Biology subjects

Wall, S.

Publications and source records attributed to Wall, S..

11 recordsLinked to original sources

bioRxiv2026

Vps35 p.D620N causes Lrrk2 kinase hyperactivity, chronic microglial activation and inflammation

Pathogenic variants in leucine-rich repeat kinase 2 (LRRK2), RAB32, and vacuolar protein sorting 35 (VPS35) cause dominantly inherited, late-onset Parkinson's disease (PD). Mutations in all three genes constitutively activate LRRK2 kinase activity, enhancing innate immune defense against pathogens; however, chronic activation is linked to dopaminergic neuronal degeneration. LRRK2 and RAB32 are highly expressed in all myeloid cells including brain microglia, whereas VPS35, a core component of the retromer, is ubiquitously expressed. Nevertheless, the VPS35 p.D620N substitution induces the greatest constitutive increase in endogenous LRRK2 kinase activity, and its consequences for immune function remain unclear. We therefore examined the transcriptomic and functional effects of wild type (WT) and Vps35 p.D620N knock-in mice (VKI) from microglia, isolated from brains of naive animals at six-month of age, and initially analyzed by single-cell RNA sequencing (scRNAseq). Despite the absence of overt behavioral differences, differential gene expression revealed genotype-dependent changes in antimicrobial humoral immunity, lysosomal stress sensing, and phagocytosis. S100 family genes and lipocalin 2 were markedly upregulated, a finding subsequently validated by gene expression and immunohistochemistry. Downregulation was also observed in pathways governing microglial regulation of synaptic transmission, neuronal development and homeostatic immune signaling. Peripherally-administered lipopolysaccharide (LPS) stimulated microglial activation and phagocytic markers in WT brain, and further increased morphological activation and synaptic engulfment in VKI animals. Compared to WT, Vps35 p.D620N drives a chronic pro-inflammatory microglial state characterized by elevated innate immune signaling, lysosomal stress and enhanced phagocytic activity. Hence, heightened microglial sensitivity, further exacerbated by a peripheral immune challenge, offers a parsimonious, if multicellular, explanation for the multifactorial etiology of PD, and may help to account for its penetrance and variable expressivity. Together, these findings provide mechanistic insight into how retromer dysfunction and LRRK2 kinase hyperactivity intersect with microglial biology to influence PD pathogenesis, potentially promoting synaptic remodeling and neurodegenerative vulnerability.

neuroscience↗

bioRxiv2024

Simultaneous Overexpression of Three Enzymes of Chloroplast Metabolism Fails to Improve CO2 Assimilation or Biomass.

Ensuring an adequate food supply amidst a growing global population and climate change challenges, necessitates innovative strategies to enhance crop productivity. Previous studies have demonstrated that the simultaneous stimulation of different photosynthesis-related processes can increase the rate of photosynthetic carbon assimilation and plant biomass. This study evaluates an approach based on modelling aimed at simultaneously increasing photosynthetic and sink capacities in Nicotiana tabacum by overexpressing three key enzymes: Sedoheptulose-1,7-bisphosphatase (SBPase), Fructose-1,6-bisphosphate aldolase (FBP Aldolase), and ADP-glucose pyrophosphorylase (AGPase). Our results showed that this strategy does not significantly improve growth or carbon assimilation in Nicotiana tabacum under the tested conditions. This suggests that while the model informing our work offers a valuable framework, its application may require adjustments based on species and environmental conditions. Future research should explore these genetic modifications in species with larger sink capacities and under a range of growth conditions to fully realize the potential of photosynthetic optimization.

plant biology↗

bioRxiv2024

Discovery and Characterization of a Pan-betacoronavirus S2-binding antibody

SUMMARY/ABSTRACTThree coronaviruses have spilled over from animal reservoirs into the human population and caused deadly epidemics or pandemics. The continued emergence of coronaviruses highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using LIBRA-seq, we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these antibodies, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryo-EM structure of 54043-5 bound to the pre-fusion S2 subunit of the SARS-CoV-2 spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses. Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses, including ADCC and ADCP. In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit.

molecular biology↗

bioRxiv2023

Do calcium channel blockers applied to cardiomyocytes cause increased channel expression resulting in reduced efficacy?

