Biology subjects

Menon, R.

Publications and source records attributed to Menon, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Molecular MRI of Neuroinflammation in Alzheimer's Disease using a Folate-targeted Nanoprobe

Background: Neuroinflammation, driven by activated microglia, plays a central role in the pathogenesis of Alzheimer's disease (AD). Non-invasive imaging of neuroinflammation holds promise for advancing our understanding of disease mechanisms and evaluating anti-inflammatory therapeutic strategies. The folate receptor (FR), specifically its {beta} isoform, has been identified as a marker of pro-inflammatory myeloid cells in peripheral inflammatory diseases; however, its association with AD neuroinflammation remains unknown. In this work, we first determined FR expression in microglia in mouse models of AD and subsequently evaluated molecular MRI (mMRI) using a folate-targeted nanoprobe for in vivo imaging of the folate receptor expression. Methods and results: Microglial activation and FR expression in APP/PS1 and P301S transgenic mouse models of AD was measured using flow cytometry. A FR-targeted nanoprobe for mMRI was prepared by functionalizing high T1-relaxivity liposomal gadolinium nanoparticle with folic acid. Following intravenous injection, localization of the nanoprobe in the brains of aged transgenic and wild-type mice was measured using T1-weighted MRI. Post-mortem microscopy measured nanoprobe localization relative to microglia and amyloid pathology. In both mouse models, FR{beta} was significantly (p < 0.05) upregulated in pro-inflammatory microglia expressing TNF and IL-1{beta}. The folate-targeted nanoprobe demonstrated MR signal enhancement in the cortical and hippocampal regions of transgenic mice but not in wild type mice; non-targeted nanoprobe control did not demonstrate signal enhancement in brain of transgenic mice. Microscopy confirmed colocalization of FR-targeted nanoprobe with IBA1-positive microglia/macrophages and amyloid plaques. Conclusions: Pro-inflammatory microglia exhibit elevated levels of FR, and its measurement by non-invasive mMRI is a promising marker of neuroinflammation in AD.

neuroscience↗

bioRxiv2026

Voluntary engagement predicts recovery across rehabilitation time points after experimental spinal cord injury

Rehabilitation is the cornerstone of clinical care following spinal cord injury (SCI) and is frequently incorporated into preclinical studies to evaluate emerging therapies. However, the variables that influence the effectiveness of rehabilitation interventions in rodent models remain poorly characterized, limiting the translational value of preclinical research. Here, we performed a meta-analysis of 150 preclinical studies comprising more than 3000 rodents and 292 effect sizes to identify such factors associated with successful rehabilitation after SCI. Rehabilitation improved functional outcomes across multiple behavioral domains, with larger effects observed in thoracic than cervical injury models. Meta-regression identified environmental enrichment as the most effective strategy, particularly when combined with task-specific training. Longer rehabilitation duration was associated with improved recovery, whereas greater daily exposure to forced rehabilitation was associated with smaller gains. In contrast, prolonged access to voluntary rehabilitation did not show this relationship. Rehabilitation improved outcomes when initiated at all time points after injury, with greater benefits when initiated during the late subacute and intermediate phases. Rehabilitation approaches associated with higher stress burden produced reduced benefits, suggesting that stress may limit rehabilitation-induced recovery. Collectively, these findings identify rehabilitation type, duration, and delivery context as important determinants of recovery after SCI and support a broad therapeutic window for intervention. Our results favor low-stress, voluntary rehabilitation strategies that promote sustained engagement and provide principles for designing effective and biologically appropriate rehabilitation strategies, potentially improving translational success for emerging SCI therapies. One Sentence SummarySustained voluntary rehabilitation promotes functional recovery across stages of experimental spinal cord injury, whereas prolonged forced training may reduce its benefits.

neuroscience↗

bioRxiv2026

Oxytocin receptor Gαi signaling drives valence reassignment to facilitate reversal of social trauma-induced avoidance

