Biology subjects

Pandey, S.

Publications and source records attributed to Pandey, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Vir2vec: A Genome-Wide Viral Embedding

Genomic language models (gLMs) are powerful numerical surrogates for DNA, but existing architectures focus primarily on human DNA or limited viral sets, and no dedicated benchmark exists for viral genome understanding. Here we introduce Vir2vec (from 17M to 422M parameters), decoder-only gLMs continually pretrained on a curated pan-viral corpus of 565,747 complete genomes across 295 species. We also present the viral Genome Understanding Evaluation (vGUE), a benchmark probing viral representations across broad organism discrimination, evolutionary signatures, intra-genus separation, variant subtyping, and host tropism. Evaluated as frozen feature extractors under nested cross-validation, Vir2vec achieves top balanced accuracy across 5 of 7 vGUE tasks, outperforming human-trained (MistralDNA), viral-specific (ModernBERTvirus), and broad biological foundation (Evo1) model. Furthermore, Vir2vec displays robust zero-shot generalization to unseen viral families. Finally, we introduce an argmax-routed SHAP explainability framework that projects feature attributions directly onto single-codon coordinates, correctly isolating key receptor-binding domain mutations driving mouse host adaptation. Vir2vec and vGUE provide a foundation for viral surveillance and discovery pipelines.

bioinformatics↗

bioRxiv2025

Projection-defined ventral tegmental area neurons exhibit distinct fentanyl-induced molecular and functional adaptations that differentially support drug-context associations

RationaleSynthetic opioids like fentanyl are contributing to unprecedented overdose rates, yet the neural circuitry underlying fentanyl-associated behaviors remains poorly understood. The ventral tegmental area (VTA) projects to both the nucleus accumbens (NAc) and prefrontal cortex (PFC), forming distinct pathways that are implicated in drug-cue associations, though their specific roles in fentanyl-context encoding are not well defined. ObjectivesThis study aimed to determine how VTA-NAc and VTA-PFC circuits contribute to fentanyl-context associations, and to assess the role of downstream dopamine receptor signaling in fentanyl context-seeking. MethodsMale and female mice underwent fentanyl conditioned place preference (CPP; 0.2 mg/kg). We locally inhibited dopamine D1 or D2 receptors in NAc or PFC during CPP expression. We used fiber photometry calcium imaging to measure activity in VTA-NAc and VTA-PFC projection neurons, and chemogenetic inhibition to suppress activity during CPP expression. ResultsFentanyl CPP expression was attenuated by blocking D1 but not D2 receptors in PFC, and D2 but not D1 receptors in NAc. We found both VTA-NAc and VTA-PFC exhibited increased calcium activity during fentanyl exposure and during entries to the fentanyl-paired context. We further identified a functional role for VTA-NAc, as chemogenetic inhibition of VTA-NAc, but not VTA-PFC, reduced fentanyl context-seeking. ConclusionsWhile both VTA-NAc and VTA-PFC pathways are recruited by fentanyl exposure, fentanyl context-seeking relies on different downstream dopamine receptors in NAc vs PFC. Further, activity in VTA-NAc functionally supports the expression of fentanyl CPP. Together, these findings indicate that VTA circuits differentially contribute to fentanyl context-seeking.

neuroscience↗

bioRxiv2025

Cross-Fostering with control dams rescues Gut Dysbiosis and Chromatin-associated Transcriptional Changes in Offspring of Opioid-Exposed Dams

Prenatal opioid exposure disrupts gut homeostasis and causes gastrointestinal complications in offspring, but the mechanisms remain unclear. Here using a murine model of prenatal hydromorphone exposure, we examined gut microbiota, intestinal injury, transcriptomic signatures, and chromatin accessibility. Exposed pups displayed marked dysbiosis, epithelial damage, and upregulation of inflammatory gene programs accompanied by relaxed ileal chromatin. Cross-fostering to opioid-naive dams restored microbial diversity, reestablished metabolite-producing taxa, and reversed injury-associated transcriptional and chromatin changes. Fecal microbiota transplantation from exposed dams recapitulated intestinal injury, indicating a microbiome-driven mechanism. These findings reveal a novel gut-microbiome-epigenome axis underlying opioid-induced injury and highlight early microbial intervention as a potential strategy to mitigate developmental harm.

