Biology subjects

Devuyst, O.

Publications and source records attributed to Devuyst, O..

10 recordsLinked to original sources

bioRxiv2026

Base Editing as a Therapeutic Strategy for Autosomal Dominant Tubulointerstitial Kidney Disease caused by Pathogenic UMOD Variants

Autosomal dominant tubulointerstitial kidney disease caused by pathogenic UMOD variants (ADTKD-UMOD) is an untreatable monogenic kidney disease in which misfolded uromodulin is retained in the endoplasmic reticulum and exerts a toxic gain-of-function effect. Here we systematically evaluate the full spectrum of base editing strategies targeting the UMOD locus. Base editors corrected a representative missense patient variant, p.Cys170Tyr, with A-to-G conversion efficiencies of up to 83.4%, restoring uromodulin trafficking to the plasmamembrane in cell lines and in human 3D kidney tubuloids. Mutation-agnostic inactivation wasachieved by four routes: premature stop codon introduction, splice-site disruption, allele-specific stop codon introduction and promoter attenuation. Maximum on-target efficienciesranged from 44.1% to 71.9%, providing a strategy set applicable across the UMOD allelicspectrum. Endogenous UMOD expression is rarely recapitulated in human cell models,leaving strategies that act on the endogenous gene difficult to assess in patient cells. Wetherefore established CRISPR activation (CRISPRa) of the endogenous UMOD promoterand confirmed its ability to upregulate UMOD expression in human urine-derived cells. Thisapproach further enabled quantification of endogenous UMOD transcript reduction followingbase editing in HEK293 cells. These results establish base editing as a versatile approachfor ADTKD-UMOD and provide a primary human system for testing interventions targetingendogenous UMOD expression, from nucleic acid-based silencing to small molecules.

genetics↗

bioRxiv2026

Disturbed mitochondrial energy production in methylmalonic aciduria is cell-type and variant-dependent

Methylmalonic aciduria (MMA) is caused by deficiency of methylmalonyl-CoA mutase (MMUT), which catalyses the final step of propionate catabolism and fuels the tricarboxylic acid cycle for energy production. Previous studies reported disrupted mitochondrial homeostasis in MMA, including reduced mitochondrial membrane potential and increased oxidative stress, especially in energetically demanding and chronically affected tissues like brain and kidneys. However, how these changes impact mitochondrial energy production remains unclear. Here, we systematically investigated mitochondrial energy production using extracellular flux analysis in cellular models of MMA, including 293T cells, patient-derived fibroblasts, urine-derived epithelial kidney cells and induced pluripotent stem cells (iPSCs) as well as iPSC-derived neurons harbouring either complete loss (knockout, KO) or pathogenic missense variants in MMUT. We found no impact on mitochondrial energy production in MMUT-KO 293T cells and fibroblasts compared to controls. In contrast, fibroblasts and 293T cells expressing the pathogenic MMUT-p.N219Y variant showed decreased energy production. This corresponds to the altered mitochondrial membrane potential in 293T cells, but contrasts with their unchanged mitochondrial abundance. Depletion of glucose, glutamine and pyruvate from the media or provision of each individually as sole fuel source exacerbated the phenotype of MMUT-p.N219Y clones, but did not induce a phenotype in MMUT-KO 293T cells. Finally, we confirmed reduced mitochondrial energy production in patient-derived kidney cells but found no evidence in MMUT-p.N219Y iPSCs and their derived neurons. Overall, our work suggests that the impact of MMUT-deficiency on mitochondrial energy production is cell type- and variant-dependent. Further investigations should clarify molecular mechanisms and their clinical impact.

cell biology↗

bioRxiv2026

SGLT2 Inhibitors Rescue Lysosomal mTORC1 Hyperactivity and Proximal Tubulopathy in Preclinical Models of Cystinosis