In the initial hours following the application of the calcium channel blocker (CCB) nifedipine to microtissues consisting of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), we observe notable variations in the drugs efficacy. Here, we investigate the possibility that these temporal changes in CCB effects are associated with adaptations in the expression of calcium ion channels in cardiomyocyte membranes. To explore this, we employ a recently developed mathematical model that delineates the regulation of calcium ion channel expression by intracellular calcium concentrations. According to the model, a decline in intracellular calcium levels below a certain target level triggers an upregulation of calcium ion channels. Such an upregulation, if instigated by a CCB, would then counteract the drugs inhibitory effect on calcium currents. We assess this hypothesis using time-dependent measurements of hiPSC-CMs dynamics and by refining an existing mathematical model of myocyte action potentials incorporating the dynamic nature of the number of calcium ion channels. The revised model forecasts that the CCB-induced reduction in intracellular calcium concentrations leads to a subsequent increase in calcium ion channel expression, thereby attenuating the drugs overall efficacy. The data and fit models suggests that dynamic changes in cardiac cells in the presence of CCBs may be explainable by induced changes in protein expression, and that this may lead to challenges in understanding calcium based drug effects on the heart unless timings of applications are carefully considered.

biophysics↗

bioRxiv2020

Cross-reactive coronavirus antibodies with diverse epitope specificities and extra-neutralization functions

The continual emergence of novel coronavirus (CoV) strains, like SARS-CoV-2, highlights the critical need for broadly reactive therapeutics and vaccines against this family of viruses. Coronavirus spike (S) proteins share common structural motifs that could be vulnerable to cross-reactive antibody responses. To study this phenomenon in human coronavirus infection, we applied a high-throughput sequencing method called LIBRA-seq (Linking B cell receptor to antigen specificity through sequencing) to a SARS-CoV-1 convalescent donor sample. We identified and characterized a panel of six monoclonal antibodies that cross-reacted with S proteins from the highly pathogenic SARS-CoV-1 and SARS-CoV-2 and demonstrated a spectrum of reactivity against other coronaviruses. Epitope mapping revealed that these antibodies recognized multiple epitopes on SARS-CoV-2 S, including the receptor binding domain (RBD), N-terminal domain (NTD), and S2 subunit. Functional characterization demonstrated that the antibodies mediated a variety of Fc effector functions in vitro and mitigated pathological burden in vivo. The identification of cross-reactive epitopes recognized by functional antibodies expands the repertoire of targets for pan-coronavirus vaccine design strategies that may be useful for preventing potential future coronavirus outbreaks.

immunology↗

bioRxiv2020

Computational prediction of drug response in short QT syndrome type 1 based on measurements of compound effect in stem cell-derived cardiomyocytes

Short QT (SQT) syndrome is a genetic cardiac disorder characterized by an abbreviated QT interval of the patients electrocardiogram. The syndrome is associated with increased risk of arrhythmia and sudden cardiac death and can arise from a number of ion channel mutations. Cardiomyocytes derived from induced pluripotent stem cells generated from SQT patients (SQT hiPSC-CMs) provide promising platforms for testing pharmacological treatments directly in human cardiac cells exhibiting mutations specific for the syndrome. However, a difficulty is posed by the relative immaturity of hiPSC-CMs, with the possibility that drug effects observed in SQT hiPSC-CMs could be very different from the corresponding drug effect in vivo. In this paper, we apply a multistep computational procedure for translating measured drug effects from these cells to human QT response. This process first detects drug effects on individual ion channels based on measurements of SQT hiPSC-CMs and then uses these results to estimate the drug effects on ventricular action potentials and QT intervals of adult SQT patients. We find that the procedure is able to identify IC50 values in line with measured values for the four drugs quinidine, ivabradine, ajmaline and mexiletine. In addition, the predicted effect of quinidine on the adult QT interval is in good agreement with measured effects of quinidine for adult patients. Consequently, the computational procedure appears to be a useful tool for helping predicting adult drug responses from pure in vitro measurements of patient derived cell lines. Author summaryA number of cardiac disorders originate from genetic mutations affecting the function of ion channels populating the membrane of cardiomyocytes. One example is short QT syndrome, associated with increased risk of arrhythmias and sudden cardiac death. Cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) provide a promising platform for testing potential pharmacological treatments for such disorders, as human cardiomyocytes exhibiting specific mutations can be generated and exposed to drugs in vitro. However, the electrophysiological properties of hiPSC-CMs differ significantly from those of adult native cardiomyocytes. Therefore, drug effects observed for hiPSC-CMs could possibly be very different from corresponding drug effects for adult cells in vivo. In this study, we apply a computational framework for translating drug effects observed for hiPSC-CMs derived from a short QT patient to drug effects for adult short QT cardiomyocytes. For one of the considered drugs, the effect on adult QT intervals has been measured and these measurements turn out to be in good agreement with the response estimated by the computational procedure. Thus, the computational framework shows promise for being a useful tool for predicting adult drug responses from measurements of hiPSC-CMs, allowing earlier identification of compounds to accurately treat cardiac diseases.

