microRNAs within the endogenous spliceosome of breast cancer cells act on novel nuclear targets

Many cancers in humans are signified by alteration in gene expression mediated by splicing and microRNAs (miRNAs). While almost all studies on miRNAs focus on their cytoplasmic regulatory roles, recent observations identify miRNAs in the nucleus, where their roles remain to be discovered. Here we provide evidence for an overlooked role of nuclear miRNAs from the spliceosomal fraction from breast-derived cell-lines that represent an increasing degree of cancer progression from non-malignant (MCF-10A) to intermediate (MCF-7) and highly metastatic (MDA-MB-231). Analyzing RNA-seq data revealed selected spliceosomal pre-miRNA fragments and mature miRNAs, many of which are cancer-associated. Specifically, the fraction of mature miRNAs increased along with the tumorigenesis level, from 20% in MCF-10A to 60% in MDA-MB-231. We focused on miR-7704 that was exclusively identified in the spliceosomal fraction. miR-7704 genomic position overlaps HAGLR, a long non-coding RNA which is known to coordinate with cancer progression. Quantifying miR-7704 expression in the three breast-derived cell-lines showed a decrease in miR-7704 expression and a parallel increase in HAGLR levels which follows the cellular malignancy level. We further demonstrated that miR-7704 downregulation increased the level of HAGLR and that miR-7704 expression correlates with cell-division length. Remarkably, a third of the abundant spliceosomal miRNAs (e.g. miR-100, miR-30a, and let-7 family members) display a decrease in expression along with the malignancy index, which is in contrast to their reported expression trend in the cytosol. Altogether, we report on novel roles for miRNAs in the spliceosome and suggest the potential for miRNAs as attractive tumorigenesis indicators.