Biology subjects

Toussaint, C.

Publications and source records attributed to Toussaint, C..

5 recordsLinked to original sources

bioRxiv2026

Multimodal temporal mapping of macrophage transcriptome remodeling during Salmonella infection

Macrophages are equipped to eliminate invading pathogens, yet several intracellular bacteria exploit them as replicative niches. Salmonella enterica serovar Typhimurium subverts host immunity by injecting effector proteins that remodel macrophage functions. While macrophages typically induce a pro-inflammatory program upon bacterial invasion, Salmonella can redirect them toward an anti-inflammatory and replication-permissive state via manipulation of the NF-{kappa}B and STAT3 host transcription factors. How the integration of the effects on these two transcription factors and potentially others underpins this reprogramming remains poorly charted. Here, we use a multipronged approach combining a bacterial reporter, temporal single-cell RNA-seq with RNA metabolic labeling, transcription factor (TF) footprinting, and single-cell CRISPR perturbations to dissect macrophage polarization dynamics during early infection. We catch the bifurcation during infection, where a subset of macrophages transition toward the anti-inflammatory phenotype. This shift involves the activation of Salmonella pathogenicity island 2 (SPI2) leading to both the dampening of the initial NF-{kappa}B-driven inflammatory program and the induction of specific transcriptional modules beyond NF-{kappa}B and STAT3, with possible contributions from AP-1 and Maf family members. Together, our study uncovers host decision points in macrophage polarization circuitry and reveals a vulnerability exploited by Salmonella to modulate host immunity. HIGHLIGHTSO_LITemporal scRNA-seq defines the emergence of inflammatory and anti-inflammatory macrophage states concomitant with Salmonella Typhimurium SPI2 induction. C_LIO_LIA critical decision point for infection outcome is reached by 6 hours post-infection. C_LIO_LIMacrophage reprogramming is associated with widespread chromatin remodeling and dynamic transcription factor binding. C_LIO_LISingle-cell perturb-seq experiment uncovers Cybb and Foxo1 as modulators of infection outcome in Hoxb8 macrophages. C_LI

genomics↗

bioRxiv2026

Leishmaniamajor co-opts IL-7 feedback in monocytes to suppress CD4⁺ T-cell immunity

During immune responses, pro-and anti-inflammatory mechanisms must be balanced to ensure pathogen clearance while limiting tissue damage. Monocyte-derived cells contribute to both processes, yet the underlying regulatory circuits remain incompletely defined. Here, we show that a subset of PDPN+IL-7R+ monocyte-derived cells that impair effector CD4 T cell-mediated control of intracellular pathogens, and thus perpetuate the infection. Fibroblast-derived IL-7 drives this immunosuppressive program, which is up-regulated in response to IFN{gamma}. We thus uncover a cytokine-dependent feedback circuit in which elevated IFN{gamma} induces IL-7 production by fibroblasts, licensing immunosuppressive monocyte-derived cells that restrain CD4 T cell responses. This mechanism links excessive inflammation to immune suppression at the expense of pathogen control. Targeting this feedback loop may enable therapeutic strategies that enhance antimicrobial immunity while preserving tissue integrity.

immunology↗

bioRxiv2025

Developmental factors drive the compartmentalised and discontinuous maturation of the small intestinal epithelium during the early postnatal period

The temporal, spatial and cellular diversity of the small intestinal epithelium during the postnatal period, a critical time window that accompanies the transition from placental energy supply to enteral feeding, the establishment of the enteric microbiota and postnatal immune maturation, has not been systematically investigated. Here, we used laser capture microdissection and bulk RNA-Seq, proteomics, and single cell RNA-Seq to analyse the total, organ site, crypt- and villus-specific intestinal epithelium of specific pathogen-free, germ-free and Salmonella-infected mice during the postnatal period. We identified key temporal and organ-site specific expression patterns that revealed a weak effect of the microbiota but strong influence of developmental regulators during early life. We also determined age-dependent signalling pathway and transcription factor activity and characterised age- and cell type-specific developmental trajectories revealing a distinct compartmentalised maturation process along the proximal-to-distal length and crypt-villus axis and a discontinuous appearance of goblet/Paneth cell and absorptive enterocyte transcriptional profiles. Finally, we described the cell type-specific response to neonatal enteric infection. Taken together, our findings identify the epithelium as an integral element in the maturation of postnatal mucosal tissues and in the establishment of host-microbe homeostasis.

immunology↗

bioRxiv2024

Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes

Base editors create precise genomic edits by directing nucleobase deamination or removal without inducing double-stranded DNA breaks. However, a vast chemical space of other DNA modifications remains to be explored for genome editing. Here, we harness the bacterial anti-phage toxin DarT2 to append ADP-ribosyl moieties to DNA, unlocking distinct editing outcomes in bacteria versus eukaryotes. Fusing an attenuated DarT2 to a Cas9 nickase, we program site-specific ADP-ribosylation of thymines within a target DNA sequence. In tested bacteria, targeting drives efficient homologous recombination in tested bacteria, offering flexible and scar-free genome editing without base replacement nor counterselection. In tested eukaryotes including yeast, plants and human cells, targeting drives substitution of the modified thymine to adenine or a mixture of adenine and cytosine with limited insertions or deletions, offering edits inaccessible to current base editors. Altogether, our approach, called append editing, leverages the addition of a chemical moiety to DNA to expand current modalities for precision gene editing.

synthetic biology↗

bioRxiv2021

Spatial organisation and homeostasis of epithelial lineages at the gastroesophageal junction is regulated by the divergent Wnt mucosal microenvironment

The gastroesophageal junction (GEJ), where squamous and columnar epithelia meet, is a hotspot for Barretts metaplasia development, dysbiosis and carcinogenesis. However, the mechanisms regulating GEJ homeostasis remain unclear. Here, by employing organoids, bulk and single-cell transcriptomics, single-molecule RNA in situ hybridisations and lineage tracing, we identified the spatial organisation of the epithelial, stromal compartment and the regulators that maintain the normal GEJ homeostasis. During development, common KRT8 progenitors generate committed unilineage p63/KRT5-squamous and KRT8-columnar stem cells responsible for the regeneration of postnatal esophagus and gastric epithelium that meet at GEJ. A unique spatial distribution of Wnt regulators in the underlying stromal compartment of these stem cells creates diverging Wnt microenvironments at GEJ and supports their differential regeneration. Further, we show that these tissue-resident stem cells do not possess the plasticity to transdifferentiate to the other lineage with the altered Wnt signals. Our study provides invaluable insights into the fundamental process of GEJ homeostasis and is crucial for understanding disease development.

developmental biology↗