Biology subjects

Prins, S.

Publications and source records attributed to Prins, S..

9 recordsLinked to original sources

bioRxiv2026

Multi-Omic Profiling Defines the Renal Mechanisms of Cardiovascular-Kidney-Metabolic Syndrome in Pulmonary Arterial Hypertension

Background: Cardiovascular-kidney-metabolic (CKM) syndrome integrates cardiac, renal, and metabolic abnormalities that drive multi-organ injury. In pulmonary arterial hypertension (PAH), CKM manifests as systemic metabolic derangements, right ventricular dysfunction, and renal compromise. Renal dysfunction strongly predicts mortality in PAH, yet current therapies provide little renal benefit. Moreover, the mechanisms driving PAH nephropathy remain poorly understood, limiting our ability to effectively treat PAH-CKM. Methods: Single-nucleus RNA sequencing identified cell-type-specific transcriptional alterations in autopsy-derived kidneys from control (n=5) and PAH (n=4) patients. Mitochondrial, cytoplasmic, and phosphoproteomic analyses profiled proteomic alterations. AlphaFold 3/ChimeraX modeling defined the predicted structural consequences of altered protein phosphorylation. Histological analysis assessed renal fibrosis, glomerular structure, immune cell infiltration, and nephron segment density. Results: 3 of 4 PAH patients exhibited renal impairment, with a cohort mean estimated glomerular filtration rate of 61 plus or minus 36 mL/min/1.73m squared. snRNA-seq identified a distinct cellular architecture in PAH kidneys, marked by an increase in thick ascending limb, proximal tubule, and immune cell nuclei and depletion of collecting duct nuclei. Transcriptional profiling demonstrated proximal tubule and thick ascending limb cells both upregulated fatty acid oxidation, ferroptosis, and cuproptosis pathways. PAH lymphocytes displayed heightened T87 cell receptor signaling, natural killer cell-mediated cytotoxicity, and Th17 differentiation. Histological analyses demonstrated increased perivascular fibrosis, glomerular T-cell infiltration, and a reduction in glomerular basement membrane density in PAH kidneys. Mitochondrial and cytoplasmic proteomics revealed broad metabolic dysfunction characterized by impaired {beta}-oxidation, TCA cycle activity, amino acid metabolism, transsulfuration, and urea cycle pathways. Phosphoproteomics predicted increased GSK3{beta}, STK, and casein kinase activity in PAH kidneys. Finally, using the totality of our data, we nominated multiple druggable targets that could be evaluated to counteract PAH nephropathy. Conclusions: Integrated multi-omic profiling demonstrates PAH nephropathy is defined by glomerular structural remodeling, proximal nephron ferroptotic and cuproptotic signaling, amino acid metabolic dysregulation, and innate and adaptive leukocyte activation. Future studies intervening on these pathways could lead to the development of novel therapeutics to augment renal function in PAH.

molecular biology↗

bioRxiv2026

Pulmonary Arterial Hypertension Induces a Metabolic and Inflammatory Hepatopathy

Right ventricular failure (RVF) is a robust predictor of mortality in pulmonary arterial hypertension (PAH); however, the mechanisms linking RVF to end-organ dysfunction remain unclear. Hepatic impairments portend poor outcomes in PAH, but the cell-specific effects of PAH on the human liver are unknown. Here, we performed single nucleus RNA sequencing on autopsy-derived liver tissue from five PAH patients and four non-PAH controls and compared these findings to non-alcoholic steatohepatitis (NASH) and Fontan-associated liver disease (FALD). PAH hepatocytes were characterized by a pro-proliferative, Warburg-like metabolic phenotype. PAH endothelial cells (ECs) also adopted a Warburg-like profile. Although EC PI3K-Akt activation was present in PAH and FALD ECs, only PAH ECs demonstrated impaired adhesion/barrier signaling. In PAH hepatic stellate cells (HSCs), PI3K-Akt signaling was enriched, while NASH and FALD HSCs co-activated PI3K-Akt and TGF-{beta}. Activated HSC abundances were increased in PAH livers and associated with heightened central vein fibrosis. PAH and NASH macrophages showed elevated complement signaling but reduced JAK-STAT activity. PAH livers exhibited dysregulated vasoactive gene expression, increased interleukin-6 expression in HSCs, and suppressed hepatocyte ketone metabolism. Correlational analysis demonstrated that HSC HIF-1 activation was associated with PAH severity. In total, these findings define the metabolic and inflammatory hepatopathy of PAH.

