Biology subjects

Tiwari, R.

Publications and source records attributed to Tiwari, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Distilling Trial-Level EEG Variability into Participant Representations: Neurophysiologically Constrained Graph Learning in ADHD

Extracting stable individual-level representations from noisy and variable trial-wise EEG remains a major challenge in computational cognitive neuroscience. We developed a spatiotemporal graph attention network to analyze Go/NoGo EEG from children and adolescents with and without ADHD. The framework combines ERP-informed temporal windows, phase-synchrony graph priors, and trial-to-participant transfer learning, making both information routing and representation geometry explicitly testable. The model learned reproducible attention trajectories, yet ADHD and control participants did not differ reliably in spatial attention allocation. Instead, group-related structure emerged in compact participant-level embeddings that distilled trial-level variability and retained discriminative information beyond convolutional representations. Performance exceeded a convolutional neural network comparison, but the central advance is methodological: neurophysiologically constrained graph learning can reveal where diagnostically relevant information emerges within the analytical pipeline. This provides a framework for developing auditable cognitive-neurophysiological markers of neurodevelopmental variation.

neuroscience↗

bioRxiv2026

Fluorosphere-Assisted Nano-Biosensor for Detection of Circulating microRNAs in Non-Small Cell Lung Cancer

Non-small-cell lung cancer (NSCLC) diagnosis is challenged owing to the need for reliable, non-invasive biomarkers. Circulating cell-free microRNAs (ccf-miRNAs) are promising candidates, but their low levels and short sequences in blood complicate detection. In this study, a novel nano-hybrid fluorescent array was developed to enable rapid and sensitive identification of NSCLC-related ccf-miRNAs. The array consists of poly(T)-modified fluorescent nano-polystyrene beads for capturing target miRNAs, and fluorophore-labeled, sequence-specific locked nucleic acid (LNA) probes for their detection. This design forms a sandwich structure with the target miRNA. Nano cytometry and fluorescence microscopy assessed both the capture and specificity of detection. The assay was tested on plasma samples for miR-16-5p and U6, evaluating selectivity, sensitivity, and reproducibility. The results showed that the poly(T)-modified beads efficiently captured the target miRNAs, and the LNA probes accurately distinguished the sequences. The assay enabled direct detection of miR-16-5p and U6 from plasma without amplification, demonstrating high selectivity, sensitivity, and reproducibility. Combining enrichment with nano-polystyrene beads and sequence-specific LNA probes addressed the main challenges of ccf-miRNA detection, namely their low abundance and short sequence length. As ccf-miRNAs are linked to NSCLC progression, this method could assist in early diagnosis, disease monitoring, and assessment of treatment response. The target-independent nature of the poly(T) capture layer allows for easy calibration to new miRNAs by changing the LNA probes, rendering it suitable for multiplex detection in clinical settings. However, further preclinical and clinical studies are needed before adoption in routine practice. This nano-hybrid fluorescent array presents a rapid and reliable approach for detecting low-abundance ccf-miRNAs in plasma. Its encouraging performance and flexible design show potential for future application in NSCLC diagnosis and monitoring, subject to additional confirmation.

molecular biology↗

bioRxiv2026

Comparative Analysis of Ultrafine Particulate Matter, Black Carbon, and Polystyrene Nanoplastics Identifies Mitochondrial Stress Adaptation as a Conserved Mechanism of Immunotoxicity

