Agathe Subtil

Understanding Chlamydia trachomatis infection requires physiologically relevant models tailored to various research questions. One of the main sites of C. trachomatis infection is the columnar epithelium of the endocervix; therefore, a model that accurately mimics the environment of endocervical epithelium is essential. Polarized cell models provide a valuable solution, offering a cost-effective yet biologically relevant alternative to conventional 2D culture systems and more complex and costly 3D or animal models. Immortalized human endocervical epithelial cells (A2EN cells) form a polarized monolayer on transwell membranes, reproducing key in vivo features, including tight junctions, mucus secretion, proinflammatory cytokine production, and hormone receptor expression, when maintained at low passage. This chapter outlines protocols for generating a polarized A2EN culture and assessing polarization through morphological, biochemical, and functional assays. Furthermore, we describe how C. trachomatis development can be monitored in polarized cells through microscopy, flow cytometry, immunofluorescence, and reinfection assays.

Chlamydia trachomatis , an intracellular bacterium, hijacks metabolites from the host cell for its own proliferation. We provide evidence of global hypermethylation of the host proteome, including histones during the late stages of infection. Single-cell analyses revealed co-occurrence of several methylated residues on histones while infection did not alter S-adenosylmethionine levels. Histone hypermethylation correlated positively with bacterial load and was prevented by antibiotic treatment. Mapping of trimethylation of histone 3 at residues K4 and K9 revealed a broad distribution throughout chromatin. Nuclear fractions of infected cells exhibited a fourfold decrease in demethylase activity against H3K4me3 and a twofold increase in succinate concentration, a competitive inhibitor for the demethylase co-factor α-ketoglutarate. Supplementation of the culture medium with dimethyl-ketoglutarate (DMKG) or with iron, a second co-factor of histone lysine demethylases, reduced histone hypermethylation. DMKG supplementation modified the transcription of about one third of the infection-responsive genes, indicating that histone hypermethylation contributes to modulating the transcriptional response of the host to infection. Finally, chemical inhibition of histone demethylases in a mouse model of infection showed a moderate benefit regarding the outcome of infection. Overall, our data show that the metabolic pressure exerted by a pathogen with an intracellular lifestyle drives epigenetic changes in infected cells.

The inflammation induced by Chlamydia trachomatis infection in the female genital tract can have severe consequences. Recent observations in women and mice infected with Chlamydia suggest that type I interferon (IFN-I) may have deleterious effects. This study aimed to elucidate the consequences of IFN-I production on C. trachomatis -induced inflammation in epithelial cells and the molecular pathway(s) involved. We showed that the combination of IFN-I and Chlamydia resulted in a stronger induction of inflammation than Chlamydia alone, while IFN-I alone had no effect. Inhibiting AKT and mTOR, but not silencing STAT1 , significantly attenuated the synergistic effect between IFN-I and bacteria on inflammation. Inhibition of ERK also blocked this synergistic effect, although ERK was not activated by IFN-I. We hypothesized that IFN-I enhanced the expression of a pathogen recognition receptor of the host, thereby potentiating detection of the bacteria and the subsequent inflammatory response. IFN-I, but not C. trachomatis infection, increased the expression of Toll-like receptor 3 (TLR3), and silencing or knocking-out TLR3 prevented the synergistic effect between infection and IFN-I. Furthermore, our data support the presence of dsRNA in infected cells and the activation of the MAPK/ERK and AP-1/ATF2 signaling cascades downstream of TLR3. Taken together, our data demonstrate that IFN-I exacerbates the host inflammatory response triggered by Chlamydia by increasing TLR3 expression and activation, leading to hyperinflammation. The identified signaling cascades represent potential targets for therapeutic intervention to limit tissue damage upon Chlamydia infection. IMPORTANCE: The effect of the production of IFN-I upon infection by Chlamydia trachomatis is not well understood. We showed that IFN-I exacerbated Chlamydia -induced inflammation in epithelial cells. This synergy was mediated by the IFN-induced upregulation of Toll-like receptor 3 (TLR3) expression, which facilitated sensing of Chlamydia and amplified the inflammatory response. We identified the signaling cascades involved upstream and downstream of TLR3 signaling. By exacerbating the pro-inflammatory response of epithelial cells, IFN-I might contribute to the hyperinflammation experienced by some individuals. The signaling pathways we uncovered can serve as a starting point for novel therapeutic strategies to alleviate tissue damage upon Chlamydia infection.

