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Context-Dependent miRNA Regulatory Landscapes in Breast Cancer Uncovered by Network Community Structure

Newby, E.; Davis, E.; Dhawan, A.

2025-08-11 cancer biology
10.1101/2025.08.07.669176 bioRxiv
Show abstract

Dysregulated microRNA (miRNA) expression is strongly linked to breast cancer, but their full impact on the transcriptome remains unexplored. To address this knowledge gap, we constructed a bipartite regulatory network of miRNAs and their mRNA targets using paired expression data from The Cancer Genome Atlas (TCGA). This network enables a comprehensive investigation of each miRNAs systems level properties in breast cancer. Community analyses revealed 17 distinct regulatory communities, which define the coordinated functions of miRNA. These community-level insights uncovered novel collective miRNA functional associations. For example, the analysis reveals a link between the miR-29 family and the epithelial-to-mesenchymal transition (EMT) that is shared across breast cancer molecular subtypes. This suggests that the miR-29 family can uniquely be used as a key regulator of EMT across breast cancers. This network-centric approach highlights coordinated miRNA expression in breast cancer, integrating network medicine principles with miRNA biology to identify novel therapeutic targets.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.