Biology subjects

Masereeuw, R.

Publications and source records attributed to Masereeuw, R..

12 recordsLinked to original sources

bioRxiv2026

Gentamicin impairs nephron development in iPSC-derived kidney organoids and disrupts proximal tubular lysosomal function

Gentamicin is an aminoglycoside antibiotic used to treat Gram-negative bacterial infections. However, its clinical use is limited by nephrotoxicity, affecting approximately 10 - 20% of treated patients. Nevertheless, gentamicin remains widely used due to its high potency, low cost, and low incidence of bacterial resistance and hypersensitivity. Importantly, gentamicin crosses the placental barrier and is administered to neonates, including preterm infants in whom nephrogenesis is still ongoing, raising concerns about its effects on kidney development. Current knowledge of this risk relies largely on rodent studies, which fail to fully recapitulate human kidney physiology. Here, we developed human-relevant in vitro models to investigate the impact of gentamicin on kidney development and to unravel the dynamic cellular responses underlying gentamicin-induced impairment. Kidney organoids differentiated from induced pluripotent stem cells (iPSC) and magnetically sorted proximal tubule cells were used to model immature kidney and immature proximal cells, respectively. Organoids were continuously exposed to gentamicin (0.25 - 1.5 mM) throughout development (d7+18), while megalin-expressing proximal tubule cells were exposed for 24 hours to explore the cellular mechanisms underlying gentamicin toxicity. Intracellular concentrations of the gentamicin congeners C1, C1a, and C2/C2a/C2b were quantified by LC-MS/MS. Gentamicin exposure impaired organoid growth, and nephron formation and maturation. Additionally, gentamicin induced lipid accumulation and reduced lysosomal area in proximal tubule cells, indicating disrupted cellular metabolism and homeostasis. In conclusion, iPSC-derived kidney organoids provide a suitable platform to further investigate gentamicins impact on kidney development and studying co-treatments to mitigate its adverse effects.

pharmacology and toxicology↗

bioRxiv2026

Autologous Immune Cell Assay to Investigate risk of Processed- and Novel Food-Induced type 2 Inflammation in Peanut Allergy

Peanut allergy represents a major food-allergy burden, raising concerns about food processing and novel dietary products. Current diagnostics assess primarily allergic endpoints rather than immune mechanisms initiating and maintaining type 2 inflammation, particularly DC2-mediated Th2 polarization. Here, an in vitro autologous monocyte-derived dendritic cell (moDC)-T cell and B cell assay has been established to study immunomodulatory effects induced by unprocessed (P-D) and processed (P-DH (heated) or P-DHG (heated and glycated)) peanut proteins and emerging foods (protein concentrates or whole biomass), related to ex vivo DC2-T cell reactions. CD14+ monocytes, CD4+ T cells and CD19+ B cells were isolated from six peanut-allergic patients PBMCs. MoDCs generated with IL4/GM-CSF were exposed (48h) to type 2 polarizing cytokine (DC2) mix, or DC2 mix combined with the food samples. Next, DC2s were co-cultured with T cells (5d), followed by B cells incubation with DC2/T cell supernatant and food samples (10d). Supernatants and cells were analyzed for Th1/Th2/Th-regulatory (Treg) cells, IgE and IgG profiles. DC2 induced a strong Th2 phenotype and activity, P-D DC2 further enhanced IL13 secretion and %Tregs. P-DH DC2 favored Th2, whereas P-DHG DC2 increased IFN{gamma}, with neither increasing %Treg. All increased CD40L+CD25+ memory Th2 cells. Wheat, whey and seaweed biomass had little effect, whereas algae DC2 showed distinct immunomodulatory, adjuvant-like activity. In conclusion, this autologous in vitro assay captures peanut-specific and generic Th2 responses and reactivity to food samples, supporting its use as additional tool to assess type 2-driving potential and allergenicity of emerging foods and processing methods in peanut-allergic patients. Clinical trial registrationThe current in vitro study was conducted in accordance with the Declaration of Helsinki and approved by the Medical Ethics Review Committee (METC) of the Erasmus MC (NL79534.078.21 MEC-2021-0905) and registrated at International Clinical Trials Registry Platform (NL-OMON51765). Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/705773v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1f42191org.highwire.dtl.DTLVardef@c7e4baorg.highwire.dtl.DTLVardef@1798547org.highwire.dtl.DTLVardef@11d0d96_HPS_FORMAT_FIGEXP M_FIG C_FIG Immune cell illustrations were adapted (1, 2) with permission; permission conveyed through Copyright Clearance Center, Inc. Capsule summaryThe autologous moDC-T cell-B cell in vitro assay may be used to assess whether processing methods or new foods might have intrinsic capacity to affect type 2 inflammation in peanut-allergic patients.

