Identification of human miR-1839-5p by small RNA-seq, a miRNA enriched in neoplastic tissues.

Abstract

MicroRNAs (miRNAs) modulate gene expression through destabilization or translational inhibition of cytoplasmic transcripts or by transcriptional regulation through binding to genomic DNA. Although miRNAs are globally down-regulated in cancer, some are overexpressed in neoplastic tissues, playing key roles in tumorigenesis (oncomiRs), sometimes behaving as effective cancer markers. Using total RNA from human uterus adenocarcinoma and non-neoplastic uterus, we conducted a small RNA-sequencing experiment followed by prediction of novel miRNAs using MirDeep* software. Synteny analysis and whole genome alignments were performed using BLAST. We also evaluated expression by a reverse transcriptase-polymerase chain reaction (RT-PCR) in normal tissues of the FSD2 gene, which spans the human miR-1839-5p gene in the opposite direction. MirDeep* analysis predicted a miRNA not previously annotated in databases, identical to and likely the orthologue of mouse miR-1839-5p. Whole-genome local alignments of this miRNA revealed a single perfect hit that is indeed syntenic to mouse miR-1839-5p. Alignments with other mammalian orthologues showed considerable conservation. We validated the prediction via a stem-loop RT-PCR assay, also employed to screen RNA samples from several additional normal and cancer tissues, showing increased expression in neoplastic tissues compared to their respective non neoplastic counterparts. Human heart tissue expresses both miR-1839-5p and FSD2. Human tissues express an orthologue of mouse miR-1839-5p and, given its expression pattern, we suggest that this miRNA could be explored as a potential oncomiR or cancer marker. Also, according to the genomic organization of miR-1839-5p and FSD2, perfect complementarity exists between the two elements, making possible miRNA-directed cleavage in human cardiac tissue.