Several studies have been conducted on human exposure to ultrafine particulate matter (UFPM), Black carbon (BC), and polystyrene nanoplastics (PS-NPs). However, it remains unclear whether different chemical types of environmental nanoparticles induce a similar mitochondrial stress response or a unique particle-specific response. In the present study, we examined the molecular mechanisms underlying nanoparticle-induced mitochondrial stress response and immunotoxicity using human peripheral blood mononuclear cells exposed to UFPM, BC, and PS-NPs under similar experimental conditions. Oxidative stress, mitochondrial adaptation, respiratory chain integrity, mitochondrial integrated stress response, inflammatory signaling, and systems-level interactions between molecules were analyzed through the evaluation of the expression of NRF2, HIF-1, PGC-1, TFAM, OMA1, DELE1, mitochondrial ND1, Complex I-V, NF-{kappa}B, TNF-, and NLRP3 and the use of principal component analysis, hierarchical clustering, and correlation networks. All three nanoparticles caused oxidative stress and mitochondrial dysfunction with different kinetics and mechanisms. UFPM mostly induced an acute antioxidant response and mitochondrial adaptation; BC led to chronic mitochondrial dysfunction, chronic activation of the OMA1-DELE1-mediated mitochondrial ISR pathway, and inflammation; while PS-NPs induced low but chronic mitochondrial adaptation along with mitochondrial biogenesis and stress responses. Our systems-level analysis showed that oxidative stress, mitochondrial adaptation, mitochondrial ISR, and inflammation represent a highly connected molecular network regardless of the physicochemical nature of the nanoparticles, with the OMA1- DELE1 axis being a key regulatory node connecting mitochondrial stress response and inflammation. Overall, we have found that mitochondrial stress response is a common mechanism underlying the toxicity of chemically different nanoparticles and have also revealed particle-specific stress-response dynamics responsible for the degree and persistence of cellular damage. The current work presents novel insights into the molecular mechanisms of nanoparticle-induced immunotoxicity and suggests OMA1, DELE1, NRF2, PGC-1, TFAM, ND1, and Complex I-V as potential biomarkers.

pharmacology and toxicology↗

bioRxiv2026

Decoupled phenology and PSII thermal plasticity in seasonally dry tropical forest trees

We tested whether seasonal plasticity in photosystem II (PSII) heat tolerance aligns with leaf phenology in tropical trees, comparing evergreen and deciduous species across the wettopostwet transition in a seasonally dry tropical forest of the central Western Ghats, India. This transition, preceding droughtinduced senescence, represents the key window to assess true unstressed thermal plasticity. PSII thermal traits: damage onset (T5), damage midpoint (T50), and temperature between damage onset to full loss (T95-T5), decline width (DW) were quantified in 27 cooccurring species during the wet (27.5{square}{degrees}C) and postwet (31.6{square}{degrees}C) periods. Contrary to phenologybased predictions, PSII plasticity was not structured by leaf habit or successional status. Both T5 (+1.7{square}{degrees}C) and T50 (+0.9{square}{degrees}C) increased significantly across seasons, but responses were speciesspecific, with evergreen and deciduous trees acclimating similarly. The preventionversusforbearance tradeoff (T5 - DW relationship) remained conserved, though leaf habits diverged under postwet conditions. Thermal safety margins based on T50 were large, but T5 revealed vulnerable latesuccessional evergreens (Saraca asoca, Ficus spp.) and Careya arborea. These results show that PSII thermotolerance regulation operates largely independently of droughtavoidance phenology, indicating species identity and not leaf habit drives plasticity in PSII thermal response in seasonally dry tropical forests.

physiology↗

bioRxiv2026

An integrated resource for systems-level analysis of aging hallmarks and associated genes