immunology↗

bioRxiv2025

Loss of nephronophthisis-associated nephrocystin-1 impairs DNA damage repair in kidney organoids

Nephronophthisis (NPH) is a heterogeneous, autosomal recessive ciliopathy and an important cause of end-stage renal disease (ESRD) in children and young adults. Since its classification as ciliopathy in 2003, NPH disease causal attribution had been focused primarily on ciliary dysfunction. The finding that ciliopathy players are involved in the DNA damage response (DDR) signaling resulted in a paradigm shift in thinking on NPH disease aetiology. Mutations in NPHP1 are the leading cause of NPH, but the underlying mechanisms that lead to the disease phenotype remain poorly understood. Here, nephrocystin-1 depleted kidney organoids were generated and characterized to address this knowledge gap. We used CRISPR/Cas9 to generate NPHP1 control (NPHP1WT) and two mutant (NPHP1ko1 and NPHP1ko2) cell lines from healthy human induced pluripotent stem cells (iPSC), which then were differentiated into kidney organoids in an air-liquid interface following an optimized protocol. Upon loss of nephrocystin-1, kidney organoids showed impaired nephron structures and loss of glomerular mesangial and distal tubular cells. Furthermore, NPHP1 depleted organoids exhibited a persistent inability to repair DNA lesions and showed increased senescence and fibrosis characteristics. Dynamic subcellular localization of nephrocystin-1 in NPHP1WT, particularly its translocation to nuclei 15 min post-UVC light exposure, suggested its direct involvement in the DDR. In conclusion, a novel NPHP1-depleted kidney organoid model was established, providing a platform to comprehensively study DNA damage, senescence and fibrosis simultaneously upon nephrocystin-1 loss. This advanced model aids in the understanding of the pathophysiology of NPH and paves the way towards identifying novel druggable targets.

molecular biology↗

bioRxiv2024

A hollow fiber membrane-based liver organoid-on-a-chip model for examining drug metabolism and transport

Liver-on-a-chip models predictive for both metabolism as well as canalicular and blood transport of drug candidates in humans are lacking. Here, we established an advanced, bioengineered and animal component-free hepatocyte-like millifluidic system based on 3D hollow fiber membranes (HFMs), recombinant human laminin 332 coating and adult human stem cell-derived organoids. Organoid fragments formed polarized and tight monolayers on HFMs with improved hepatocyte-like maturation, as compared to standard 3D organoid cultures in Matrigel from matched donors. Gene expression profiling and immunofluorescence revealed that hepatocyte-like monolayers expressed a broad panel of phase I (e.g., CYP3A4, CYP2D6) and II (UGTs, SULTs) drug-metabolizing enzymes and drug transporters (e.g., OATP1B3, MDR1 and MRP3). Moreover, statically cultured monolayers displayed phase I and II metabolism of a cocktail of six relevant compounds, including midazolam and 7-hydroxycoumarin. We also demonstrated the disposition of midazolam in the basal/blood-like circulation and apical/canalicular-like compartment of the millifluidic chip. Finally, we connected the system to the other two PK/ADME-most relevant organ systems, i.e. small intestine- and kidney proximal tubule-like to study the bioavailability of midazolam and coumarin, and excretion of metformin. In conclusion, we generated a proof-of-concept liver organoid-on-a-chip model for examining metabolism and transport of drugs, which can be further developed to predict PK/ADME profiles in humans.

