Biology subjects

Kumar, P.

Publications and source records attributed to Kumar, P..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

A single catalytic domain residue regulates the substrate specificity of a mucin-type O-glycosyltransferase in salivary gland function

Human GalNAc-T1 is a ubiquitously expressed mucin-type O-glycosyltransferase that modulates various biological pathways, including immunity, extracellular matrix formation, and salivary gland development and function. However, substrates of GalNAc-T1 are mostly unknown and the mechanistic details of regulation are not well characterized. Here, we investigate the role of the Drosophila melanogaster GalNAc-T1 ortholog PGANT5 in salivary glands and provide structural and biochemical details into its mechanism of O-glycosylation. We find that loss of pgant5 causes irregular secretory granule morphology, altered mucin packaging, and disruption of secretion. Alternative splicing of pgant5 yields two isoforms, pgant5A and pgant5B, with higher expression of pgant5A in salivary glands. Rescue with pgant5A, but not pgant5B, partially restores secretory granule morphology and salivary gland function. A single residue difference within the substrate binding pockets of PGANT5A and PGANT5B increases the in vitro activity and specificity of PGANT5A towards salivary gland mucins relative to PGANT5B, corroborating the in vivo expression and role of pgant5A in salivary glands. Our data additionally provide new insights into a catalytic domain motif that regulates GalNAc-T activity. Overall, our studies illustrate how alternative splicing of an O-glycosyltransferase that results in modest amino acid changes can influence substrate specificity to regulate tissue-specific biological functions.

biochemistry↗

bioRxiv2025

CGGBP1-regulated heterogeneous C-T transition rates relate with G-quadruplex potential of terrestrial vertebrate genomes

The formation of G-quadruplexes (G4) is fundamentally linked to GC content of the DNA. There is little evidence for evolutionary selection of G4 stabilizers; G4 formation depends strictly on inherent sequence properties. Vertebrate promoters are notable for their consistently high GC-content as well as pronounced G/C strand asymmetry. Genomic GC content has changed in the course of evolution of terrestrial vertebrates, especially the amniotes but its relationship with the potential to form G4 remains less well understood. By analyzing genomes of 101 amniotes we report that lineage-specific differences in association between GC-content and G4 formation potential (pG4) in amniotes are concentrated at 1kb promoter regions. To understand possible mechanisms underlying high GC-concentrations in pG4 of mammalian and avian promoters, we test the possibility of selective cytosine methylation restriction leading to G/C-retention by CGGBP1, a protein involved in mitigation of cytosine methylation as well as G4-formation. By analyzing promoterome-wide C-T transition rates at TFBSs in pG4s we show that mammalian and avian CGGBP1s preserve C through methylation restriction. Our approach involves a combined meta-analysis of (i) genomes and promoters of 101 amniote genomes classified into reptilian, avian and mammalian classes through PQS finder and FIMO for 1019 JASPAR vertebrate motifs, (ii) recently reported global cytosine methylation patterns affected by overexpression of amniotic or non-amniotic forms of CGGBPs, (iii) and PWM reconstruction of motifs differentially enriched in pG4s showing homeothermic specific GC-retention. Our findings suggest that cytosine methylation restriction by CGGBP1 shapes G4 forming profiles of vertebrate promoters by preserving C on the G4-complementary strand resulting in minute differences in TFBSs across amniotes. HighlightsO_LIEvolution of vertebrate genome G4-forming potential mirrors that of CGGBP1. C_LIO_LICGGBP1 prevents meC-to-T mutations at pG4 sites, preserving G4-forming potential specifically in amniote promoters. C_LIO_LIpG4-TFBS mutations reveal homeothermic GC-retention bias, mirroring CGGBP1-mediated pG4 protection patterns. C_LIO_LIThe G4-forming regions most responsive to CGGBP1 exemplify this methylation-linked defense against C-to-T substitutions, distinguishing homeotherms from poikilotherms. C_LI

genomics↗

bioRxiv2025

Adipocyte IL-22RA1 signaling promotes structural and functional remodeling of white adipose tissue following acute intestinal damage.

