Defining intracellular and extracellular role of AGR2: insights of from CRISPR-targeted breast cancer cells and DIA-NN analysis

Anterior Protein Gradient-2 (AGR2) is an endoplasmic reticulum resident protein that catalyzes thiol-disulfide interchange reactions during protein maturation within the secretory pathway. Overexpression of AGR2 is prevalent in various epithelial cancers, particularly in estrogen receptor-positive (ER+) breast cancer, where it correlates with poor prognosis. Emerging evidence suggests AGR2 can also be secreted extracellularly and exert pro-tumorigenic effects similar to its intracellular counterpart, highlighting its potential role in the tumor microenvironment. However, the precise mechanism of AGR2 secretion and how it impacts on the tumor microenvironment remains unclear. This study aims to elucidate the intricate roles of both intracellular and extracellular AGR2 signaling. We employed CRISPR/Cas9 genome editing to knock out AGR2 in two ER+ breast cancer cell lines, MCF7 and T47D, resulting in two AGR2 knockout cell pools per cell line. Using cutting-edge proteomics techniques, specifically Data Independent Acquisition-Neural Network (DIA-NN) mass spectrometry, we analyzed the impact of AGR2 depletion on cellular protein expression. In the whole cell lysate proteome of MCF-7 and T47D cell lines, we identified 9698 and 9984 proteins, respectively. Among these, we discovered 119 and 601 commonly differentially expressed proteins (DEPs) in the AGR2 knockout pools of MCF-7 and T47D, respectively. Functional enrichment analysis revealed shared perturbations in transmembrane transporter activity, estrogen signaling pathways, and oxidoreductase activity. Secretome analysis identified 1041 and 1626 proteins in MCF-7 and T47D cell lines, respectively. We identified 92 and 601 DEPs in the secretomes of MCF-7 and T47D, respectively, primarily involved in protein chaperone activity, metabolic pathways, and cytoskeleton organization. Protein-protein interaction and hub gene analysis further identified potential key binding partners in the AGR2 signaling axis. In summary, our findings provide a comprehensive insight into the intricate signaling pathways involving AGR2, spanning both intracellular and extracellular proteomes. We identified a subset of proteins highly reliant on AGR2-mediated regulation, suggesting that AGR2's oxidoreductase activity may extend beyond cellular boundaries. Moreover, this study emphasizes a potential 'druggable' stage within the AGR2-dependent pathway, proposing avenues for targeted therapeutic interventions.