Chlamydia trachomatis , an obligate intracellular bacterium, develops into a vacuolar compartment called the inclusion. The bacteria import nucleoside triphosphates (NTPs) present in the inclusion lumen. It remains unclear whether nucleosides enter the inclusion lumen in their native form or as phosphorylated nucleotides. Using click chemistry coupled with fluorescence microscopy we provide evidence that cytidine requires phosphorylation by host uridine-cytidine kinase 2 (UCK2) prior to its incorporation into bacterial nucleic acids. These findings support the hypothesis that nucleosides are converted into nucleotides in the host cytoplasm prior to translocation into the inclusion lumen. Future work should therefore focus on the identification of nucleotide transporter(s) at the inclusion membrane.

Excessive inflammation upon Chlamydia trachomatis infection can cause severe damages in the female genital tract. This obligate intracellular bacterium develops mainly in epithelial cells, whose innate response contributes to the overall inflammatory response to infection. The ubiquitin-like protein interferon-stimulated gene 15 (ISG15) stimulates interferon γ (IFNγ) production and is required for bacterial clearance in several infectious contexts. Here, we describe and investigate the consequences of the increase in ISG15 expression by epithelial cells infected with C. trachomatis . Infection of HeLa cells and primary ecto-cervical epithelial cells resulted in a transcriptional upregulation of ISG15 expression. This did not involve the canonical type I interferon (IFN-I) signaling pathway and depended instead on the activation of the STING/TBK1/IRF3 pathway. The absence or reduction of ISG15 synthesis led to increased production of several cytokines and chemokines, including interleukin (IL) 6 and IL8. This implicates that ISG15 normally dampens the immune response induced by C. trachomatis infection in epithelial cells. ISG15 exerted its control from an intracellular location, but without involving ISGylation. Finally, higher levels of inflammation and delayed bacterial clearance were observed in the genital tracts of ISG15-KO mice infected by C. trachomatis compared with wild-type animals; however, IFNγ production was unchanged. Altogether, our data show that ISG15 expression acts as a brake on the immune response to C. trachomatis infection in epithelial cells and limits bacterial burden and inflammation in mice. IMPORTANCE: Infection of epithelial cells by Chlamydia trachomatis elicits an innate immune response by these cells. The signaling pathways involved, and their outcomes, are still very poorly understood. In this paper, we described how Chlamydia infection triggered the expression of ISG15, a small molecule normally associated to type I interferon (IFN-I) signaling and control of INF-γ production. ISG15 synthesis by epithelial cells attenuated their immune response to Chlamydia infection. In mice, we observed that ISG15 displayed a marginal role in modulating the production of IFN-γ, a key component of the host immune response to infection, but facilitated bacterial clearance. Overall, our study strengthens the importance of ISG15 not only in the resolution of viral but also of bacterial infection and document its role of “immune brake” in the context of Chlamydia infection.

Chlamydia trachomatis , an intracellular bacterium, highjacks metabolites from the host cell for its own proliferation. We provide evidence of global hypermethylation of the host proteome, including histones, during the late stages of infection. Single cell analyses revealed co-occurrence of several methylated residues on histones. Histone hypermethylation correlated with bacterial load and was prevented by antibiotic treatment. Mapping of trimethylation of histone 3 at residues K4 and K9 revealed a broad distribution throughout the chromatin. Nuclear fractions of infected cells exhibited a four-fold decrease of demethylase activity towards H3K4me3 and a two-fold increase in succinate concentration, a competitive inhibitor for the demethylase co-factor α-ketoglutarate. Supplementation of the culture medium with dimethyl-ketoglutarate (DMKG) or with iron, a second co-factor of histone lysine demethylases, reduced histone hypermethylation. DMKG supplementation modified the transcription of about one third of the infection-responsive genes, indicating that histone hypermethylation contributes to modulating the transcriptional response of the host to infection. Finally, chemical inhibition of histone demethylases in a mouse model of infection showed a moderate benefit regarding the outcome of infection. Overall, our data show that the metabolic pressure exerted by a pathogen with an intracellular lifestyle drives epigenetic changes in infected cells.

