Whole transcriptome sequencing of UPEC-infected testis and epididymis (5d) following depletion of CX3CR1+ macrophages

A finely tuned immune regulation within the epididymis and testis—balancing tolerance towards sperm with effective defense against infections—is essential for maintaining male fertility. This balance is especially critical in the epididymis, where sperm mature and where it is often disrupted during ascending urogenital infections. While testicular inflammation is typically reversible, the epididymis undergoes irreversible tissue remodeling, particularly in distal regions, whereas proximal regions remain mostly unaffected despite bacterial presence. We previously identified that each epididymal region has a unique immunological landscape, distinct from that of the testis. Notably, CX3CR1⁺ macrophages are the dominant immune cell type and appear central to maintaining homeostasis and orchestrating immune responses in a region-specific manner. To assess their functional role, we used a transgenic mouse model to deplete CX3CR1⁺ macrophages under steady-state and infected conditions. Whole-transcriptome analysis following E. coli infection revealed downregulation of genes linked to innate immunity and cytokine regulation, indicating that CX3CR1⁺ macrophages restrain excessive inflammation—particularly in proximal regions. Combined with histological and cellular phenotyping, our data highlight a key role for CX3CR1⁺ macrophages in preserving epithelial integrity and modulating immune responses during infection.