Aging is a complex biological process involving progressive cellular dysfunction, tissue decline, and increased susceptibility to multiple chronic diseases. A systemic view of aging through its established hallmarks provides a structured framework to understand this complexity and drive therapeutic discovery. To this end, we present AgingHallmarksDB, an interactive web platform that enables systems-level analysis of hallmark-associated gene sets. Aging-related genes were first curated from seven established resources, and those present in at least two of these resources were considered as consensus aging-related genes. Using functional annotations derived from GO, KEGG, and Reactome, a total of 3111 genes were mapped to the 11 aging hallmarks, of which 2593 were supported by additional experimental or manually curated evidence, with 1089 of these forming the consensus set. Further, AgingHallmarksDB supplements hallmarks and gene annotations with tissue or cell-type class specificity, exosomal profiles, and regulatory interactions, enabling users to perform hallmark enrichment, protein-protein and regulatory interaction-based analysis. To elucidate the interconnectedness of hallmarks, network separation and proximity analyses of hallmark-associated modules were performed, revealing functional overlap between hallmarks on the human interactome. Furthermore, the utility of AgingHallmarksDB was demonstrated through network topological and regulatory interaction analyses of common hallmark genes, hallmark enrichment and network proximity analyses of eight chronic age-related diseases and seven developmental and congenital diseases, and gene set enrichment analysis of a PM2.5-associated skin transcriptome. Together, these analyses highlight the utility of AgingHallmarksDB for aging hallmark-centred systems biology research. The resource is accessible at https://cb.imsc.res.in/aginghallmarksdb/.

bioinformatics↗

bioRxiv2026

Ketone ester supplementation in aged mice reduces activation of B cell subsets

BackgroundAging in the immune system results in increased susceptibility to infections, exacerbated autoimmunity, and reduced responsiveness to vaccines. However, there are no current established interventions for immune aging. Ketogenic diets and fasting have been researched as interventions against other aspects of aging and age-related diseases, and they work in part by increasing circulating levels of ketone bodies, which have anti-inflammatory properties and can boost T cell function. Exogenous ketones, such as ketone esters, are currently being studied as a more accessible approach to obtain the benefits of ketone bodies through direct supplementation. Here, we investigated whether ketone ester supplementation improves immune function during aging. Aged (19-month-old) C57BL/6JN mice were given a diet supplemented with the ketone ester or a control diet for 15 weeks. ResultsWe found that the ketone ester diet decreased activation of B cells, especially age-associated B cells, in the spleen. The diet also reduced the proportion of age-associated B cells defined by CD11b and CD11c expression, though not of the broader CD21-CD23- population. Despite this decrease in activation, there was no impairment in antibody production, as mice on the ketone ester diet mounted a normal response to nitrophenyl-ovalbumin immunization. The ketone ester diet also reduced glucose dependence and translation in subsets of age-associated B cells. Treating splenocytes from aged mice with {beta}-hydroxybutyrate was sufficient to suppress B cell translation and reduced mTORC1 signaling, indicating that ketone bodies act directly on B cells. {beta}-hydroxybutyrate also decreased expression of T-bet, the signature transcription factor driving the autoimmune functions of age-associated B cells. ConclusionsOur study elucidates the effect of ketone esters on B cells in the context of aging and unveils a new immunoregulatory role of ketone bodies on B cells.

immunology↗

bioRxiv2026

Oxytocin-dependent reorganization of social vs. food motivational hierarchy and corticostriatal neural activity by social isolation in rats

Animals must continuously prioritize among competing internal needs, yet the neural mechanisms that arbitrate between these drives remain poorly understood. Here, we used a behavioral paradigm in rats to quantify choice between social interaction and food seeking under varying need states. We show that social isolation selectively shifts preference toward social engagement, even under metabolic demand, indicating a reweighting of motivational priorities. Chronic local field potential recordings across prefrontal and striatal brain regions revealed that this shift is accompanied by a reconfiguration of corticostriatal theta-band coordination. Trial-by-trial analyses demonstrated that network dynamics predict behavioral choice, linking neural coordination to decision output. Pharmacological blockade of oxytocin receptors attenuated both the network reorganization and the behavioral prioritization shift, implicating oxytocin signaling in gating this process. Together, our findings identify a network-level mechanism through which internal states dynamically compete, providing a framework for understanding how the brain resolves conflicting motivational demands.

neuroscience↗

bioRxiv2025

Multi-omics Analysis of Human Blood Cells Reveals Unique Features of Age-associated Type2 CD8 Memory T cells

