{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T19:22:48Z","timestamp":1787253768542,"version":"build-2736575974"},"reference-count":50,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,6,17]],"date-time":"2025-06-17T00:00:00Z","timestamp":1750118400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AI151075"],"award-info":[{"award-number":["R01 AI151075"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p><jats:italic>Chlamydia trachomatis<\/jats:italic> (<jats:italic>Ct<\/jats:italic>) 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 <jats:italic>Ct<\/jats:italic> and host-derived immortalized cells has been performed, this study used dual RNA sequencing to examine host-pathogen interactions in <jats:italic>ex vivo<\/jats:italic> human primary endocervical stromal cells infected with <jats:italic>Ct<\/jats:italic> 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. <jats:italic>Ct<\/jats:italic> 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 <jats:italic>Ct<\/jats:italic>-host interactions, including early host immune quiescence and robust mid-infection activation of innate immunity in contradistinction to previous host and <jats:italic>Ct<\/jats:italic> findings in immortalized cell lines. The findings emphasize the utility of <jats:italic>ex vivo<\/jats:italic> human primary cell culture for investigating <jats:italic>Ct<\/jats:italic> pathogenesis using clinically relevant <jats:italic>Ct<\/jats:italic> strains and provide a foundation for future exploration of uncharacterized genes and pathways critical to <jats:italic>Ct<\/jats:italic> infection.<\/jats:p>","DOI":"10.3389\/fcimb.2025.1613922","type":"journal-article","created":{"date-parts":[[2025,6,17]],"date-time":"2025-06-17T05:29:26Z","timestamp":1750138166000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Transcriptional profiling of Chlamydia trachomatis and its host in an ex vivo endocervical primary cell culture system using dual RNA sequencing"],"prefix":"10.3389","volume":"15","author":[{"given":"Olusola","family":"Olagoke","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siddharth","family":"Chittaranjan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah","family":"Dean","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,6,17]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"2037","DOI":"10.1128\/IAI.01530-14","article-title":"Expression of the effector protein IncD in Chlamydia trachomatis mediates recruitment of the lipid transfer protein CERT and the endoplasmic reticulum-resident protein VAPB to the inclusion membrane","volume":"82","author":"Agaisse","year":"2014","journal-title":"Infect. 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