Biology subjects

Horvath, A.

Publications and source records attributed to Horvath, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Multi-scale electrophysiological characterization of human cardioids reveals progressive maturation

Background: Human induced pluripotent stem cell-derived cardiomyocytes are valuable for cardiac disease modelling and drug testing but remain limited by immature structural and electrophysiological properties in conventional two-dimensional cultures. Three-dimensional cardiac models, including cardioids, provide a more physiological environment through multicellular organization and enable tissue-level functional analysis. Their electrophysiological properties and maturation, however, remain incompletely characterized. Methods: We performed an integrated electrophysiological characterization of human cardioids over the first three weeks of maturation using sharp microelectrode recordings, calcium transient measurements, whole-cell patch clamp recordings, immunofluorescence, transcriptomic analysis, and pharmacological interventions. Results: During maturation, cardioids exhibited progressive electrophysiological maturation, characterized by more physiological resting membrane potentials (-54.0{+/-}3.1mV to -68.1{+/-}1.2mV), increased action potential amplitude (73.5{+/-}4.8mV to 101.7{+/-}2.1mV) and upstroke velocity (44.3{+/-}5mV/ms to 86.6{+/-}8.4mV/ms), and shorter action potential duration (178.9{+/-}8.7ms to 144.0{+/-}4.8ms at 1Hz stimulation). These changes were associated with progressively increased INa density and enhanced SCN5A mRNA and Nav1.5 protein expression, consistent with progressive maturation of cardiac excitability. IKr current and KCNH2/hERG expression were already present at early maturation stages and remained stable, as evidenced by preserved sensitivity to dofetilide-blockade. Pharmacological inhibition of barium- and HMR-sensitive currents altered resting membrane and/or action potential characteristics in intact cardioids, whereas in isolated cardiomyocytes classical IK1 remained undetectable and IKs was small, highlighting a certain degree of persisting immaturity of the model. Conclusions: These findings demonstrate that human cardioids undergo progressive electrophysiological maturation and provide complementary tissue- and cellular-level insights into cardiac function, establishing their suitability for investigating INa and IKr-related cardiac pathologies.

physiology↗

bioRxiv2026

Brain-wide mapping of proglucagon expression in mice identifies fasting-responsive GLP-1 neurons in the posterior hypothalamic nucleus

ObjectiveGlucagon-like peptide-1 (GLP-1), a peptide neurotransmitter in the brain, is synthesized from proglucagon, encoded by the glucagon gene (Gcg). Besides medullary GLP-1 neurons, Gcg-expressing neuron populations were identified in the olfactory bulb and basolateral amygdala. However, several lines of evidence suggest that additional Gcg neuron populations might exist. MethodsWe conducted a brain-wide mapping of Gcg-expressing cells by fluorescent in situ hybridization in C57BL/6J and FVB/Ant mice. Proglucagon and GLP-1 expression were studied with immunofluorescence. We characterized a Gcg-Cre;tdTomato mouse line and studied the expression of proglucagon-processing enzymes in Gcg-expressing neuron populations. We used adeno-associated virus-mediated tracing in Gcg-Cre mice to map the projections of hypothalamic Gcg neurons. ResultsGcg-expressing neuron populations were identified in the olfactory bulb, claustrum, piriform cortex, basolateral amygdala, posterior hippocampus, posterior hypothalamic nucleus (PH), periaqueductal gray/dorsal raphe, and dorsal nucleus of the lateral lemniscus. These neurons express lower Gcg mRNA levels than medullary GLP-1 neurons. Proglucagon and GLP-1-immunoreactivity (C-terminus) were detected in almost all Gcg-expressing neuron populations, along with the mRNAs for prohormone convertases 1/3 and 2, enzymes generating GLP-1 or glucagon, respectively. Fasting markedly increased Gcg mRNA, proglucagon and GLP-1 synthesis in the PH. PH Gcg neurons project densely to the ventral and intermediate lateral septum, preoptic region, ventrolateral preoptic nucleus, lateral hypothalamus and zona incerta, establishing close contacts with both GLP-1 receptor-positive and -negative neurons. ConclusionsProglucagon is expressed in 9 distinct neuron populations. Feeding status regulates GLP-1 synthesis in PH neurons that likely control feeding- or energy balance-related functions.

