Endoplasmic reticulum-localized TurboID-mediated labelling reveals distinct secretome profiles of MCF-10A and MDA-MB-231 cells

Breast cancer is one of the most prevalent cancers and the leading causes of cancer-related deaths. The lack of reliable biomarkers for accurate subtyping and early diagnosis continues to hinder early detection and treatment. Secretome proteins represent an accessible and valuable source of biomarkers due to their roles in cell communication, signalling and shaping the extracellular microenvironment. In this study, secretome proteins from two cell lines, MCF-10A and MDA-MB-231, representing healthy and aggressive breast cells, respectively, were labelled with ER-localized TurboID-mediated enzymatic biotinylation approach at the endoplasmic reticulum. The biotinylated samples were enriched using streptavidin-coated magnetic beads and analysed by label-free quantitation using nHPLC LC-MS/MS. The regulated proteins were subjected to bioinformatics analyses using STRING and g:Profiler tools to identify candidate biomarkers. Proteomic analysis identified 206 proteins, with approximately 82% belonged to secretome proteins. Among them, 65 were differentially regulated which were associated with hydrolytic activity, cell adhesion, and lipid metabolism. CST1, APOC1, and POSTN had previously been associated with cancer, while TEX10, LZIC, and PSMA3 were implicated in breast cancer for the first time. Our findings demonstrates extensive secretome remodelling in invasive breast cancer cells, unveiling potential secreted biomarker candidates that may improve breast cancer diagnosis and treatment strategies.