5'-Isoforms of miR-1246 Have Distinct Targets and Stronger Functional Impact Compared with Canonical miR-1246 in Colorectal Cancer Cells In Vitro

• Published in: International journal of molecular sciences 2024-02, Vol.25 (5), p.2808
• Main Authors: Lukosevicius, Rokas, Alzbutas, Gediminas, Varkalaite, Greta, Salteniene, Violeta, Tilinde, Deimante, Juzenas, Simonas, Kulokiene, Ugne, Janciauskas, Dainius, Poskiene, Lina, Adamonis, Kestutis, Kiudelis, Gediminas, Kupcinskas, Juozas, Skieceviciene, Jurgita
• Format: Article
• Language: English
• Subjects: 5′-isomiR functions in vitro; 5′-isomiRs; Base Sequence; Caco-2 Cells; Cell cycle; Colorectal cancer; Colorectal Neoplasms - pathology; Comparative analysis; CRC; Development and progression; Epigenetic inheritance; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Genes; Humans; Kinases; MicroRNA; MicroRNAs; MicroRNAs - genetics; miR-1246; RNA sequencing; targetome
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms25052808

Colorectal cancer (CRC) is a multifactorial disease involving genetic and epigenetic factors, such as miRNAs. Sequencing-based studies have revealed that miRNAs have many isoforms (isomiRs) with modifications at the 3'- and 5'-ends or in the middle, resulting in distinct targetomes and, consequently, functions. In the present study, we aimed to evaluate the putative targets and functional role of miR-1246 and its two 5'-isoforms (ISO-miR-1246_a and ISO-miR-1246_G) in vitro. Commercial Caco-2 cells of CRC origin were analyzed for the expression of WT-miR-1246 and its 5'-isoforms using small RNA sequencing data, and the overabundance of the two miR-1246 isoforms was determined in cells. The transcriptome analysis of Caco-2 cells transfected with WT-miR-1246, ISO-miR-1246_G, and ISO-miR-1246_a indicated the minor overlap of the targetomes between the studied miRNA isoforms. Consequently, an enrichment analysis showed the involvement of the potential targets of the miR-1246 isoforms in distinct signaling pathways. Cancer-related pathways were predominantly more enriched in dysregulated genes in ISO-miR-1246_G and ISO-miR-1246_a, whereas cell cycle pathways were more enriched in WT-miR-1246. The functional analysis of WT-miR-1246 and its two 5'-isoforms revealed that the inhibition of any of these molecules had a tumor-suppressive role (reduced cell viability and migration and promotion of early cell apoptosis) in CRC cells. However, the 5'-isoforms had a stronger effect on viability compared with WT-miR-1246. To conclude, this research shows that WT-miR-1246 and its two 5'-isoforms have different targetomes and are involved in distinct signaling pathways but collectively play an important role in CRC pathogenesis.