Unraveling small non-coding RNAs with a significant post-transcriptional impact on breast cancer cell signaling, using a combinational sequencing approach

Breast cancer (BrCa) is a predominant type of cancer with high mortality rates. The deregulation of cell signaling pathways is a hallmark of BrCa pathogenesis and disease progression. Aiming to explore novel post-transcriptional regulatory mechanisms influencing BrCa cell signaling, a combinational sequencing approach was employed by integrating small RNA sequencing with poly(A)-RNA sequencing, following the alteration of cell signaling using proteasome inhibitors. Pursuing a broad analysis of BrCa gene expression, cell lines deriving from the major molecular subtypes were incorporated. Gene expression changes were detected after treatment with both inhibitors, with the strongest overlap in the Luminal B and TNBC cells. The altered small non-coding RNA profiles suggested broad regulatory effects on genes central to BrCa biology and cell signaling. Interestingly, miR-489-3p and miR-876-3p were consistently downregulated and miR-1827 upregulated among the studied conditions, while other miRNAs were characterized with cell-line specific alterations. Several piRNAs, including piR-36,318, piR-39,245, and piR-36,036, were markedly induced. Specific tRNA-derived RNA fragments such as 5’-tRF-TRN-GTT11, 3’-tRF-TRQ-CTG3, i-tRF-TRQ-CTG3(1), and 5’-tRF-TRV-CAC14 stood out with a potential contribution to regulatory axes shaping BrCa biology. Furthermore, an upregulation of miR-22-5p/3p and a relevant downregulation of specific targets was observed in two TNBC cell lines of metastatic origin. The luciferase activity assay revealed a direct interaction of miR-22-5p with the components of the PI3K/AKT pathway, INSR, ITGB8, and PI3KR1. Lastly, the overexpression of mir-22 inhibited cell proliferation and migration. In conclusion, our combinational sequencing approach unraveled several small non-coding RNAs with a significant post-transcriptional impact on BrCa cell signaling.