Nuclear Roles of Spliceosome-Associated microRNAs in Neuronal Cancer Cells

MicroRNAs (miRNAs) are well-known for regulating translation in the cytoplasm, yet their roles in the nucleus remain poorly understood. Previously, we identified spliceosome-associated miRNAs implicated in tumorigenesis and metastasis in breast cancer models. Here, we investigate their nuclear functions in immortalized human cortical neurons (HCN) cell line, along with brain cancer derived cell lines of glioblastoma (U87MG) and neuroblastoma (SH-SY5Y) that are widely used as models for brain cancer research. Our findings reveal that spliceosome-associated miRNAs mark neuronal cancer cells and uncover novel nuclear targets. Interestingly, some spliceosomal miRNAs exhibit opposing regulatory effects in the nucleus compared to the cytoplasm, while some portray potential novel nuclear functions. A notable example is miR-99b, which overlaps the 5’ splice junction of the poorly characterized long non-coding RNA (lncRNA) SPACA6-AS1 and, through base-pairing, enhances SPACA6-AS1 pre-mRNA levels. These findings highlight the diverse and context-dependent functions of nuclear miRNAs in gene regulation and cancer progression, expanding our understanding of their regulatory potential beyond the cytoplasm.