Interleukin (IL)-22 has been shown to play an important role in intestinal host defense and ameliorating high-fat diet (HFD)-induced metabolic disorders primarily through signaling in intestinal epithelial cells. Adipocytes have emerged as key immune-metabolic regulators that influence intestinal inflammation in inflammatory bowel disease (IBD). However, the role of IL-22RA1 signaling in adipocytes has not been explored. In the present study, we examined the role of IL-22RA1 signaling in adipocytes in response to dextran sulfate sodium (DSS)-mediated gut inflammation. To do this, we subjected adipocyte specific Il22ra1 knockout mice (Il22ra1Adipo) to intestinal inflammation under normal chow and HFD conditions. Compared to littermate controls, Il22ra1Adipo mice displayed significant weight loss on day 9 of DSS treatment and showed altered expression of immune response- and lipid metabolism-related genes in white adipose tissue (WAT) under a normal chow diet. Notably, when mice were primed with HFD prior to DSS-induced intestinal injury, WAT from Il22ra1Adipo mice showed a significant reduction in Fabp4 expression and a marked increase in the proliferation marker Ki67. These findings indicate that loss of IL-22RA1 signaling in adipocytes disrupts adipocyte differentiation and lipid metabolism, leading to increased proliferation of preadipocytes or stromal cells without proper maturation. Importantly, this altered adipose tissue response occurred despite similar levels of colonic inflammation between knockout and control mice, suggesting a critical role for adipocyte IL-22RA1 signaling in maintaining metabolic and inflammatory homeostasis in WAT during combined metabolic and intestinal inflammatory stress.

pathology↗

bioRxiv2025

Defining the Mycobacterium tuberculosis Pangenome and Suggestions for a New Composite Reference Sequence

Mycobacterium tuberculosis (Mtb) causes tuberculosis (TB), a global disease with diverse clinical and microbiological manifestations. Studies into the biological causes of this phenotypic diversity have been largely limited to a few reference strains. A pangenome approach is likely to provide new insights. Pangenomic tuberculosis studies have been limited the availability of only fragmented genome sequences and error-prone reference genomes. We used a de novo assembly pipeline that generates extremely complete and accurate whole genome sequences to generate 50 closed Mtb genomes across all seven major lineages. We identified 3,377 core gene clusters and 379 accessory clusters. Analysis showed multi-copy core clusters were largely due to gene fragmentation (76%), paralogs (12%), nearly identical gene duplications (4%), or combinations (8%). Sixteen hypervariable regions (HVRs) were identified, including novel paralogs and variable PE/PPE genes. We consolidated these findings into a Pangenome Gene Reference Resource (PGRR) for precision alignment. Our study demonstrates the closed nature of the Mtb pangenome, with most variation in accessory genes and HVRs. The PGRR provides a foundation for improved drug/vaccine target discovery and highlights the need to move beyond the commonly used H37Rv strain to study Mtb genetic and phenotypic diversity. IMPORTANCETuberculosis (TB), caused by Mycobacterium tuberculosis, affects millions globally. Genetic differences among Mtb strains have been difficult to resolve due to incomplete genome references. We sequenced and analyzed complete genomes of 50 Mtb strains from all lineages, identifying 16 hypervariable regions and 3,498 core gene clusters whose diversity mostly stemmed from gene fragmentation, paralog duplication and deletion events and differences in the PE/PPE gene family representation. These differences may explain many of the varied clinical manifestations of TB. We created Pangenome Gene Reference Resource to unify genetic data for precise comparison studies to aid in developing new drugs vaccines and other interventions against this disease.

