hsa-miR-1246 is Consistently Overexpressed in Spheroid-Derived Cancer Stem Cells From Multiple Tumor Types

Tumors consist of various cell types, including a small population of cancer stem cells (CSCs), which are linked to metastasis, drug resistance, and recurrence. Maintaining the CSC phenotype requires regulation of molecules, including miRNAs; they are small non-coding RNAs involved in processes such as proliferation, differentiation, invasion, and apoptosis. However, miRNAs involved in CSC generation and maintenance remain largely unidentified. In this study, we aimed to identify miRNAs associated with CSC populations by studying the miRNA profiles in Spheroids-Derived cancer stem cells (SDCSCs) from different cancer cell lines. Firstly, we used small RNA sequencing by Illumina to identify differentially expressed miRNAs from SDCSCs compared with adherent cells from lung cancer cell line. MiRNAs with P < .05 and fold change >1.0 were considered significant. Next, we conducted a meta-analysis to integrate expression data from studies performed under same conditions from several tumor cell lines such as ovarium, breast, colorectal cancer cell lines. We reanalyzed microarrays and RNA sequencing data. For integration we employed the Robust Rank Aggregation approach. We identified only one upregulated miRNA, the hsa-miR-1246 with a P-value 1.6356^-5. hsa-miR-1246 showed consistent overexpression in CSC-enriched spheroids, with fold changes ranging from 2.4 to 3.8 (P < .05) across studies. Bioinformatics analysis revealed that hsa-miR-1246 interacts with cyclins, GSK3B, and other experimentally validated targets, which were related to the cell cycle (FDR 8,40E-03) and the regulation of transcription from RNA polymerase II (FDR 8,30E-03). Our results provide the first integrative study showing that hsa-miR-1246 is consistently overexpressed from cancer stem cells in different tumor cell lines, suggesting a direct link between its oncogenic activity and the CSC phenotype. Since our analysis demonstrates that miR-1246 overexpression is highly specific to CSCs rather than differentiated tumor cells, its detection in patients could serve as an indirect indicator of CSC abundance and tumor aggressiveness. This provides new biological insight into the cellular origin of this miRNA and supports its potential use as a biomarker of stemness and therapeutic target in cancer. Additional studies using in vivo models and functional knockdown experiments will be important to validate these findings and better define the role of hsa-miR-1246 in CSC regulation.