pharmacology and toxicology↗

bioRxiv2023

A novel KCNJ16 kidney organoid model recapitulates the disease phenotype and shows restoration of lipid accumulation upon treatment with statins

Backgroundthe KCNJ16 gene has been associated with a novel kidney tubulopathy phenotype, viz. disturbed acid-base homeostasis, hypokalemia and altered renal salt transport. KCNJ16 encodes for Kir5.1, which together with Kir4.1 constitutes a potassium channel located at kidney tubular cell basolateral membranes. Preclinical studies provided mechanistical links between Kir5.1 and a disease phenotype, however, the disease pathology remains poorly understood. Here, we aimed at generating and characterizing a novel advanced in vitro human kidney model that recapitulates the disease phenotype to investigate further the pathophysiological mechanisms underlying the disease and potential therapeutic interventions. Methodswe used CRISPR/Cas9 to generate KCNJ16 mutant (KCNJ16+/- and KCNJ16-/-) cell lines from healthy human induced pluripotent stem cells (iPSC) KCNJ16 control (KCNJ16WT). The iPSCs were differentiated following an optimized protocol into kidney organoids in an air-liquid interface. ResultsKCNJ16-depleted kidney organoids showed transcriptomic and potential functional impairment of key voltage-dependent electrolyte and water-balance transporters. We observed cysts formation, lipid droplet accumulation and fibrosis upon Kir5.1 function loss. Furthermore, a large scale, glutamine tracer flux metabolomics analysis demonstrated that KCNJ16-/- organoids display TCA cycle and lipid metabolism impairments. Drug screening revealed that treatment with statins, particularly the combination of simvastatin and C75, prevented lipid droplet accumulation and collagen-I deposition in KCNJ16-/- kidney organoids. Conclusionsmature kidney organoids represent a relevant in vitro model for investigating the function of Kir5.1. We discovered novel molecular targets for this genetic tubulopathy and identified statins as a potential therapeutic strategy for KCNJ16 defects in the kidney. Significance StatementIn this study, the use of CRISPR/Cas9 technology resulted in the establishment of a KCNJ16-depleted kidney organoid model, instrumental in elucidating the pathophysiology of the recently reported KCNJ16-associated kidney tubulopathy. Our study substantiates the role of Kir5.1 (KCNJ16) in kidney disease, confirming already described phenotypes, as well as aiding to gain insight in the causal role of Kir5.1 loss in the disease phenotype. Our approach increases the knowledge on KCNJ16-related kidney phenotype, and it states the importance of combining CRISPR/Cas9 technology and advanced in vitro models for complex disease modeling and therapy testing. Furthermore, we encourage the application of our approach to the in vitro modeling of rare and/or underrepresented genetic kidney diseases, for which the availability of patient material is limited.

cell biology↗

bioRxiv2023

Gene surgery as a potential treatment option for Nephropathic Cystinosis in vitro

Nephropathic cystinosis is a rare monogenetic kidney disease caused by mutations in the lysosomal transporter cystinosin (encoded by CTNS) that, to date, has no cure. The hallmark of this disease is lysosomal accumulation of cystine and decline in proximal tubular function leading to kidney failure early in life. In this project, we developed a novel gene repair strategy using CRISPR/Cas9 Homology-Independent Targeted Integration (HITI) to restore CTNS. A novel, non-viral peptide-mediated approach was used to deliver the Cas9-guideRNA ribonucleoprotein (RNP) complex and repair templates to conditionally immortalized proximal tubule epithelial cell (ciPTEC) lines. The repair constructs contained either mCherry (1.7 kb), the CTNS Superexon (1.7 Kb) or both (3.2 Kb). The results demonstrated that the smaller mCherry construct achieved a higher repair efficiency (63%) compared to the CTNS-mCherry construct (16%). Clonal expansion of repaired cells showed restoration of lysosomal cystine levels in 70-75% of the clones, which was accompanied by improved mitochondrial bioenergetics. In conclusion, CRISPR/Cas9 HITI can be used to precisely insert repair templates into the genome, resulting in a functional cystinosin restoration, and a reversal of the cystinotic disease phenotype.