microbiology↗

bioRxiv2025

Perinatal Exposure to Metal Mixtures Disrupts Neuronal Function and Behavior

BackgroundEnvironmental exposure to heavy metals such as lead (Pb), arsenic (As), hexavalent chromium [Cr(VI)], and cadmium (Cd), (PACC), is linked to neurodevelopmental disorders. These metals often co-occur in contaminated environments, but their combined effects on brain development remain poorly understood. ObjectiveTo test the hypothesis that perinatal exposure to a mixture of environmentally relevant levels of Pb, As, Cd, and Cr(VI), causes developmental defects in cognition, behavior, and neuronal function. MethodsFemale C57BL/6J mice were exposed to either a single metal or the PACC mixture in drinking water. Exposure began two weeks preconception and continued until weaning at postnatal day 21. Juvenile mice were tested at 4-5 weeks of age in open field (locomotion), novel object recognition (short-term memory), Y-maze (working memory), and elevated plus maze (anxiety-like behavior). A subset of animals underwent Whole-cell patch-clamp recordings in the medial prefrontal cortex (mPFC) and hippocampal CA1 neurons. ResultsPerinatal exposure to PACC metal mixture increased anxiety-like behavior and impaired short-term memory but not locomotion or working memory. Pyramidal neurons in mPFC and hippocampal CA1 displayed increased intrinsic excitability, mPFC neurons also showed elevated amplitude in spontaneous excitatory postsynaptic currents. DiscussionOur findings suggest that perinatal exposure to the PACC metal mixture impairs cognition, increases anxiety-like behavior, and alters neuronal function in specific brain regions of juvenile mice, leading to disruption in neuronal function and behavior later in life. Further studies are needed to provide mechanistic insight into how perinatal heavy metal exposure affects neuronal development. HighlightsO_LIPerinatal exposure to a metal mixture including lead (Pb), arsenic (As), hexavalent chromium (Cr(VI)), and cadmium (Cd), collectively termed PACC metal mixture--impairs cognition and increases anxiety in mice. C_LIO_LINeuronal excitability and synaptic transmission are altered in medial prefrontal cortex after PACC metal mixture exposure. C_LIO_LIPACC mixture exposure decreases short-term memory in both males and females, and increases anxiety in males C_LIO_LIPrincipal component and clustering analyses reveal that PACC mixture exposure and control mice form distinct, nonoverlapping populations in physiological-behavioral space. C_LIO_LIEnvironmentally relevant PACC metal mixtures exert stronger effects than individual metals alone. C_LI

pharmacology and toxicology↗

bioRxiv2025

Repurposing Melatonin in dual-mode for Wilson disease therapy as a Copper Chelator and an antioxidant agent

Loss-of-function mutations in copper-ATPase ATP7B underlie Wilson disease (WD), a disorder characterized by hepatic copper accumulation and severe hepato-neuropathology. Existing chelation therapeutics remove excess copper but lack intrinsic antioxidant capacity and frequently cause systemic toxicity. Here we evaluate melatonin, an FDA-approved indoleamine with antioxidant and putative metal-chelating activity, as a candidate therapeutic for WD. In ATP7B-/- hepatocytes, melatonin restored copper-induced reactive oxygen species (ROS) to basal levels, reduced apoptosis twofold, and attenuated Nrf2 nuclear translocation leading to reduction of Hemoxygenase-1 abundance. Live-cell ratiometric analysis of GSSG/GSH using GRX1-roGFP2 expressed in melatonin-treated ATP7B-/- hepatocytes revealed a significant reduction in intensity-ratio, indicating an effective mitigation of copper-induced glutathione oxidation. Isothermal calorimetric titration revealed moderate Cu2+ affinity (K ITC=4.54 x 103 M-{superscript 1}), rationalized by MD-simulations showing an interaction energy of 18.5 x 10-3 kcal{middle dot}mol-{superscript 1} via amide-Cu{superscript 2} coordination. In-cellulo studies also revealed that copper-induced vesicularized ATP7B reinstates to Golgi in melatonin-treated hepatocytes. In vivo, melatonin treatment reduced copper-induced oxidative stress in zebrafish embryos and lowered copper burden in Caenorhabditis elegans WD model. Our studies revealed that encapsulation of melatonin within an engineered polymeric nanocapsules having dithiol linkers, susceptible to cleavage by GSH, extended melatonins circulatory half-life ten-fold and enhanced its ROS-scavenging efficacy three-fold relative to free melatonin. This work introduces a unique dual-function therapeutic strategy that integrates antioxidant activity with copper chelation, simultaneously addressing copper overload and redox imbalance. Repurposing melatonin, with its established clinical safety, offers rapid and cost-effective translational pathway toward WD-therapy while providing a generalizable platform for redox- and metal-associated disorders.