microbiology↗

bioRxiv2025

CNNM1 is Involved in Spermatogonial Stem Cell Maintenance in the Mouse

Male reproductive development starts early during embryogenesis with the formation of spermatogonial stem cells (SSCs) from their neonatal precursors, the gonocytes. Previously, we reported high levels of CNNM1 expression in the testicular germ cells of neonatal mice, which were maintained in the SSCs of pubertal and adult mice. CNNM1 exhibited a progressive decline in expression levels as the SSCs progressed through the spermatogenic differentiation sequence. However, the specific functional role of CNNM1 during spermatogenesis remains elusive. Here, we studied the expression pattern of Cnnm1 during gonocyte to spermatogonia transition (GST), and expression levels were found to be higher at the initial establishment phase of SSCs marked with a higher rate of cell proliferation. GDNF-mediated self-renewal/proliferation of the C18-4 spermatogonial cell line enhanced the expression of CNNM1. Overexpression of CNNM1 in C18-4 spermatogonial cell lines resulted in the upregulation of genes involved in cell proliferation, nucleic acid metabolism, male germ cell development and various pathways involved in cell cycle regulation, whereas CNNM1 knockdown altered the cell cycle progression. Based on the expression analysis and proteome profiling, we conclude that CNNM1 regulates and maintains the self-renewal, proliferation, and survival of mouse spermatogonial cells. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=196 HEIGHT=200 SRC="FIGDIR/small/683346v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@7aa116org.highwire.dtl.DTLVardef@e5c74borg.highwire.dtl.DTLVardef@17f23f4org.highwire.dtl.DTLVardef@11795a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Right-Lateralized Maladaptive Topological Reorganization in Hyperthyroidism

Hyperthyroidism (HT) has been associated with cognitive impairments, but the structural connectomic and molecular mechanisms underlying these deficits remain poorly understood. In this study, we investigated large-scale brain network reorganization using structural connectivity derived from diffusion MRI in patients with 30 hyperthyroidism and 28 matched control participants. Subject level connectomes were analyzed to characterize network topology, with a specific focus on hub architecture, nodal alterations, and hemispheric reorganization. To probe molecular underpinnings, we integrated normative neurotransmitter receptor and transporter density maps with network metrics, assessing their correspondence to observed connectomic disruptions. Individuals with hyperthyroidism exhibited increased structural connectivity, particularly in mid- and long-range connections, alongside disrupted network topology. These changes were characterized by reduced modularity, increased characteristic path length and hub reorganization, most prominently in subcortical and right-hemisphere regions. Importantly, network alterations were functionally relevant, as metrics showed significant associations with clinical and cognitive variables, including FT4 levels, BMI, and perceptuomotor performance in the hyperthyroid group. Spatial neuromolecular correspondence analyses further revealed that DAT, 5-HT2A, and NET were closely aligned with topological changes. Moreover, neurotransmitter-weighted within-module degree z-scores moderately predicted TSH levels in HT. Our findings demonstrate that hyperthyroidism is associated with an increase in redundant, spatially extended white matter connections and a marked right-lateralized asymmetry in network organization. Furthermore, serotonergic (5-HT1a) and dopaminergic (DAT) systems consistently contributed to the modulation of intra-modular hubness, suggesting their role in maladaptive structural reorganization that may underlie perceptuomotor dysfunction in hyperthyroidism.

neuroscience↗

bioRxiv2025

IRG1/itaconate/NRF2/GSH axis in tumor-associated macrophages drives therapy resistance and immune evasion in BRCA1-deficient breast cancer

Tumor-associated macrophages (TAMs) are major contributors to immunosuppression and therapeutic resistance, including resistance to PARP inhibitors (PARPi) in BRCA1-deficient breast cancer. However, the mechanisms underlying TAM-mediated PARPi resistance remain unclear. Here, we demonstrate that TAM-derived glutathione (GSH) impairs the efficacy of PARPi by protecting tumor cells from DNA damage and ferroptosis while suppressing STING-mediated immune activation. Mechanistically, STAT5-driven upregulation of the IRG1/itaconate axis in TAMs rewires mitochondrial metabolism and activates NRF2-dependent GSH biosynthesis. GSH is subsequently released into the tumor microenvironment, where it is taken up by tumor cells, protecting them from PARPi-induced cytotoxicity and dampening immune responses. Pharmacological inhibition of IRG1 reverses these effects, restoring PARPi sensitivity and enhancing anti-tumor immunity in BRCA1-deficient tumor models. Collectively, these findings uncover a TAM-specific immunometabolic program that limits PARPi efficacy and highlight the IRG1/NRF2/GSH axis as a promising therapeutic target to improve treatment outcomes in BRCA1-associated breast cancer.

