Biology subjects

Kapoor, A.

Publications and source records attributed to Kapoor, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Systematic genome analysis enables long-overdue taxonomic reorganization of genus Orthoflavivirus; potential assignment of over 50 new species

Members of the Orthoflavivirus genus in the family Flaviviridae are primarily vector-transmitted RNA viruses infecting humans, other mammals and birds, including major pathogens such as tick borne encephalitis, West Nile, Zika and dengue viruses. Vector-borne flaviviruses are assigned to the Euflavivirus subgenus of orthoflaviviruses, with more divergent largely unclassified insect-specific flaviviruses, including cell fusing agent virus assigned to the second subgenus, Fusivirus. The currently classified 57 orthoflavivirus species have traditionally been assigned descriptively on the basis of their genome and antigenic relatedness, ecology and host and vector tropisms, although many more orthoflavi-like viruses remain unassigned. To investigate whether species might be demarcated using a fixed genetic divergence threshold, we examined distributions of pairwise distances in NS5 and E genes (which encode the RNA-dependent RNA polymerase and envelope protein, respectively) of classified orthoflaviviruses. Demarcation thresholds of 0.1 in the two regions would be most parsimonious with current euflavivirus classification. Exceptions include species in the tick-borne encephalitis virus complex with divergences below the threshold, and dengue virus types currently assigned to a single species that are substantially above. Application of the proposed thresholds would provide the means to establish 25 new euflavivirus and 33 new fusivirus species and reconcile several anomalies and inconsistencies in the current species taxonomy. The use of a species demarcation threshold brings consistency with the classification of viruses in other families. A robust and evolutionarily consistent framework furthermore enables taxonomic assignments of the numerous currently unassigned orthoflaviviruses that lack the phenotypic descriptions required for the current species definition.

microbiology↗

bioRxiv2026

The Neuro-Immune Axis in Glioma Spontaneous Remission: Evidence from Population-Level Latent Variable Modelling and Transcriptomic Profiling

Gliomas are primary brain tumours that develop from neural stem or progenitor cells containing oncogenic alterations. Gliomas undergo remission with partial or complete disappearance of the disease, and in rare instances, spontaneous remission. Spontaneous remission happens without treatment or with inadequate medical intervention. This is a rare but well-documented phenomenon and has been observed across various tumour types, including gliomas, with varying frequency. While historically viewed as clinical anomalies, we hypothesize that SR may be driven by a measurable, latent neuro-immune axis specifically, autonomic vagal nerve modulation of the tumour microenvironment (TME) via the cholinergic anti-inflammatory pathway. Using a Gamma frailty Cox proportional hazards model on a SEER cohort of 6,939 glioma patients, we identified a latent biological variable (Z) that explains 27.1% of survival variance independent of age, grade, treatment, and tumour location. To determine the molecular basis of this latent survival advantage, we applied parallel frailty and Cox models to the TCGA Lower Grade Glioma and Glioblastoma (LGG+GBM) cohorts. Clinical validation confirmed expected hazards for age and grade, with the frailty model achieving high predictive accuracy (5-year AUC = 0.840; 10-year AUC = 0.841). Transcriptomic integration revealed that the alpha7 nicotinic acetylcholine receptor (CHRNA7) is highly protective, inversely correlating with biological frailty (r = -0.285, p < 0.0001). Conversely, pro-inflammatory cytokines (IL6) and M2 macrophage markers (CD163) positively correlated with frailty. Grade-stratified Cox regression and Kaplan-Meier analyses confirmed that CHRNA7 confers a significant survival advantage entirely independent of tumour grade. Single-cell RNA-sequencing data (Core GBmap) confirmed that CHRNA7 and TLR4 are expressed heavily on tumour-associated macrophages and microglia, rather than malignant cells. Our in-silico integration suggests that high vagal tone releases acetylcholine, binding to alpha7nAChR on TME macrophages. This triggers a signalling cascade that dampens the IL-6 production required for glioma proliferation, effectively halting tumour growth. Ongoing in vitro wet-lab experiments utilizing specific alpha7nAChR agonists (GTS-21) and physiological stress models aim to clinically validate this vagal-immune mechanism.