cell biology↗

bioRxiv2025

Crosstalk Between Phosphorylation and Ubiquitination Controls the Fate and Function of Strigolactone Signal Transducers

Strigolactones (SL) are pivotal plant hormones that sculpt plant architecture by modulating shoot branching, root development, and meristem activity. While transcriptional responses downstream of SL perception have been well explored, the role of post-translational regulation fine-tuning these responses remains less understood. In this study, we identify a dual-layered regulatory module involving MPK4-mediated phosphorylation and MAX2-dependent ubiquitination that synergistically control the stability and function of BRC1, a key SL-responsive transcription factor. Phosphorylation by MPK4 stabilizes BRC1, enhancing its activity and SL sensitivity, whereas loss of phosphorylation leads to BRC1 degradation and functional inactivation. BRC1, in turn, directly activates MPK4 transcription, establishing a positive feedback loop that amplifies SL signaling. Genetic analyses of the brc1-2 x mpk4 double mutant reveals phenotypic defects and SL insensitivity additive to those observed in the brc1-2 and mpk4 single mutants, indicating that MPK4 and BRC1 act in parallel yet converging pathways downstream of SL. Additionally, MAX2 functions as a regulatory checkpoint that degrades non-phosphorylated MPK4 and BRC1, thereby resetting the signaling circuit to ensure accurate and timely response. Together, these findings illuminate a finely-tuned regulatory module integrating phosphorylation and ubiquitination to control the intensity and duration of SL responses, suggesting a model for hormone-driven developmental plasticity in plants.

molecular biology↗

bioRxiv2025

Spatial and Single-Cell Dissection of Fibroblast Subpopulation Reprogramming Driving Stromal Collapse in Breast Cancer Lymph Node Metastasis

ObjectiveThis study aimed to define conserved molecular drivers of breast cancer lymph node metastasis (LNM) through an unbiased, multi-omics approach, resolving spatial and cellular mechanisms of stromal reprogramming. MethodsWe integrated three bulk RNA-seq datasets (GSE110590, GSE193103, GSE209998) to identify differentially expressed genes (DEGs) in LNMs versus primary tumors. Tissue-specific genes were excluded where possible. Single-cell (scRNA-seq; GSE225600) and spatial transcriptomics (Visium) from primary/metastatic tissues were analyzed using Seurat and spacexr. Fibroblast subclusters were isolated for functional enrichment. Clinical validation included genetic alteration profiling (cBioPortal), survival analysis (KM Plotter), and stage-specific expression dynamics (TNMplot). Therapeutic candidates were screened via CTD. FindingsBulk RNA-seq identified three genes consistently downregulated in lymph node metastases compared to primary tumors: MAB21L1, F2RL2, and COL6A6 (log2FC [≤] -2.62; adj. p < 0.05). Single-cell RNA-seq analysis revealed that all three DEGs converged exclusively within specific fibroblast subpopulations in primary tumors; these DEGs were not enriched in other cell types. DEG-expressing fibroblasts orchestrated complementary protective barriers: F2RL2+ fibroblasts mediated immune crosstalk (via CXCL14, C1S) and TGF-{beta} balance; COL6A6+ fibroblasts reinforced ECM structure (COL6A6/COL6A3) and inhibited Wnt signaling (SFRP2); MAB21L1+ fibroblasts suppressed SMAD signaling (through NR2F1 upregulation) and blocked cell migration. Metastatic niches exhibited significant depletion of protective fibroblast subpopulations (F2RL2+: reduced from 1.9% to 0.1%; COL6A6+: reduced from 3.1% to 1.3%); this depletion coincided with ECM dissolution and disrupted spatial coordination of immune markers (proximity-dependent HLA-DRA/CXCL9 expression). High expression of these DEGs correlated with improved recurrence-free survival (e.g., COL6A6: HR = 0.19, p = 0.002); genomic deletions of the DEGs were significantly more frequent in metastases versus primary tumors (e.g., MAB21L1 deep deletion: 9.13% vs. 0.57%). ConclusionAn unbiased transcriptomic approach revealed specialized fibroblast subpopulations as central gatekeepers against LNM via ECM, immune, and signaling barriers. Their erosion drives stromal collapse in metastasis. Epigenetic modulators (Valproic Acid, Vorinostat) were prioritized for therapeutic restoration of suppressive stroma.