Traumatic social experiences often generate social deficits that form the core symptom of psychopathologies like social anxiety disorder (SAD). The failure to overwrite these aversive social associations is a fundamental barrier to recovery from SAD. Using the mouse social fear conditioning (SFC) paradigm, we identify a discrete population of oxytocin receptor (OXTR)-expressing neurons in the caudal lateral septum (LScOXTR) that act as a critical hub for adaptive learning during social fear extinction. Using calcium imaging in mice undergoing extinction training, we show that successful valence reassignment is best predicted by the precise temporal inhibition of LScOXTR neurons during the contact phase of social investigation. This contact-associated suppression of LScOXTR neurons was absent in mice that failed to extinguish fear. Notably, successful extinction was also associated with enhanced oxitocinerg innervation within the LSc. Chemogenetic silencing of LScOXTR neurons prior to extinction impaired extinction, indicating that a specific temporal activity pattern of LScOXTR neurons is necessary for adaptive learning. Pharmacological dissection of downstream OXTR signaling revealed that selective activation of Gi-coupled, but not Gq-coupled, signaling accelerated extinction and promoted social approach. Our findings establish that extinction success is governed by the temporally precise, Gi-mediated silencing of LScOXTR neurons during social contact, revealing a novel mechanism for adaptive social valence processing with direct implications for treatment-resistant SAD.

neuroscience↗

bioRxiv2026

An Integrated Atlas of the Human Kidney Spanning Health and Diseases

The human kidney contains highly specialized cell populations. Despite numerous single-cell and single-nucleus transcriptomics studies, differences in cohorts, technologies, analytical pipelines, and annotation frameworks have limited the ability to define consensus kidney cell states, identify disease-associated populations and interpret kidney disease genetic susceptibility. Here, we assembled 18 human kidney single-cell and single-nucleus RNA-sequencing datasets spanning 232 donors and five major disease contexts into a uniformly processed and computationally integrated Human Kidney Cell Atlas (HKCA), comprising over one million high-quality cells (816,895) and nuclei (215,308). The HKCA resolves 63 cell types and 120 harmonized cell states, including rare epithelial and stromal populations associated with kidney diseases . Integration with spatial transcriptomics, intercellular communication networks, and human genetic association data further defined the anatomical context and disease relevance of these populations. The HKCA also provides a framework for automated annotation of independent kidney human and mouse datasets. Together, the HKCA establishes a comprehensive reference for human kidney biology, enabling disease interpretation and genetic risk localization at cellular resolution.

genomics↗

bioRxiv2026

Comparative Modelling of Actin-Tropomyosin Interfaces

Tropomyosins are coiled-coil dimers that polymerize head-to-tail along actin filaments. They stabilize distinct filament populations and regulate the access of myosins and actin-binding proteins in both muscle and non-muscle contexts. Despite their central regulatory role, how filament length and isoform identity of different tropomyosin homologues might modulate actin affinity is not completely understood, especially across species. Here, we present a stepwise computational docking pipeline combining AlphaFold2-Multimer coiled-coil models, experimentally informed residue-level restraints, and pseudo-energy analysis via PPCheck to build and evaluate actin-tropomyosin co-polymer models for three isoforms: human TPM1 (hTPM1; 284 residues), human TPM4 (hTPM4; 248 residues), and Schizosaccharomyces pombe Cdc8 (SpCdc8; 161 residues). Interface energetics reveal a consistent hierarchy in which the shortest filament, SpCdc8, achieves the most stabilizing and residue-rich actin contacts, consistent with reduced cumulative geometric penalty along the actin helix. Among human isoforms, hTPM1 forms stronger interfaces with actin than hTPM4. The hTPM1-actin model also exhibits higher contact density and additional energetic hotspots, in agreement with the experimentally established slower exchange kinetics of TPM1 isoforms on actin filaments relative to TPM4. Hotspot mapping identifies conserved acidic residues at equivalent positions across all three isoforms, emphasizing the importance of electrostatic anchor points in maintaining interface integrity across diverse evolutionary contexts. Modeling of four temperature-sensitive SpCdc8 mutations (A18T, R21H, E31K and E129K) reveals that these substitutions substantially destabilize the coiled-coil dimer without significantly affecting actin interactions, suggesting that subtle regulatory failure arises from compromised longitudinal cable continuity rather than from direct loss of actin affinity. Taken together, our results support a hierarchical model of tropomyosin dimer stability, actin-tropomyosin recognition in which filament length imposes a geometric baseline on interface stability, onto which isoform-specific sequence evolution superimposes functional tuning. The tropomyosin homologues we studied appear to retain conserved electrostatic hotspots thereby providing a common structural scaffold across tissues and organisms.

