Proximity labeling and SILAC based proteomic approach identifies proteins at the interface of homotypic and heterotypic cancer cell interactions

Cellular communication, particularly between different types of cancer cells, plays a crucial role in tumor progression and invasion. This study employed a combinatory approach of horseradish peroxidase (HRP)-dependent proximity biotinylation and stable isotope labeling by amino acids in cell culture (SILAC) to identify proteins involved in homotypic (same cell type) and heterotypic (different cell types) interactions in breast cancer cell lines. Epithelial (MCF7) and mesenchymal (MDA-MB-231) breast cancer cells were co-cultured to model these interactions. HRP was targeted to the extracellular leaflet of the plasma membrane in 'bait' cells to label proximal proteins in 'prey' cells. Prey cells were metabolically labeled with heavy isotopes, enabling differentiation of self-biotinylated proteins from those of interacting cells. Mass spectrometry analysis identified cell surface and extracellular proteins enriched at the interface of cell interactions. The study revealed distinct and common proteomic profiles for homotypic and heterotypic interactions and demonstrating that the methodology effectively maps the proteome of cancer cell interactions. This approach provides insights into the molecular mechanisms of cancer cell communication, potentially informing therapeutic strategies to inhibit tumor invasion.