Biology subjects

Wen, X.

Publications and source records attributed to Wen, X..

At least 19 recordsLinked to original sources

bioRxiv2026

DEPICT enables sample-centric therapeutic prioritization across evolving and spatially heterogeneous tumor states

Accurate treatment selection remains a major challenge in precision oncology because tumors with similar genomic alterations can respond differently to therapy. Most drug-response models evaluate individual drugs or drug-sample pairs, whereas clinical decision-making requires therapies to be prioritized within each tumor context. Here we present DEPICT (Drug Efficacy Prediction via Integrated ConText), a sample-centric deep learning framework that reframes drug-response prediction as the relative prioritization of therapies within an individual tumor context. DEPICT integrates transcriptomic and mutational features with prior alteration-therapy relationship and was trained on 231,880 cell line-drug pairs comprising 941 cancer cell lines and 289 compounds. Without retraining, DEPICT retained predictive performance in independently profiled cell lines, experimentally induced drug-resistant states and matched primary lung tumors and patient-derived organoids. Representations learned exclusively from bulk pharmacogenomic data further captured progressive drug-response states at single-cell resolution and outperformed existing single-cell drug-response inference methods. Applied to spatial transcriptomic data, DEPICT resolved clone-associated therapeutic heterogeneity within individual lung tumors, and predicted regional differences were recapitulated in matched multiregional organoid drug-response assays. These findings establish sample-centric therapeutic prioritization as a transferable strategy for modeling dynamic and spatially heterogeneous drug vulnerabilities across biological scales.

bioinformatics↗

bioRxiv2026

A learned oral signal drives long-lasting thirst satiation

Drinking quenches thirst long before the ingested water has been absorbed. Here we investigate the mechanism by combining sham drinking, which uncouples water ingestion from rehydration, with recordings of thirst-promoting neurons in the brain. We show that sham drinking suppresses thirst and rapidly inhibits thirst-promoting neurons despite no water absorption. Remarkably, this suppression of thirst neurons in the absence of rehydration is proportional to the amount of water consumed and persists for tens of minutes after drinking has stopped. This sustained inhibition is triggered by passage of water through the oral cavity, but not licking or swallowing alone, and undergoes extinction with repeated sham drinking, indicating it is learned. Complementary experiments using hypertonic saline demonstrate this learning is bidirectional. These findings reveal that the experience of rapid thirst quenching is not a hard-wired response to the consumption of water, but rather a learned prediction of future bodily state.

neuroscience↗

bioRxiv2026

Prevention of Unc13a cryptic splicing is sufficient to preserve memory

TDP-43 dysfunction is thought to underlie frontotemporal dementia and limbic-predominant age-related TDP-43 encephalopathy, neurodegenerative dementias currently without effective therapy. Therapeutic strategies are designed to correct individual cryptic targets of TDP-43, such as UNC13A, whereby its cryptic splicing compromises synaptic function, yet the sufficiency of such an approach to prevent memory deficits is unclear. Using a forebrain neuron-specific TDP-43 knockout mouse model that recapitulates TDP-43 dysfunction occurring during early stages of human disorders, we found here that prevention of cryptic splicing to include that of Unc13a attenuated memory deficits. We show that genetic ablation of Unc13a cryptic exon solely in such TDP-43 knockout mice is sufficient to preserve cognition, supporting the clinical value of targeting UNC13A to mitigate memory deficits. Prevention of cryptic splicing of multiple targets of TDP-43 additionally attenuate neuron loss. For optimal outcomes in TDP-43 related dementias, these findings thus strongly support strategies designed to repress cryptic splicing of multiple targets of TDP-43, including UNC13A.

pathology↗

bioRxiv2026

Planning in Nonhuman Primates Emerges from Structure Knowledge and is Distinct from Attention, Working Memory, Effort Control, and Learning

Forward planning involves mentally simulating future choices. Such mental simulation may constitute an independent cognitive operation, or it may be intricately linked to canonical cognitive operations supporting working memory of choice options, covert attentional information sampling, forming memory models of problem structure and effort control for pursuing future goals. Here, we test the relative independence of planning in non-human primates with an object-sequence planning task assessed together with an assay of simpler cognitive tasks. The sequence task unexpectedly masked objects at future serial positions probing NHPs to plan ahead serial future choices. We found that five of six subjects planned ahead 2-3 ordinal positions. Planning depth was predicted by knowledge of the serial structure but constituted a unique cognitive factor that was distinct from sequence memory, object memory, and learning efficacy. Similarly, planning was segregated from working memory capacity, attention, inhibitory control and effort control. These findings suggest that planning ahead constitutes a separate construct not reducible to other domain-general cognitive operations, and emerges in NHPs that successfully form an internal model of the problem structure.