genetics↗

bioRxiv2025

Indirect pathway neurons in the tail of the striatum regulate inhibitory control over sensory driven behavior

Inhibitory control, or the ability to withhold action in certain situations, is behaviorally essential. Disrupted inhibitory control is linked to various neuropsychiatric symptoms, making it critical to understand the underlying neural basis. We examined how the tail of the striatum (TS), a major basal ganglia sensory hub, regulates actions to sensory stimuli. Mice performed an auditory Go/NoGo task where we recorded cell-specific activity of TS neurons. Both major striatal types were active during target sounds, but non-target sounds preferentially engaged indirect pathway neurons. Temporarily silencing this activity increased errors to non-target stimuli, indicating a role in suppressing inappropriate action. In mice deficient for the synaptic adhesion molecule Neurexin1, a gene linked to autism spectrum disorder and ADHD, TS indirect pathway recruitment was reduced, and these mice demonstrated auditory-specific inhibitory control deficits. Altogether, these findings highlight a subcortical target to potentially improve attentional and behavioral regulation in neurodevelopmental disorders. TeaserPosterior striatal circuits control sensory-guided actions and are disrupted in a rodent model of neurodevelopmental disorders.

neuroscience↗

bioRxiv2025

Microbial Scl1 Activates TGFBR1 receptor kinase signalling to Drive Fibrosis-Inflammation Axis in Alcohol-Associated Liver Disease

Background and AimsAlcohol consumption alters gut microbiota, which can affect metabolism, immune regulation, and signalling pathways and lead to alcohol-associated liver disease (ALD). We investigated how alcohol-associated gut microbiota (AGMs) modulate liver kinome signalling to drive inflammation and fibrosis in ALD. MethodLiver kinome and metaproteome changes were studied in rats (n=6/group) colonized with stool of severe alcohol-related hepatitis (SAH) patients (SAH[->]healthy-rats) or healthy human donors (HD[->]ALD-rats). AGM-associated liver kinome changes were cross-correlated with bacterial genera. A bacterial protein; Streptococcal collagen-like protein 1 (Scl1) was identified with affinity for TGF{beta}R1. This was validated by molecular docking and immunoprecipitation-LCMS assay. Expression of Streptococcus pneumonia and pyogenes was done in stool of SAH patients (n=10). Also, Scl1 was quantified in patient stool (n=24) and liver tissue (n=19) samples. Validation was performed by assessing Scl1 level in plasma and Streptococcus level in stool samples before and after fecal microbiota transplantation (FMT) in SAH patients. ResultsStool metaproteomics showed significant increase in 10 bacterial genera (Streptococcus, Staphylococcus, and Clostridium) in SAH[->]Healthy-rats, mirroring changes seen in ALD-rats (FC>1.5, p<0.05). Clusters of Orthologous Groups analysis indicated increased post-translational modifications (PTMs) and decreased lipid metabolism in ALD-rats and SAH[->]Healthy-rats. Liver kinome profiling showed 85 upregulated kinases in SAH[->]Healthy-rats, with 34 overlapping with ALD-rats, associated with inflammation (Mapk14, Map3k10 and others), fibrosis (Tgfbr1, Igf1r, and others), lipid metabolism (Cdk14, Cdk18) and regeneration (Met, Bmpr1a and others). FMT from healthy human-donors to ALD-rats reversed the expression of Streptococcus (10-fold), Staphylococcus (3-fold), and Clostridium (5-fold), along with 18 kinases associated with inflammation (Btk, Camk4, Nuak1) and fibrosis (Tgfbr1, Col4a1, Fgfr2 and others). Strong association (r{superscript 2}>0.9, p<0.05) was seen between Streptococcus abundance and fibrosis and inflammation-related kinases. Level of Scl1 was significantly high in SAH and ALD-rat stool samples (FC>2, p<0.05). It showed strong affinity for TGF{beta}R1, as validated by molecular docking (>86%confidence) and immunoprecipitation assays (>100FC,p<0.05), indicating it as a potential ligand for TGF{beta}R1. Concordantly, expression of Scl1 was highest amongst all the known ligands for TGF{beta}R1 (p<0.05) suggesting Scl1 is a major contributor for TGF{beta}R1 activation and its downstream signalling in these patients. Following fecal microbiota transplantation, expression of Scl1 in plasma and Streptococcus levels in stool were significantly reduced by 2.1-folds and 1.9 folds respectively in SAH patients. Further, Scl1 levels SAH plasma is capable of predicting poor therapeutic response and 30-day mortality with high accuracy (AUC=0.92, cutoff >70 normalized abundance). ConclusionAlcohol induced gut dysbiosis alters the liver kinome, promoting inflammation, fibrosis, and lipid dysregulation. Streptococcal Scl1 is identified as a bacterial protein mimicking human collagen and capable of activating fibrotic signalling pathway through TGF{beta}R1in liver and is capable of predicting poor response in SAH. FMT from healthy donor restores microbial imbalance and harmful microbial-host interactions.