neuroscience↗

bioRxiv2026

Comparative transcriptomics analysis of histone deacetylases, transcription factors, and ion channel genes in human iPSC-cardiomyocytes vs. the adult human heart

Epigenetic modulators such as histone deacetylases (HDACs) and histone acetyltransferases (HATs) are known master regulators of gene expression that substantially impact cardiac electrophysiology. Novel pharmacological agents, HDAC inhibitors, are rapidly emerging as treatments for cancer and immune diseases, and their effects on cardiac ion channels (ICs) are of great interest. We used small interfering RNAs to individually suppress each of the known HDACs, including sirtuins (SIRTs), in human induced pluripotent stem-cell-derived cardiomyocytes (hiPSC-CMs), iCell2. Follow-up deep-sequencing allowed comparison to identically processed and normalized RNA sequencing data from adult human left ventricle (LV) from the GTEx database. The transcriptomics analysis revealed high similarity of gene expression patterns for cardiac ICs (with some differences in calcium influx and calcium buffering related genes), as well as strong co-regulation by cardiac transcription factors (TFs) and HDACs/SIRTs in both hiPSC-CMs and the adult LV. Partial least square regression models helped visualize links between HDACs/HATs, TFs, and cardiac ICs and helped identify potential key regulators of cardiac IC transcription. Powerful TFs, including MEF2A, GATA4, 6 exerted positive effect on IC genes while RUNX1 and SHMT2 were distinct negative regulators in both sample types; TRIM28 was found to serve opposite roles in the two sample types. In functional measurements, HDAC suppression primarily increased excitability, while SIRT suppression decreased excitability, in line with transcriptomic links. Our analysis offers insights about the role of epigenetic modifiers in regulating cardiac electrophysiology and informs the utility of hiPSC-CM as a scalable experimental model for cardiotoxicity testing of HDAC inhibitors.

bioengineering↗

bioRxiv2025

Infarctsize-AI: an efficient infarct size image analysis tool for small rodent myocardial infarction studies

BackgroundMyocardial infarct size (IS) is the gold standard end-point in shorth-term studies on cardioprotection. However, IS quantification in rodent models with standard Evans Blue and 2,3,5-triphenyltetrazolium chloride (TTC) staining is time-consuming and prone to inter-observer variance. Therefore, we aimed to develop an artificial intelligence (AI)-based application to reduce time and inter-observer variability of IS analysis in rodent acute myocardial infarction (MI) models. MethodsWe used TTC/Evans blue-stained heart slice images of independent laboratories from previously published projects. Rat (n = 325 and 248 slices) and mouse (n = 77 slices) datasets were used to train deep learning segmentation models with three different neural network architectures, which were combined into a single AI analysis. AI analysis was compared with manual analysis on rat data from a training laboratory (internal data, n = 496 slices, n = 41 whole-hearts) and data from independent laboratories (external data, n = 60 and 62 slices). Additionally, two independent evaluators performed manual and AI-assisted analysis, consisting of AI-analysis and its manual correction, on internal (n = 36 slices) and external data (n = 37 slices). ResultsLins concordance correlation coefficient (CCC) between IS/AAR values from manual and AI analysis was 0.844 with 95% CI of [0.814; 0.869] for images of internal data heart slices. On external data heart slices, AI accurately annotated slice area and AAR but failed to annotate infarcted area. On internal whole-heart data, CCC between AI and AI-assisted IS/AAR was 0.894 with 95% CI of [0.812; 0.942]. AI-assisted analysis reduced evaluation time on both internal and external datasets and increased region overlap for AAR between the two independent evaluators on dependent data. ConclusionsAI-assisted analysis significantly reduced analysis time and inter-observer variability. For optimal performance, lab-specific AI training is recommended. Infarctsize-AI is available at https://infarctsize.com. Translational perspectiveMyocardial infarct size (IS) is the gold-standard end-point in shorth-term studies to assess potential cardioprotective therapies against acute myocardial infarction (AMI). However, IS quantification in rodent AMI models is time-consuming and prone to inter-observer variance. Therefore, we developed an AI-based software that can reduce analysis time and inter-observer variability and facilitate documentation, which facilitates the clinical translation of potential cardioprotective therapies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=34 SRC="FIGDIR/small/688527v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@187c938org.highwire.dtl.DTLVardef@1ab8bb4org.highwire.dtl.DTLVardef@160dc68org.highwire.dtl.DTLVardef@264617_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Murder in cold blood? Forensic and bioarchaeological identification of the skeletal remains of Bela, Duke of Macso (c. 1245-1272)

