Single-cell atlas of patient-derived cervical organoids uncovers epithelial immune heterogeneity and intercellular crosstalk during Chlamydia infection

The uterine cervix is a critical mucosal interface that balances immune defense and reproductive function, yet how its distinct epithelial compartments coordinate responses to infection remains unclear. Here, we integrate patient-derived 3D cervical organoids, single-cell transcriptomics and native tissue analysis to construct a high-resolution atlas of epithelial cell diversity and immune dynamics during Chlamydia trachomatis infection. We demonstrate that cervical organoids precisely mirror native tissue at both transcriptional and cellular levels, identifying epithelial subtypes with region-specific immune specializations. Upon infection, ectocervical epithelia reinforce barrier integrity, whereas endocervical epithelia, particularly uninfected bystander cells, exhibit extensive transcriptional reprogramming characterized by robust interferon activation, antigen presentation, and antimicrobial defense. Infection profoundly reshapes epithelial intercellular communication, positioning bystander cells as central signaling hubs that coordinate immune responses and tissue regeneration. Our findings highlight a sophisticated epithelial-intrinsic immune network critical for cervical mucosal defense and establish a physiologically relevant platform for studying human host-pathogen interactions and guiding targeted mucosal therapies against reproductive tract infections and pathologies.