Biology subjects

Yilmaz, G.

Publications and source records attributed to Yilmaz, G..

3 recordsLinked to original sources

bioRxiv2025

Vascular transcriptional and metabolic changes precede progressive intra-renal microvascular rarefaction in autosomal dominant polycystic kidney disease

BackgroundThe mechanisms contributing to progressive kidney damage in autosomal dominant polycystic kidney disease (ADPKD) remain unclear. Renal microvascular (MV) rarefaction plays an important role in kidney disease, but its natural history, underlying mechanisms, and contributions to renal disease progression in ADPKD remain unknown. We hypothesized that intrarenal MV rarefaction is present early on and is preceded by vascular transcriptional and metabolic changes. MethodsPkd1RC/RC and WT mice (n=16 each) were studied at 1, 6, and 12 months. Total kidney volume (TKV) was measured in vivo (MRI), whereas renal MV architecture (3D-micro-CT), capillary density, perivascular fibrosis, and histomorphometric parameters were assessed ex vivo. In randomly selected Pkd1RC/RC and WT kidneys (n=5, each/timepoint), mRNA-sequencing was performed to identify differentially expressed vasculature-related genes (DEGs). Next, in young individuals with ADPKD and matched controls (n=10 each), plasma cellular energy metabolites were determined (LC-MS/MS), validated in an extended cohort (n=32 and n=16, respectively), and correlated with markers of disease severity and progression. Gene-metabolite interaction networks were generated to integrate DEGs in Pkd1RC/RC at 1 month with metabolites dysregulated in individuals with ADPKD. ResultsRenal MV density was preserved at 1 month but progressively decreased at 6 and 12 months, associated with capillary loss and perivascular fibrosis. A total of 110, 48, and 201 DEGs were identified at 1, 6, and 12 months, respectively. Plasma gamma-aminobutyric acid (GABA) and homocysteine (Hcy) levels were higher in individuals with ADPKD versus controls, interacted with DEGs implicated in inflammatory and innate immune response and Hcy metabolism, and correlated with TKV and renal blood flow. ConclusionsOur data demonstrates that intrarenal MV abnormalities present early in ADPKD and are preceded by vascular transcriptional and metabolic changes. The renal microcirculation may constitute an important therapeutic target in ADPKD, and its underlying biomarkers may serve to monitor its progression. TRANSLATIONAL STATEMENTWe provide the first longitudinal and most comprehensive analysis of the intrarenal microvascular network in a slowly progressive orthologous model of ADPKD and integrate the findings with studies in a young cohort of ADPKD individuals. Our integrated preclinical and clinical data identify vasculature-related pathways that could be targeted for therapeutic interventions and contribute promising, noninvasive biomarkers in patients with ADPKD. Furthermore, because alterations of the intrarenal microcirculation may affect drug delivery, a better understanding of its longitudinal changes may aid in treatment management.

physiology↗

bioRxiv2024

Gut Microbiome Perturbation Affected Conjugative Transfer of Antimicrobial Resistance Genes

The global spread of antimicrobial resistance genes (ARGs) poses a significant threat to public health. While antibiotics effectively treat bacterial infections, they can also induce gut dysbiosis, the severity of which varies depending on the specific antibiotic treatment used. However, it remains unclear how gut dysbiosis affects the mobility and dynamics of ARGs. To address this, mice were pre-treated with streptomycin, ampicillin, or sulfamethazine, and then orally inoculated with Salmonella enterica serovar Typhimurium and S. Heidelberg carrying a multi-drug resistance IncA/C plasmid. The streptomycin pre- treatment caused severe microbiome perturbation, promoting high-density colonization of S. Heidelberg and S. Typhimurium, and enabling IncA/C transfer from S. Heidelberg to S. Typhimurium and a commensal Escherichia coli. The ampicillin pre-treatment induced moderate microbiome perturbation, supporting only S. Heidelberg colonization and IncA/C transfer to commensal E. coli. The sulfamethazine pre-treatment led to mild microbiome perturbation, favoring neither Salmonella spp. colonization nor conjugative plasmid transfer. The degree of gut dysbiosis also influenced the enrichment or depletion of ARGs associated with mobile plasmids or core commensal bacteria, respectively. These findings underscore the significance of pre-existing gut dysbiosis induced by various antibiotic treatments on ARG dissemination and may inform prudent antibiotic use practices.

microbiology↗

bioRxiv2020

Pseudomonas aeruginosa biofilms display carbohydrate ligands for CD206 and CD209 that interfere with their receptor function

Bacterial biofilms represent a challenge to the healthcare system because of their resilience against antimicrobials and immune attack. Biofilms consist of bacterial aggregates embedded in an extracellular polymeric substance (EPS) composed of carbohydrate polymers, nucleic acids and proteins. Carbohydrates within P. aeruginosa biofilms include neutral and mannose-rich Psl, and cationic Pel composed of N-acetyl-galactosamine and N-acetyl-glucosamine. Here we show that P. aeruginosa biofilms display ligands for the C-type lectin receptors mannose receptor (MR, CD206) and Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin (DC-SIGN, CD209). Binding of MR and DC-SIGN to P. aeruginosa biofilms is carbohydrate-and calcium-dependent and extends to biofilms formed by clinical isolates. Confocal analysis of P. aeruginosa biofilms shows abundant DC-SIGN ligands among bacteria aggregates while MR ligands concentrate into discrete clusters. DC-SIGN ligands are also detected in planktonic P. aeruginosa cultures and depend on the presence of the common polysaccharide antigen. Carbohydrates purified from P. aeruginosa biofilms are recognised by DC-SIGN and MR; both receptors preferentially bind the high molecular weight fraction (HMW; >132,000Da) with KDs in the nM range. HMW preparations contain 74.9-80.9% mannose, display -mannan segments and alter the morphology of human dendritic cells without causing obvious changes in cytokine responses. Finally, HMW interferes with the endocytic activity of cell-associated MR and DC-SIGN. This work identifies MR and DC-SIGN as receptors for bacterial biofilms and highlights the potential for biofilm-associated carbohydrates as immunomodulators through engagement of C-type lectin receptors. Author SummarySelective engagement of pattern recognition receptors during infection guides the decision-making process during induction of immune responses. This work identifies mannose-rich carbohydrates within bacterial biofilms as novel molecular patterns associated with bacterial infections. P. aeruginosa biofilms and biofilm-derived carbohydrates bind two important lectin receptors, MR (CD206) and DC-SIGN (CD209), involved in recognition of self and immune evasion. Abundance of MR and DC-SIGN ligands in the context of P. aeruginosa biofilms could impact immune responses and promote chronic infection.

microbiology↗