Aging impacts immune function, but the mechanisms driving age-related changes in immune cell subsets remain unclear. To explore age-dependent changes in immune cell populations, we analyzed human peripheral blood mononuclear cells (PBMCs) from a cohort of healthy donors aged 20-82 years using a 36-color spectral flow cytometry panel focused on T cells. We identified a unique population of memory CD8 T cells, which lack CXCR3 and produce a Th2-like cytokine response, accumulate with age. We discovered an age-dependent bias in naive CD8 T cells toward Th2 cytokine production, accompanied by transcriptional and epigenetic changes supporting this phenotype. Moreover, health outcome association analysis linked the accumulation of these unique CXCR3- central memory CD8 T cells to asthma, chronic liver conditions, and type 2 diabetes. Together, our results support the model that an age-dependent drift in epigenetic regulation towards a Th2-like phenotype drives a pathogenic Th2-like immune population.

immunology↗

bioRxiv2025

Airborne Nanoplastics Perturb Mitochondrial Complex I via the ND6 Axis: Polymer-Specific Mitoepigenetic Remodeling Integrating Experimental, In Silico, and Machine Learning Analyses

Airborne nanoplastics constitute an emerging class of environmental contaminants, but their mitoepigenetic effects on human immune cells have not been systematically investigated. Ex vivo human lymphocytes were used to investigate integrated mitochondrial, epigenetic, and inflammatory responses induced by polystyrene (PS), polypropylene (PP), and polyvinyl chloride (PVC) nanoplastics. Fluorescence microscopy at multiple exposure time points and flow cytometry confirmed efficient cellular internalization and progressive intracellular accumulation of nanoplastics. Exposure elicited coordinated transcriptional remodeling of genes regulating mitochondrial dynamics (DRP1, MFN1), mitochondrial DNA encoded oxidative phosphorylation components (MT-ATP6, MT-COX1, MT-ND6), DNA repair (OGG1, APE1), DNA methylation machinery (DNMT1, DNMT3a, DNMT3b), and mitochondrial-associated miRNAs (miR-21, miR-34a, miR-155). Functional analyses revealed polymer and time-dependent disruption of mitochondrial membrane potential and respiratory chain activities, with Complex I identified as the primary site of vulnerability. Correlation analysis showed strong positive associations among DRP1, OMA1, DELE1, and ND6 (r > 0.9, R{superscript 2} > 0.8, p < 0.001), reflecting coordinated mitochondrial stress and epigenetic signaling, while negative correlations between DRP1 and MFN1 (r = -0.54, R{superscript 2} = 0.29, p < 0.01) and between APE and ND6 (r {approx} -0.42, R{superscript 2} {approx} 0.18, p < 0.05) highlight antagonistic regulation and impaired mitochondrial network stability linked to Complex I dysfunction. In silico docking of oxidized nanoplastic oligomers identified high-affinity interactions at the Complex I Fe-S cluster and cofactor-binding sites, suggesting direct interference with electron transfer. A random forest-based model accurately predicted MT-ND6 expression from Complex I activity (R{superscript 2} > 0.85), establishing a data-driven Complex I-ND6 axis. Collectively, these findings demonstrate that airborne nanoplastics induce integrated mitoepigenetic and immunometabolic dysregulation, underpinned by coordinated and antagonistic regulatory interactions in lymphocytes.

molecular biology↗

bioRxiv2025

Large differences in photorespiration and its temperature response among temperate trees

