Integrative Re-analysis of miRNA–mRNA Regulatory Networks and Functionally Enriched Pathways in Triple-Negative Breast Cancer

Background: Triple-negative breast cancer (TNBC) is an aggressive and molecularly heterogeneous subtype of breast cancer. Although microRNAs play an important role in post-transcriptional gene regulation, the regulatory networks involved in TNBC remain incompletely understood. Re-analysis of publicly available expression datasets provides a practical and cost-effective approach to identify potential regulatory relationships and generate hypotheses for further investigation. Methods: Public TNBC miRNA (GSE38167, Agilent GPL14943) and mRNA (GSE61723, Affymetrix GPL16686) datasets were independently analysed using GEO2R with Benjamini-Hochberg false discovery rate (FDR) correction. Features meeting the criteria of FDR < 0.05 and |log₂FC| ≥ 1 were retained. Experimentally supported miRNA-target interactions obtained from miRTarBase were filtered according to inverse-expression patterns. The resulting network was analysed for highly connected nodes using igraph, while functional enrichment analysis was performed using g:Profiler across GO, KEGG and Reactome databases. Results: The analysis identified 702 differentially expressed miRNA probes and 319 significant mRNA transcript features. Following inverse-expression filtering, 689 candidate interactions involving 151 unique miRNAs and 76 target genes were retained. Functional enrichment analysis identified 463 significant terms associated with extracellular space, CXCR chemokine receptor binding, growth factor activity, cell migration and proliferation. Integration of three enriched KEGG pathways – ECM-receptor interaction, cytokine-cytokine receptor interaction and AMPK signalling-with hub interactions resulted in nine prioritized regulatory axes converging on CCNA2, CXCL11 and FN1, with downregulated miRNAs paired with upregulated target genes. Conclusion: This integrative re-analysis narrowed a large transcriptomic candidate space to nine pathway-contextualized miRNA-mRNA regulatory hypotheses. These findings provide a reproducible framework and a basis for subsequent experimental validation of the identified regulatory mechanisms in TNBC models.