biophysics↗

bioRxiv2020

Identifying drug response by combining measurements of the membrane potential, the cytosolic calcium concentration, and the extracellular potential in microphysiological systems

Cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) offer a new means to study and understand the human cardiac action potential, and can give key insight into how compounds may interact with important molecular pathways to destabilize the electrical function of the heart. Important features of the action potential can be readily measured using standard experimental techniques, such as the use of voltage sensitive dyes and fluorescent genetic reporters to estimate transmembrane potentials and cytosolic calcium concentrations. Using previously introduced computational procedures, such measurements can be used to estimate the current density of major ion channels present in hiPSC-CMs, and how compounds may alter their behavior. However, due to the limitations of optical recordings, resolving the sodium current remains difficult from these data. Here we show that if these optical measurements are complemented with observations of the extracellular potential using multi electrode arrays (MEAs), we can accurately estimate the current density of the sodium channels. This inversion of the sodium current relies on observation of the conduction velocity which turns out to be straightforwardly computed using measurements of extracellular waves across the electrodes. The combined data including the membrane potential, the cytosolic calcium concentration and the extracellular potential further opens up for the possibility of accurately estimating the effect of novel drugs applied to hiPSC-CMs.

bioengineering↗

bioRxiv2019

Improved computational identification of drug response using optical measurements of human stem cell derived cardiomyocytes in microphysiological systems

Cardiomyocytes derived from human induced pluripotent stem cells hold great potential for drug screening applications. However, their usefulness is limited by the relative immaturity of cells electro-physiological properties as compared to native cardiomyocytes in the adult human heart. In this work, we extend and improve on methodology to address this limitation, building on previously introduced computational procedures which predict drug effects for mature cells based on changes in optical measurements of action potentials and Ca2+ transients made in stem cell derived cardiac microtissues. This methodology quantifies ion channel changes through the inversion of data into a mathematical model, and maps this response to a mature phenotype through the assumption of functional invariance of fundamental intracellular and membrane channels during maturation.\n\nHere we utilize an updated action potential model to represent both immature and mature cells, apply an IC50-based model of dose-dependent drug effects, and introduce a continuation-based optimization algorithm for analysis of dose escalation measurements using five drugs with known effects. The improved methodology can identify drug induced changes more efficiently, and quantitate important metrics such as IC50 in line with published values. Consequently, the updated methodology is a step towards employing computational procedures to elucidate drug effects in mature cardiomyocytes for new drugs using stem cell-derived experimental tissues.