bioinformatics↗

bioRxiv2026

Exofection as a Therapeutic Modality: Restoring P-gp Activity via Trophoblast-Derived EV in Neuroinflammatory Disorders

BackgroundP-glycoprotein (P-gp/ABCB1) is a key efflux transporter that maintains barrier integrity by clearing xenobiotics and toxic metabolites. At the feto-maternal interface, trophoblast-derived extracellular vesicles (CTC-EVs) naturally and transiently transfer functional P-gp to maternal decidual cells, restoring lost and or reduced P-gp function (exofection) to sustain pregnancy homeostasis. A similar loss of P-gp at the blood brain barrier (BBB) contributes to impaired amyloid-{beta} (A{beta}) clearance and neuroinflammation in Alzheimers disease. We investigated whether CTC-EV-mediated exofection could restore P-gp function in human brain endothelial cells (hBECs) and enhance A{beta} clearance under inflammatory and neurodegenerative conditions. MethodsCTC-EVs were isolated and characterized by nanoparticle tracking analysis and western blotting for P-gp and EV markers. Transcriptomic profiling of CTC-EVs identified enrichment of transporter-related genes, including solute carriers and ABC transporters, along with inflammatory mediators. Network analysis revealed coordinated modules linking EV cargo to transporter regulation, endocytosis/trafficking pathways, and inflammatory remodeling processes converging on BBB efflux activity. hBECs were exposed to LPS (500 ng/mL, 48 h) with or without CTC-EVs. P-gp expression was assessed by immunofluorescence (mean fluorescence intensity, MFI) and western blotting, while functional efflux was measured using Calcein-AM assays. A{beta} oligomer transport was evaluated using a transwell hBEC model. In vivo, 3xTg-AD mice received intravenous CTC-EVs (1x10L/day for 5 days), followed by assessment of P-gp expression, A{beta} burden, and neuroinflammatory markers. Pharmacokinetic studies in P-gp knockout mice were conducted to confirm functional transporter recovery. ResultsLPS exposure significantly reduced P-gp expression in hBECs (41.3% decrease in MFI, p=0.0084), which was restored by CTC-EVs (46.7% increase vs. LPS, p=0.0121). Exofection increased P-gp by a 2.1-fold following EV treatment as determined by western blot. Functional assays demonstrated enhanced efflux, with a 38.5% reduction in intracellular Calcein fluorescence (p<0.001). Network-informed mechanisms supported coordinated regulation of transporter and trafficking pathways. CTC-EVs improved A{beta} transport across inflamed hBEC monolayers. In vivo, EV-treated 3xTg-AD mice exhibited increased P-gp expression in the frontal cortex (38.6%) and hippocampus (42.1%), reduced A{beta} plaque burden (27.9%), and decreased inflammatory markers (IL-1{beta} and TNF-, p<0.05). In P-gp knockout mice, EVs reduced brain drug accumulation by 22.4% (p=0.032), confirming restoration of transporter function. ConclusionCTC derived EVs are natural carriers of functional transporter proteins and restore efflux capacity in compromised endothelial barriers. Integration of transcriptomic and network analyses highlights coordinated regulation of transporter, trafficking, and inflammatory pathways underlying exofection. This reproductive biology inspired strategy offers a promising therapeutic approach for enhancing A{beta} clearance and mitigating neuroinflammation in Alzheimers disease.

pharmacology and toxicology↗

bioRxiv2026

From Stress to Survival: Trophoblast-Derived Extracellular Vesicle Proteome Captures Aspirin-Driven Cellular Reprogramming in a Preeclampsia Model.