Cancer Biology↗

bioRxiv2026

Airspace miR-146a levels in ventilated patients decrease with age and correlate with mortality

The acute respiratory distress syndrome is a heterogenous syndrome characterized by the rapid development of respiratory failure. Nearly 40% of patients who develop ARDS will die, and there is growing interest in identification of biomarkers to identify patients at risk of death and/or inform treatment decisions. Most prior work on biomarkers in ARDS has focused on the plasma compartment, but there is concern that circulating biomarkers may not reflect alveolar pathobiology. The anti-inflammatory microRNA-146a has been shown to be upregulated in inflammatory cells in human bronchoalveolar lavage fluid, but it is not known if these levels correspond with outcomes. We measured miR-146a expression by digital droplet PCR in human biospecimens from four different cohorts of patients with respiratory failure requiring mechanical ventilation - two plasma cohorts, one bronchoalveolar lavage cohort, and one heat moisture exchange (HME) filter fluid cohort. We found that miR-146a was detectible in plasma, bronchoalveolar lavage fluid, and HME fluid. However, only when measured in the alveolar space, was miR-146a expression significantly lower in older adults and those who died. It did not correlate with outcomes when measured in plasma. To our knowledge, this is the first report that nucleotides can be measured in HME fluid and builds upon expanding literature that circulating biomarkers may not reflect complex biology of the alveolar microenvironment during ARDS.

molecular biology↗

bioRxiv2026

GPU accelerated population genetics statistics using pg_gpu

Population genetics summary statistics--diversity, divergence, linkage disequilibrium, selection scans, and dimensionality reduction--are fundamental across human, agricultural, and ecological genomics. As whole-genome sequencing datasets have grown to hundreds of thousands of individuals, the cost of computing these statistics on conventional CPU implementations has become a major bottleneck: windowed scans of a single chromosome arm can take hours to days, and computation of pairwise linkage-disequilibrium statistics useful for demographic inference scales as O(n2) in sample size, often exceeding wall-clock budgets entirely. We present pg_gpu, a Python library implementing a comprehensive catalog of population-genetics summary statistics as fused CUDA kernels on NVIDIA GPUs. pg_gpu covers eleven categories spanning diversity and neutrality tests, divergence, admixture, the site-frequency spectrum, linkage disequilibrium, haplotype-based selection scans, dimensionality reduction (PCA, randomized PCA, local PCA / lostruct), distance distributions, relatedness, resampling, and a generalized weighted-SFS framework for custom{omega} estimators. On the full Ag1000G Phase 3 chromosome 3R arm (2,940 haplotypes, 10.9 million variants) pg_gpu agrees with scikit-allel and PLINK2 to machine precision while delivering a median 139x and maximum 1,096x speedup. For the multi-population LD statistics used by moments for demographic inference, pg_gpu is a drop-in replacement that yields a ~1,750-fold speedup over the native implementation. Whole chromosome arm scans, lostruct screens, and calculation of LD statistics complete on a single NVIDIA A100 in seconds to a few minutes.

evolutionary biology↗

bioRxiv2026

Screening metatranscriptomes for ultrastable RNA secondary structures reveals hidden bacteriophages and novel capsid nanomaterials

Metatranscriptomics has transformed our view of RNA bacteriophage diversity, revealing vast numbers of single-stranded RNA (ssRNA) phages whose protein capsids can be engineered for biotechnology applications. However, many ssRNA phages remain hidden from current detection methods, which require protein-level similarity to known phages. Here we show that RNA structure provides an additional signal for the detection of ssRNA phages in metatranscriptomes, including hidden phages missed by prior protein-based methods. By computationally folding each contig and screening for exceptionally stable RNA secondary structures, we find evidence of thousands of previously unrecognized phages encoding novel coat proteins. We express a library of 12,000 such coat proteins in E. coli and find that most assemble into nuclease-resistant capsids. We determine the 3D structure of one such capsid by cryo-electron microscopy and demonstrate that it can be disassembled and reassembled in vitro to package heterologous RNA--a key step toward repurposing these particles as RNA delivery vehicles. We compile the newly discovered ssRNA phages with previously known ones into a database that contains sequence and structural information for over 460,000 unique RNA molecules and over 100,000 distinct coat proteins, providing a comprehensive resource for microbiology and nanomaterials research.

biochemistry↗

bioRxiv2026

Annexin A2 Regulates Surfactant Dysfunction During Injurious Ventilation.

