Biology subjects

van Zonneveld, A. J.

Publications and source records attributed to van Zonneveld, A. J..

3 recordsLinked to original sources

bioRxiv2025

Cell Type-Specific and Diabetic Kidney Disease-Associated Expression of Long Non-Coding RNAs in Human Kidneys

BackgroundLong non-coding RNAs (lncRNAs) play essential roles in cellular processes, often exhibiting cell type-specific expression and influencing kidney function. While single-cell RNA sequencing (scRNA-seq) has advanced our understanding of cellular specificity, past studies focus solely on protein-coding genes. We hypothesize that lncRNAs, due to their cell-specific nature, have crucial functions within particular renal cells and thereby play essential roles in renal cell function and disease. MethodsUsing single-nucleus RNA sequencing (snRNA-seq) data from kidney samples of five healthy individuals and six DKD patients, we explored the non-coding transcriptome. Cell type-specific lncRNAs were identified, and their differential expression in DKD was assessed. Integrative analyses included expression quantitative trait loci (eQTL), genome-wide association studies (GWAS) for estimated glomerular filtration rate (eGFR), and gene regulatory networks. Functional studies focused on TARID, a lncRNA with podocyte-specific expression, to elucidate its role in podocyte health. Resultswe identified 349 lncRNAs with cell type-specific expression across kidney cell types. Of these, 104 lncRNAs were differentially expressed in DKD. Integrative analyses, including eQTL data, GWAS results for eGFR and gene regulatory networks, pinpointed TARID, a podocyte-specific lncRNA, as a key candidate upregulated in DKD. Functional studies confirmed TARIDs podocyte-specific expression and revealed its central role in actin cytoskeleton reorganization, a critical process in podocyte health. ConclusionsOur study provides a comprehensive resource of single-cell lncRNA expression in the human kidney and highlights the importance of cell type-specific lncRNAs in kidney function and disease. Specifically, we demonstrate the functional relevance of TARID in podocyte health. This work underscores the utility of integrating scRNA-seq with functional genomics to uncover novel regulatory mechanisms in kidney biology. Key pointsO_LIThis provides a resource for kidney (cell type-specific) lncRNA expression and demonstrates the importance of lncRNAs in renal health. C_LIO_LIWe identified 349 cell type-specific lncRNAs in the human kidney, with 104 showing altered expression in diabetic kidney disease (DKD). C_LIO_LITARID, a podocyte-specific lncRNA upregulated in DKD, is crucial for actin cytoskeleton reorganization in podocytes. C_LI

bioinformatics↗

bioRxiv2023

Tracer-based metabolomics for profiling nitric oxide metabolites in a 3D microvessel-on-a-chip model

Endothelial dysfunction is a common denominator in cardiovascular diseases (CVDs) associated with diabetes, hypertension, obesity, renal failure or hypercholesterolemia. In these disease states, circulating adverse metabolic or hemostatic risk factors drive the progression of inflammation, thrombosis, platelet activation and atherosclerosis. A hallmark of endothelial dysfunction is the reduced bioavailability of nitric oxide (NO), a signaling molecule essential for vascular homeostasis. Numerous studies have focused on NO synthesis by endothelial cells (ECs) using in vitro cultures to understand the pathophysiology of endothelial dysfunction. A limitation of these studies is that the expression of the NO-generating enzyme, endothelial nitric oxide synthase (eNOS), in physiological conditions is modulated by the exposure of the ECs to laminar shear stress, a stimulus that is clearly lacking in most two-dimensional (2D) cultures. Here we developed a tracer-based metabolomics approach to measure NO-specific metabolites with mass spectrometry (MS) and show the impact of unidirectional fluid flow on metabolic parameters associated with NO synthesis using 2D and three-dimensional (3D) platforms. Specifically, we tracked the conversion of stable-isotope labeled NO substrate L-Arginine to L-Citrulline and L-Ornithine to determine eNOS activity. We demonstrated that when human coronary artery endothelial cells (HCAECs) cultured in media containing 13C6,15N4-L-Arginine treated with eNOS stimulator - vascular endothelial growth factor (VEGF), eNOS inhibitor - L-NAME and arginase inhibitor - S-(2- boronoethyl)-L-cysteine (BEC), their downstream metabolites - 13C6,15N3 L-Citrulline and 13C5,15N2 L- Ornithine showed clear responses as measured using Ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS). In this study, we also assessed the NO metabolic status of a static 2D culture, a 3D microvessel model with bidirectional flow, and our 3D model with unidirectional fluid flow generated by a microfluidic pump. Compared to 2D culture, our 3D model showed significant effects in the control and microvessels exposed to VEGF when Citrulline/Ornithine ratio was analyzed. The obtained result indicates that the 2D static culture mimics more endothelial dysfunction status. Our detection method and 3D model with a unidirectional fluid flow provides a more representative physiological environment that exhibits perfect model to study endothelial dysfunction.

cell biology↗

bioRxiv2022

Highly potent antisense oligonucleotides (ASOs) targeting the SARS-CoV-2 RNA genome

Currently the world is dealing with the third outbreak of the human-infecting coronavirus with potential lethal outcome, cause by a member of the Nidovirus family, the SARS-CoV-2. The severe acute respiratory syndrome coronavirus (SARS-CoV-2) has caused the last worldwide pandemic. Successful development of vaccines highly contributed to reduce the severeness of the COVID-19 disease. To establish a control over the current and newly emerging coronaviruses of epidemic concern requires development of substances able to cure severely infected individuals and to prevent virus transmission. Here we present a therapeutic strategy targeting the SARS-CoV-2 RNA using antisense oligonucleotides (ASOs) and identify locked nucleic acid gapmers (LNA gapmers) potent to reduce by up to 96% the intracellular viral load in vitro. Our results strongly suggest promise of our preselected ASOs for further development as therapeutic or prophylactic anti-viral agents. One sentence summaryASOs (LNA gapmers) targeting the SARS-CoV-2 RNA genome have been effective in viral RNA (load) reduction in vitro.

molecular biology↗