Canonical and non-canonical miRNA degradation shapes state transitions and stemness in breast cancer

Area of Science:

• Molecular Biology
• Cancer Research
• Epigenetics

Background:

• Target-directed microRNA degradation (TDMD) is a key mechanism controlling microRNA (miRNA) stability.
• The role of TDMD in human cancers, particularly breast cancer, is not well understood.
• Understanding miRNA turnover is crucial for deciphering cancer progression and therapeutic resistance.

Purpose of the Study:

• To define the landscape of TDMD in different breast cancer subtypes.
• To investigate the functional impact of TDMD on miRNA regulation and cancer phenotypes.
• To uncover novel TDMD mechanisms and their implications in therapeutic response.

Main Methods:

• CRISPR interference (CRISPRi) for ZSWIM8 depletion.
• miRNA sequencing (miRNA-seq) to profile miRNA levels.
• RNA immunoprecipitation sequencing (RIP-seq) and crosslinking immunoprecipitation (CLIP) to map miRNA-binding sites.
• Single-cell transcriptomics to analyze cellular heterogeneity.

Main Results:

• Identified 19 high-confidence TDMD substrates, including miR-29b-3p and miR-33a/b-5p, demonstrating TDMD's role in shaping miRNA target repression.
• TDMD of miR-29b-3p correlates with epithelial-mesenchymal transition plasticity and identifies a stem-like, tumor-initiating subpopulation in triple-negative breast cancer.
• Discovered a non-canonical, ZSWIM8/proteasome-independent TDMD pathway involving SERPINE1-triggered miR-30c-5p degradation, which confers paclitaxel resistance and enhances tumor-sphere formation.

Conclusions:

• TDMD is a significant regulatory layer in cancer, linking miRNA decay to cellular state transitions and treatment outcomes.
• Regulated miRNA decay contributes to aggressive breast cancer phenotypes and therapeutic resistance.
• This study provides a framework for investigating TDMD's role in cancer biology and developing novel therapeutic strategies.