The Acute Respiratory Distress Syndrome (ARDS) is a life-threatening cause of respiratory failure, and patients who develop ARDS frequently require mechanical ventilation, which puts them at risk of developing ventilator induced lung injury (VILI). Both VILI and ARDS can induce pulmonary surfactant dysfunction, but the mechanisms are not known. Here we report a novel role for a phospholipid binding protein, Annexin A2 (AnxA2), in the regulation of surfactant composition and function following injurious ventilation. Wild type and AnxA2-/-mice were subjected to injurious ventilation and we found that AnxA2-/- mice developed stiffer lungs following VILI that was not due to differences in barrier permeability or inflammation. Furthermore, we found that pulmonary surfactant from AnxA2-/- mice had reduced surface tension lowering properties and that this was due to a reduction in 1-palmitoyl-2-oleoylphosphatidylglycerol, or POPG. Quantitative analysis of surface tension-surface area hysteresis loops obtained from surfactant isolated from AnxA2-/- mice showed a defect in phase transitions during compression. In summary, Annexin A2 regulates surfactant function during injurious ventilation and may serve as a novel therapeutic target to prevent surfactant dysfunction in patients with ARDS who require mechanical ventilation.

molecular biology↗

bioRxiv2026

Fluorescence based microviscosity mapping in membraneless organelles

Membraneless organelles (MLOs) are cellular biomolecular condensates formed by liquid-liquid phase separation. Their biological functions are intimately linked to their material properties including viscosity. Condensate viscosity is determined by the size, shape, concentration and molecular interactions between MLOs components. It impacts the diffusion of MLOs constituents and the selective permeability of the condensate, thereby regulating the rate of biochemical reactions. Viscosity modifications associated with liquid-to-gel transition of the condensates are related to pathologies. Current experimental approaches for characterizing the material properties of cellular condensates remain limited. In this study, we report the use of BODIPY-based molecular rotors, in combination with fluorescence lifetime imaging microscopy (FLIM), to monitor the microviscosity of cellular MLOs directly in living cells. The fluorescence lifetime of BODIPY derivatives increases with the viscosity of their microenvironment, enabling quantitative assessment of microviscosity within condensates. HaloTag technology was employed to specifically label MLO components. Our findings reveal that the nucleolus exhibits higher viscosity than the surrounding nucleoplasm and that microviscosity varies across nucleolar sub-compartments. Furthermore, nucleolar reorganization induced by inhibition of rRNA synthesis results in a measurable increase in microviscosity. Finally, we demonstrate that the microviscosity of stress granules is lower than that of the nucleolus. Overall, presented results demonstrate the strong potential of the BODIPY based molecular rotors as a versatile and powerful tools for probing the material properties of cellular MLOs.

biophysics↗

bioRxiv2025

Acoustic Coupling for Double-Blind Human Low-Intensity Focused Ultrasound Neuromodulation

ObjectiveLow-intensity focused ultrasound (LIFU) is a non-invasive neuromodulation technique with the potential for precise targeting of small and deep human brain circuitry. To ensure rigorous and reproducible effects, it is necessary to implement double-blinding to mitigate potential experimental biases. This study innovates on previous ultrasound coupling methods by embedding a 3D-printed thermoplastic disc in a high-density gel-polymer matrix to create identical gel-plastic coupling devices that either transmit (verum) or block (sham) ultrasound. MethodsWe evaluated varying thicknesses (1.5 mm, 2,0 mm, 2.5 mm) and infill densities (25%, 50%, 75%, and 100%) of Acrylonitrile Butadiene Styrene (ABS) for insertion loss and effects on beam characteristics across relevant human neuromodulation frequencies from 0.2 - 1 MHz. ResultsABS at 1.5 mm thickness and 50 % infill had the lowest insertion loss at 0.50 MHz of 0.9 {+/-} 0.04 dB demonstrating acoustic transparency suitable for a verum device. For the sham device, we introduced an internal air gap that produced 31 dB insertion loss at 0.50 MHz. The verum device demonstrated minimal effects on the beam shape with a radial peak shift of 0.3 {+/-} 0.2 mm and an average axial shift of 0.5 mm. DiscussionThis novel gel-plastic coupling device can be tailored to most LIFU transducer shapes and is designed to support double-blind protocols by maintaining visual and tactile indistinguishability while controlling transmitted energy. This method provides a cost-effective and easily implementable solution for double-blinding in human LIFU studies to improve the reliability and rigor of experimental outcomes.