Photorespiration significantly influences terrestrial carbon fluxes, yet empirical measurements of its variability across tree species and temperature conditions remain limited, constraining predictions of vegetation and climate models. We quantified apparent photorespiratory CO2 loss (Lapp) and its temperature response for seven temperate broadleaf tree species in northern Europe, using in situ O2-shift measurements in Uppsala, Sweden during peak summer. Apparent loss was derived as the difference between net CO2 assimilation under ambient (Anet) and O2-free conditions at three leaf temperatures (25, 30, and 35 {degrees}C), spanning typical and heat-wave scenarios. Apparent photorespiratory CO2 loss showed pronounced interspecific variation and increased with temperature, while net photosynthesis remained relatively stable. The ratio of apparent loss to net photosynthesis ({phi} = Lapp/Anet) rose sharply with temperature, reaching species-mean values up to 0.94 at 35 {degrees}C, indicating that photorespiration can represent nearly the entirety of net carbon gain under heat stress even when leaves remain net CO2 sinks. Suppression of photorespiration under N2 and associated changes in leaf temperature systematically reallocated photosynthetic electron transport: the fraction of ambient electron transport rate (ETR) allocated to net CO2 assimilation declined with temperature, whereas the complementary fraction allocated to apparent photorespiratory loss and other O2-dependent sinks increased, with ETR-based apparent loss and its proportional expression rising steeply across the 25-35 {degrees}C range. Together, these in situ flux and partitioning measurements reveal high variability and strong temperature sensitivity in apparent photorespiration among temperate trees. Compared to crop-based parameterisations, the {phi} values we report for temperate trees are substantially higher and more temperature-dependent, providing species-specific constraints that can improve Farquhar-von Caemmerer-Berry-type vegetation model representations of photorespiration in forest ecosystems.

plant biology↗

bioRxiv2025

Modes of action and in planta antifungal activity of Olea europaea defensin OefDef1.1-derived peptide variant

Peptide-based biopesticides represent a promising strategy for sustainable disease control in agriculture. Synthetic antifungal peptides incorporating the {gamma}-core motif of plant defensins offer multiple modes of action (MoA) and potential as biofungicides. We investigated a synthetic variant of the olive defensin OefDef1.1 for antifungal activity, structure-function relationships, and MoA against Botrytis cinerea, the necrotrophic pathogen causing gray mold. A disulfide-bridged peptide, GMAOe1C_V1*, derived from OefDef1.1 (G32-Y53) and modified with hydrophobic amino acid substitutions, inhibited B. cinerea growth in vitro and reduced lesion formation in detached leaves. Foliar application of GMAOe1C_V1* suppressed disease symptoms in pepper plants. Mechanistically, GMAOe1C_V1* rapidly permeabilized fungal plasma membranes and accumulated in vacuoles, triggering vacuolar expansion and cell death. It also inhibited protein synthesis in vitro and in vivo, suggesting a role as a translation inhibitor. Alanine scanning mutagenesis of the non-disulfide bridged variant identified the 7RHSKH11 motif as essential for antifungal activity. Circular dichroism revealed an unstructured conformation with minimal secondary structure. Transcriptomic analysis of GMAOe1C_V1* treated B. cinerea germlings showed downregulation of genes involved in mitochondrial function and amino acid biosynthesis. These findings demonstrate the potential of an olive defensin-derived peptide as a bio-inspired antifungal agent with multifaceted MoA, supporting its development for crop protection.

plant biology↗

bioRxiv2025

A programmable genetic platform for engineering noninvasive biosensors

Creating genetic sensors for noninvasive visualization of biological activities in deep, optically opaque tissues holds immense potential for basic research and the development of genetic and cell-based therapies. MRI stands out among deep-tissue imaging methods for its ability to generate high-resolution images without ionizing radiation. However, the adoption of MRI as a mainstream biomolecular technology has been hindered by the lack of adaptable methods to link molecular events with genetically encodable MRI contrast. To address this challenge, we introduce universal reporter circuit-based activatable sensors (URCAS), a highly programmable platform for the systematic creation of genetic sensors for MRI. In developing URCAS, we engineered protease-activatable MRI reporters using two distinct approaches: protein stabilization and subcellular trafficking. We established the applicability of URCAS in five diverse mammalian cell types and showcased its versatility by assembling a toolkit of genetic sensors for viral proteins, small-molecule drugs, logic gates, protein-protein interactions, and calcium, without requiring new customization for each target. Our findings suggest that URCAS provides a modular, programmable platform for streamlining the development of noninvasive, nonionizing, and genetically encoded sensors for biomedical research and in vivo diagnostics.