In 1915, the remains of a male were discovered in a 13th-century monastery on Margaret Island, Budapest. Historical context suggested that the remains may belong to Duke Bela of Macso (c. 1245-1272), grandson of King Bela IV of Hungary (House of Arpad) and son of Duke Rostislav (Rurik dynasty). We applied a complex approach to identify the individual and reconstruct the circumstances of his death. Radiocarbon dating, when adjusted for freshwater reservoir effects linked to a high-protein diet, placed the burial in the mid-13th century. Skeletal features corresponded to a young adult male. Stable isotope and dental calculus analyses indicated a high-status diet rich in animal proteins and C3 cereals. Ancient DNA confirmed descent from King Bela III (Arpad dynasty) and Y-chromosomal affiliation with the Rurikid lineage. Forensic evidence revealed 26 perimortem injuries, suggesting a coordinated, premeditated assassination involving at least three assailants. The pattern of injuries indicates both planning and intense emotional involvement. Our findings provide the first genetic identification of a medieval royal, and resolve a century-old archaeological question, and illustrate the power of integrating multidisciplinary methods to confirm historical hypotheses and reconstruct violent deaths from the past with unprecedented detail. TeaserWith unprecedented details, this study shows the impact of integrating multidisciplinary methods to confirm historical hypotheses and reconstruct violent deaths from the past.

genetics↗

bioRxiv2025

Contrastive learning of adverse events to provide effective and interpretable vector representations for machine-assisted pharmacovigilance

Post-marketing surveillance is crucial for drug safety, yet the tools of pharmacovigilance rely solely on text-based data that may limit the applicability of contemporary machine learning methodologies in the support of decision making. Here, we adapt contrastive learning algorithms to generate adverse event vector representations from spontaneous reports to serve as general machine-readable resources for pharmacovigilance applications. We present comprehensive analyses of the resulting representations through density-based clustering, semantic evaluation and comparison of multivariate dispersions, revealing patterns that reflect both functional and causal relations of the adverse events while also capturing drug-safety related information better than existing medical terminologies and encoder-only large language models (LLMs). Furthermore, we demonstrate the applicability of the representations as input features in our downstream model, outperforming the reporting odds ratio method commonly used by regulatory agencies (AUROC: 0.88 vs 0.75) and LLM-based representations (AUROC: 0.88 vs 0.83) on drug-event causality prediction benchmarks. As such, this is the first demonstration of an interpretable adverse event vector representation that can be utilized for training arbitrary models, enabling wider and more effective applications of machine learning in pharmacovigilance.

pharmacology and toxicology↗

bioRxiv2025

Novel insights into the genetic architecture and mechanisms of host/microbiome interactions from a multi-cohort analysis of outbred laboratory rats

The intestinal microbiome influences health and disease. Its composition is affected by host genetics and environmental exposures. Understanding host genetic effects is critical but challenging in humans, due to the difficulty of detecting, mapping and interpreting them. To address this, we analysed host genetic effects in four cohorts of outbred laboratory rats exposed to distinct but controlled environments. We found that polygenic host genetic effects were consistent across environments. We identified three replicated microbiome-associated loci, one of which involved a sialyltransferase gene and Paraprevotella. We found a similar association in a human cohort, between ST6GAL1 and Paraprevotella, both of which have been linked with immune and infectious diseases. Moreover, we found evidence of indirect genetic effects on microbiome phenotypes, which substantially increased their total genetic variance. Finally, we identified a novel mechanism whereby indirect genetic effects can contribute to "missing heritability".

genetics↗

bioRxiv2025

The Cause of Most Common Antler Abnormality is Not a Fracture But an Osteomyelitis Like Disease the Pedunculitis Chronica Deformans