neuroscience↗

bioRxiv2025

Screen-VarCal: An Interpretable Probabilistic Framework for Recalibrating ACMG Rule-Based Variant Classification in Preventive Medicine

Motivationhole-genome sequencing (WGS) is increasingly used for preventive genomics, yet rule-based ACMG engines such as InterVar were tuned for high pre-test probability diagnostics. In screening contexts, these heuristics can inflate pathogenic/likely pathogenic (P/LP) calls, prompting unnecessary follow-up. We sought an interpretable, data-driven recalibration tailored to proactive use. ResultsAcross 20 WGS cases, InterVar flagged 109 variants as P/LP; only 18 (16.5%) were concordant with ClinVar P/LP assertions. The remaining 83.5% were largely absent from Clin-Var (n=68) or mapped to benign/likely benign (n=13). Nearly all flagged variants (96%) were heterozygous, predominantly in autosomal recessive genes (e.g., FAM20C, MTMR2 ), indicating a dominant carrier inflation effect; recurrent loci (e.g., ATXN3, FAM20C ) further amplified yield. We introduce Screen-VarCal, an interpretable probabilistic framework that combines logistic regression with isotonic adjustment to align InterVar outputs with observed ClinVar P/LP distributions. Screen-VarCal reduced false positives by[~] 60% while retaining all ClinVar-concordant findings and yields calibrated probabilities with coefficients that transparently link ACMG evidence categories (PVS/PS/PM/PP/BS/BP) and zygosity to risk.

bioinformatics↗

bioRxiv2025

Microbiota/gut/neuron axis promotes Drosophila ageing via Acetobacter, Tachykinin, and TkR99D

Gut microbiota exert an evolutionarily conserved influence on ageing, from invertebrates to humans. How do microbes that are physically confined to the gut lumen affect the systemic physiological process of ageing? In female Drosophila, we show that microbiota increase expression of the peptide hormone Tachykinin (Tk), which corresponds to reduced lifespan. Tk is required for microbiota to shorten lifespan, with knockdown rendering flies constitutively long-lived even in the presence of an intact microbiota. This lifespan extension does not come with canonical costs to fecundity or feeding, but impacts on triacylglyceride (TAG) storage suggest adaptive functions in metabolic homeostasis. In flies with defined (gnotobiotic) microbiotas, we show that we can model Tk-dependent effects of microbiota on lifespan and TAG by monoassociation with Acetobacter pomorum. These effects require Tk in the midgut, and the cognate TK receptor TkR99D in neurons, implicating a microbiota-gut-neuron relay. This relay also appears to compromise gut barrier function in aged flies, indicating roles in healthspan as well as lifespan. However, the effect of TkR99D is independent of its reported role in insulin signalling and adipokinetic hormone signalling which, respectively, are canonical regulators of lifespan and TAG metabolism, suggesting a non-canonical role for TkR99D elsewhere in the nervous system. Altogether our results implicate a microbiota-gut-neuron axis in ageing, via a specific bacterium modulating activity of a specific and evolutionarily-conserved hormone.

genetics↗

bioRxiv2025

SCOPE: Revealing Hidden Mechanisms in Phenotypic Screens Through Target and Pathway Enrichment

