gene expression, at some extent the transcription of an RNA can be inferred from the chromatin status of its promoter (Corces et al, 2018;Duren et al, 2017;Liu et al, 2018). Since mounting evidence has shown that vtRNAs expression is tightly controlled by chromatin accessibility, dependent on nucleosome positioning and promoter DNA methylation (Ahn et al, 2018;Fort et al, 2018;Helbo et al, 2015Helbo et al, , 2017Lee et al, 2014aLee et al, , 2014bPark et al, 2017;Sallustio et al, 2016;Treppendahl et al, 2012), the chromatin structure is a suitable surrogate marker of vtRNA transcription and could be used as a proxy of their expression.…”