BackgroundLow-dose aspirin (LDA) reduces preeclampsia (PE) risk by up to 40%, yet its molecular effects on chorion trophoblast cells (CTCs) a fetal membrane lineage at the feto-maternal interface remain obscure. CTCs form a structural and immunoregulatory barrier whose dysfunction drives inflammation-associated membrane pathology in PE. Extracellular vesicles (EVs) released by CTCs may encode cellular stress and adaptation states, offering a molecular window into aspirins timing-dependent effects on PE risk modification. MethodsHuman CTCs were challenged with cigarette smoke extract (CSE) to model oxidative stress-driven PE pathology. Two paradigms were tested: (1) prophylactic aspirin (4 and 40 {micro}g/ml) before and/or flanking CSE, and (2) therapeutic aspirin after CSE challenge. EVs were isolated via ultracentrifugation and size exclusion chromatography, characterized by nanoparticle tracking and immunoblotting, and profiled by quantitative mass spectrometry. Network pathway analysis and machine-learning biomarker selection defined EV-encoded molecular states. ResultsCTC-derived EVs from CSE-exposed cells carried a PE-like proteomic signature marked by suppressed VEGF/ECM remodeling, activated TNF-p53 apoptotic signaling, and heightened inflammation. Prophylactic low-dose aspirin shifted EV cargo toward preserved angiogenic capacity (VEGFA, COL1A1, MMP14) with attenuated apoptotic and NF-{kappa}B signatures. High-dose aspirin produced broad transcriptional suppression without vascular benefit in EVs. Therapeutic aspirin partially rescued injury-associated EV cargo but failed to restore angiogenic signatures. Machine-learning analysis of EV proteomes identified a prophylactic biomarker panel anchored by HSPA8, SERPINF2, COL4A1, and PLOD1, linked to angiogenic recovery and redox balance. ConclusionsCTC-derived EV proteomic signatures capture dose-and timing-dependent aspirin effects, positioning the chorion as a pharmacological "secondary responder" favoring cellular resilience over classical anti-inflammatory suppression. EV-based molecular profiling might offer a framework for stratifying aspirin responders from non-responders toward personalized PE prevention.

cell biology↗

bioRxiv2026

SpliceRead: Improving Canonical and Non-Canonical Splice Site Prediction with Residual Blocks and Synthetic Data Augmentation

Accurate splice site prediction is fundamental to understanding gene expression and its associated disorders. However, most existing models are biased toward frequent canonical sites, limiting their ability to detect rare but biologically important non-canonical variants. These models often rely heavily on large, imbalanced datasets that fail to capture the sequence diversity of non-canonical sites, leading to high false-negative rates. Here, we present SpliceRead, a novel deep learning model designed to improve the classification of both canonical and non-canonical splice sites using a combination of residual convolutional blocks and synthetic data augmentation. SpliceRead employs a data augmentation method to generate diverse non-canonical sequences and uses residual connections to enhance gradient flow and capture subtle genomic features. Trained and tested on a multi-species dataset of 400- and 600-nucleotide sequences, SpliceRead consistently outperforms state-of-the-art models across all key metrics, including F1-score, accuracy, precision, and recall. Notably, it achieves a substantially lower non-canonical misclassification rate than baseline methods. Extensive evaluations, including cross-validation, cross-species testing, and input-length generalization, confirm its robustness and adaptability. SpliceRead offers a powerful, generalizable framework for splice site prediction, particularly in challenging, low-frequency sequence scenarios, and paves the way for more accurate gene annotation in both model and non-model organisms.The open sourced code of SpliceRead and a detailed documentation is available at The open-sourced code of SpliceRead and detailed documentation are available at https://github.com/OluwadareLab/SpliceRead.