Phenotypic screening enables discovery of small molecules without requiring predefined targets, but mechanistic interpretation remains challenging due to polypharmacology and pathway complexity. We developed SCOPE (Screening Compound Ontology for Pathway Enrichment), a KNIME-based computational framework that resolves the molecular drivers of phenotypic activity by linking compound-level screening data to annotated targets and pathways. SCOPE integrates multi-source target annotations and performs statistical enrichment to identify shared mechanisms of action. Applied to a high-throughput screen for modulators of ER-stress induced secretion of endoplasmic reticulum (ER) resident proteins, a process known as exodosis, SCOPE identified calcium signaling as the most enriched KEGG pathway without prior biological context. Target enrichment revealed G protein-coupled receptors (GPCRs) involved in inositol 1,4,5-trisphosphate receptors (IP3Rs)-mediated signaling, with widespread antagonism among hit compounds implicating this pathway in the regulation of exodosis. Notably, SCOPE uncovered a novel role for the histamine receptor HRH1, which was validated by RNAi knockdown and pharmacological inhibition, implicating HRH1 as a potential therapeutic target in ER stress-related disorders. These results highlight SCOPEs potential to deconvolute phenotypic screens and uncover actionable mechanisms in complex cellular systems.

bioinformatics↗

bioRxiv2025

Adaptation of the Chlorella photosynthetic electron transport chain to environmental light conditions

In photosynthetic organisms, the process of photosystem II-cyclic electron flow (PSII-CEF) protects against degradation of the active D1 protein subunit of photosystem II in high light environments. By comparing the photophysiology of the extreme-light (2000 {micro}Ein/m2/s) desert alga Chlorella ohadii to the low-light (20 {micro}Ein/m2/s) aquatic alga Chlorella sp. NIES 642, we can monitor how natural adaptations resulting in differing levels of PSII-CEF affect the photosynthetic electron transport chain. Modeling of chlorophyll fast repetition rate fluorometry shows distinct backward transitions of the Kok cycle in C. ohadii, which are absent in NIES 642. Increase in PSII-CEF also has a positive effect on the occurrence of miss parameters in the water oxidizing complex. Fluorescent Q A- reoxidation kinetics detail that the majority of reaction centers in C. ohadii are performing electron transfer to oxidized QB under saturating light conditions. A combination of kinetic observations excludes plastocyanin as a potential external electron carrier in the mechanistic path of PSII-CEF and suggests that photosystem I-cyclic electron flow works in tandem with PSII-CEF. The combination of these two alternative flow mechanisms expedite electron transfer downstream of PSII and optimize ATP production, respectively. Utilizing 77K spectrofluorometry, congruent photosystem stoichiometry is found between both Chlorella species, despite a 100-fold growth light intensity difference. Electrochromic shift measurements show that C. ohadii has diminished changes to both trans-membrane potential and {Delta}pH during operation of photosynthesis compared to NIES 642, and that excess addition of N,N-dicyclohexylcarbodiimide to Chlorella cells has an inhibitory effect on the photosynthetic electron transport chain.

biochemistry↗

bioRxiv2025

Massively parallel reporter assays identify functional enhancer variants at QT interval GWAS loci

Genome-wide association studies (GWAS) have identified >30 loci with multiple common noncoding variants explaining interindividual electrocardiographic QT interval (QTi) variation. Of the many types of noncoding functional elements, here we sought to identify transcriptional enhancers with sequence variation and their cognate transcription factors (TFs) that alter the expression of proximal cardiac genes to affect QTi variation. We used massively parallel reporter assays (MPRA) in mouse cardiomyocyte HL-1 cells to screen for functional enhancer variants among 1,018 QTi-associated GWAS variants that overlap candidate cardiac enhancers across 31 loci. We identified 445 GWAS variant-containing enhancers of which 79 showed significant allelic difference in enhancer activity across 21 GWAS loci, with multiple enhancer variants per locus. Of these, we predicted differential binding by cardiac TFs, including AP-1, ATF-1, GATA2, MEF2, NKX2.5, SRF and TBX5 which are known to play key roles in development and homeostasis, at 49 enhancer variants. Finally, we used expression quantitative trait locus mapping and predicted promoter-enhancer contacts to identify 14 candidate target genes through analyses of 36 enhancer variants at 16 loci. This study provides strong evidence for 14 cardiac genes, 10 of them novel, impacting on QTi variation, beyond explaining observed genetic associations.

genetics↗

bioRxiv2025

Integrated analysis of protein sequence and structureredefines viral diversity and the taxonomy of the Flaviviridae