biophysics↗

bioRxiv2018

Metabolically-Driven Maturation of hiPSC-Cell Derived Heart-on-a-Chip

Human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CM) are a promising in vitro tool for drug development and disease modeling, but their immature electrophysiology limits diagnostic utility. Tissue engineering approaches involving aligned 3D cultures enhance hiPSC-CM structural maturation but are insufficient to induce mature electrophysiology. We hypothesized that mimicking post-natal switching of the hearts primary ATP source from glycolysis to fatty acid oxidation could enhance electrophysiological maturation of hiPSC-CM. We combined hiPSC-CM with microfabricated culture chambers to form 3D cardiac microphysiological systems (MPS) that enhanced immediate microtissue alignment and tissue specific extracellular matrix (ECM) production. Using Robust Experimental design, we identified a maturation media that improved calcium handling in MPS derived from two genetically distinct hiPSC sources. Although calcium handling and metabolic maturation were improved in both genotypes, there was a divergent effect on action potential duration (APD): MPS that started with abnormally prolonged APD exhibited shorter APD in response to maturation media, whereas the same media prolonged the APD in MPS that started with aberrantly short APD. Importantly, the APD of both genotypes was brought near the range of 270-300ms observed in human left ventricular cardiomyocytes. Mathematical modeling explained these divergent phenotypes, and further predicted the response of matured MPS to drugs with known pro-arrhythmic effects. These results suggest that systematic combination of biophysical stimuli and metabolic cues can enhance the electrophysiological maturation of hiPSC-derived cardiomyocytes. However, they also reveal that maturation-inducing cues can have differential effects on electrophysiology depending on the baseline phenotype of hiPSC-CM. In silico models provide a valuable tool for predicting how changes in cellular maturation will manifest in drug responsiveness.

bioengineering↗

bioRxiv2018

Inversion and computational maturation of drug response using human stem cell derived cardiomyocytes in microphysiological systems

While cardiomyocytes differentiated from human induced pluripotent stems cells (hiPSCs) hold great promise for drug screening, the electrophys-iological properties of these cells can be variable and immature, producing results that are significantly different from their human adult counterparts. Here, we describe a computational framework to address this limitation, and show how in silico methods, applied to measurements on immature cardiomyocytes, can be used to both identify drug action and to predict its effect in mature cells. Our synthetic and experimental results indicate that optically obtained waveforms of voltage and calcium from microphysiological systems can be inverted into information on drug ion channel blockage, and then, through assuming functional invariance of proteins during maturation, this data can be used to predict drug induced changes in mature ventricular cells. Together, this pipeline of measurements and computational analysis could significantly improve the ability of hiPSC derived cardiomycocytes to predict dangerous drug side effects.

biophysics↗

bioRxiv2017

Transcriptomes of major renal collecting-duct cell types in mouse identified by single-cell RNA-Seq

Prior RNA sequencing (RNA-Seq) studies have identified complete transcriptomes for most renal epithelial cell types. The exceptions are the cell types that make up the renal collecting duct, namely intercalated cells (ICs) and principal cells (PCs), which account for only a small fraction of the kidney mass, but play critical physiological roles in the regulation of blood pressure, extracellular fluid volume and extracellular fluid composition. To enrich these cell types, we used fluorescence-activated cell sorting (FACS) that employed well established lectin cell surface markers for PCs and type B ICs, as well as a newly identified cell surface marker for type A ICs, viz. c-Kit. Single-cell RNA-Seq using the 1C- and PC-enriched populations as input enabled identification of complete transcriptomes of A-ICs, B-ICs and PCs. The data were used to create a freely-accessible online gene-expression database for collecting duct cells. This database allowed identification of genes that are selectively expressed in each cell type including cell-surface receptors, transcription factors, transporters and secreted proteins. The analysis also identified a small fraction of hybrid cells expressing both aquapor{inverted exclamation}n-2 and either anion exchanger 1 or pendrin transcripts. In many cases, mRNAs for receptors and their ligands were identified in different cells (e.g. Notch2 chiefly in PCs vs Jag1 chiefly in ICs) suggesting signaling crosstalk among the three cell types. The identified patterns of gene expression among the three types of collecting duct cells provide a foundation for understanding physiological regulation and pathophysiology in the renal collecting duct.\n\nSIGNIFICANCE STATEMENTA long-term goal in mammalian biology is to identify the genes expressed in every cell type of the body. In kidney, the expressed genes (\"transcriptome\") of all epithelial cell types have already been identified with the exception of the cells that make up the renal collecting duct, responsible for regulation of blood pressure and body fluid composition. Here, a technique called \"single-cell RNA-Seq\" was used in mouse to identify transcriptomes for the major collecting-duct cell types: type A intercalated cells, type B intercalated cells and principal cells. The information was used to create a publicly-accessible online resource. The data allowed identification of genes that are selectively expressed in each cell type, informative for cell-level understanding of physiology and pathophysiology.

physiology↗