The loss of lysosomal cystine transporter cystinosin (CTNS) disrupts kidney proximal tubule (PT) function, causing cystinosis - a prototypical lysosomal storage disorder characterized by cystine accumulation and metabolic dyshomeostasis. Cystine storage disrupts lysosomal nutrient sensing and downstream mTORC1 signalling, driving loss of PT differentiation and proximal tubulopathy. Here, using cross-species disease models, differentiated cellular systems, lysosome-based assays, and transcriptomics profiling, we demonstrate that sodium-glucose co-transporter 2 (SGLT2) inhibitors (empagliflozin or dapagliflozin) ameliorate proximal tubulopathy in cystinosis. In CTNS-deficient PT cells, SGLT2 inhibition restores lysosome proteolysis, autophagic flux, metabolic homeostasis, and epithelial differentiation and function, independently of cystine clearance. Mechanistically, SGLT2 inhibition reduces the assembly of the v-ATPase-Ragulator-Rag scaffolding complex at lysosomes, thereby decoupling cystine storage from pathological mTORC1 activation. These effects reprogram PT metabolic trajectories and differentiation states, mitigating proximal tubulopathy across zebrafish and rodent models of cystinosis. Together, these findings define a lysosome-metabolism crosstalk that links glucose handling to mTORC1 regulation and provide a rationale for repurposing SGLT2 inhibitors as a disease-modifying therapy for cystinosis and related lysosome-driven PT disorders.

pathology↗

bioRxiv2025

A Novel Zebrafish Luminescent Biosensor for Kidney Tubulopathy, Metal Toxicity, and Drug Screening

An efficient endo-lysosomal pathway is crucial to mediate the reabsorption and processing of ultrafiltered solutes including low-molecular-weight (LMW) proteins by the epithelial cells lining the proximal tubule (PT) of the kidney. The zebrafish pronephros is increasingly used as a model system for congenital or acquired disorders that impair the endocytic uptake in PT cells, that cause an inappropriate loss of solutes and LMW proteins in the urine. Here, we describe a new reporter zebrafish line, termed[1/2] vdbp-NanoLuc, in which the vitamin D-binding protein is coupled to NanoLuc luciferase, for rapid, large-scale detection of PT dysfunction and LMW proteinuria. We demonstrate the reliability and value of the[1/2] vdbp-NanoLuc biosensor in fish models of monogenic endolysosomal diseases, gentamicin and cisplatin-induced nephrotoxicity, and metal contamination. This novel system provides mechanistic insights into the cadmium- and copper-induced PT dysfunction and, when combined with a swimming test, a platform for drug screening to alleviate cisplatin toxicity.

pharmacology and toxicology↗

bioRxiv2025

A Drosophila model for Dent disease reveals impaired ER export of Cubilin as pathogenic mechanism

Mutations in the CLCN5 gene encoding the chloride-hydrogen exchanger ClC-5 cause Dents disease, a genetic disorder of the endolysosomal pathway in the proximal tubules of the kidneys. Many patients also develop glomerular lesions, but the underlying mechanism is unclear. We have established an in vivo model for Dents disease using Drosophila nephrocytes that share similarities with podocytes and proximal tubular cells. Upon depletion of ClC-c, the fly homologue of CLCN5, the endocytic receptor Cubilin was lost from the cortex of nephrocytes, which led to a strong decrease in albumin uptake and slit diaphragm (SD) turnover. Moreover, the actin and microtubular cytoskeleton as well as Rab11-marked recycling endosomes showed a strong cortical accumulation, whereas cholesterol-enriched autophagic compartments emerged in the perinuclear area. Cubilin exhibited a mild mislocalization to cortical early and late endosomal compartments and, in addition, strongly accumulated in the endoplasmic reticulum (ER). This was accompanied by a fragmentation of the ER morphology and an increase in ER exit sites and associated Golgi stacks. These secretory pathway phenotypes were also observed upon silencing of a subunit of the vacuolar H+-ATPase (V-ATPase) suggesting that they depend on acidification. Therefore, we speculate that ClC-c and the V-ATPase together acidify the Golgi to allow proper glycosylation and surface trafficking of Cubilin (or its binding partner Amnionless). Interestingly, ER retention of Cubilin was confirmed in ClC-5 knockout mice, underscoring the relevance of this pathomechanism for Dents disease. Translational statementIn this work, we study the function of the fly ortholog of CLCN5 whose mutations cause Dents disease, a devastating hereditary kidney disease. By demonstrating that the protein uptake receptor Cubilin is retained in the ER upon ClC-c/ClC-5 depletion in flies and mice, we provide an unexpected new disease mechanism for this disease. Future therapeutic strategies may be directed at improving ER export through acidification of the Golgi apparatus.

