Biology subjects

Horvath, M.

Publications and source records attributed to Horvath, M..

12 recordsLinked to original sources

bioRxiv2026

Structural Basis for Nucleobase Activation by the Adenine DNA Glycosylase MutY

MutY excises adenine (A) from 8-oxo-guanine:adenine (OG:A) lesions in DNA to initiate base excision repair (BER) and thereby prevent mutations. A catalytic Glu, found at position 43 in the enzyme from Geobacillus stearothermophilus (Gs MutY), protonates the nucleobase at N7 to labilize the N-glycosidic bond. The resulting oxocarbenium ion transition state is stabilized by a covalent DNA-enzyme intermediate and resolved by nucleophilic attack to yield the beta-anomer abasic AP site product. The retaining SN1 mechanism for MutY posits deprotonation of the nucleophile by the catalytic Glu. Here we tested kinetic and structural consequences of Glu replacement and found that E43Q and E43S substitution variants were severely impaired, retained measurable activity, but engage the substrate nucleobase in an anti conformation, rotated by 180 {degrees} from the syn conformation seen in previous substrate complexes. The enzyme-generated AP product is observed in its alpha-anomer configuration for these Glu-replacement variants. Comparison with inverting adenine glycosylases that act on RNA or nucleosides shows that MutYs mechanism is uniquely reliant on one catalytic residue for both leaving group and nucleophile activation, a situation that may serve to ensure only rare adenines paired with OG are excised.

biochemistry↗

bioRxiv2025

Predicting TCR antigen specificity at proteome-scale with synthetic immune cells and machine learning

TCR specificity to peptide-HLA antigens is central to immunology, impacting responses in infection, autoimmunity and cancer. Achieving precise recognition while avoiding off-target reactivity is critical for effective immunity and safe therapeutic interventions. Comprehensive, proteome-wide specificity profiling of TCRs is challenging with current methods, which notably lack integrated machine learning for large-scale analysis. Here, we report a synthetic immune cell system coupled with machine learning to enable TCR functional and specificity mapping of peptide-HLA antigens at proteome-scale. Multi-step immunogenomic engineering of synthetic antigen-presenting cells (APCs) was performed to enable stable mono-allelic integration and precise display of peptide antigens and HLA class I from a defined genomic locus, ensuring genomically-encoded antigen presentation. Compatible with a synthetic TCR displaying T cell system, this platform incorporates a fluorescent reporter of cytokine-mediated signaling for real-time activation detection in both synthetic APCs and T cells. We combined this screening with diverse peptide antigen libraries and deep sequencing to train supervised machine learning models. These models were applied to predict TCR specificity to peptide-HLA antigens across the entire human proteome. Experimental validation confirmed novel off-targets for therapeutic TCR candidates, including for a clinically-approved TCR therapeutic. This integrated synthetic immune cell and machine learning approach provides unprecedented proteome-wide peptide-HLA specificity mapping to support the development of safer TCR-based therapies. One sentence summaryWe present a synthetic immune cell platform integrated with machine learning that enables prediction of TCR specificity to peptide-HLA antigens at proteome-scale.

immunology↗

bioRxiv2025

Host-specific bacterial modulation of airway gene expression and alternative splicing

The human microbiome varies extensively between individuals. While there are numerous studies investigating the effects of inter-individual differences on microbiome composition, there are few studies investigating inter-individual effects on microbial modulation of the host, or host-specific effects. To address this knowledge gap, we colonized human bronchial epithelial air-liquid interface tissue cultures generated from six different adults with one of three phylogenetically diverse bacteria and compared how each microbe differentially modulated host gene expression in each of the six donors. Microbial treatment had the strongest effect on transcription, followed by donor-specific effects. Gene pathways differed markedly in their donor- and microbe-specificity; interferon expression was highly donor-dependent while transcription of epithelial barrier and antibacterial innate immunity genes were predominantly microbially driven. Moreover, we evaluated whether microbial regulation of alternative splicing was modulated by donor. Strikingly, we found significant non-redundant, donor-specific regulation of alternative splicing exclusively in the Gram-positive commensal microbes. These findings highlight that microbial effects on the human airway epithelium are not only species-specific but also deeply individualized, scoring the importance of host context in shaping microbe-induced transcriptional and splicing responses.

microbiology↗

bioRxiv2025

Early Candida - Oral Tumor Interactions Suggest miRNA-Mediated Regulation of Inflammatory and Tumor-associated processes

