Spliceosomal miR-99b Regulates SPACA6-AS1 Pre-mRNA Levels and Promotes Malignant Phenotypes in Breast Cancer

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression primarily in the cytoplasm. However, emerging evidence highlights their additional roles in the nucleus. In particular, spliceosomal miRNAs have been implicated in novel regulatory functions, including the modulation of gene expression. Here, we investigate the nuclear role of spliceosomal miR-99b in breast cancer cells, focusing on its interaction with the long non-coding RNA (lncRNA) SPACA6-AS1. Using non-tumorigenic (MCF-10A) and breast cancer cell lines (MCF-7 and MDA-MB-231), we demonstrate that spliceosomal miR-99b expression increases with malignancy and correlates with elevated SPACA6-AS1 pre-mRNA levels. Notably, miR-99b exhibits full complementarity to the 5′ splice junction of SPACA6-AS1, suggesting a direct role in splicing regulation. Functional assays reveal that inhibition of miR-99b reduces SPACA6-AS1 pre-mRNA levels, whereas its overexpression enhances pre-mRNA accumulation, indicating that miR-99b promotes the formation or stabilization of the unspliced transcript. Furthermore, increased miR-99b expression is associated with altered ratios of SPACA6 isoforms, supporting a broader role in RNA-level regulation of gene expression. Phenotypically, miR-99b enhances breast cancer cell migration and is required for efficient invasion, particularly in highly aggressive cancerous cells. Our findings uncover a novel nuclear function of miR-99b in modulating lncRNA splicing and gene expression. This spliceosomal miR-99b–SPACA6-AS1 axis represents a previously unrecognized regulatory pathway that contributes to breast cancer progression and may provide a potential target for diagnostic and therapeutic strategies.