bioinformatics↗

bioRxiv2026

Sex-dependent involvement of lateral septum astrocytes in social fear: Role of oxytocin receptor signaling

Astrocytes are now widely recognized as important modulators of synaptic plasticity and socio-emotional behaviors. Recent studies highlight their involvement in anxiety- and depressive-like behaviors, particularly via oxytocin (OXT) signaling. While the specific contributions of astrocytes remain largely unexplored, the role of OXT receptor (OXTR) signaling in the lateral septum (LS) in regulating social fear expression has been well characterized. Here, we studied the differential contribution of astrocytic OXTR signaling using a social fear conditioning (SFC+) paradigm. We found the highest abundance of astrocytes, and especially of OXTR-expressing (OXTR+) astrocytes, within the caudal LC (LSc) compared to the rostral LS in both male and female mice. Interestingly, female mice displayed a significantly higher number of astrocytes and OXTR+ astrocytes in the LSc in comparison to males. However, social fear acquisition resulted in dynamic changes in LSc astrocytic morphology and calcium activity in male mice. Furthermore, we showed that pre-SFC acquisition pharmacology-induced loss of local astrocytic function facilitated the extinction of social fear in males. In support, astrocyte-specific OXTR knockdown in the LSc also facilitated social fear extinction in both males and females. Taken together, our study identifies OXTR-signaling in LSc astrocytes as a crucial component in the mechanisms underlying the regulation of social fear in a sex-dependent manner.

neuroscience↗

bioRxiv2026

Prenatal Exposure to Bacterial Extracellular Vesicles Influences Fetal Gut Immunity and Immune Programming

BackgroundThe fetal immune system undergoes pivotal development during gestation, preparing for postnatal antigenic challenges. Bacterial extracellular vesicles (bEVs), bioactive particles shed by bacteria, are emerging as modulators of host immunity. However, their role in shaping fetal intestinal immune development remains largely unexplored. ObjectivesThis study aimed to investigate the effects of bEV exposure on lymphoid and myeloid populations in the fetal murine gut, focusing on their role in priming intestinal immunity, promoting differentiation, and modulating immune cell phenotypes in both normal and germ-free (GF) environments. Materials and MethodsWe used a murine model to evaluate the immune-modulating effects of bEVs during fetal development. bEVs were isolated from bacterial cultures and introduced into the amniotic sac of embryonic day 15.5 (E15.5) fetuses through intra-amniotic injection. Fetal and neonatal mice were either raised under conventional conditions (normal environment, NE) or in germ-free (GF) environments to assess microbiota-dependent effects. Immune profiling of fetal (E17) and postnatal (4 weeks) gut tissues was performed using high-dimensional mass cytometry (CyTOF) in both conventionally housed and germ-free (GF) mice. Clustering and differential expression analyses identified lymphoid and myeloid subpopulations, including progenitors, antigen-presenting cells, and intestinal stem cells (ISCs). secondary immune challenge (LPS or TSST-1) was conducted in postnatal bEV-primed mice to assess immune memory responses. ResultsbEV exposure significantly increased the prevalence of CD45- CD24+ CD44+ ISCs, promoting intestinal renewal and defense via differentiation into Paneth and tuft cells. These ISCs exhibited potential antigen-presenting capabilities through MHC expression. CD45+ lymphoid progenitors were upregulated, highlighting their role in early differentiation pathways. Myeloid progenitors, particularly monocyte-dendritic progenitor subsets, showed a bias toward antigen-presenting phenotypes.Germ-free models revealed heightened sensitivity to bEVs, with pronounced activation of progenitors and a reduction in exhaustion markers. Interestingly, macrophage and neutrophil populations displayed dose-dependent modulation, with low bEV concentrations promoting their expansion and higher doses leading to reduced incidence. Our findings suggest that bEVs act as immune priming agents in the fetal gut, promoting progenitor expansion and differentiation while preparing the intestine for postnatal challenges. Differences in responses between NE and GF models emphasize the importance of environmental influences, including microbiota, on bEV-mediated immune modulation. ConclusionbEVs play a pivotal role in shaping fetal intestinal immunity by priming lymphoid and myeloid progenitors and enhancing ISC function. These results open potential avenues for leveraging bEVs in immunomodulation and vaccine strategies. Future studies should explore the functional responses of bEV-primed cells and their translational relevance in humans.