biochemistry↗

bioRxiv2026

Multimodality Molecular Profiling Nominates Targetable Mechanisms in Progressive RV Dysfunction

BackgroundRight ventricular dysfunction (RVD) is a robust predictor of mortality in multiple cardiovascular diseases. Currently, it remains unclear whether the severity of RVD corresponds to distinct cellular and molecular alterations, and this has important implications for defining optimal therapeutic targets. To address this knowledge gap, we performed a multi-omics evaluation of pulmonary artery banded (PAB) pigs with differing degrees of RV compromise. MethodsPAB pigs were stratified into mild and severe RVD groups using an RV ejection fraction cutoff of 35%. RV tissue from control, mild RVD, and severe RVD animals was analyzed using single-nucleus RNA sequencing, mitochondrial and cytoplasmic proteomics, and phosphoproteomics. Histological analyses corroborated multi-omic findings. ResultsCardiac MRI revealed progressive structural and functional alterations in mild and severe RVD pigs. snRNAseq demonstrated that advancing RVD was associated with loss of cardiomyocytes, accumulation of efferocytosis-impaired macrophages, and dysregulated endothelial cells and pericytes. Combined transcriptomic and proteomic analyses showed escalating impairments of complex cardiomyocyte metabolism with worsening RVD. RV microvasculature was compromised with severe RVD as there were alterations in endothelial cell/pericyte genetic regulation, co-localization patterns in RV sections, and ectopic cardiomyocyte HIF1 expression. Analysis of both mitochondrial and global proteostasis revealed greater compromise in mitochondrial proteostasis, including downregulation of mitochondrial proteases, chaperones, and ribosomes. Paradoxically, cytoplasmic ribosomes were upregulated in severe RVD. The predicted kinome and phosphatome were uniquely altered in mild RVD as compared to severe RVD. Finally, integration of multi-omic approaches identified insufficient mitochondrial unfolded protein response, impaired macrophage efferocytosis, and activation of the ribotoxic stress response as potential contributors to severe RVD. ConclusionsOur multi-omic analysis defines the cellular and molecular landscape of progressive RVD and nominates druggable pathways that may promote progressive RV dysfunction. Future studies are needed to determine how targeting these pathways influences RV phenotypes.

physiology↗

bioRxiv2026

Proteomics Defines Shared and Divergent Alterations in the Right Atrium and Right Ventricle in Porcine Right Heart Failure

Right heart failure is due to both right atrial and right ventricular dysfunction. While the two chambers are distinct, the proteomic response to pressure overload is undefined. Here, we used quantitative proteomics to evaluate changes in both chambers in pulmonary artery banded pigs. We found common alterations in oxidative phosphorylation, ribosome regulation, integrin-mediated adhesion, and glycolysis enzymes. However, the right atrium had more pronounced deficits in the TCA cycle and branched chain amino acid metabolism. Thus, these data highlight metabolic pathways that could be evaluated to selectively enhance right atrial function.

biochemistry↗

bioRxiv2024

Energetics of the outer retina II: Calculation of a spatio-temporal energy budget in retinal pigment epithelium and photoreceptor cells based on quantification of cellular processes