cancer biology↗

bioRxiv2025

Neuroinflammatory Stress Preferentially Impacts Synaptic MAPK Signaling and Mitochondria in Excitatory Neurons

BackgroundUnderstanding synapse-specific effects of neuroinflammation can provide mechanistic and therapeutically relevant insights across the spectrum of neurological diseases. MethodsWe applied neuron-specific proteomic biotinylation in vivo, differential centrifugation of brain for crude synaptosome enrichment (P2 fraction) and mass spectrometry (MS) analysis of biotinylated proteins to derive native-state proteomes of Camk2a-positive neurons and their corresponding P2 synaptic compartments. Next, in an in vivo model of systemic lipopolysaccharide (LPS) dosing, we examined the effects of neuroinflammation on whole neuron and synaptic compartments using a combination of MS, network analysis, confirmatory biochemical and ultrastructural assays and integrative approaches across our mouse-derived and existing human datasets. ResultsUltrastructural and biochemical analyses of P2 fractions verified enrichment in synaptic elements, including synaptic vesicles and mitochondria. MS of biotinylated proteins from Camk2a-specific bulk brain homogenates (whole neuron) and P2 fractions (synaptosome) showed enrichment of >1000 proteins, consistent with neuron-specific biotinylation, also confirmed by immunofluorescence microscopy. Camk2a-specific synaptic proteome revealed molecular signatures related to mitochondrial function, synaptic transmission, protein translation. LPS-treated mice displayed body weight loss and neuroinflammation, characterized by glial activation, increased pro-inflammatory cytokine levels and upregulated expression of Alzheimers disease (AD)-related microglial genes. LPS-induced neuroinflammation exerted distinct effects on the synaptic proteome, including increased mitochondrial and reduced cytoskeletal-synaptic proteins, while suppressed synaptic MAPK signaling. Importantly, these changes were not observed at the whole neuron level, indicating unique vulnerability of the synapse to neuroinflammation. In line with synapse proteomic and signaling changes, LPS altered the ultrastructure of asymmetric synapses, suggesting dysregulation of excitatory neurotransmission. Co-expression network analysis of Camk2a neuronal proteins further resolved mitochondria- and synapse-specific protein modules, some of which were neuroinflammation-dependent. Neuroinflammation increased levels of a mitochondria-enriched module, and decreased levels of a pre-synaptic vesicle module, without impacting a post-synaptic membrane module. LPS-dependent mitochondrial and LPS-independent post-synaptic modules in mouse neurons mapped to post-mortem human AD brain proteomic modules which were decreased in cases with AD dementia and positively correlated to cognitive function, including pro-resilience markers for AD. ConclusionOur findings using native-state proteomics of Camk2a neurons combined with synaptosome enrichment identify proteome-level mechanisms of early synaptic vulnerability to neuroinflammation relevant to AD.

neuroscience↗

bioRxiv2025

Oxidative stress-induced proteolytic activation of polyphenol oxidase triggers an oxidized flavonoids-mediated stress signaling in Camellia sinensis

Environmental perturbations often increase reactive oxygen species (ROS) production, inducing oxidative damage to various biomolecules. The cellular system utilizes ROS or ROS-generated metabolites to instigate signaling pathways, resulting in acclimation, growth inhibition, or programmed cell death (PCD) for sustaining stress. Various stress-generated or stress-activated signaling components and downstream pathways are identified in model plants; however, they are largely unexplored in non-model plants. Here, we report a stress-induced proteolytic activation of an evolutionarily conserved chloroplast-localized enzyme, polyphenol oxidase (PPO), that oxidizes catechins into theaflavins (TFs) and initiates a stress signaling under drought in Camellia sinensis (Tea). Germplasm-based analysis revealed a heightened proteolytic activation of PPO and consequent TFs accumulation in drought-susceptible genotypes. Transcriptome analysis revealed that PPO activation and TFs accumulation were linked to the activation of UPR(unfolded protein response)-like response, which was reinforced by virus-induced silencing and overexpression of PPO, and direct feeding of TFs in tea plants. Pharmacological treatments revealed that TFs interact with HSP90, activating a canonical IRE-bZIP60-dependent ER stress pathway resulting in PCD. Similar proteolytic activation of PPO and subsequent instigation of stress signaling in other plant species (tomato and wheat) demonstrated that PPO acts as an evolutionarily conserved stress sensor, instigating an inter-organelle communication in plants. Significance statementPPO, an evolutionarily conserved and chloroplast/plastid localized enzyme, senses stress and undergoes proteolytic activation to generate oxidized flavonoids/quinones that function as signaling molecules in Tea and likely in other plants. The oxidized flavonoids modulate protein folding machinery and augment folding stress, especially in the ER, inducing canonical IRE1-bZI60-dependent PCD. The finding shows that specific secondary metabolites likely have roles in instigating intra- and intercellular communication to sustain the adversities of stress in different plant species.