Excessive inflammation upon C. trachomatis infection can cause severe damages in the female genital tract. This obligate intracellular bacterium develops mainly in epithelial cells, whose innate response contributes to the overall inflammatory response to infection. The ubiquitin-like protein interferon-stimulated gene 15 (ISG15) stimulates interferon γ (IFNγ) production and is required for bacterial clearance in several infectious contexts. Here, we describe and investigate the consequences of the increase in ISG15 expression by epithelial cells infected with C. trachomatis . Infection of HeLa cells and primary ecto-cervical epithelial cells resulted in a transcriptional up-regulation of ISG15 expression. This did not involve the canonical IFN-I signaling pathway and depended instead on the activation of the STING/TBK1/IRF3 pathway. Absence or reduction of ISG15 synthesis led to increased production of several cytokines and chemokines including interleukin (IL) 6 and IL8, implicating that ISG15 normally dampens the immune response induced by C. trachomatis infection in epithelial cells. ISG15 exerted its control from an intracellular location, but without involving ISGylation. Finally, higher levels of inflammation and delayed bacterial clearance were observed in the genital tracts of ISG15-KO mice infected by C. trachomatis compared to wild type animals, however IFNγ production was unchanged. Altogether, our data show that ISG15 expression acts as a brake on the immune response to C. trachomatis infection in epithelial cells and limits bacterial burden and inflammation in mice.

Intracellular trafficking is mediated by transport carriers that originate by membrane remodeling from donor organelles. Tubular carriers contribute to the flux of membrane lipids and proteins to acceptor organelles, but how lipids and proteins impose a tubular geometry on the carriers is incompletely understood. Using imaging approaches on cells and in vitro membrane systems, we show that phosphatidylinositol-4-phosphate (PI4P) and biogenesis of lysosome-related organelles complex 1 (BLOC-1) govern the formation, stability, and functions of recycling endosomal tubules. In vitro, BLOC-1 binds and tubulates negatively charged membranes, including those containing PI4P. In cells, endosomal PI4P production by type II PI4-kinases is needed to form and stabilize BLOC-1-dependent recycling endosomal tubules. Decreased PI4KIIs expression impairs the recycling of endosomal cargoes and the life cycles of intracellular pathogens such as Chlamydia bacteria and influenza virus that exploit the membrane dynamics of recycling endosomes. This study demonstrates how a phospholipid and a protein complex coordinate the remodeling of cellular membranes into functional tubules.

The obligate intracellular bacteria Chlamydia trachomatis store glycogen in the lumen of the vacuoles in which they grow. Glycogen catabolism generates glucose-1-phosphate (Glc1P), while the bacteria can take up only glucose-6-phosphate (Glc6P). We tested whether the conversion of Glc1P into Glc6P could be catalyzed by a phosphoglucomutase (PGM) of host or bacterial origin. We found no evidence for the presence of the host PGM in the vacuole. Two C. trachomatis proteins, CT295 and CT815, are potential PGMs. By reconstituting the reaction using purified proteins, and by complementing PGM deficient fibroblasts, we demonstrated that only CT295 displayed robust PGM activity. Intriguingly, we showed that glycogen accumulation in the lumen of the vacuole of a subset of Chlamydia species (C. trachomatis, C. muridarum, C. suis) correlated with the presence, in CT295 orthologs, of a secretion signal recognized by the type three secretion (T3S) machinery of Shigella. C. caviae and C. pneumoniae do not accumulate glycogen, and their CT295 orthologs lack T3S signals. In conclusion, we established that the conversion of Glc1P into Glc6P was accomplished by a bacterial PGM, through the acquisition of a T3S signal in a “housekeeping” protein. Acquisition of this signal likely contributed to shaping glycogen metabolism within Chlamydiaceae.