bioengineering↗

bioRxiv2022

Differentiated kidney tubular cell-derived extracellular vesicles enhance maturation of tubuloids

Advanced kidney in vitro models such as organoids or tubuloids still lack the intrinsic expression of various transport proteins needed for active secretory function. Extracellular vesicles (EVs), cell-derived structures that constitute the organs microenvironment, are known to regulate various cellular processes, including kidney development and regeneration across the nephron. In this study, we propose a new application of renal tubular epithelial cell EVs as modulators for tubuloid functional maturation by increasing the levels of various differentiation markers such as organic anion transport 1 (OAT1), a protein involved in endogenous waste excretion. First, we show that EVs from engineered proximal tubule cells increased the expression of several transcription factors and epithelial transporters in tubuloids that resulted in improved cellular transport capacity. Next, a more in-depth proteomic data analysis demonstrated that EVs can trigger various biological pathways, including mesenchymal-to-epithelial transition, which is crucial in the tubular epithelial maturation process. Moreover, we demonstrated that EV-treated tubuloid-derived cells in a 3D tubular conformation as part of a bioartificial kidney can generate a tight polarized epithelial monolayer with formation of dense cilia structures. In conclusion, EVs from renal tubular epithelial cells can phenotypically improve tubuloid maturation, thereby enhancing their potential as preclinical models and functional units in regenerative therapies.

cell biology↗

bioRxiv2020

Topographic Guidance in Melt-Electrowritten Tubular Scaffolds Enhances Engineered Kidney Tubule Performance

To advance the engineering of kidney tubules for future implantation, constructs should be both self-supportive and yet small-sized and highly porous. Here, we hypothesize that the fabrication of small-sized porous tubular scaffolds with a highly organized fibrous microstructure by means of melt-electrowriting (MEW) allows the development of self-supported kidney proximal tubules with enhanced properties. A custom-built MEW device was used to fabricate tubular fibrous scaffolds with small diameter sizes (O = 0.5, 1, 3 mm) and well-defined, porous microarchitectures (rhombus, square, and random). Human umbilical vein endothelial cells (HUVEC) and human conditionally immortalized proximal tubular epithelial cells (ciPTEC) were seeded into the scaffolds and tested for monolayer formation, integrity, and organization, as well as for extracellular matrix (ECM) production and renal transport functionality. Tubular scaffolds were successfully manufactured by fine control of MEW instrument parameters. A minimum inner diameter of 0.5 mm and pore sizes of 0.2 mm were achieved. CiPTEC formed tight monolayers in all scaffold microarchitectures tested, but well-defined rhombus-shaped pores outperformed and facilitated unidirectional cell orientation, increased collagen type IV deposition, and expression of the renal transporters and differentiation markers organic cation transporter 2 (OCT2) and P-glycoprotein (P-gp). To conclude, we present smaller diameter engineered kidney tubules with microgeometry-directed cell functionality. Due to the well-organized tubular fiber scaffold microstructure, the tubes are mechanically self-supported, and the self-produced ECM constitutes the only barrier between the inner and outer compartment, facilitating rapid and active solute transport.

bioengineering↗

bioRxiv2020

The lysosomal V-ATPase B1 subunit in proximal tubule is linked to nephropathic cystinosis

Variants in ATP6V1B1, the gene encoding the B1 subunit of the vacuolar H+-ATPase lead to distal renal tubular acidosis and hearing loss of variable degree. Apart from metabolic acidosis, a 23-month-old girl with pathogenic ATP6V1B1 variants presented with increased granulocyte cystine levels, and symptoms of renal Fanconi syndrome, indicating an unknown link to proximal tubulopathy and cystinosis, a disorder of the proximal tubule caused by variants in the CTNS gene. Here, we demonstrated that ATP6V1B1 is expressed in proximal tubules of human kidney tissue, though to a lesser extent than in distal tubules. Further, we used CRISPR/Cas9 technology to selectively knockout ATP6V1B1 or CTNS in human renal proximal tubule cells and performed a full metabolomic and proteomic analysis to compare their phenotype to isogenic control cells. In line with the clinical data, the loss of ATP6V1B1 disrupted the chemiosmotic coupling between the lysosomal V ATPase B1 subunit and cystinosin and resulted in intralysosomal accumulation of cystine and autophagy activation in renal proximal tubule cells. In conclusion, we identified ATP6V1B1 as a central player in renal proximal tubule cells, regulating lysosomal cystine transport and autophagy, and its absence can lead to proximal tubule dysfunction.