cell biology↗

bioRxiv2024

AQP1- A regulatory factor associated with brown adipose tissue silencing

The activation of non-shivering thermogenesis (NST) in brown adipose tissue (BAT) by environmental cold challenge yields strong metabolic benefit in the face of diet-induced obesity (DIO). Yet, a critical barrier to leveraging brown fat NST for therapeutic use against metabolic disease is that BAT is silenced and inactive at physiological ambient temperature conditions in humans. The mechanisms that govern this silencing process remain poorly understood. Here, we identified a putative BAT-silencing factor, aquaporin-1 (AQP1), in brown fat from wild-type (WT) mice via proteomics analysis. We generated the first BAT-specific AQP1 knockout mice (AQP1-KO) and revealed that AQP1-KO could activate NST under BAT silencing environmental conditions and that the AQP1-KO mice were significantly protected against DIO and metabolic dysfunction compared to Flox controls. We found that AQP1-KO mice on high fat diet (HFD) had reduced weight gain through reductions in fat mass, improved glucose tolerance, and increased whole body energy expenditure compared to Flox control mice. Mechanistically, we show that AQP1 ablation in mice had upregulated gene expression related to the electron transport chain (ETC) and mitochondrial translation contributing to the activation of NST under BAT environmental silenced conditions. Significance StatementNovel strategies to combat obesity-associated metabolic dysfunction are urgently needed to curb the growing obesity epidemic. Investigation of brown adipose tissue (BAT) silencing mechanisms may reveal novel therapeutic targets that when ablated, can activate BAT to increase energy expenditure and protect subjects against the metabolic dysfunction associated with obesity. We have identified Aquaporin 1 (AQP1) as a putative BAT silencer regulatory factor and show through the generation of the first BAT-specific aquaporin-1 knockout (AQP1-KO) mouse that BAT can be activated under environmental silencing conditions. We further show that these mice are protected against diet-induced obesity, with improved glucose tolerance, and increased energy expenditure. These findings highlight AQP1 as a promising therapeutic target in the emerging research field of BAT silencers.

molecular biology↗

bioRxiv2022

Allelic and Gene Dosage Effects Involving Uromodulin Aggregates Drive Autosomal Dominant Tubulointerstitial Kidney Disease

Missense mutations in the UMOD gene encoding uromodulin cause autosomal dominant tubulointerstitial kidney disease (ADTKD), one of the most common monogenic kidney diseases. A pressing need for ADTKD is to bridge the gap between postulated gain-of-function mutations and organ damage - a prerequisite for therapeutic development. Based on two missense UMOD mutations associated with divergent progression of ADTKD, we generated UmodC171Y and UmodR186S knock-in mice that showed strong allelic and gene dosage effects, with distinct dynamic pathways impacting on uromodulin trafficking, formation of intracellular aggregates, activation of ER stress, unfolded protein and immune responses, kidney damage and progression to kidney failure. Deletion of the wild-type Umod allele in heterozygous UmodR186S mice increased the formation of uromodulin aggregates and ER stress, indicating a protective role of wild-type uromodulin. Studies in kidney tubular cells confirmed biochemical differences between distinct uromodulin aggregates, with activation of specific quality control and clearance mechanisms. Enhancement of autophagy by starvation and mTORC1 inhibition decreased the uromodulin aggregates, suggesting a therapeutic strategy. These studies substantiate a model for allelic effects and the role of toxic aggregates in the progression of ADTKD-UMOD, with relevance for toxic gain-of-function mechanisms and for strategies to improve clearance of mutant uromodulin.