microbiology↗

bioRxiv2025

Liver Kinome Profiling Identifies PS1145 as a Potential Therapeutic molecule for amelioration of Systemic Inflammation in Alcohol-related Liver Disease

Background and aimsAlcohol-related liver disease (ALD) has high mortality due to systemic inflammation. We analysed liver and monocyte kinome profiles in a chronic ethanol-fed pre-clinical rat model to identify therapeutic targets that could mitigate inflammation in ALD. MethodKinome profile was performed in liver and circulating monocytes at baseline, and after 8,12,16,20 and 24-weeks of 40% ethanol administration. Pathway-specific inhibitors, including PS1145 (IKK-phosphorylation inhibitor), PH-797804 (MAPK14 inhibitor), resveratrol and prednisolone were tested for their anti-inflammatory effects in ALD-rats, PBMC from patients and NIAAA mouse model. ResultsKinome profiling identified 497 liver and 345 monocyte kinases in ALD rats (FDR<0.01). A time-dependent increase in MAPK14-associated kinases was observed in both tissues (FC>1.5, p<0.05). By 24 weeks, 172 liver and 48 monocyte kinases were significantly upregulated, particularly those linked to MyD88-TLR4, PI3K-Akt, TNF, TGF{beta}, and cellular senescence pathways. Key contributors included TGF{beta}R1, ROS-generating kinases, and IL-1-driven MAPK14 and IKK phosphorylation. Targeting this axis, PS1145 (an IKK inhibitor) suppressed NF{kappa}B activation and inflammation in THP1 and HepG2 cells, as well as PBMCs from healthy and SAH patients, outperforming PH797804, resveratrol, and prednisolone (p<0.05, FC>1.5). PS1145 significantly reduced IL-6, TNF, and NF{kappa}B, while increasing IL-10. In vivo, PS1145 treatment in the NIAAA mouse model markedly reduced hepatic steatosis, cellular stress and inflammatory pathways (cytokine signalling, IL-36 signalling and others) more effectively than standard therapies, Notably, it also downregulated IL36R, impairing TLR receptor dimerization, suggesting a dual mechanism of action (p<0.05) highlighting its therapeutic potential in ameliorating systemic inflammation in ALD. ConclusionOur study highlights the key role of MAPK14 and MYD88-TLR4 pathway kinases in driving systemic inflammation in SAH. The IKK inhibitor PS1145, by blocking both IKK phosphorylation and TLR dimerization, effectively suppresses inflammatory signalling and improves liver pathology, positioning it as a promising targeted therapy for ALD.