pharmacology and toxicology↗

bioRxiv2020

A combined microphysiological-computational omics approach in dietary protein evaluation

The ever-growing world population puts pressure on food security. To tackle this, waste stream proteins and novel protein sources need to be evaluated for nutritional value, which requires information on digesta peptide composition in comparison to established protein sources and coupling to biological parameters. Here, we present a novel combined experimental and computational approach comparing seventeen protein sources with cows whey protein (WPC) as benchmark. In vitro digestion was followed by proteomics analysis and statistical model clustering based on Bayesian Information Criterion. Next, we incorporated functional protein data after evaluating the effects of eighteen protein digests on intestinal barrier integrity, viability, brush border enzyme activity and immune parameters using a bioengineered intestine. Our data show that a holistic approach allows evaluating a dietary proteins potential for delivery of bioactive peptides, where protein source (animal, plant or novel source-derived) does not seem to be the driving force for clustering.

bioengineering↗

bioRxiv2020

Cysteamine-bicalutamide combination treatment restores alpha-ketoglutarate and corrects proximal tubule phenotype in cystinosis

Nephropathic cystinosis is a severe monogenetic kidney disorder caused by mutations in CTNS, encoding the lysosomal transporter cystinosin, resulting in lysosomal cystine accumulation. The sole treatment, cysteamine, slows down the disease progression, but does not correct the established proximal tubulopathy. Here, we developed a new therapeutic strategy by applying an omics-based strategy to expand our knowledge on the complexity of the disease and prioritize drug targets in cystinosis. We identified alpha-ketoglutarate as a key metabolite linking cystinosin loss, lysosomal autophagy defect and proximal tubular impairment in cystinosis. This insight offered a bicalutamide-cysteamine combination treatment as a novel dual target pharmacological approach for the phenotypical correction of cystinotic proximal tubule cells, patient-derived kidney tubuloids and cystinotic zebrafish.

pharmacology and toxicology↗

bioRxiv2019

Action of cocaine involves depletion of dopaminergic and serotonergic storage vesicles

Cocaine is known to increase the extracellular levels of dopamine (DA) and serotonin (5-HT) by inhibiting the neuronal reuptake of these monoamines. However, individuals with reduced monoamine reuptake transporter expression do not display a reduction in cocaine intake, suggesting that a mechanism other than inhibition of monoamine reuptake contributes to the rewarding and addictive effects of the psychostimulant. Here we report that cocaine depletes the dopaminergic and serotonergic storage vesicles of the rat nucleus accumbens. This cocaine-induced vesicle depletion gave rise to acute increases in the extracellular levels of DA and 5-HT, which in turn correlated with monoamine-type-specific changes in behavior. Both the neurochemical and behavioral responses to cocaine varied among individual animals, which was not due to individual differences in the reuptake of DA and 5-HT, but rather to individual differences in their vesicular release. Furthermore, we found that reserpine-induced depletion of storage vesicles reduced both short and long access cocaine self-administration, and the degree of reduction was linked to the vesicular storage capacity of the animals. In conclusion, we demonstrate a novel mechanism by which cocaine increases the extracellular concentrations of accumbal DA and 5-HT, namely via release from storage vesicles. Furthermore, individual differences in cocaine-induced vesicular monoamine release shape individual differences in not only the acute behavioral and neurochemical effects of the stimulant, but also in its intake. Thus, intracellular storage vesicles represent an attractive novel drug target to combat psychostimulant addiction.

neuroscience↗