developmental biology↗

bioRxiv2026

P-glycoprotein exofection between fetal and maternal cells as a mechanism of intercellular material transfer at the feto maternal interface

Cells can recover lost protein functions through a process we term exofection, in which extracellular vesicles deliver functional molecular cargo to recipient cells and transiently reprogram their activity. Here we show that exosomes derived from fetal chorion trophoblast cells (CTCs) restore P-glycoprotein (P-gp) efflux transporter function in inflammation-impaired maternal decidual cells (DECs) at the feto-maternal interface. CTCs maintain high P-gp expression under inflammatory stress, whereas DECs exhibit marked downregulation of transporter genes and proteins. Proteomic analysis revealed that CTC-derived exosomes package P-gp as a stable cargo that enters DECs through clathrin- and heparan sulfate-dependent uptake pathways. Delivery of CTC exosomes reinstated P-gp abundance and efflux capacity in LPS-stimulated or P-gp-deficient DECs, as shown by calcein efflux and immunofluorescence assays. In pregnant P-gp knockout mice, exosome treatment restored systemic clearance of the P-gp substrate tacrolimus and improved pharmacokinetic parameters. These findings establish exofection as a naturally occurring mechanism of transporter rescue at the feto-maternal interface, where fetal exosomes compensate for inflammation-induced maternal loss of efflux capacity. By restoring P-gp-mediated barrier function, exofection provides a protective strategy that limits the accumulation of xenobiotics and cytokines in maternal tissues and safeguards the fetus. This work reveals a previously unrecognized form of intercellular communication with broad implications for fetal protection, placental biology, cellular engineering, and the delivery of therapeutic proteins. One Sentence SummaryExofection is identified as a novel mechanism of transient cellular engineering via exosome-mediated functional protein delivery between cells.

developmental biology↗

bioRxiv2025

Dapagliflozin mitigates hypoxia-induced metabolic stress, kidney tubular cell death and fibrosis

Sodium-glucose co-transporter 2 inhibitors (SGLT2-i) slow progression of kidney disease but therapeutic mechanisms remain elusive. Here we report the beneficial effect of dapagliflozin on hypoxia-mediated kidney tubular epithelial cell injury, a contributing factor to kidney disease progression, using a human pluripotent stem cell (hPSC)-derived hypoxic kidney organoid model. Hypoxic organoids showed increased expression of Hypoxia Inducible Factor (HIF)-associated transcriptional targets, decreased tricarboxylic acid (TCA) cycle metabolites and mitochondrial {beta}-oxidation protein expression, and activated unfolded protein response. A transcriptional signature derived from hypoxic organoids 1) identified a subgroup of individuals whose kidney disease subsequently progressed, and 2) correlated with worse tubular injury. Dapagliflozin enhanced mitochondrial stress response resulting in reversed hypoxia-induced tubular epithelial cell apoptosis, reactive oxygen species (ROS) accumulation, and organoid fibrosis. These results indicate that dapagliflozin may contribute to improved kidney disease outcomes by attenuating hypoxia-induced metabolic stress-mediated tubular epithelial cell injury.

