Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level

Apoptosis is an essential defensive mechanism against tumorigenesis. Proteins of the B-cell lymphoma-2 (Bcl-2) family regulate programmed cell death by the mitochondrial apoptosis pathway. In response to intracellular stress, the apoptotic balance is governed by interactions of three distinct subgroups of proteins; the activator/sensitizer BH3 (Bcl-2 homology 3)-only proteins, the pro-survival, and the pro-apoptotic executioner proteins. Changes in expression levels, stability, and functional impairment of pro-survival proteins can lead to an imbalance in tissue homeostasis. Their overexpression or hyperactivation can result in oncogenic effects. Pro-survival Bcl-2 family members carry out their function by binding the BH3 short linear motif of pro-apoptotic proteins in a modular way, creating a complex network of protein-protein interactions. Their dysfunction enables cancer cells to evade cell death. The critical role of Bcl-2 proteins in homeostasis and tumorigenesis, coupled with mounting insight in their structural properties, make them therapeutic targets of interest. A better understanding of gene expression, mutational profile, and molecular mechanisms of pro-survival Bcl-2 proteins in different cancer types, could help to clarify their role in cancer development and may guide advancement in drug discovery. Here, we shed light on the pro-survival Bcl-2 proteins in breast cancer using different bioinformatic approaches, linking -omics with structural data. We analyzed the changes in the expression of the Bcl-2 proteins and their BH3-containing interactors in breast cancer samples. We then studied, at the structural level, a selection of interactions, accounting for effects induced by mutations found in the breast cancer samples. We find two complexes between the up-regulated Bcl2A1 and two down-regulated BH3-only candidates (i.e., Hrk and Nr4a1) as targets associated with reduced apoptosis in breast cancer samples for future experimental validation. Furthermore, we predict L99R, M75R as damaging mutations altering protein stability, and Y120C as a possible allosteric mutation from an exposed surface to the BH3-binding site. Author summary Apoptosis is a form of cellular suicide. When the process of apoptosis is disrupted, cells that should have been eliminated may survive. The cellular decision-making between cell survival and cell death is orchestrated by interactions between three subgroups of Bcl-2 proteins. One of these, the pro-survival Bcl-2 subgroup, can enable cancer cells to escape cell death with impact on cancer development. Because of their role in cancers, pro-survival proteins are promising therapeutic targets for anti-cancer treatments. Despite progress in drug development, a common trait is that the available compounds could suffer in selectively targeting certain pro-survival proteins. We believe that additional knowledge on the alterations of the different pro-survival proteins in different cancer types, coupled with a better understanding of their interactions and functionality, will provide foundations for the development of new drugs with increased specificity. Here, we shed light on the role of the pro-survival proteins in breast cancer, by bridging different bioinformatic methods, linking the analysis of changes in gene expression with the study of structural ensembles of proteins. Our results highlight the prospects of an integrative bioinformatics approach for a comprehensive view of pro-survival proteins and their interactions in a specific cancer type.