Abstract 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 (miRNAs) in breast cancer cells, has lagged behind. To address this knowledge gap, we performed RNA sequencing (RNA-seq) to identify differential transcripts between 3D and 2D cell cultures and to identify novel potential therapeutic targets. Our data showed that the Hs-578T breast cancer cells orchestrate their growth as stellated 3D cell structures over an extracellular matrix protein-enriched scaffold. Expression profiling data revealed that 88 lncRNAs, 218 miRNAs, and 2806 mRNAs were modulated in Hs-578T cells under 3D conditions. Regulated protein-encoding genes were associated with cell proliferation, migration, and chemoresistance. Interestingly, analyses of lncRNA/miRNA/mRNA coregulatory networks reveal positive regulation of a set of hypoxia-responsive genes, including the hypoxia-inducible factor 1 subunit alpha (HIF1A). Moreover, we found that the lncRNA Small nucleolar RNA host gene 7 (SNHG7) may regulate multiple miRNAs, which, in turn, could modulate hypoxia-responsive genes through the SNHG7/miR-486-3p/HIF1A axis. Functional analysis showed that SNHG7 and HIF1A expression was upregulated, whereas miR-486-3p was downregulated under 3D culture conditions, which correlated with poor overall survival in breast cancer patients. Subsequent experiments on the 3D microenvironment demonstrate that SNHG7 knockdown inhibits both cell proliferation and invasion and promotes apoptosis, thereby sensitizing cancer cells to cisplatin. Furthermore, a significant increase in hypoxic regions within the internal structures was observed in SNHG7-deficient 3D cultures. In conclusion, our findings suggest that 3D microenvironment-induced transcriptional changes contribute to breast cancer progression, highlighting SNHG7 as a potential target for RNA-based therapies.
Salinas-Vera et al. (Thu,) studied this question.