Investigating the Prognostic and Therapeutic Potential of MicroRNAs (miRNAs) and Piwi-Interacting Small RNAs (piRNAs) in Breast Cancer

Background

Breast cancer’s(BC) heterogeneous nature highlights the importance of understanding its underlying regulatory mechanisms. Therefore, identifying novel prognostic biomarkers and therapeutic targets is crucial for advancing the current standard of care for BC.

Methods

Ninety-six BC samples underwent miRNAome and piRNAome profiling. Relapse-free survival (RFS) analysis was conducted using RStudio 2023.09.1, while miRNA and piRNA mapping and quantification employed CLC Genomics Workbench 20.2. IDEP.951 was used for differential expression analysis. Cancer hallmark assessments utilized clonogenic assays, three-dimensional organotypic culture, live-dead staining, and cell cycle analysis. Target Scan and Ingenuity Pathway Analysis were used for miRNA target identification.

Results

Hierarchical clustering identified miRNAs associated with luminal, HER2, and basal BC subtypes. Hsa-miR-5683 emerged as a potential prognostic biomarker, showing a favorable correlation with RFS, and suppressing tumorigenicity in triple-negative breast cancer (TNBC) models. Transcriptomic profiling of hsa-miR-5683 overexpressing TNBC revealed a role in regulating key oncogenic pathways. Integration of downregulated genes and CRISPR-Cas9 perturbational effects identified 11 bona fide gene targets for hsa-miR-5683 essential for TNBC viability. BC patients' clustering based on piRNA expression was less prominent when compared to miRNA-based clustering. Survival analysis identified several prognostic piRNAs, among which hsa-piR-775 correlated with better prognosis and suppressed tumorigenicity of TNBC models.

Conclusions

Our data provide a comprehensive miRNA and piRNA expression atlas in BC underscoring their prognostic and therapeutic significance unraveling the intricate miRNAs-mediated regulatory network in TNBC.