plant biology↗

bioRxiv2025

Nanophotonic neural probes for in vivo photostimulation, electrophysiology, and microfluidic delivery

Implantable silicon neural probes with integrated optical emitters and electrodes are emerging tools for simultaneous optogenetic stimulation and electrophysiological recording in deep brain regions. In parallel, neural probes with microfluidic channels have been developed for localized drug delivery and neurochemical sampling. However, thus far, such fluidic probes have lacked optical and electrical functionalities or been limited to a low number of optical emitters and/or electrodes, constraining their utility in multimodal investigations of neural circuits. Here, we introduce foundry-fabricated silicon nanophotonic neural probes with monolithically integrated microfluidics. Each probe has 16 silicon nitride grating coupler emitters, 18 titanium nitride microelectrodes, and one embedded microfluidic channel. We evaluate the photonic, electrophysiological, and microfluidic functionalities in vivo in optogenetic, blue-light-sensitive mice. With our multifunctional neural probes, we demonstrate local suppression of epileptic seizure activity (induced by microfluidic injection of 4-aminopyridine) using photostimulation. Through foundry-compatible microfluidics integration, this work advances the versatility of nanophotonic neural probes and presents new possibilities for multimodal neuroscience experiments leveraging this scalable neurotechnology.

neuroscience↗

bioRxiv2025

Molecular docking of Pyocyanin from Pseudomonas aeruginosa with NADPH oxidase and Toll-like receptor 4 : Exploring the Link Between Oral Microbiome and Oral Cancer Pathogenesis

Oral cancer is among the leading cancers in India, with its progression influenced not only by genetic and environmental factors but also by dysbiosis in the oral microbiome. Pseudomonas aeruginosa, an opportunistic Gram-negative bacterium, has been implicated in oral carcinogenesis through the action of its virulence factor, pyocyanin--a redox-active phenazine that induces reactive oxygen species (ROS), promoting oxidative stress, immune dysregulation, and inflammation. Despite evidence linking pyocyanin to ROS-related pathways, its molecular interaction with key host proteins like NADPH oxidase and Toll-like receptor 4 (TLR4) remains unexplored. The present study aims to investigate the molecular interactions of pyocyanin with NADPH oxidase and TLR4 through molecular docking, aiming to elucidate its role in oxidative and inflammatory mechanisms associated with oral cancer pathogenesis. The structures of pyocyanin and the NADPH oxidase (NOX2) and TLR4 target proteins were retrieved from PubChem and RCSB PDB, respectively. CASTp was used to identify potential binding pockets. Molecular docking was performed using the HADDOCK server. The docked complexes were analyzed based on HADDOCK scores, binding energies, RMSD, and buried surface area. Interaction profiles were visualized using BIOVIA Discovery Studio. Among the docking clusters, Cluster 6 for the NOX2-pyocyanin complex showed a favorable HADDOCK score (84.4 {+/-} 2.9), low RMSD (0.2 {+/-} 0.0), and substantial buried surface area (456.1 {+/-} 13.2 [A]2). For the TLR4-pyocyanin complex, Cluster 1 exhibited the most favorable interaction profile with a HADDOCK score of 25.0 {+/-} 5.5 and a Z-score of -2.3. Binding site prediction and hydropathy analysis supported the structural feasibility of pyocyanin interaction with both targets. This study provides structural insights into the potential interaction of pyocyanin with NADPH oxidase and TLR4, supporting its role in modulating oxidative stress and inflammatory signaling pathways. These findings enhance our understanding of oral microbiome-host interactions and their contribution to oral cancer pathogenesis.

