Transcriptional profiling of Chlamydia trachomatis and its host in an ex vivo endocervical primary cell culture system using dual RNA sequencing

Olusola Olagoke¹Siddharth Chittaranjan¹Deborah Dean^2,3,4,5*

• ¹Department of Pediatrics, School of Medicine, University of California San Francisco, San Francisco, California, United States
• ²Departments of Medicine and Pediatrics, Division of Infectious Diseases and Global Health, University of California San Francisco School of Medicine, San Francisco, United States
• ³Department of Bioengineering, University of California San Francisco and Berkeley School of Engineering, Berkeley, United States
• ⁴Bixby Center for Global Reproductive Health, University of California San Francisco, San Francisco, United States
• ⁵Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, United States

Chlamydia trachomatis (Ct) is an obligate intracellular bacterium that causes significant ocular and urogenital morbidity worldwide. Understanding host-pathogen interactions is challenging but dual RNA sequencing offers simultaneous transcriptome data for comprehensive interrogations into these interactions. While transcriptional profiling of both Ct and hostderived immortalized cells has been performed, this study used dual RNA sequencing to examine host-pathogen interactions in ex vivo human primary endocervical stromal cells infected with Ct strain E/Bour. At 1-hour post-infection (1hpi), 168 differentially expressed host genes (DEGs) were identified, 40% of which were non-coding RNAs, novel proteins, or pseudogenes. Pathway analysis revealed no significant enrichment at this stage, indicating a quiescent host response. At 24hpi, 212 DEGs were identified, with strong upregulation of interferon-stimulated genes and activation of the cGAS-STING and RLR pathways, despite the absence of detectable type I interferons. Pro-inflammatory and leukocyte recruitment genes were also highly expressed, suggesting an immunoreactive phenotype at this later stage. Ct transcriptomics identified 331 early and 903 mid-infection genes. Inclusion-membrane genes peaked at 1hpi, while hemolysin-like and polymorphic membrane protein genes were upregulated at 24hpi. Enrichment analysis identified pathways related to catalytic activity, host modulation, and bacterial survival. This study demonstrates distinct temporal dynamics in Cthost interactions, including early host immune quiescence and robust mid-infection activation of innate immunity in contradistinction to previous host and Ct findings in immortalized cell lines. The findings emphasize the utility of ex vivo human primary cell culture for investigating Ct pathogenesis using clinically relevant Ct strains and provide a foundation for future exploration of uncharacterized genes and pathways critical to Ct infection.