A comparative analysis of CXCR4 gene expression from published datasets and cell surface protein levels in breast and...

The CXCL12/CXCR4 signaling axis is a critical mediator of cancer metastasis, particularly in the homing of breast and prostate cancer cells to the bone. Consequently, characterizing the CXCR4 status of preclinical cancer models is essential for designing meaningful experiments. However, prior reports show conflicting CXCR4 status in these models, with reported positivity rates varying from <5 % to >90 % across studies, highlighting the urgent need for systematic comparison. This study provides a systematic comparison of CXCR4 expression patterns by analyzing gene expression data from breast cancer cell lines (MDA-MB-231, MDA-MB-468) and prostate cancer cells (PC3) across multiple published datasets using batch effect correction. Additionally, flow cytometry experiments were conducted to directly quantify CXCR4 surface protein levels in these same cell lines, integrating transcriptomic analyses with proteomic evidence. The comparative analysis revealed a marked divergence between transcript abundance and surface protein expression. The highly metastatic MDA-MB-231 cells exhibited the highest levels of CXCR4 mRNA, which correlated with a strong enrichment of metastasis-related signaling pathways. Conversely, MDA-MB-468 and PC3 cells displayed relatively lower CXCR4 transcript levels but contained a significantly higher proportion of CXCR4-positive cells at the protein level. These findings indicate that high transcriptional activity does not necessarily translate to high surface protein availability, likely due to active post-translational regulation, such as rapid receptor internalization. Overall, these results emphasize the importance of validating both gene and protein expression in specific cell line models prior to conducting CXCR4-focused mechanistic or therapeutic studies. Such validation is crucial, as expression patterns may vary considerably between laboratories due to differences in passage number, culture conditions, and genetic drift.