animal behavior and cognition↗

bioRxiv2026

Unraveling the Mechanism of HIV-1 Hypersusceptibility to Tenofovir Imparted by Islatravir Resistance Mutations

In response to the newly approved antiretroviral therapy (ART) islatravir (ISL), the M184V and A114S resistance mutations have emerged in the human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT). These mutations markedly hypersensitize RT to the globally administered ART tenofovir disoproxil fumarate (TDF). We have solved six structures - four by X-ray crystallography and two by cryo-EM - that capture the single- and double-mutant RTs during inhibitor incorporation and demonstrate the role of the mutations in altering protein-antiviral interactions. These snapshots reveal that the smaller, more flexible TDF diphosphate (TDF-DP) can better accommodate mutation-induced active site changes than ISL triphosphate (ISL-TP). Structural differences between the two inhibitors are consistent with biochemical determination of inhibitory constants (Kis), highlighting differences at the step of inhibitor incorporation. Virological evaluation of ISL and TDF combinations reveals additive inhibition of HIV-1. Given the converse ISL hypersusceptibility imparted by the TDF-resistant K65R mutation, we propose ISL and TDF as a combination that can inspire future therapeutic options.

biochemistry↗

bioRxiv2026

Nephrotoxicity of Immune Checkpoint Inhibitors in Mice with a Human Immune System

IntroductionImmune checkpoint inhibitors (ICIs) enhance antitumor responses by blocking inhibitory receptors, including PD-1 and CTLA-4. Overactivation can trigger systemic toxicity akin to autoimmune diseases, including kidney manifestations. We sought to 1) profile immune signaling and 2) interrogate potential mechanisms of ICI-related kidney injury in a Human Immune System (HIS) tumor-bearing mouse model treated with nivolumab and ipilimumab. MethodsImmunodeficient BRGS (BALB/c-Rag2nullIl2r{gamma}nullSirpNOD) neonates were engrafted with human CD34+ cells to generate HIS-BRGS mice. Human MDA-MB-231 tumor cells were implanted subcutaneously; once tumors reached [~]150 mm3, mice received weekly intraperitoneal vehicle (PBS) or ICI (nivolumab 20 mg/kg + ipilimumab 10 mg/kg) for 4 weeks (Veh BRGS n=4; ICI BRGS n=6; Veh HIS-BRGS n=7; ICI HIS-BRGS n=7). Kidneys were evaluated by histopathology (H&E, TEM), flow cytometry for human immune phenotypes, multiplex ELISA (80 human proteins; 10 injury biomarkers), bulk RNA sequencing, and targeted qPCR. Pearson correlations identified predictors of histopathological injury. ResultsRenal vasculitis and interstitial nephritis were observed only in ICI-treated HIS-BRGS mice. These kidneys showed a shift toward CD4+ T-cell enrichment with an increased TNF- production capacity compared to CD8+ counterparts. Toxicity was accompanied by increased renal concentrations of human cytokines, chemokines, and soluble receptors. ICI treatment significantly elevated serine proteases (Granzyme A/B) and NGF-{beta}, while decreasing IL-4. Interstitial nephritis correlated with renal PD-1 and MIF. Renal vasculitis correlated with kidney PD-1, CCL1, MIF, Granzyme A, IL-15, and BAFF. Traditional injury biomarkers (KIM-1, NGAL) remained unchanged; however, a trending decrease in EGF was observed. ConclusionsOur study suggests that shifts in human T-cell populations and specific immune proteins could serve as promising biomarkers and mechanistic targets for ICI nephrotoxicity. The tumor-bearing HIS-BRGS mouse model reproducibly recapitulates the histopathological and immunological features of human ICI-induced nephrotoxicity and represents a validated preclinical platform for testing novel therapeutic interventions to preserve kidney function during cancer immunotherapy. Translational StatementImmune checkpoint inhibitor (ICI)-associated nephrotoxicity occurs in up to 25% of treated patients, yet the immunological mechanisms driving renal injury remain poorly characterized due to the scarcity of human biopsy material and the absence of robust preclinical models that recapitulate human immune responses. This study demonstrates that tumor-bearing humanized immune system (HIS) mice treated with combined nivolumab and ipilimumab reproducibly develop renal vasculitis and interstitial nephritis mediated by a human CD4+ T cell-dominant infiltrate, mirroring the clinicopathological features reported in patients with ICI-associated acute kidney injury. By integrating histopathology, flow cytometry, multiplex proteomics, and transcriptomics, we identify a coordinated immune network, including IL-15, CCL1, MIF, GZMA, and BAFF, that correlates with the severity of renal pathology and represents tractable mechanistic targets and candidate biomarkers. These findings provide a validated preclinical platform for dissecting irAE mechanisms and testing novel therapeutic strategies to preserve kidney function during cancer immunotherapy.