bioinformatics↗

bioRxiv2025

The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data

The Data Distillery Knowledge Graph (DDKG) is a framework for semantic integration and querying of biomedical data across domains. Built for the NIH Common Fund Data Ecosystem, it supports translational research by linking clinical and experimental datasets in a unified graph model. Clinical standards such as ICD-10, SNOMED, and DrugBank are integrated through UMLS, while genomics and basic science data are structured using ontologies and standards such as HPO, GENCODE, Ensembl, STRING, and ClinVar. The DDKG uses a property graph architecture based on the UBKG infrastructure and supports ontology-based ingestion, identifier normalization, and graph-native querying. The system is modular and can be extended with new datasets or schema modules. We demonstrate its utility for informatics queries across eight use cases, including regulatory variant analysis, tissue-specific expression, biomarker discovery, and cross-species variant prioritization. The DDKG is accessible via a public interface, a programmatic API, and downloadable builds for local use.

bioinformatics↗

bioRxiv2025

Mechanism-Guided Engineering of Fluorinase Unlocks EfficientNucleophilic Biofluorination

The fluorinase enzyme, the only known biocatalyst forming stable carbon-fluorine bonds, operates with extremely low efficiency, catalyzing one reaction every 2-12 minutes. This severely limits its utility for sustainable biofluorination, and its sluggish activity remains poorly understood. We suppressed its aggregation through directed mutagenesis and elucidated the kinetic mechanism using a novel mathematical framework that fits complex kinetic and oligomerization data. This analysis revealed that >80% of enzyme molecules are inactive under standard conditions due to two dead-end pathways. The designed W50F+A279R mutant preferentially formed hexamers and displayed enhanced catalytic efficiency in this oligomeric state. When coupled with mechanism-based optimization of the reaction medium, including enzymatic removal of the inhibitory product, the catalytic turnover rate reached 12.5 {+/-} 2.1 min-{superscript 1}, representing [~]60-fold increase compared with previously reported turnover rates of the wild-type enzyme. Our work provides a mechanistic blueprint for fluorinase enhancement and a generalizable mathematical framework for analyzing kinetics of multimeric enzymes.

biochemistry↗

bioRxiv2025

Structural Validation of the Intermediate Leptomeningeal Layer in the Human Central Nervous System

Traditionally, the human central nervous system (CNS) is described as having three meningeal layers, from outer to inner: dura mater, arachnoid mater, and pia mater. The arachnoid and pia mater are called the leptomeninges, and the space between them is filled with cerebrospinal fluid (CSF). Using gross dissection, light microscopy, and ultrastructural analysis of fresh postmortem and cadaveric CNS specimens spanning fetal to adult ages (N=61), we demonstrate a fibrocellular intermediate leptomeningeal layer (ILL) from the cortex to the caudal end of the spinal cord. The ILL divides the subarachnoid space (SAS) into two distinct structural compartments, through which vessels and nerves pass. The ILL shows unique structural features, such as dips into the brains sulci and fissures, as a double-fold membrane that bears intra-layer trabeculae, carries vessels, and forms the perivascular sheath. Moreover, throughout the CNS, it appears to be a non-sieved barrier, characterized by the presence of tight and adherens junctions. ILL, predominantly in the spinal cord, contains macrophage-like cells, indicating its layer-specific immune properties. The ILL warrants recognition as a distinct human meningeal layer with potential barrier and immune functions. SignificanceO_ST_ABSAn Intermediate Leptomeningeal Layer encloses the Central Nervous System in HumansC_ST_ABSThe integrated analysis of our macroscopic, microscopic, and ultrastructural study provides robust support for an intermediate leptomeningeal layer (ILL) in the subarachnoid space (SAS) of the human central nervous system (CNS) along the entire neural axis. The ILL is a fibrocellular macroscopic structure, with restricted permeability, that divides the cerebrospinal fluid (CSF)-filled SAS into two distinct structural compartments. Uniquely, ILL revealed the presence of cells with macrophage-like properties, suggesting a possible role in immune surveillance. The ILL may redefine the established concept of protective coverings of CNS, CSF circulation dynamics, and the role of leptomeninges in health and disease, including drug delivery.

neuroscience↗

bioRxiv2025

Gut microbial metabolites butyrate and acetate limit Zika virus replication and associated ocular manifestations via the G-protein coupled receptor 43/FFAR2.