When simultaneously present, oral cancer and oral candidiasis are associated with high mortality. Recently, fungi-driven OSCC has emerged as a recognized phenomenon, that is triggered by Candida and sustained by several pro-tumor mechanisms. This study aimed to deepen our understanding and investigate how these mechanisms are regulated at the early stages of fungi-tumor interactions. Post-transcriptional regulation was examined through the analysis of miRNA (miR) responses in a metastatic cell line. We characterized early tumor responses to two common oral yeasts, C. albicans, frequently responsible for oral infections, and C. parapsilosis, a yeast with mostly commensal behavior in this niche. Exposed to C. albicans, tumor cells exhibited overexpression of inflammatory and pro-tumor pathways. This was also mirrored at the miR-level. Intriguingly, this species induced upregulation of oncogenic miRs, while simultaneously downregulated tumor-suppressive miRs. miR-target analyses revealed targets primarily to be involved in inflammation (TNFa signaling via NFKB), albeit tumor progression was also heavily influenced based on the targets identified within the PanCancer Progression Panel. Several miR-target pairs were identified with TRIB1-miR-30c-1-3p highlighted at the route of inflammation, and MMP3-miR-374a-3p and JUN-miR-1268b/miR-16-1-3p/miR-30c-1-3p at the route of OSCC progression. These findings highlight that C. albicans drives OSCC progression, in part, through miR regulation. Contrarily, C. parapsilosis elicited tumor responses predominantly related to hypoxia and metabolic regulation, followed by a mild activation of inflammatory and tumorigenic processes. No significant miR-regulatory responses were identified. To sum up, we added a new layer to fungi-tumor interactions and identified regulatory elements, that might hold future translational potential. ImportancePrevious studies have shown that yeast carriage in the oral cavity of oral cancer patients is significantly higher than those of healthy individuals. Additionally, the abundance of fungal cells is higher at malignant epithelial surfaces compared to the unaffected mucosal tissues. These observations indicated a direct interaction between mouth residing yeasts and oral tumorous cells. We have previously demonstrated that certain Candida species actively contribute to tumor progression in metastatic oral epithelial cells via various mechanisms including the promotion of migration, MMP activity or oncometabolite secretion. In this study, our findings demonstrate, that fungi-driven OSCC progression is also evident at the level of miRNA regulation, when C. albicans is present. In this context, the fungus might also enhance existing post-transcriptional regulatory mechanisms in the malignant oral epithelium. This behavior seems to be species-specific, as another common resident of the oral microflora, C. parapsilosis does not trigger such an effect.

microbiology↗

bioRxiv2024

Structure of human MUTYH and functional profiling of cancer-associated variants reveal an allosteric network between its cluster cofactor and active site required for DNA repair

MUTYH is a clinically important DNA glycosylase that thwarts mutations by initiating base-excision repair at 8-oxoguanine (OG):A lesions. The roles for its [4Fe-4S] cofactor in DNA repair remain enigmatic. Functional profiling of cancer-associated variants near the [4Fe-4S] cofactor revealed that most variations abrogate both retention of the cofactor and enzyme activity. Surprisingly, R241Q and N238S retained the metal center and bound substrate DNA tightly but were completely inactive. We solved the crystal structure of human MUTYH bound to a transition state mimic and this revealed that Arg241 and Asn238 build an H-bond network connecting the [4Fe-4S] cluster to the catalytic Asp236 that mediates base excision. The structure of the bacterial MutY variant R149Q, along with molecular dynamics simulations of the human enzyme, show the cofactor functions to position and activate the catalytic Asp. These results suggest that allosteric cross-talk between the DNA binding [4Fe-4S] cofactor and the base excision site regulate DNA repair.

biochemistry↗

bioRxiv2023

Species- and strain-effects in interferon, innate immunity, and barrier transcriptional response of microbiome interactions of 3D respiratory epithelial cultures

The microbiome modulates the respiratory epitheliums immunomodulatory functions. To explore how the microbiomes biodiversity affects microbe-epithelial interactions, we screened 58 phylogenetically diverse microbes for their transcriptomic effect on tracheobronchial air-liquid interface cell (ALI) cultures. We found distinct species- and strain-level differences in host innate immunity, and epithelial barrier response. Strikingly, we found that host interferon, an antiviral immune response, was one of the most variable host processes, and this variability was not driven by microbial phylogenetic diversity, bioburden, nor by the microbes ability to stimulate other innate immunity pathways. Our study provides a foundation for understanding how the respiratory microbiomes biodiversity affects epithelial, and particularly, antiviral innate immunity.

microbiology↗

bioRxiv2023

High-Throughput Bioprinting of the Nasal Epithelium using Patient-derived Nasal Epithelial Cells

