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

ABSTRACT: 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 (LogFC ≥ 1.5 or ≤ −1.5, p.adj value <0.05). 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE232952 | GEO | 2023/05/20

REPOSITORIES: GEO

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Project description:Purpose:Triple negative breast cancer (TNBC) commonly metastasizes to the brain and predicts poor prognosis with limited therapeutic options. TNBC frequently harbors BRCA mutations translating to platinum sensitivity; platinum response may be augmented by additional suppression of DNA repair mechanisms through poly(ADP-ribose)polymerase (PARP) inhibition. We evaluated brain penetrance and efficacy of Carboplatin +/- the PARP inhibitor ABT888, and investigated gene expression changes in murine intracranial (IC) TNBC models stratified by BRCA and molecular subtype status. Experimental design:Athymic mice were inoculated intra-cerebrally with BRCA-mutant: SUM149 (basal), MDA-MB-436 (claudin-low), or BRCA-wild-type: MDA-MB-468 (basal), MDA-MB-231BR (claudin-low) TNBC cells and treated with PBS control (IP, weekly), Carboplatin (50mg/kg/week, IP), ABT888 (25mg/kg/day, OG), or their combination. DNA-damage (?-H2AX) and apoptosis (cleaved-Caspase-3(cC3)) were assessed via IHC of IC tumors. Gene expression of BRCA-mutant IC tumors was measured. Results: Carboplatin+/-ABT888 significantly improved survival in BRCA-mutant IC models compared to control, but did not improve survival in BRCA-wild-type IC models. Carboplatin+ABT888 revealed a modest survival advantage versus Carboplatin in BRCA-mutant models. ABT888 yielded a marginal survival benefit in the MDA-MB-436 but not in the SUM149 model. BRCA-mutant SUM149 expression of ?-H2AX and cC3 proteins was elevated in all treatment groups compared to Control, while BRCA-wild-type MDA-MB-468 cC3 expression did not increase with treatment. Carboplatin treatment induced common gene expression changes in BRCA-mutant models.Conclusions: Carboplatin+/-ABT888 improves survival in BRCA-mutant IC TNBC models with corresponding DNA damage and gene expression changes. Combination therapy represents a promising treatment strategy for patients with TNBC brain metastases warranting further clinical investigation. reference x sample

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

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