Biology subjects

Goemans, C.

Publications and source records attributed to Goemans, C..

4 recordsLinked to original sources

bioRxiv2025

Volumetric imaging and single-cell RNAseq atlases identify cellular mechanisms of human dental pulp response during tooth decay progression

Dental pulp responses to dental decay, the most prevalent chronic disease worldwide, involve remodeling processes similar to those observed in other human pathological conditions. By integrating volumetric imaging and single-cell analysis across different disease stages in human samples, we uncovered the natural history of dental pulp responses to decay. At early stages, we observed an arterialization of the capillary networks and progressive outward remodeling of the larger vessels. Neurogenesis of nerve endings and the reprogramming of perivascular progenitor cells into fibroblasts are also observed, initiating the physiological reparative response of the stroma. Pathological angiogenesis and nerve regression combined with dental pulp fibrosis at later stages of tooth decay determine irreversible pulpitis. These results provide a basis for understanding dental tissue response to injury, driving a paradigm shift in patient management. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/653296v1_ufig1.gif" ALT="Figure 1"> View larger version (71K): org.highwire.dtl.DTLVardef@15d1d86org.highwire.dtl.DTLVardef@3d556corg.highwire.dtl.DTLVardef@b33e32org.highwire.dtl.DTLVardef@1b84a1a_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2024

Reversal of vein of Galen aneurysmal malformation by stimulation of flow-mediated vessel fusion

Congenital vascular malformations arise from defective homeostatic development of the vascular tree1. The aneurysmal malformation of the Vein of Galen (VGAM) is the most frequent neurovascular malformation in neonates, with limited therapeutic options and poor outcomes in the most severe cases2. This congenital disease is consecutive to germline genetic mutation of RASA1 or EPHB43,4, but little is known about the mechanisms leading to its development. We generated mutant rasa1a and ephb4a deficiency models in zebrafish reproducing the genetic and structural characteristics of the VGAM in the dorsal longitudinal vein of the cerebral vasculature. We link the development of the malformation to a failure of the fusion of precursor blood vessels into a draining vessel for the choroidal type malformations and to a failure to constrict for the mural type malformations. The fusion process is driven by blood flow, sensed and integrated by endothelial cells. RASA1 deficiency destabilizes the homeostatic response to blood flow and contributes to impaired flow-mediated activation of MAPK and PI3K signaling. We targeted these defective mechanotransduction mechanisms pharmacologically in both rasa1a and ephb4a mutant models, successfully reestablishing the fusion and constriction processes in preexisting malformations. This work identifies molecular actors of the flow-mediated blood vessel fusion mechanism, a specific angiogenetic program, and provides ground for treating VGAM and other vascular remodeling disorders.

developmental biology↗

bioRxiv2024

Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics

By acquiring or evolving resistance to one antibiotic, bacteria can become resistant to a second one, due to shared underlying mechanisms. This is called cross-resistance (XR) and further limits therapeutic choices. The opposite scenario, in which initial resistance leads to sensitivity to a second antibiotic, is termed collateral sensitivity (CS) and can inform cycling or combinatorial treatments. Despite their clinical relevance, our current knowledge of such interactions is limited, mostly due to experimental constraints in their assessment and lack of understanding of the underlying mechanisms. To fill this gap, we used published chemical genetic data on the impact of all Escherichia coli non-essential genes on resistance/sensitivity to 40 antibiotics, and devised a metric that robustly discriminates between known XR and CS antibiotic interactions. This metric, based on chemical genetic profile (dis)similarity between two drugs, allowed us to infer 404 XR and 267 CS interactions, thereby expanding the number of known interactions by more than 3-fold - including reclassifying 116 previously reported interactions. We benchmarked our results by validating 55 out of 59 inferred interactions via experimental evolution. By identifying mutants driving XR and CS interactions in chemical genetics, we recapitulated known and uncovered previously unknown mechanisms, and demonstrated that a given drug pair can exhibit both interactions depending on the resistance mechanism. Finally, we applied CS drug pairs in combination to reduce antibiotic resistance development in vitro. Altogether, our approach provides a systematic framework to map XR/CS interactions and their mechanisms, paving the way for the development of rationally-designed antibiotic combination treatments.

systems biology↗

bioRxiv2023

The killing of human gut commensal E. coli ED1a by tetracycline is associated with severe ribosome dysfunction

Ribosomes translate the genetic code into proteins. Recent technical advances have facilitated in situ structural analyses of ribosome functional states inside eukaryotic cells and the minimal bacterium Mycoplasma. However, such analyses of Gram-negative bacteria are lacking, despite their ribosomes being major antimicrobial drug targets. Here we compare two E. coli strains, a lab E. coli K-12 and human gut isolate E. coli ED1a, for which tetracycline exhibits bacteriostatic and bactericidal action, respectively. The in situ ribosome structures upon tetracycline treatment show a virtually identical drug binding-site in both strains, yet the distribution of ribosomal complexes clearly differs. While K-12 retains ribosomes in a translation competent state, tRNAs are lost in the vast majority of ED1a ribosomes. A differential response is also reflected in proteome-wide abundance and thermal stability assessment. Our study underlines the need to include molecular analyses and to consider gut bacteria when addressing antibiotic mode of action. O_LSTHIGHLIGHTSC_LST* Ribosome structures of gram-negative bacteria are analyzed in situ * Tetracyline is bactericidal to gut isolate despite identical ribosome structures * When antibiotic is bacteriostatic, ribosomal translation competent states are retained * When antibiotic is bactericidal, cells rapidly accumulate P-tRNAs-deficient ribosomes GRAPHICAL ABSTRACT

biophysics↗