Rewiring of the transcriptome of breast cancer cells in 3D organotypic cultures promotes cancer progression through SNHG7/miR-486-3P/HIF1A axis

Three-dimensional (3D) organotypic cell cultures more accurately recapitulate the spatial architecture, biological, and epigenetic features of tumors than traditional two-dimensional (2D) monolayer models, thus representing an innovative approach in cancer research. However, the impact of the 3D microenvironment on the reprogramming of non-coding RNAs, including long non-coding RNAs (lncRNAs) and microRNAs in breast cancer cells, remains unexplored. To fill this knowledge gap, we performed RNA sequencing to identify the differential transcriptome of 3D versus 2D cell cultures and novel potential therapeutic targets. Our data showed that the Hs-578T breast cancer cells grew as stellated 3D structures over an extracellular matrix protein- enriched scaffold. Expression profiling data revealed that 88 lncRNAs, 218 microRNAs, and 2,806 mRNAs were modulated in Hs-578T cells under 3D conditions. Regulated protein-encoding genes were found to be associated with cell proliferation, migration, and chemoresistance. Interestingly, coregulatory network analyses reveal a positive regulation of a set of hypoxia-responsive genes related to the lncRNA-SNHG7/miR-486-3p/HIF1A axis in 3D cultures. SNHG7 and HIF1A expression were upregulated, whereas miR-486-3p was downregulated in 3D cultures, correlating with poor overall survival in cancer patients. Functional studies in the 3D environment indicate that the knockdown of SNHG7 abolishes cell proliferation and invasion, while activating apoptosis, thereby sensitizing cancer cells to cisplatin. Furthermore, a significant increase in hypoxic internal regions was found in SNHG7-deficient 3D structures. In conclusion, our data suggested that the 3D architecture of cells reprograms the transcriptional programs of breast cancer cells. Importantly, SNHG7 plays a key role in cancer progression, representing a promising novel therapeutic target for breastcancer.