The Flaviviridae are a family of non-segmented positive-sense enveloped RNA viruses containing significant pathogens including hepatitis C virus and yellow fever virus. Recent large-scale metagenomic surveys have identified many diverse RNA viruses related to classical orthoflaviviruses and pestiviruses but quite different genome lengths and configurations, and with a hugely expanded host range that spans multiple animal phyla, including molluscs, cnidarians and stramenopiles,, and plants. Grouping of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flavivirus and flavi-like viruses into four divergent clades and multiple lineages within them was congruent with helicase gene phylogeny, PPHMM profile comparisons, and comparison of RdRP protein structure predicted by AlphFold2. These results support their classification into the established order, Amarillovirales, in three families (Flaviviridae, Pestiviridae, and Hepaciviridae), and 14 genera. This taxonomic framework informed by RdRP hallmark gene evolutionary relationships provides a stable reference from which major genome re-organisational events can be understood.

microbiology↗

bioRxiv2024

ZFAND6 is a subunit of a TRAF2-cIAP E3 ubiquitin ligase complex essential for mitophagy

The A20 ubiquitin-editing enzyme is a critical negative regulator of NF-{kappa}B signaling and inflammation. While the mechanisms by which A20 restricts inflammation have been extensively studied, the physiological functions of other A20-like proteins are largely unknown. Here, we report a previously unknown function of the A20 family member ZFAND6 as a novel regulator of mitophagy. Deletion of ZFAND6 in bone marrow-derived macrophages (BMDMs) promotes the upregulation of reactive oxygen species (ROS) and the accumulation of damaged mitochondria due to impaired mitophagy. Consequently, mitochondrial DNA (mtDNA) is released into the cytoplasm, triggering the spontaneous expression of interferon-stimulated genes (ISGs) in a cGAS-STING dependent manner, which leads to enhanced viral resistance in vitro. However, mice lacking ZFAND6 exhibit increased morbidity and mortality upon challenge with a sublethal dose of influenza A virus (IAV) due to impaired myeloid cell activation and diminished type I IFN signaling. Mechanistically, ZFAND6 bridges a TRAF2-cIAP1 interaction, which is required for the initiation of ubiquitin-dependent mitophagy. Our results suggest that ZFAND6 is a subunit of a TRAF2-cIAP E3 ligase complex that promotes the clearance of damaged mitochondria by mitophagy to maintain mitochondrial homeostasis.

immunology↗

bioRxiv2024

Development of quantitative high-throughput screening assays to identify, validate, and optimize small-molecule stabilizers of misfolded β-glucocerebrosidase with therapeutic potential for Gaucher disease and Parkinson's disease

Glucocerebrosidase (GCase) is implicated in both a rare, monogenic disorder (Gaucher disease, GD) and a common, multifactorial condition (Parkinsons disease); hence, it is an urgent therapeutic target. To identify correctors of severe protein misfolding and trafficking obstruction manifested by the pathogenic L444P-variant of GCase, we developed a suite of quantitative, high-throughput, cell-based assays. First, we labeled GCase with a small pro-luminescent HiBiT peptide reporter tag, enabling quantitation of protein stabilization in cells while faithfully maintaining target biology. TALEN-based gene editing allowed for stable integration of a single HiBiT-GBA1 transgene into an intragenic safe-harbor locus in GBA1-knockout H4 (neuroglioma) cells. This GD cell model was amenable to lead discovery via titration-based quantitative high-throughput screening and lead optimization via structure-activity relationships. A primary screen of 10,779 compounds from the NCATS bioactive collections identified 140 stabilizers of HiBiT-GCase-L444P, including both pharmacological chaperones (ambroxol and non-inhibitory chaperone NCGC326) and proteostasis regulators (panobinostat, trans-ISRIB, and pladienolide B). Two complementary high-content imaging-based assays were deployed to triage hits: the fluorescence-quenched substrate LysoFix-GBA captured functional lysosomal GCase activity, while an immunofluorescence assay featuring antibody hGCase-1/23 provided direct visualization of GCase lysosomal translocation. NCGC326 was active in both secondary assays and completely reversed pathological glucosylsphingosine accumulation. Finally, we tested the concept of combination therapy, by demonstrating synergistic actions of NCGC326 with proteostasis regulators in enhancing GCase-L444P levels. Looking forward, these physiologically-relevant assays can facilitate the identification, pharmacological validation, and medicinal chemistry optimization of new chemical matter targeting GCase, ultimately leading to a viable therapeutic for two protein-misfolding diseases. Significance StatementGaucher disease, the inherited deficiency of glucocerebrosidase, is caused by biallelic, loss-of-function mutations in the gene GBA1, which is also the most frequent genetic risk factor for Parkinsons disease. While the development of small-molecule stabilizers of glucocerebrosidase is being considered for both disorders, discovery and optimization of lead compounds is limited by the lack of robust cell-based assays amenable to high-throughput screening format. We developed a comprehensive assay pipeline for preclinical discovery of glucocerebrosidase modulators and began by screening libraries enriched with bioactive compounds with known mechanisms of action. The screen identified chemical matter with established relevance to glucocerebrosidase, provided an atlas of potential new molecular targets regulating the GBA1 pathway, and produced a set of promising potential therapeutics.