Human nasal epithelial cells (hNECs) are an essential cell source for the reconstruction of the respiratory pseudostratified columnar epithelium composed of multiple cell types in the context of infection studies and disease modeling. Hitherto, manual seeding has been the dominant method for creating nasal epithelial tissue models. However, the manual approach is slow, low-throughput and has limitations in terms of achieving the intricate 3D structure of the natural nasal epithelium in a uniform manner. 3D Bioprinting has been utilized to reconstruct various epithelial tissue models, such as cutaneous, intestinal, alveolar, and bronchial epithelium, but there has been no attempt to use of 3D bioprinting technologies for reconstruction of the nasal epithelium. In this study, for the first time, we demonstrate the reconstruction of the nasal epithelium with the use of primary hNECs deposited on Transwell inserts via droplet-based bioprinting (DBB), which enabled high-throughput fabrication of the nasal epithelium in Transwell inserts of 24-well plates. DBB of nasal progenitor cells ranging from one-tenth to one-half of the cell seeding density employed during the conventional cell seeding approach enabled a high degree of differentiation with the presence of cilia and tight-junctions over a 4-week air-liquid interface culture. Single cell RNA sequencing of these cultures identified five major epithelial cells populations, including basal, suprabasal, goblet, club, and ciliated cells. These cultures recapitulated the pseudostratified columnar epithelial architecture present in the native nasal epithelium and were permissive to respiratory virus infection. These results denote the potential of 3D bioprinting for high-throughput fabrication of nasal epithelial tissue models not only for infection studies but also for other purposes such as disease modeling, immunological studies, and drug screening.

bioengineering↗

bioRxiv2021

Candida albicans enhances the progression of oral squamous cell cancrinoma in vitro and in vivo

Oral squamous cell carcinoma (OSCC) is a serious health issue worldwide. OSCC is highly associated with oral candidiasis, although it is unclear whether the fungus promotes the genesis and progression of OSCC or cancer facilitates the growth of the fungus. Therefore, we investigated whether Candida could directly influence OSCC development and progression. Our in vitro results suggest that the presence of live C. albicans, but not C. parapsilosis, enhances the progression of OSCC by stimulating the production of matrix metalloproteinases, oncometabolites, pro-tumor signaling routes, and overexpression of prognostic marker genes associated with metastatic events. We also found that oral candidiasis triggered by C. albicans enhanced the progression of OSCC in vivo through the induction of inflammation and overexpression of metastatic genes and markers of epithelial-mesenchymal transition. Taken together, these results suggest that C. albicans actively participates in the complex process of OSCC progression.

microbiology↗

bioRxiv2021

Oral epithelial cells distinguish between Candida species with high or low pathogenic potential through miRNA regulation

Oral epithelial cells monitor microbiome composition and initiate immune response upon dysbiosis, as in case of Candida imbalances. Comparison of healthy oral epithelial cell responses revealed that the inability of C. parapsilosis to induce a robust antifungal response was due to activation of various inflammation-independent pathways, while C. albicans robustly activated inflammation cascades. Regarding posttranscriptional regulation, several miRNAs were altered by both species. For C. parapsilosis, the applied dose directly correlated with changes in transcriptomic responses. Carbohydrate metabolism, hypoxia- and cardiovascular development-related responses dominate after C. parapsilosis stimulus, whereas C. albicans altered inflammatory responses. Subsequent analyses of HIF1- and HSC-activation pathways predicted target genes through which miRNA-dependent regulation of yeast-specific functions may occur, supporting the observed responses. Thus, C. parapsilosis is recognized as a commensal at low doses by the oral epithelium; however, increased fungal burden activates different pathways, some of which overlap with inflammatory processes induced by C. albicans. Impact statementAltered miRNA regulation discriminates between C. albicans and C. parapsilosis in human oral epithelial cells

microbiology↗

bioRxiv2020

Snca-GFP knock-in mice reflect patterns of endogenous expression and pathological seeding