Short-chain fatty acids (SCFAs) are gut microbial metabolites produced by gut microbiota from dietary fiber. SCFAs have shown both pro- and anti-viral roles among different viruses, and are known to regulate immune functions during infections. However, their role against the Zika virus (ZIKV) in general and ocular infection, in particular, has never been investigated. In the present study, we aimed to examine the role of three SCFA derivatives: phenylbutyrate (PBA), sodium butyrate (NaB), and sodium acetate (NaAC), on ZIKV replication and associated ocular complications using primary human trabecular meshwork cells (HTMCs) and an IFNAR1-deficient mouse model of ocular infection. Our findings reveal that PBA and NaAc treatment dramatically suppressed the ZIKV replication in HTMCs. NaB showed a slightly less effect than PBA and NaAc. PBA and NaAc treatment significantly attenuated the ZIKV-induced inflammatory cytokine, interferons, and interferon-stimulated genes response via antagonizing the RIG-I/NF{kappa}B/MAPKs/STAT1-3 signaling pathways. We discovered that ZIKV induces the expression of free fatty acid receptor 2 (FFAR2)/ GPR43 in HTMCs, which is further potentiated by PBA/NaAc. Pharmacological inhibition of FFAR2 abrogated the protective abilities of PBA/NaAc and significantly increased viral replication. Blocking FFAR2 receptors promoted ZIKV-induced cell death, which was suppressed by PBA and NaAc. Mechanistically, butyrate and acetate inhibited ZIKV binding and cellular entry and inactivated the virus before internalization. PBA and NaAc treatment in mice attenuated the ZIKV-induced ocular manifestations (intraocular pressure, RPE/retinal atrophy, and anterior segment inflammation), which was abrogated by FFAR2 inhibition. Collectively, our findings indicate that SCFA treatment is an effective approach to limit ZIKV replication and associated ocular damage and may be worth exploring as a means to treat or prevent ZIKV-induced ocular complications in humans. ImportanceZIKV is known to cause severe ocular manifestations in in-utero exposed infants; however, the molecular mechanisms of ZIKV-induced ocular complications remain unknown. SCFAs have demonstrated both pro- and anti-viral roles against different viruses; however, their role against ZIKV is unknown. We showed that SCFAs butyrate and acetate suppress ZIKV transmission and associated ocular complications. The anti-ZIKV activity of these SFACs is mediated via FFAR2, and pharmacological inhibition of FFAR2 promotes ZIKV-induced inflammatory and cell death responses, as well as ocular malformations.

microbiology↗

bioRxiv2025

Cognition-centric brain activity across diverse imaging tasks constrains the representation of mental health in task-evoked brain function

Large-scale neuroimaging studies best powered to investigate mental health biomarkers continue to administer a set of in-scanner tasks that, to date, yield weak brain-mental health associations. Triangulating the source of these weak associations is critical to directing the focus of future work. Using these tasks strong brain-cognition associations as a positive control, we analyzed potential sources of weak brain-mental health associations across five popular fMRI tasks and dozens of task-evoked brain networks. Across tasks and networks, latent mental health factors showed substantially weaker brain associations than cognition despite comparable measurement reliability and greater interindividual variability. Moreover, increasing brain-feature dimensionality improved cognitive but not mental health signal, and task-evoked network profiles were 1.8-2.3 times more homogeneous and 3.5 times lower-dimensional than mental health profiles. Findings implicate a signal evocation bottleneck: common fMRI tasks elicit little interindividual variation in mental health-related brain activity relative to the diversity of mental health itself. Overall, these findings motivate a shift in focus to the development and use of tasks in large-scale studies more explicitly designed to evoke mental health-relevant brain activity. Significance StatementIdentification of robust individual-specific mental health-related brain signals from fMRI remains elusive, limiting the clinical utility of brain imaging. To investigate why, we systematically evaluated brain signals evoked by tasks used by the Human Connectome Project-Young Adult study, which are now commonly included in many large-scale neuroimaging studies. Our findings suggest that, more so than analytical or measurement constraints on detecting these signals, a primary limitation is a failure of these prevalent fMRI tasks to evoke mental health-relevant brain signals in the first place. These findings suggest that progress in psychiatric neuroimaging may require tasks more explicitly designed to evoke mental health-relevant brain activity.