Climate change is increasing the incidence of certain diseases in wildlife, offering a deeper understanding of their underlying causes. Traditionally, the most common antler abnormalities have been attributed to trauma, based on their morphology. However, this explanation does not account for the epidemic-like spread of abnormalities in specific regions, suggesting that they might be a previously undescribed aspect of this anomaly. In fallow deer (Dama dama), using advanced medical diagnostic tools, we identified an osteomyelitis-like condition, Pedunculitis Chronica Deformans (PCD) which is also observed in other Cervidae. The incidence of this disease shows a strong correlation with the production of mycotoxins by molds that are becoming more prevalent with global warming. Mycotoxins can inhibit wound healing through scar formation after the antlers are cast, leading to the development of PCD. In this report we characterize PCD pathomorphology and introduce a scoring system to differentiate it from other deformities. Moreover, we argue that the most common anomalies such as fractures, antler losses, fatal meningoencephalitis and brain abscesses are complications of PCD. Our research underscores the potential of antlers to serve as biomarkers for mycotoxin exposure.

zoology↗

bioRxiv2024

Structures of aberrant spliceosome intermediates on their way to disassembly

Intron removal during pre-mRNA splicing is of extraordinary complexity and its disruption causes a vast number of genetic diseases in humans1. While key steps of the canonical spliceosome cycle have been revealed by combined structure-function analyses2,3, structural information on an aberrant spliceosome committed to premature disassembly is not available. Here, we report two cryo-EM structures of post-Bact spliceosome intermediates from S. pombe primed for disassembly. We identify the DEAH-box helicase - G patch protein pair (Gih35-Gpl1, homologous to human DHX35-GPATCH1) and show how it maintains catalytic dormancy. In both structures, Gpl1 recognizes a remodeled active site introduced by an over-stabilization of the U5 loop I interaction with the 5 exon leading to a single nucleotide insertion at the 5splice site. Remodeling is communicated to the spliceosome surface and the Ntr1 complex that mediates disassembly is recruited. Our data pave the way for a targeted analysis of splicing quality control.

biochemistry↗

bioRxiv2024

Deep skin fibroblast-mediated macrophage recruitment supports acute wound healing

Epithelial and immune cells have long been appreciated for their contribution to the early immune response after injury; however, much less is known about the role of mesenchymal cells. Using single nuclei RNA-sequencing, we defined changes in gene expression associated with inflammation at 1-day post-wounding (dpw) in mouse skin. Compared to keratinocytes and myeloid cells, we detected enriched expression of pro-inflammatory genes in fibroblasts associated with deeper layers of the skin. In particular, SCA1+ fibroblasts were enriched for numerous chemokines, including CCL2, CCL7, and IL33 compared to SCA1-fibroblasts. Genetic deletion of Ccl2 in fibroblasts resulted in fewer wound bed macrophages and monocytes during injury-induced inflammation with reduced revascularization and re-epithelialization during the proliferation phase of healing. These findings highlight the important contribution of deep skin fibroblast-derived factors to injury-induced inflammation and the impact of immune cell dysregulation on subsequent tissue repair.

cell biology↗

bioRxiv2024

Transcriptomic Meta-analysis Identifies Long Non-Coding RNAs Mediating Zika's Oncolytic Impact in Glioblastoma Multiforme

Glioblastoma multiforme (GBM) is an aggressive and lethal form of brain cancer with few effective treatments. In this context, Zika virus has emerged as a promising therapeutic agent due to its ability to selectively infect and kill GBM cells. To elucidate these mechanisms and expand the landscape of oncolytic virotherapy, we pursued a transcriptomic meta-analysis comparing the molecular signatures of Zika infection in GBM and neuroblastoma (NBM). Over-representation analysis of dysregulated coding genes showed significant enrichment of tumor necrosis factor (TNF), NF-{kappa}B, and p53 signaling pathways. A refined list of long non-coding RNAs consistently dysregulated in Zika-infected GBMs was also developed. Functional review of these candidates revealed their potential regulatory role in Zika-mediated oncolysis. We performed validation of the less-researched targets in adult and pediatric GBM cell lines and found significant differential regulation, as predicted. Altogether, our results provide novel insights into the molecular mechanisms underlying the effect of Zika on GBM. We highlight potential therapeutic targets that could be further interrogated to improve the efficacy of tumor cell death and the utility of Zika as an adjuvant virotherapy for GBM and other related cancers.