bioengineering↗

bioRxiv2025

Longitudinal Multi-Organ Transcriptomic Atlas of Salt-Induced Hypertension

BACKGROUNDSalt-sensitive hypertension is a prevalent and clinically significant subtype of hypertension, where increased dietary salt intake elevates blood pressure and causes injury to multiple organ systems. Despite extensive research, dynamic molecular changes and conserved versus organ-specific transcriptional programs in hypertensive multi-organ damage remain poorly understood. Defining complex molecular pathways both in a temporal sequence and in an organ-specific manner is essential for developing targeted, precision therapies to mitigate hypertensive disease burden. METHODSWe generated a longitudinal multi-organ transcriptomic atlas of salt-sensitive hypertension using RNA sequencing of kidney cortex, kidney medulla, heart, and liver from Dahl salt-sensitive rats across four disease stages. A comprehensive bioinformatic analysis mapped dynamic transcriptional programs, evaluated 50 biological pathways, and defined upstream regulators. Histological and biochemical assays complemented transcriptomic analysis, while integration with human genome-wide association studies (GWAS) and compound-transcriptome analysis provided translational insights and identified candidate therapeutics. RESULTSSalt-induced hypertension elicited both shared and tissue-specific transcriptional programs that evolved with disease progression. The kidney medulla showed robust early immune activation with metabolic suppression, while the cortex exhibited transient metabolic activation before declining and initiating immune activation. The liver and heart showed time-dependent metabolic and inflammatory remodeling. Cross-organ comparisons revealed a shared early proliferative response that converged on proinflammatory and fibrotic signatures. Upstream regulator analysis identified 79 time- and tissue-specific transcription factors associated with gene expression dynamics. GWAS integration analysis revealed endocrine signaling, ion transport, lipid metabolism, and detoxification as conserved pathways across species, underscoring the translational relevance of the model and study. Predictive compound- transcriptome analyses identified kinase inhibitors targeting phosphoinositide 3-kinase, mechanistic target of rapamycin and cyclin-dependent kinases as top candidates to counteract maladaptive transcriptional programs. CONCLUSIONSThis study defines temporal and tissue-specific transcriptomic remodeling in salt-sensitive hypertension and highlights the need for precision interventions to prevent progressive organ damage.

physiology↗

bioRxiv2025

Enabling Organ- and Injury-Specific Nanocarrier Targeting via Surface-Functionalized PEG-b-PPS Micelles for Acute Kidney Injury

While nanomedicine holds great promise for kidney disease, targeted delivery remains a major challenge. Most nanocarriers rely on passive accumulation or epithelial-specific ligands, limiting their utility in complex, inflamed renal environments. In acute kidney injury (AKI), inflammation and vascular dysfunction play central roles, yet targeting strategies beyond the tubule remain underexplored. Here, dual-ligand micelles are developed to enhance nanocarrier localization to the inflamed kidney by simultaneously engaging both organ- and injury-specific cues. Poly(ethylene glycol)-block-poly(propylene sulfide) (PEG-b-PPS) micelles were engineered to display two peptide ligands: CLPVASC, which preferentially distributes to the kidney, and CYNTTTHRC, which binds selectively to inflamed endothelium. These targeting motifs were incorporated via lipid-anchored peptide amphiphiles, enabling modular surface functionalization without disrupting micelle morphology, size, or charge. In vitro, dual-targeted micelles demonstrated enhanced uptake by human endothelial cells exposed to hypoxia-reoxygenation. In vivo, following unilateral renal ischemia-reperfusion injury (IRI) in mice, targeted micelles achieved selective accumulation in the injured kidney, outperforming both non-targeted controls and contralateral kidneys. Off-target distribution to liver, lung, and spleen was markedly reduced, confirming the spatial precision of the dual-ligand approach. This strategy offers a scalable, modular, and biologically informed platform for precision delivery in AKI and related inflammatory conditions.