genetics↗

bioRxiv2022

Lysosomal cystine export regulates mTORC1 signaling to guide kidney epithelial cell fate specialization

Differentiation is critical for cell fate decisions, but the signals involved remain unclear. The kidney proximal tubule (PT) cells reabsorb disulphide-rich proteins through endocytosis, generating cystine via lysosomal proteolysis. Here we report that defective cystine mobilization from lysosomes through cystinosin (CTNS), which is mutated in cystinosis, diverts PT cells towards growth and proliferation, disrupting their functions. Mechanistically, cystine storage stimulates Ragulator-Rag GTPase-dependent recruitment of mechanistic target of rapamycin complex 1 (mTORC1) and its constitutive activation. Re-introduction of CTNS restores nutrient-dependent regulation of mTORC1 in knockout cells, whereas cell-permeant analogues of L-cystine, accumulating within lysosomes, render wild-type cells resistant to nutrient withdrawal. Therapeutic mTORC1 inhibition corrects lysosome and differentiation downstream of cystine storage, and phenotypes in a zebrafish model of cystinosis. Thus, cystine serves as a lysosomal signal that tailors mTORC1 and metabolism to direct epithelial cell fate decisions. These results identify mechanisms and therapeutic targets for dysregulated homeostasis in cystinosis.

cell biology↗

bioRxiv2020

Proteomic and transcriptomic profiling reveal different aspects of aging in the kidney

The kidney is an excellent model for studying organ aging. Kidney function shows steady decline with age and is easy to assay using urine or blood samples. However, little is known about the molecular changes that take place in the kidney during the aging process. In order to better understand the molecular changes that occur with age, we measured mRNA and protein levels in 188 genetically diverse mice at ages 6, 12, and 18 months. We observed distinctive change in mRNA and protein levels as a function of age. Changes in both mRNA and protein are associated with increased immune infiltration and decreases in mitochondrial function. Proteins show a greater extent of change and reveal changes in a wide array of biological processes including unique, organ-specific features of aging in kidney. Most importantly, we observed functionally important age-related changes in protein that occur in the absence of corresponding changes in mRNA. Our findings suggest that mRNA profiling alone provides an incomplete picture of molecular aging in the kidney and that examination of changes in proteins is essential to understand aging processes that are not transcriptionally regulated.

systems biology↗

bioRxiv2019

Mechanical activation of TRPV4 channels controls albumin reabsorption by proximal tubule cells.

The proximal tubule (PT) mediates the endocytosis of essential substances filtered through the glomerulus, including albumin and a large variety of low molecular weight proteins that would otherwise be lost in urine. Variations in the amount of ultrafiltrate delivered to the PT modulate protein endocytosis. Here we show that TRPV4 ion channel is expressed at the basolateral side of PT cells. Mechanical activation of TRPV4 by cell stretching induces an entry of Ca2+ into the cytosol, which promotes endocytosis. Trpv4-/- mice present only a mild PT dysfunction in basal conditions but they exhibit a much more severe proteinuria than Trpv4+/+ mice when the permeability of glomerular filter is altered by systemic delivery of angiotensin II or antibodies against the glomerular basement membrane. These results emphasize the importance of TRPV4 channel in PT pressure sensing and provide insights into the mechanisms controlling protein reabsorption and potential targets for treating tubular proteinuria. SummaryThe proximal tubule (PT) mediates the endocytosis of albumin and low molecular weight proteins. Gualdani et al. report that variations in the amount of ultrafiltrate delivered to the PT activate TRPV4 ion channel expressed at the basolateral side of PT cells, which modulates protein endocytosis.

physiology↗