Alpha-synuclein (aSyn) participates in synaptic vesicle trafficking and synaptic transmission, but its misfolding is also strongly implicated in Parkinsons disease (PD) and other neurodegenerative disorders known as synucleinopathies where misfolded aSyn accumulates in different regions of the central and peripheral nervous systems. Although increased aSyn expression levels or altered aggregation propensities likely underlie familial PD with SNCA amplification or mutations, the majority of synucleinopathies arise sporadically, indicating that disease can develop under normal levels of wildtype aSyn. We report here the development and characterization of a mouse line expressing an aSyn-GFP fusion protein under the control of native Snca regulatory elements. Regional and subcellular localization of the aSyn-GFP fusion protein in brains and peripheral tissues of knock-in (KI) mice are indistinguishable from that of wildtype littermates. Importantly, similar to wildtype aSyn, aSyn-GFP disperses from synaptic vesicles upon membrane depolarization, indicating that the tag does not alter normal aSyn dynamics at synapses. In addition, intracerebral injection of aSyn pre-formed fibrils into KI mice induced the formation of aSyn-GFP inclusions with a distribution pattern similar to that observed in wildtype mice, albeit with attenuated kinetics due to the GFP tag. We anticipate that this new mouse model will facilitate in vitro and in vivo studies requiring in situ detection of endogenous aSyn, therefore providing new insights into aSyn function in health and disease. Significance StatementAlpha-synuclein (aSyn) participates in synaptic vesicle function and represents a major component of the Lewy pathology found in Parkinsons and related neurodegenerative diseases. The function of aSyn and the sequence of events leading to its aggregation and neurotoxicity are not fully understood. Here we present a new mouse model in which Enhanced Green Fluorescence Protein (GFP) has been knocked-in at the C-terminal of the Snca gene. The resulting fusion protein shows identical expression and localization to that of wildtype animals, is functional, and is incorporated into pathological aggregates in vitro and in vivo. This new tool allows for monitoring aSyn under a variety of physiological and pathological conditions, and may uncover additional insights into its function and dysfunction.

neuroscience↗

bioRxiv2020

A Shift from Value- to Saliency- Neural Encoding of Subjective Value in Combat Veterans with PTSD during Decision Making under Uncertainty

Military personnel engaged in combat are vulnerable to Posttraumatic Stress Disorder (PTSD), following traumatic experiences in the battlefield. Prior research has mostly employed fear-related paradigms to unravel neural underpinnings of fear dysregulation in individuals with PTSD. The ability to acquire and update fear responses depends critically on the individuals ability to cope with uncertainty, yet the role of individual uncertainty attitudes in the development of trauma-related psychopathology has hardly been examined. Here, we investigated the association between PTSD-related alterations and the subjective valuation of uncertain outcomes during decision-making. We used a monetary gambling paradigm inspired by behavioral economics in conjunction with fMRI and explored neural markers of both vulnerability and resilience to PTSD in a group of combat veterans. Behaviorally, PTSD symptom severity was associated with increased aversion to uncertainty. Neurally, activity in the ventromedial prefrontal cortex (vmPFC) during valuation of uncertain options was associated with PTSD symptoms, an effect which was specifically driven by numbing symptoms. Moreover, the neural encoding of the subjective value of those uncertain options was markedly different in the brains of veterans diagnosed with PTSD, compared to veterans who experienced trauma but did not develop PTSD. Most notably, veterans with PTSD exhibited enhanced representations of the saliency of rewards and punishments in the neural valuation system, especially in ventral striatum, compared with trauma-exposed controls. Our results point to a link between the function of the valuation system under uncertainty and the development and maintenance of PTSD symptoms, and stress the significance of studying reward processes in PTSD.

neuroscience↗

bioRxiv2020

Potent inhibitors of toxic alpha-synuclein oligomers identified via cellular time-resolved FRET biosensor.

Preventing or reversing the pathological misfolding and self-association of alpha-synuclein (aSyn) can rescue a broad spectrum of pathological cellular insults that manifest in Parkinsons Disease (PD), Dementia with Lewy bodies (DLB), and other alpha-synucleinopathies. We have developed a high-throughput, FRET-based drug discovery platform that combines high-resolution protein structural detection in living cells with an array of functional and biophysical assays to identify novel lead compounds that protect SH-SY5Y cells from aSyn induced cytotoxicity as well as inhibiting seeded aSyn aggregation, even at nanomolar concentrations. Our combination of cellular and cell-free assays allow us to distinguish between direct aSyn binding or indirect mechanisms of action (MOA). We focus on targeting oligomers with the requisite sensitivity to detect subtle protein structural changes that may lead to effective therapeutic discoveries for PD, DLB, and other alpha-synucleinopathies. Pilot high-throughput screens (HTS) using our aSyn cellular FRET biosensors has led to the discovery of the first nanomolar-affinity small molecules that disrupt toxic aSyn oligomers in cells and inhibit cell death. Primary neuron assays of aSyn pathology (e.g. phosphorylation of mouse aSyn PFF) show rescue of pathology for two of our tested compounds. Subsequent seeded thioflavin-t (ThioT) aSyn aggregation assays demonstrate these compounds deter or block aSyn fibril assembly. Other hit compounds identified in our HTS are known to modulate oxidative stress, autophagy, and ER stress, providing validation that our biosensor is sensitive to indirect MOA as well.

neuroscience↗