neuroscience↗

bioRxiv2025

Identification of Potential Oral Cancer-Specific Biomarker in Oral Potentially Malignant Disorders for Early Detection of Malignancy: A Systematic Review

Oral malignancies are increasing and significantly contribute to cancer-related mortality. Oral Potentially Malignant Diseases (OPMDs) share several characteristics with Oral Cancer (OC) and have the potential to undergo malignant transformation. Beyond clinical and visual similarities, OC and OPMDs also exhibit common molecular alterations at the genomic and transcriptional levels. Identifying commonly mutated genes between OC and OPMDs may enhance early detection strategies. Therefore, we conducted a systematic review analyzing mutated genes from 25 studies (selected from 331 studies using the PRISMA flowchart) that investigated gene mutations in OC and OPMDs through whole-exome sequencing analysis. Across these studies, we identified a total of 7,564 mutated genes: 6,885 from OC studies and 579 from OPMD studies. Of these, 311 genes were found to be common between OCs and OPMDs. To further assess their relevance, these genes were categorized into High (N=5), Medium (N=20), and Low-frequency (N=386) groups, and their distribution was compared between OC and OPMD studies. Based on these comparisons, four genes: TP53, PIK3CA, FAT1, and TTN were identified as showing comparable mutation patterns between OC and OPMDs, suggesting their potential role as early biomarkers for malignant transformation. Furthermore, FAT1 and TTN may serve as promising candidates for assessing the likelihood of Oral Cancer development in OPMDs.

cancer biology↗

bioRxiv2025

AF2Rank Revisited: Reproducing AlphaFold-Based Structure Evaluation and a Hypothesis for Context-Aware Refinement (CAR-AF)

Protein structure prediction has undergone transformative advancements with AlphaFold2 achieving near-experimental accuracy across extensive protein datasets. This study reproduces and validates the AF2Rank pipeline, which utilizes AlphaFolds intrinsic confidence metrics--predicted Local Distance Difference Test (pLDDT) and predicted Template Modeling score (pTM)--to evaluate and rank decoy protein structures without dependence on multiple sequence alignments (MSAs). The pipeline was implemented locally using the Rosetta decoy dataset, overcoming reproducibility challenges such as software dependency conflicts, residue indexing inconsistencies, and system-level execution issues. This framework successfully enabled high-confidence evaluation of over 1000 decoys for a benchmark target (1a32), with ongoing expansion to 133 protein targets. Notably, we discovered that AlphaFold confidence metrics encode protein-specific "fingerprints," enabling reverse classification of structures to their source proteins. Our XGBoost-based classifier achieved 61.5% accuracy across 133 distinct protein targets, substantially exceeding random chance (0.75%). Feature importance analysis revealed that traditional energy functions (Rosetta normalized score, 26%) and derived interaction features (pLDDT-pTM ratio, 16%) provide the strongest discriminative power, suggesting AlphaFold metrics capture meaningful biological and structural information beyond generic quality assessment. Building upon this foundation, a novel hypothesis is introduced: Context-Aware Refinement of AlphaFold Predictions (CAR-AF). This approach postulates that AlphaFold-predicted structures may be further improved through refinement in the presence of their native binding partners--such as receptors or ligands--thereby producing conformations that are both structurally and functionally enhanced. The proposed methodology comprises four stages: generation of initial predictions via AlphaFold, structural modeling of relevant binding partners, docking of predicted proteins into these biological contexts, and refinement of the resulting complexes using molecular modeling tools such as Rosetta or HADDOCK. Structural and energetic metrics including TM-score, RMSD, and binding energy will be used to assess potential improvements in predictive quality.

bioinformatics↗