cancer biology↗

bioRxiv2024

scSNViz: a user-friendly toolset for visualization and analysis of Cell-Specific Expressed SNVs

SummaryAccurately characterizing expressed genetic variation at the single-cell level is essential for understanding transcriptional heterogeneity, allelic regulation, and mutational dynamics within complex tissues. However, few tools enable comprehensive visualization and quantitative analysis of expressed variants across individual cells. scSNViz is an R package for the exploration, quantification, and visualization of expressed single-nucleotide variants (SNVs) from cell-barcoded single-cell RNA sequencing (scRNA-seq) data. The software supports estimation of variant allele fractions, clustering of SNV expression profiles, and 2D and 3Dl visualization of individual SNVs or user-defined SNV groups. Beyond visualization, scSNViz facilitates investigation of cell-, cluster-, or lineage-specific variant expression patterns, as well as allelic dynamics including imprinting, random allele inactivation, and transcriptional bursting. It interoperates seamlessly with established single-cell frameworks - Seurat for clustering, Slingshot for trajectory inference, scType for cell-type annotation, and CopyKat for copy-number profiling - enabling integrative multi-omic analyses of expressed variation. Availability and ImplementationscSNViz is implemented in R and freely available at https://github.com/HorvathLab/scSNViz (DOI: 10.5281/zenodo.17307516). The package includes comprehensive documentation and example workflows designed for users with limited bioinformatics experience.

genomics↗

bioRxiv2024

Genome-Wide Association Study in Outbred Heterogeneous Stock Rats Identifies Multiple Loci for the Incentive Salience of Reward Cues.

Addiction vulnerability is associated with the tendency to attribute incentive salience to reward predictive cues; both addiction and the attribution of incentive salience are influenced by environmental and genetic factors. To characterize the genetic contributions to incentive salience attribution, we performed a genome-wide association study (GWAS) in a cohort of 1,645 genetically diverse heterogeneous stock (HS) rats. We tested HS rats in a Pavlovian conditioned approach task, in which we characterized the individual responses to food-associated stimuli ("cues"). Rats exhibited either cue-directed "sign-tracking" behavior or food-cup directed "goal-tracking" behavior. We then used the conditioned reinforcement procedure to determine whether rats would perform a novel operant response for unrewarded presentations of the cue. We found that these measures were moderately heritable (SNP heritability, h2 = .189-.215). GWAS identified 14 quantitative trait loci (QTLs) for 11 of the 12 traits we examined. Interval sizes of these QTLs varied widely. 7 traits shared a QTL on chromosome 1 that contained a few genes (e.g. Tenm4, Mir708) that have been associated with substance use disorders and other mental health traits in humans. Other candidate genes (e.g. Wnt11, Pak1) in this region had coding variants and expression-QTLs in mesocorticolimbic regions of the brain. We also conducted a Phenome-Wide Association Study (PheWAS) on other behavioral measures in HS rats and found that regions containing QTLs on chromosome 1 were also associated with nicotine self-administration in a separate cohort of HS rats. These results provide a starting point for the molecular genetic dissection of incentive salience and provide further support for a relationship between attribution of incentive salience and drug abuse-related traits.

neuroscience↗

bioRxiv2023

Exponential increase in QTL detection with increased sample size.

Power analyses are often used to determine the number of animals required for a genome wide association analysis (GWAS). These analyses are typically intended to estimate the sample size needed for at least one locus to exceed a genome-wide significance threshold. A related question that is less commonly considered is the number of significant loci that will be discovered with a given sample size. We used simulations based on a real dataset that consisted of 3,173 male and female adult N/NIH heterogeneous stock (HS) rats to explore the relationship between sample size and the number of significant loci discovered. Our simulations examined the number of loci identified in sub-samples of the full dataset. The sub-sampling analysis was conducted for four traits with low (0.15 {+/-} 0.03), medium (0.31 {+/-} 0.03 and 0.36 {+/-} 0.03) and high (0.46 {+/-} 0.03) SNP-based heritabilities. For each trait, we sub-sampled the data 100 times at different sample sizes (500, 1,000, 1,500, 2,000, and 2,500). We observed an exponential increase in the number of significant loci with larger sample sizes. Our results are consistent with similar observations in human GWAS and imply that future rodent GWAS should use sample sizes that are significantly larger than those needed to obtain a single significant result.

