FREM1 Serves as a Novel Therapeutic Target in Breast Cancer through Basement Membrane-Based Prognostic Modeling with Integrated Bioinformatics and Experimental Validation

Background​​ : Breast cancer remains the leading cause of cancer-related mortality in women worldwide, with metastatic disease posing significant therapeutic challenges. While immunotherapy has shown promise, tumor immune evasion limits its efficacy. The basement membrane (BM), a specialized extracellular matrix structure, plays a crucial yet understudied role in breast cancer progression and immune modulation. This study aims to investigate the prognostic value and therapeutic potential of BM-related genes in breast cancer.​​ Methods​​ : We integrated transcriptomic data from TCGA and GEO databases to construct a BM-related gene signature. Unsupervised clustering stratified patients into molecular subtypes, while differential expression analysis identified key BM-associated genes. Functional enrichment analyses (GO, KEGG, GSEA) elucidated biological pathways, and immune microenvironment characterization was performed using ESTIMATE and CIBERSORT. Machine learning approaches pinpointed critical BM-related genes, which were subsequently validated through in vitro experiments.​​ Results​​ : Breast cancer patients were classified into high- and low-BM groups, with the low-BM cohort exhibiting worse prognosis. Pathway analysis revealed significant enrichment in immune regulation, ECM remodeling, and cytokine signaling. FREM1 emerged as a top protective gene through machine learning. Experimental validation using low-FREM1-expressing breast cancer cell lines demonstrated that FREM1 overexpression (confirmed by qPCR and Western blot) significantly suppressed tumor cell proliferation, as evidenced by decreased Ki-67 expression and reduced EdU incorporation.​​ Conclusion​​ : Our study establishes BM-related genes as novel prognostic biomarkers and therapeutic targets in breast cancer. FREM1 in particular functions as a tumor suppressor by inhibiting cancer cell proliferation, highlighting its potential for therapeutic exploitation. These findings provide critical insights into BM-mediated tumor progression and suggest new avenues for targeted breast cancer therapy.