bioengineering↗

bioRxiv2025

Accumulation of SA-βGal High Cells in Human Naive T Cell Compartments Reveals a Stress-Adapted, Senescent-Like State

Aging is associated with a decline in immune function termed immunosenescence, characterized by accumulation of senescent-like immune cells and chronic inflammation, known as inflammaging. While senescence-associated {beta}-galactosidase (SA-{beta}Gal) activity is a well-established senescence marker, its functional significance and the precise cellular subsets affected within the T cell compartment remain unclear. Here, we identify and characterize a previously unrecognized subset of naive CD4 and CD8 T cells displaying high SA-{beta}Gal activity that significantly increases with age. Despite exhibiting hallmark features of senescence such as DNA damage, nuclear envelope disruption, loss of heterochromatin, and pronounced dysregulation of autophagy and lysosomal pathways, these SA-{beta}Gal-high naive T cells notably lack the canonical senescence marker p21CIP1 and retain robust proliferative capacity upon activation. Remarkably, naive CD4 SA-{beta}Gal-high T cells acquire cytotoxic properties including NK-like features, granzyme secretion, and the ability to induce paracrine DNA damage in endothelial cells. Mechanistically, we demonstrate that impaired autophagic flux contributes significantly to this phenotype. Our findings address critical knowledge gaps regarding the nature and functional plasticity of senescence-like states in naive T cells, highlighting a novel link between lysosomal-autophagic dysfunction, cellular stress adaptation, and inflammaging. Understanding this unique T cell population provides important insights into immune aging and offers potential targets to mitigate age-associated immune dysfunction and chronic inflammation.

immunology↗

bioRxiv2025

Endothelial Prolyl Hydroxylase 3 Mitigates Maladaptive Inflammation to Promote Post-Ischemic Kidney Repair

Acute kidney injury (AKI) is a major health concern and well-established risk factor for the development of chronic kidney disease (CKD). Tissue hypoxia is a prominent feature of the injured kidney that shapes the biological behavior of parenchymal and immune cells. Endothelial cells have important immunomodulatory roles, but the impact of dysregulated oxygen sensing on their responses remains poorly understood. By leveraging a combination of conditional mouse strains, single-cell analyses of mouse and human samples, and in vitro experiments, we demonstrate that the oxygen sensor PHD3 in the endothelium suppresses maladaptive inflammatory responses, thereby promoting kidney repair. Specifically, post-ischemic inactivation of endothelial PHD3, but not PHD1, leads to maladaptive kidney repair, characterized by increased fibrosis and inflammation. scRNA-seq analysis of the postischemic endothelial PHD3-haplodeficient kidney shows an endothelial IFN-{gamma} gene signature, resembling the responses seen in patients with severe AKI. By performing loss- and gain-of-function experiments in vitro, we demonstrate that PHD3 regulates IFN-{gamma} responsive pro-inflammatory signatures in a HIF-dependent manner. Consistent with this, simultaneous deletion of ARNT in endothelial PHD3-deficient mice restored kidney repair. Thus, our findings provide novel mechanistic insights into endothelial oxygen sensing and the AKI-to-CKD transition, highlighting potential therapeutic avenues for mitigating disease progression. TRANSLATIONAL STATEMENTUsing a genetic approach, we identified endothelial PHD3 as a critical regulator of kidney repair. Post-ischemic loss of endothelial PHD3--but not PHD1--led to maladaptive outcomes marked by increased injury, fibrosis, and inflammation. Mechanistically, we show that PHD3 restrains IFN-{gamma}-driven pro-inflammatory signaling through a HIF-dependent pathway. These findings reveal a central role for endothelial oxygen sensing in dictating kidney recovery and underscore the importance of cellular context in responses to hypoxia. Given the expanding clinical use of non-selective PHD inhibitors, our work highlights the need for more targeted, cell-specific approaches to modulate hypoxia pathways in kidney disease.