The outer retina (OR) is highly energy demanding. Impaired energy metabolism combined with high demands are expected to cause energy insufficiencies that make the OR susceptible to complex blinding diseases such as age-related macular degeneration (AMD). Here, anatomical, physiological and quantitative molecular data were used to calculate the ATP expenditure of the main energy-consuming processes in three cell types of the OR for the night and two different periods during the day. The predicted energy demands in a rod dominated (perifovea) area are 1.33 x 1013 ATP/s/mm2 tissue in the night and 6.53 x 1012 ATP/s/mm2 tissue during the day with indoor light conditions. For a cone-dominated foveal area the predicted energy demands are 6.44 x 1012 ATP/s/mm2 tissue in the night and 6.75 x 1012 ATP/s/mm2 tissue with indoor light conditions during daytime. We propose the likely need of for diurnal/circadian shifts in energy demands to efficiently stagger all energy consuming processes. Our data provide insights into vulnerabilities in the aging OR and suggest that diurnal constraints may be important when considering therapeutic interventions to optimize metabolism.

systems biology↗

bioRxiv2024

Energetics of the outer retina I: Estimates of nutrient exchange and ATP generation.

Photoreceptors (PRs) are metabolically demanding and packed at high density, which presents a challenge for nutrient exchange between the associated vascular beds and the tissue. Motivated by the ambition to understand the constraints under which PRs function, in this study we have drawn together diverse physiological and anatomical data in order to generate estimates of the rates of ATP production per mm2 of retinal surface area. With the predictions of metabolic demand in the companion paper, we seek to develop an integrated energy budget for the outer retina. It is known that rod PR number and the extent of the choriocapillaris (CC) vascular network that supports PRs both decline with age. To set the outer retina energy budget in the context of aging we demonstrate how, at different eccentricities, decline CC density is more than matched by rod loss in a way that tends to preserve nutrient exchange per rod. Together these finds provide an integrated framework for the study of outer retinal metabolism and how it might change with age.

systems biology↗

bioRxiv2022

K978C CFTR restores essential epithelial function with greater efficiency than wildtype CFTR when expressed in CF airway cells.

Class Ia/b CFTR variants cause severe cystic fibrosis (CF) lung disease in ~10% of CF patients and are untreatable with small molecule pharmaceuticals. Genetic replacement strategies offer a potential cure for all patients but so far, have displayed limited efficiency in vivo. We hypothesised that increasing protein abundance and/or activity of introduced CFTRs would more effectively restore function to CF bronchial epithelial cells (CFBE) in the presence of CF sputum (CFS) than wildtype (WT)-CFTR. We investigated codon optimised CFTR (hCAI), increased open probability CFTR (K978C) and codon optimised plus K978C (h^K978C) as candidates for gene therapy. Transfection of HEK293T with hCAI and h^K978C produced ~10-fold more CFTR protein than WT or K978C CFTRs. hCAI and h^K978C also displayed ~4-fold greater anion transport than WT in a halide-sensitive YFP quenching assay. However, functionality of modified CFTR cDNAs expressed in CFBE were profoundly different. 10% transduction of CFBE with K978C, compared to 22% transduction with WT, restored Cl- transport to similar levels as that recorded from non-CF cells. K978C increased ASL height and pH more effectively than WT-CFTR, while hCAI and h^K978C had limited impact. Further investigation indicated that codon optimised CFTRs mis-localised in CFBE and compromised vectoral Cl- transport. These data provide further evidence that codon optimised CFTR cDNAs may be unsuitable for gene therapy practices that employ high activity promoters. However, increased activity CFTR cDNAs such as K978C, that potentially mimic the effect of potentiators, may provide more potent recovery of function than WT-CFTR cDNA in CF airways. Significance StatementCystic fibrosis (CF) disease is associated with genetic malfunction of the Cl- channel CFTR, leading to dehydration and decreased pH in the fluid lining the airways. Replacement of CFTR by gene therapy/gene editing offers potential therapeutic benefit but efficiency is poor. We show that gain of activity K978C CFTR under the control of a high activity promoter fully restored Cl- transport, hydration and pH to CF bronchial epithelial cells (CFBE) in the presence of CF sputum and more efficiently than wild type CFTR. Codon optimised forms of CFTR were much less effective and proteins were mis-localised/mis-processed in CFBE. Thus, K978C could offer improved therapeutic potential.