genetics↗

bioRxiv2022

Analysis of the abomasal transcriptome of LDA affected cattle

Left displacement of the abomasum (LDA) is a common condition in Holstein population mainly occur around the time of parturition. The entrapped abomasum located between the rumen and the abdominal wall caused by the abomasal hypomotility. The heritability of LDA estimated higher than for other bovine diseases but a number of management and nutritional conditions are also affecting the disease appearance. Genome studies revealed many significant genomic regions associated with LDA, although an RNA sequencing analysis of abomasum is missing from the literature. Within the framework of this research, we tried to patch up this area missing from the literature and to reveal the genetic causes and a complex interaction between the endocrine and neuromuscular pathways behind the symptoms of the disease with the help of transcriptomic analysis.

bioinformatics↗

bioRxiv2022

Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex.

The S. pombe orthologue of the human PAXT complex, Mtl1-Red1 Core (MTREC), is an eleven-subunit complex which targets cryptic unstable transcripts (CUTs) to the nuclear RNA exosome for degradation. It encompasses the canonical poly(A) polymerase Pla1, responsible for polyadenylation of nascent RNA transcripts as part of the cleavage and polyadenylation factor (CPF/CPSF). In this study we identified and characterised the interaction between Pla1 and the MTREC complex core component Red1 and analysed the functional relevance of this interaction in vivo. Our crystal structure of the Pla1-Red1 complex showed that a 58-residue fragment in Red1 binds to the RNA recognition motif domain of Pla1 and tethers it to the MTREC complex. Structure-based Pla1-Red1 interaction mutations showed that Pla1, as part of MTREC complex, hyper-adenylates CUTs for their efficient degradation. Interestingly, the Red1-Pla1 interaction was also required for the efficient assembly of the fission yeast facultative heterochromatic islands. Together, our data suggest a complex interplay between the RNA surveillance and 3-end processing machineries.

molecular biology↗

bioRxiv2022

CovidOutcome2: a tool for SARS-CoV2 mutation identification and for disease severity prediction

Our goal was to develop a platform, CovidOutcome2, capable of predicting disease severity from viral mutation profiles using automated machine learning (autoML) and deep neural networks applied to the available large corpus of sequenced SARS-CoV2 genomes. CovidOutcome2 accepts either user-submitted genomes or user defined mutation combinations as the input. The output is a predicted severity score plus a list of identified, annotated mutations and their functional effects in VCF format. The best model performance is a ROC-AUC 0.899 for the model including patient age and ROC-AUC 0.83 for the model without patient age. AvailabilityCovidOutcome is freely available online under the URL https://www.covidoutcome.bio-ml.com as well as in a standalone version https://github.com/bio-apps/covid-outcome.

bioinformatics↗

bioRxiv2022

Extracellular vesicles carrying HIV-1 Nef induce trained immunity in myeloid cells

SummaryPersistent inflammation is a hallmark of HIV infection and is not reversed after suppression of viral replication by anti-retroviral therapy (ART). One explanation for chronic inflammation in ART-treated HIV-infected individuals is hyperreactivity of the myeloid cells due to a phenomenon called trained immunity. Here, we demonstrate that human monocyte derived macrophages originating from monocytes initially treated with extracellular vesicles containing HIV-1 protein Nef (exNef), but differentiating in the absence of exNef, released increased levels of pro-inflammatory cytokines after lipopolysaccharide stimulation. This effect was associated with epigenetic changes related to inflammation and cholesterol metabolism pathways, upregulation of the lipid rafts, and was blocked by methyl-{beta}-cyclodextrin, statin, and inhibitor of activity of lipid raft-associated receptor IGF1R. Bone marrow-derived macrophages from exNef-injected mice had higher abundance of lipid rafts and produced elevated levels of TNF. These phenomena are consistent with trained immunity and may contribute to persistent inflammation and co-morbidities in HIV-infected individuals.

immunology↗