LncRNA SOX9-AS1 triggers a transcriptional program involved in metabolic reprogramming, cell migration and invasion in triple-negative breast cancer

The regulatory role of the lncRNA SOX9-AS1 in TNBC and basal-like subtypes is poorly understood. We performed SOX9-AS1 gene silencing using two short-harping constructs, which were transfected in MDA-MB-468 and HCC1187 TNBC cell lines that had high SOX9-AS1 expression, and the genome-wide RNA-seq analysis of both transfects was performed. Data showed that 351 lncRNAs and 740 mRNAs were differentially expressed in MDA-MB-468. Meanwhile 56 lncRNAs and 100 mRNAs were also severally modulated in HCC1187 cells. Pathway analysis revealed that the protein-encoding genes potentially regulates metabolic reprogramming, and epithelial-mesenchymal transition. SOX9-AS1 is a master regulator of a plethora of genes that can reflect our understanding of the important role of this lncRNA in the molecular cell biology of TNBC and basal-like subtypes.