Unveiling the complexity of Beclin-1 splicing and its role in autophagy regulation in breast cancer

Autophagy maintains cellular homeostasis by degrading unnecessary or damaged proteins and organelles. The study focuses on Beclin-1 (BECN1), a key regulator of autophagy, whose expression in is frequently found decreased in breast cancers due to monoallelic deletion. In this work, we primarily aim to show that BECN1 undergoes post-transcriptional alternative splicing to generate three additional protein isoforms which are characterized for their structural and functional roles in autophagy in cancer cells. We have determined that the Alpha isoform is involved in stimulating mitophagy. Additionally, the Beta isoform restricts it, while Gamma has a minimal impact on the autophagic flux. Second, we also demonstrated how different environments affect the BECN1 gene expression in breast cancer cells. By comparing traditional 2D cell cultures with more advanced and physiologically relevant in-vitro 3D models, this research concludes new insights into the unique patterns of BECN1 splicing. A key highlight of the work showed relatively higher expression of protein isoform Alpha than the wild-type BECN1 in the triple negative breast cancer spheres indicating their possible roles in tumor progression. These findings not only deepen our understanding of BECN1's role in breast cancer but also highlight how the environment around cells can influence gene expression.