GPNMB Mediated Immune Modulation in Triple Negative Breast Cancer: Transcriptomic Analysis of GPNMB Knockdown in TAM CoCultures Reveals Therapeutic Targeting Opportunities

Abstract Triple Negative Breast Cancer (TNBC) can be regarded as one of the most aggressive and therapeutically chal- lenging forms of cancer. It is responsible for 10–15% of all breast cancer cases worldwide along with significantly low success rate in prognosis when compared to hormone receptor positive (ER, PR, HER2) tumors. The immunosup- pressive tumor microenvironment (TME) characterized by abundant tumor associated macrophages (TAMs) with M2-like pro tumoral phenotypes, plays a critical role in TNBC progression and also in therapy failure. Glycoprotein non-metastatic melanoma protein B(GPNMB) has emerged as one of the key immunomodulatory factors with the ability to polarize macrophages toward immunosuppressive states and facilitating immune evasion. This analyti- cal study presents a comprehensive transcriptomic analysis of GPNMB knockdown (siGPNMB1 and siGPNMB2) in co-cultured TNBC cancer cells with THP1 derived macrophages when compared to control conditions. Using RNAseq differential gene expression (DGE) analysis with DESeq2 and pathway enrichment analysis through Gene Set Enrichment Analysis (GSEA), we were able to identify 232 genes which show significant differential expres- sion. GPNMB knockdown resulted in substantial downregulation of pro-tumoral inflammatory programs including IL6-JAK-STAT3 signalling, TGFβ signalling, and epithelial mesenchymal transition (EMT), while upregulating ox- idative phosphorylation and MYC target pathways. Our findings demonstrate that GPNMB functions as a critical orchestrator of macrophage mediated immune suppression in TNBC, making it an attractive therapeutic target for re-educating the TME and enhancing anti tumor immunity.