molecular biology↗

bioRxiv2021

Can two wrongs make a right? F508del-CFTR ion channel rescue by second-site mutations in its transmembrane domains

Deletion of phenylalanine 508 (F508del), in the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel, is the most common cause of cystic fibrosis (CF). F508 is located on nucleotide-binding domain 1 (NBD1) in contact with cytosolic extensions of transmembrane helices, in particular intracellular loop 4 (ICL4). We carried out a mutagenesis scan of ICL4 by introducing five or six second-site mutations at eleven positions in cis with F508del, and quantifying changes in membrane proximity and ion-channel function of CFTR. The scan strongly validated the effectiveness of R1070W at rescuing F508del defects. Molecular dynamics simulations highlighted two features characterizing the ICL4/NBD1 interface of F508del/R1070W-CFTR: flexibility, with frequent transient formation of interdomain hydrogen bonds, and loosely stacked aromatic sidechains, (F1068, R1070W, and F1074, mimicking F1068, F508 and F1074 in wild-type CFTR). F508del-CFTR had a distorted aromatic stack, with F1068 displaced towards space vacated by F508. In F508del/R1070F-CFTR, which largely retained F508del defects, R1070F could not form hydrogen bonds, and the interface was less flexible. Other ICL4 second-site mutations which partially rescued F508del-CFTR are F1068M and F1074M. Methionine side chains allow hydrophobic interactions without the steric rigidity of aromatic rings, possibly conferring flexibility to accommodate the absence of F508 and retain a dynamic interface. Finally, two mutations identified in a yeast scan (A141S and R1097T, on adjacent transmembrane helices linked to ICL1 and ICL4) also partially rescued F508del-CFTR function. These studies highlight the importance of hydrophobic interactions and conformational flexibility at the ICL4/NBD1 interface, advancing understanding of the structural underpinning of F508del dysfunction.

biophysics↗

bioRxiv2019

High-content assay for precision medicine discovery in cystic fibrosis.

CFTR, a plasma membrane anion channel, plays a key role in controlling transepithelial fluid movement. Excessive activation results in intestinal fluid loss during secretory diarrhoeas, while CFTR mutations underlie cystic fibrosis (CF). Anion permeability depends both on how well CFTR channels work (permeation/gating) and on how many are present at the membrane (reflecting folding, trafficking, metabolic stability). Recently, treatments with two drug classes targeting CFTR - one boosting ion-channel function (potentiators), the other increasing plasma membrane density (correctors) - have provided significant health benefits to CF patients. Here we present an image-based fluorescence assay that can rapidly and simultaneously estimate both CFTR ion-channel function and the proteins proximity to the membrane. We monitor F508del-CFTR, the most common CF-causing variant, and confirm rescue by low temperature, CFTR-targeting drugs and second-site revertant mutation R1070W. In addition, we characterize a panel of 62 CF-causing mutations. Our measurements correlate well with published data (electrophysiology and biochemistry), further confirming validity of the assay. Finally, we profile effects of acute treatment with approved potentiator drug VX-770 on the rare-mutation panel. Mapping the potentiation profile on CFTR structures raises mechanistic hypotheses on drug action, suggesting that VX-770 might allow an open-channel conformation with an alternative arrangement of domain interfaces around site 1. The assay is a valuable tool for investigation of CFTR molecular mechanisms, allowing accurate inferences on gating/permeation. In addition, by providing a two-dimensional characterization of the CFTR protein, it could better inform development of single-drug and precision therapies addressing the root cause of CF disease.

pharmacology and toxicology↗