molecular biology↗

bioRxiv2024

Targeting ZNF638 activates antiviral immune responses and potentiates immune checkpoint inhibition in glioblastoma

Viral mimicry refers to the activation of innate anti-viral immune responses due to the induction of endogenous retroelement (RE) expression. Viral mimicry has been previously described to augment anti-tumor immune responses and sensitize solid tumors to immunotherapy including colorectal cancer, melanoma, and clear renal cell carcinoma. Here, we found that targeting a novel, master epigenetic regulator, Zinc Finger Protein 638 (ZNF638), induces viral mimicry in glioblastoma (GBM) preclinical models and potentiates immune checkpoint inhibition (ICI). ZNF638 recruits the HUSH complex, which precipitates repressive H3K9me3 marks on endogenous REs. In GBM, ZNF638 is associated with marked locoregional immunosuppressive transcriptional signatures, reduced endogenous RE expression and poor immune cell infiltration (CD8+ T-cells, dendritic cells). ZNF638 knockdown decreased H3K9-trimethylation, increased cytosolic dsRNA and activated intracellular dsRNA-signaling cascades (RIG-I, MDA5 and IRF3). Furthermore, ZNF638 knockdown upregulated antiviral immune programs and significantly increased PD-L1 immune checkpoint expression in patient-derived GBM neurospheres and diverse murine models. Importantly, targeting ZNF638 sensitized mice to ICI in syngeneic murine orthotopic models through innate interferon signaling. This response was recapitulated in recurrent GBM (rGBM) samples with radiographic responses to checkpoint inhibition with widely increased expression of dsRNA, PD-L1 and perivascular CD8 cell infiltration, suggesting dsRNA-signaling may mediate response to immunotherapy. Finally, we showed that low ZNF638 expression was a biomarker of clinical response to ICI and improved survival in rGBM patients and melanoma patients. Our findings suggest that ZNF638 could serve as a target to potentiate immunotherapy in gliomas.

cancer biology↗

bioRxiv2024

Antimicrobial Potential and Characterization of Silver Nanoparticles Synthesized from Ocimum Sanctum Extract

The growing resistance of microbes to conventional antibiotics and the environmental impact of chemical synthesis methods highlight the urgent need for effective and sustainable antimicrobial agents. In this study, we address these challenges by synthesizing silver nanoparticles (AgNPs) using Ocimum sanctum leaf extract, a green and efficient method. We confirmed AgNPs synthesis through UV-vis spectroscopy, observing a Surface Plasmon Resonance (SPR) peak centered at 420 nm. X-ray Diffraction (XRD) analysis showed intense peaks at 37.81{degrees}, 45.01{degrees}, 63.91{degrees}, and 78.0{degrees}, corresponding to Braggs reflections at 111, 200, 220, and 311, respectively, with an average particle size of approximately 18 nm calculated using Scherrers formula. The reduction of Ag+ was monitored using Atomic Absorption Spectroscopy (AAS), which revealed a rapid decrease from 2.73 ppm to 0.023 ppm within four minutes, driven by the active reducing agents in the O. sanctum extract. The Scanning Electron Microscope (SEM) image confirmed the spherical shape of the AgNPs, with an average size of 23.82 {+/-} 4.17 nm. Fourier Transform Infrared (FTIR) spectroscopy identified absorption peaks at 1635 cm-1 and 3430 cm-1, associated with the amide I bond of proteins and OH stretching in alcohols and phenolic compounds, respectively. The synthesized AgNPs exhibited significant antimicrobial activity, demonstrated by a dose-dependent inhibitory effect against bacterial strains. The inhibition zone measured 6 mm at the lowest concentration of 5 {micro}g/L and increased progressively to 14 mm at the highest concentration of 25 {micro}g/L, indicating strong antimicrobial potential even at low dosages.

biochemistry↗