cell biology↗

bioRxiv2025

GRAYU: Graph-based Database integrating Ayurvedic formulations, medicinal plants, phytochemicals and diseases

The translation of Indias extensive traditional knowledge on indigenous medicinal plants into modern therapeutic solutions is contingent upon a systematic framework. While traditional Indian medicine offers a rich source of therapeutic leads, this knowledge is often not structured for modern computational analysis, creating a barrier to systematic drug discovery. To this end, we present GRAYU, a curated and comprehensive online database that integrates data across multiple categories, connecting 1039 traditional formulations to 12,949 indigenous plants, 129,542 phytochemicals, and 13,480 indicated diseases. It also provides insights into 1,382,362 plant-phytochemical, 116,824 plant-disease, 2,405 plant-formulation, and 4,087 formulation-disease associations. Case studies on phytochemical analogs, sustainable plant substitution, and disease-network pharmacology showcased the potential of integrative graphs to decode shared molecular signatures and therapeutic networks across traditional Ayurvedic formulations. GRAYU represents a user-friendly resource for researchers to investigate complex bio-associations and formulate novel therapeutic hypotheses, with insights from traditional Indian medicine. GRAYU is available at https://caps.ncbs.res.in/GRAYU/.

bioinformatics↗

bioRxiv2025

Cellular and Spatial Drivers of Unresolved Injury and Functional Decline in the Human Kidney

Building upon a foundational Human Kidney resource, we present a comprehensive multi-modal atlas that defines spatially resolved versus unresolved repair states and mechanisms in human kidney disease. Homeostatic interactions between injured kidney epithelium and its surrounding milieu determine successful repair outcomes, while pathogenic signaling promotes unresolved inflammation and fibrosis leading to chronic disease. We integrated multiple single-cell and spatial modalities across [~]700 samples from >350 patients ([~]250 research biopsies), analyzing [~]1.7 million cells alongside complementary mouse multi-omic profiles spanning acute-to-chronic injury and aging (>300,000 cells) and spatial transcriptomic analysis of >150 human biopsies. This cross-species atlas delineates functional pathways and druggable targets across the nephron and defines gene regulatory networks and chromatin landscapes governing tubular, fibroblast, and immune cell transitions from injury to either recovery or failed repair states. We identified distinct cellular states associated with specific pathological features that show dynamic distributions between acute kidney injury (AKI) and chronic kidney disease (CKD), organized within unique spatial niches that reveal progression mechanisms from early injury to unresolved disease. Gene regulatory analyses prioritized key transcription factor activities (SOX4, SOX9, NFKB1, REL, KLFs) and their target networks establishing disease states and tissue microenvironments. These regulatory programs were directly linked to clinical outcomes, identifying molecular signatures of recovery and secreted biomarkers predictive of AKI-to-CKD progression, providing a key resource for therapeutic development and precision medicine approaches in kidney disease.

molecular biology↗

bioRxiv2025

Methylphenidate-induced reductions in choice impulsivity are associated with alterations in cortico-striatal beta oscillations.

Impulsive choice- preferring small, immediate rewards over larger, delayed reward- is a hallmark of many psychiatric disorders. Methylphenidate, a dopamine and noradrenaline transporter inhibitor, reduces impulsivity, but the neural mechanisms underlying this effect remain unclear. Identifying a neurophysiological signature of methylphenidates action could be used clinically to predict treatment response and guide drug development. To this end, we recorded local field potentials (LFP) from 32 electrodes spanning cortico-striatal circuits in rats performing a temporal discounting task, under saline or methylphenidate treatment conditions. Methylphenidate decreased beta frequency (15-30 Hz) power and connectivity for small, immediate rewards while simultaneously increasing beta power for large, delayed rewards. Reduced connectivity in cortico-striatal networks during small rewards predicted increased preference for delayed rewards. These findings suggest that methylphenidate influences discounting behavior by modulating reward-evoked beta oscillations in cortico-striatal networks. Thus, beta oscillations may serve as a translational biomarker of treatment responsivity to monoaminergic drugs, providing a circuit-level assay to measure and predict changes in impulsive behavior.