pharmacology and toxicology↗

bioRxiv2025

Metabolomic Profiling of Ashwagandha (Withania somnifera): Linking Bioactive Compounds to Functional Therapeutic Roles

IntroductionWithania somnifera (Ashwagandha) is a widely used medicinal plant with established roles in traditional systems of medicine. Known for diverse pharmacological effects, including neuroprotection, hepatoprotection, enhancement of male fertility, and anti-inflammatory activity. Despite its longstanding use, a deeper understanding of its phytochemical composition and bioactive mechanisms is required to bridge traditional knowledge with modern therapeutic applications. MethodsA comprehensive metabolomics profiling of Withania somnifera was performed to identify and quantify its bioactive secondary metabolites. Focus was placed on major classes such as alkaloids, phenolic compounds, and terpenoids. Known compounds were annotated and categorized based on their abundance, chemical class, and reported biological functions. Particular attention was given to compounds implicated in neuroprotection, liver health, reproductive support, and inflammation-modulation. ResultsThe analysis revealed a rich but low-abundance of known metabolites. Alkaloids such as Gentianaine (8.44%) and Sauroxine (2.94%), and phenolics like Mulberrofuran A (14.58%) and Sulphuretin (9.61%), were among the most prominent. These compounds are associated with antioxidative, anti-inflammatory, and neuroregenerative activities. Terpenoids including Pinocarvone and Ergosterol contributed to hepatoprotective and anti-inflammatory properties. Compounds such as Gomphrenin-I, Sitosterol, Pfaffic acid, beta-Carotene and others (>3%) supported spermatogenesis, while Embelin and Kievitone enhanced oxidative stress response. Although most identified compounds were individually present in low percentages (<0.30%), their collective activity suggests synergistic effects. ConclusionMetabolomic analysis of Withania somnifera confirms high abundance of bioactive secondary metabolites that have hepatoprotective, neuroprotective, anti-oxidant and spermatogenesis-enhancing effects. These findings justify protective and beneficial effect of Withania in promoting stress relief, energy, and overall wellness. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/659832v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1ae8e5forg.highwire.dtl.DTLVardef@105300corg.highwire.dtl.DTLVardef@1958320org.highwire.dtl.DTLVardef@d3ba13_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

Complement C3aR deletion does not attenuate neurodegeneration in a tauopathy model or alter acute inflammation-induced gene expression changes in the brain

Aberrant activation of the classical complement pathway in the brain is implicated in contributing to synapse loss and neurodegeneration in various neurodegenerative conditions. Given that C3aR is a druggable target in the complement pathway, we evaluated the potential of C3aR KO to rescue neurodegeneration in a tauopathy model and neuroinflammatory responses in an acute endotoxemia model. We found that C3aR KO did not rescue tau pathology, microglia activation markers, neurodegeneration, or behavioral abnormalities in tauopathy model mice. While we found that endotoxemia resulted in numerous transcriptional changes including distinct alterations in subpopulations of microglia, astrocytes and oligodendrocytes, C3aR KO did not impact these alterations. Together, our results suggest that the beneficial effects of blocking the complement classical pathway in neurodegeneration models is likely independent of C3aR activation and raise questions about the rationale for therapeutically targeting C3aR for neurodegenerative disease.

neuroscience↗

bioRxiv2025

A slow and clathrin-dependent mode of compensatory endocytosis in hippocampal boutons at near-physiological temperature

The mode of presynaptic compensatory endocytosis has been controversial for decades. Recently, an ultrastructural study on synaptic membrane retrieval following synaptic vesicle fusion revealed an ultrafast mechanism of endocytosis in mouse hippocampal synapses at physiological temperature. Using live cell imaging of single-vesicle exo- and endocytosis in mouse hippocampal synapses, combined with accelerated optogenetic acidification of synaptic vesicles, we found that compensatory endocytosis occurs mostly through a slow clathrin-dependent and actin-independent mode at both room and physiological temperatures.