pharmacology and toxicology↗

bioRxiv2024

Identification of candidate causal cis-regulatory variants underlying electrocardiographic QT interval GWAS loci

Identifying causal variants among tens or hundreds of associated variants at each locus mapped by genome-wide association studies (GWAS) of complex traits is a challenge. As vast majority of GWAS variants are noncoding, sequence variation at cis-regulatory elements affecting transcriptional expression of specific genes is a widely accepted molecular hypothesis. Following this cis-regulatory hypothesis and combining it with the observation that nucleosome-free open chromatin is a universal hallmark of all types of cis-regulatory elements, we aimed to identify candidate causal regulatory variants underlying electrocardiographic QT interval GWAS loci. At a dozen loci, selected for higher effect sizes and a better understanding of the likely causal gene, we identified and included all common variants in high linkage disequilibrium with the GWAS variants as candidate variants. Using ENCODE DNase-seq and ATAC-seq from multiple human adult cardiac left ventricle tissue samples, we generated genome-wide maps of open chromatin regions marking putative regulatory elements. QT interval associated candidate variants were filtered for overlap with cardiac left ventricle open chromatin regions to identify candidate causal cis-regulatory variants, which were further assessed for colocalizing with a known cardiac GTEx expression quantitative trait locus variant as additional evidence for their causal role. Together, these efforts have generated a comprehensive set of candidate causal variants that are expected to be enriched for cis-regulatory potential and thereby, explaining the observed genetic associations.

genetics↗

bioRxiv2024

Functional characterization of QT interval associated SCN5A enhancer variants identify combined additive effects

Several empirical and theoretical studies suggest presence of multiple enhancers per gene that collectively regulate gene expression, and that common sequence variation impacting on the activities of these enhancers is a major source of inter-individual variability in gene expression. However, for vast majority of genes, enhancers and the underlying regulatory variation remains unknown. Even for the genes with well-characterized enhancers, the nature of the combined effects from multiple enhancers and their variants, when known, on gene expression regulation remains unexplored. Here, we have evaluated the combined effects from five SCN5A enhancers and their regulatory variants that are known to collectively correlate with SCN5A cardiac expression and underlie QT interval association in the general population. Using small deletions centered at the regulatory variants in episomal reporter assays in a mouse cardiomyocyte cell line we demonstrate that the variants and their flanking sequences play critical role in individual enhancer activities, likely being a transcription factor (TF) binding site. By performing oligonucleotide-based pulldown assays on predicted TFs we identify the TFs likely driving allele-specific enhancer activities. Using all 32 possible allelic synthetic constructs in reporter assays, representing the five biallelic enhancers in tandem in their genomic order, we demonstrate combined additive effects on overall enhancer activities. Using transient enhancer assays in developing zebrafish embryos we demonstrate the four out the five enhancer elements act as enhancers in vivo. Together, these studies extend the previous findings to uncover the TFs driving the enhancer activities of QT interval associated SCN5A regulatory variants, reveal the additive effects from allelic combinations of these regulatory variants, and prove their potential to act as enhancers in vivo.

genetics↗