neuroscience↗

bioRxiv2025

A Genome Sequence Variant Monitoring Program for Seasonal Influenza A H3N2 and Respiratory Syncytial Virus A using Wastewater-Based Surveillance in Ontario, Canada

Seasonal respiratory viruses, such as the Influenza A virus and the respiratory syncytial virus, are responsible for over a billion infections worldwide each year resulting in a substantial burden on health care systems. Surveillance of these viruses, including their prevalence in communities and their evolution, are essential for informing public health decisions and recommending vaccine formulations and schedules. Typically, these viruses are monitored using clinical samples from patients seeking medical attention. Recently, wastewater-based surveillance (WBS) has been leveraged to understand transmission dynamics and genome evolution of SARS-CoV-2 and seasonal respiratory viruses. To further the utility of WBS we developed and implemented novel tiled-amplicon sequencing assays to identify and track Influenza A virus H3N2 and respiratory syncytial virus A circulating in Southern Ontario, Canada. We also developed virus specific deconvolution tools to estimate the abundance of mixed lineages in wastewater. These assays were able to accurately determine which lineages were circulating in wastewater with high sensitivity and specificity. If implemented in regular surveillance programs, they could be used to inform real-time public health decisions and determine potential disease surge with impact on emergency room visits and hospitalization, as well as track which emerging strains will become predominant in the future and determine which strains should be the focus of seasonal vaccines.

genomics↗

bioRxiv2025

Mapping Functional Homologies Between Human and Marmoset Brain Networks Using Movie-Driven Ultra-High Field fMRI

Naturalistic stimuli, such as movies, offer a powerful tool for probing functional brain organization across species. Using movie-driven functional magnetic resonance imaging (md-fMRI), we recorded brain activity in humans and awake marmosets exposed to the same dynamic audiovisual stimulus. We applied tensor independent component analysis (tICA) to identify functional networks in each species, hierarchically clustered these components, and examined their within- and between-species temporal correlations to assess functional homologies. We found strong interspecies correspondence in core sensory networks, particularly those involved in visual and auditory processing, suggesting conserved mechanisms for sensory integration. In contrast, networks associated with higher-order cognition, including prefrontal and temporoparietal areas, were observed primarily in humans, highlighting species-specific specializations. These findings demonstrate the value of naturalistic paradigms and data-driven approaches in revealing both shared and divergent brain network architectures. By openly sharing our data and analysis pipelines, we aim to support future comparative studies and advance the marmoset as a model for investigating the evolutionary foundations of brain function.

neuroscience↗

bioRxiv2025

Systematic evaluation of single-cell multimodal data integration for comprehensive human reference atlas.

The integration of multimodal single-cell data enables comprehensive organ reference atlases, yet its impact remains largely unexplored, particularly in complex tissues. We generated a benchmarking dataset for the renal cortex by integrating 3 and 5 scRNA-seq with joint snRNA-seq and snATAC-seq, profiling 119,744 high-quality nuclei/cells from 19 donors. To align cell identities and enable consistent comparisons, we developed the interpretable machine learning tool scOMM (single-cell Omics Multimodal Mapping) and systematically assessed integration strategies. "Horizontal" integration of scRNA and snRNA-seq improved cell-type identification, while "vertical" integration of snRNA-seq and snATAC-seq had an additive effect, enhancing resolution in homogeneous populations and difficult-to-identify states. Global integration was especially effective in identifying adaptive states and rare cell types, including WFDC2-expressing Thick Ascending Limb and Norn cells, previously undetected in kidney atlases. Our work establishes a robust framework for multimodal reference atlas generation, advancing single-cell analysis and extending its applicability to diverse tissues.

genomics↗