neuroscience↗

bioRxiv2025

Protein-primed DNA homopolymer synthesis by an antiviral reverse transcriptase

Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign DNA for degradation1. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this strategy by leveraging DNA synthesis instead2,3. We and others recently showed that DRT2 systems use an RNA template to assemble a de novo gene, leading to expression of an antiviral effector protein, Neo4,5. It remains unknown whether similar mechanisms of defense are employed by other DRT families. Focusing on DRT9, here we uncover an unprecedented mechanism of DNA homopolymer synthesis, in which viral infection triggers polydeoxyadenylate (poly-dA) accumulation in the cell to drive abortive infection and population-level immunity. Cryo-EM structures reveal how a conserved noncoding RNA serves as both a structural scaffold and reverse transcription template to direct hexameric complex assembly and RNA-templated poly-dA synthesis. Remarkably, biochemical and functional experiments identify conserved tyrosine residues within the reverse transcriptase itself that prime DNA synthesis, leading to the formation of high-molecular weight protein-DNA covalent adducts. Synthesis of poly-dA in vivo is regulated by the competing activities of phage-encoded triggers and host-encoded silencers of DRT9. Collectively, our work unveils a novel nucleic acid-driven defense system that expands the paradigm of bacterial immunity and broadens the known functions of reverse transcriptases.

molecular biology↗

bioRxiv2025

Predictive Modeling of acute Graft-versus-Host-Disease using Machine Learning on Immune Cell and Cytokine Profiles at Engraftment

BackgroundAcute Graft-versus-Host-Disease (aGvHD) is a major immune complication following allogenic hematopoietic stem cell transplantation (Allo-HSCT), initiated by conditioning regimen-associated tissue damage. It involves the complex interplay of immune cells and cytokines. Our study aims to leverage machine learning (ML) algorithms on the immune and cytokine profile of Allo-HSCT recipients to develop biomarker-based classification models to predict the onset of aGvHD at the time of engraftment. Materials and MethodsSeventy patients diagnosed with hematological disorders who had undergone Ist Allo-HSCT were recruited from All India Institute of Medical Sciences, New Delhi, India. Peripheral blood (PB) was collected from the patients at the time of engraftment, and the immune cell subtypes and cytokine profiles were analyzed using flow cytometry and ELISA respectively. The individual cell counts were then processed using basic ML models, including support vector classifier with RBF kernel, Decision Tree, and Random Forest, chosen for their mathematical simplicity and feature importance advantage of Decision Trees and Random Forests. Various data settings were utilized in the study: combined immune and cytokine counts, immune cell counts only, cytokine counts only, T-cell counts only, NK cell counts only, dendritic cell counts only, and B-cell counts only. These configurations were selected to investigate how different data sets impact the prediction of aGvHD before its onset. ResultsAt the engraftment flow cytometric analysis of reconstituted lymphocytes in patients who developed aGvHD revealed that there was a remarkable decrease in the ratio of CD4+/CD8+ T-cell and Tregs, with an increase in the cytotoxic regulatory NK-cell, dendritic cells, and B-cell. The levels of pro-inflammatory cytokines (IFN-{gamma}, IL-1{beta}, IP-10, TNF-, IL-17, IL-12p70, MIP-1, MIP-1{beta}, RANTES), and Th17-and Th1-cells were elevated with consequent decline of the levels of anti-inflammatory cytokine IL-10, IL-2, IL-4 and Th2-, Th9-cells. Machine learning based on 48 parameters [all immune cell subsets n=34 and all cytokines (n=14)]. The correlation heat map shows a higher correlation of aGvHD with the cytokine profile with or without immune cells (accuracy: 1), T-cell alone (accuracy: 0.96); NK-cell alone (accuracy: 0.93); dendritic cells alone (accuracy: 0.90), B-cell alone (accuracy: 0.86). ConclusionThe current models classify perfectly, indicating the potential for a ML algorithm in predicting the onset of aGvHD. However, a study with a larger sample size is required to validate these classification models and mitigate the risk of overfitting observed due to the consistently high performance. The study also highlights the potential of cytokine profiles as a viable alternative to T-cell counts, as evidenced by the correlation heat map and classifier models. These findings provide valuable insights into dataset requirements and future directions for integrating ML models into aGvHD prediction.

immunology↗

bioRxiv2025

A Drd1-cre mouse line with nucleus accumbens gene dysregulation exhibits blunted fentanyl seeking

The synthetic opioid fentanyl remains abundant in the illicit drug supply, contributing to tens of thousands of overdose deaths every year. Despite this, the neurobiological effects of fentanyl use remain largely understudied. The nucleus accumbens (NAc) is a central locus promoting persistent drug use and relapse, largely dependent on activity of dopamine D1 receptors. NAc D1 receptor-expressing medium spiny neurons (D1-MSNs) undergo molecular and physiological adaptations that contribute to negative affect during fentanyl abstinence, but whether these neuroadaptations also promote fentanyl relapse is unclear. Here, we obtained Drd1-cre120Mxu mice to investigate D1-dependent mechanisms of fentanyl relapse. We serendipitously discovered this mouse line is resistant to fentanyl seeking, despite similar intravenous fentanyl self-administration, and greater fentanyl-induced locomotion, compared to wildtype counterparts. In drug naive mice, we found Drd1-cre120Mxu mice have elevated D1 receptor expression in NAc, alongside increased expression of MSN marker genes Chrm4 and Penk. We show Drd1-cre120Mxu mice have increased sensitivity to the D1 receptor agonist SKF-38393, and exhibit divergent expression of MSN markers, opioid receptors, glutamate receptor subunits, and TrkB after fentanyl self-administration that may underly blunted fentanyl seeking. Finally, we show fentanyl-related behavior is unaltered by chemogenetic manipulation of D1-MSNs in Drd1-cre120Mxu mice. Conversely, chemogenetic stimulation of putative D1-MSNs in wildtype mice recapitulated the blunted fentanyl seeking of Drd1-cre120Mxu mice, supporting a role for aberrant D1-MSN signaling in this behavior. Together, our data uncover alterations in NAc gene expression and function with implications for susceptibility and resistance to developing fentanyl use disorder.

neuroscience↗

bioRxiv2025

Integrated Cross-Disease Atlas of Human And Mouse Astrocytes Reveals Heterogeneity and Conservation of Astrocyte Subtypes in Neurodegeneration

Astrocytes play a pivotal role in central nervous system homeostasis and neuroinflammation. Despite advancements in single-cell analyses, the heterogeneity of reactive astrocytes in neurodegenerative diseases, particularly across species, remains understudied. Here, we present an integrated atlas of 187,000 astrocytes from mouse models of Alzheimers (AD) and multiple sclerosis (MS) alongside 438,000 astrocytes from AD, MS, and Parkinsons (PD) patients. Our analysis identified four distinct mouse astrocyte clusters, including two disease-associated astrocyte (DAA) clusters, DAA1 and DAA2. DAA1 displayed reactivity resembling responses to acute stimuli, including endotoxemia, while DAA2 expressed well-known AD risk genes. In an AD model, DAA1 and DAA2 exhibited distinct spatial relationships to amyloid plaques. In humans, we identified eight distinct astrocyte clusters, encompassing homeostatic and disease-associated subtypes. Cross-species analysis linked disease-associated clusters while also highlighting divergent expression in others. Our astrocyte atlas is available through a user-friendly, searchable website: http://research-pub.gene.com/AstroAtlas/.

neuroscience↗

bioRxiv2024

Sporophyte Directed Gametogenesis via the Ubiquitin Proteasome System

Plants alternate between diploid sporophyte and haploid gametophyte generations. In mosses which retain features of ancestral land plants, the gametophyte is dominant and has an independent existence. However, in flowering plants the gametophyte has undergone evolutionary reduction to just a few cells enclosed within the sporophyte. The gametophyte is thought to retain genetic control of its development even after reduction. Here we demonstrate that male gametophyte development in Arabidopsis, long considered to be autonomous, is also under genetic control of the sporophyte via a repressive mechanism involving large-scale regulation of protein turnover. We identify an Arabidopsis gene SHUKR as an inhibitor of male gametogenesis. SHUKR is unrelated to proteins of known function and acts sporophytically in meiosis to control gametophyte development by negatively regulating expression of a large set of ubiquitination genes specific to post-meiotic gametogenesis. This control is late-emerging as SHUKR homologs are found only in eudicots. We show that SHUKR is rapidly evolving under positive selection suggesting that variation in control of protein turnover during male gametogenesis has played an important role in evolution within eudicots.

plant biology↗