pharmacology and toxicology↗

bioRxiv2026

Sequence Design and Phylogenetic Inference with Generative Flow Networks

Phylogenetic inference remains computationally challenging due to the exponentially growing tree topology search space, and current methods rely heavily on multiple sequence alignments (MSAs) which are expensive and error-prone. We propose AncestorGFN, a proof-of-concept approach leveraging Generative Flow Networks (GFlowNets) for simultaneous sequence generation and phylogenetic exploration without requiring explicit MSAs. Our method learns to generate sequences matching a target distribution while the flow trajectories implicitly encode structural relationships among sequences. We demonstrate that greedy traceback on maximum-flow trajectories recovers shared intermediate states suggestive of common ancestry, and evaluate on the let-7 microRNA family where the learned flow structure qualitatively captures phylogenetic branching patterns. Furthermore, beam search at inference time discovers novel sequences clustering near known targets, suggesting applications in de novo sequence design. This work establishes an initial foundation for alignment-free phylogenetic exploration using generative models.

synthetic biology↗

bioRxiv2026

Structural Basis of Polypurine Track Strand Displacement by HIV-1 Reverse Transcriptase

To complete reverse transcription, HIV-1 reverse transcriptase (RT) must displace the RNase H-resistant polypurine tract (PPT) primers. This enables synthesis of the long terminal repeats and formation of the central cDNA flap. However, the molecular mechanism of this PPT strand displacement (SD) has remained unknown, and no structural data exist on how a retroviral polymerase execute these reactions. We report the first cryo-EM structures of HIV-1 RT bound to nucleic acid substrates containing either a PPTRNA or PPTDNA displacement strand, with incoming dATP positioned at the polymerase catalytic site. These structures reveal key features of the PPT displacement mechanism by RT. Specifically, we observed a binding mode where the template nucleotide (T1) base-paired to the first displacement nucleotide (D1) undergoes a 90{degrees} rotation relative to the preceding template base (T0). This sharp template flip positions D1 [~]30 [A] away from the primers 3-end and is coordinated by RTp66 residues at the SD interface: F61 and R78 contact T1/T0 to drive template translocation, while W24 engages both T1 and D1 to stabilize the displacement strand. Biochemical and virological mutagenesis experiments confirm that interactions with F61 and R78 are essential for both canonical cDNA polymerization and SD, whereas the W24-nucleotide interactions are required exclusively for SD but are dispensable for standard cDNA synthesis. These results contribute to the structural and functional understanding of PPT strand displacement by HIV-1 RT and reveal a distinct mechanistic vulnerability for the design of next-generation antiretrovirals.

biochemistry↗

bioRxiv2026

MAMGL: A memory-augmented meta-graph learning framework for adolescent major depression disorder diagnosis

BackgroundAdolescent major depressive disorder (AMDD) is a prevalent and heterogeneous psychiatric condition that emerges during a critical period of brain development. Neuroimaging-based biomarkers derived from resting-state functional magnetic resonance imaging (rs-fMRI) hold promise for objective diagnosis; however, pronounced inter-individual variability and limited sample sizes pose major challenges for robust model development. MethodsWe propose a memory-augmented Meta-Graph Convolutional Network (BrainMetaGCN) to classify AMDD using rs-fMRI functional connectivity. Individual functional connectivity matrices were constructed by parcellating rs-fMRI time series into cortical regions of interest and computing pairwise correlations. A meta-graph generator dynamically learned subject-specific graph structures, which were processed by lightweight graph convolutional layers. A memory neural network was incorporated to encode population-level prototypical connectivity patterns and generate individualized representations via attention-based retrieval. Model performance was evaluated across multiple independent datasets and compared with state-of-the-art deep learning approaches. Additionally, network interpretability was examined through cortical hierarchy analysis and functional enrichment of discriminative network components. ResultsThe proposed BrainMetaGCN consistently outperformed baseline models, including convolutional and transformer-based approaches, achieving higher accuracy, area under the receiver operating characteristic curve, sensitivity, and specificity. Memory-module-derived functional networks exhibited clear modular organization and showed a significant positive correlation with cortical functional hierarchy, supporting their neurobiological validity. Functional enrichment analyses implicated synaptic transmission, axon guidance, receptor tyrosine kinase signaling, and immune-related pathways, suggesting neurodevelopmental and neuroimmune mechanisms underlying AMDD. Ablation analyses confirmed that memory augmentation and dynamic meta-graph construction were critical for robust performance under small-sample conditions. ConclusionsThis study introduces a robust and interpretable memory-augmented graph learning framework for AMDD classification. By effectively balancing individual specificity and population-level generalization, BrainMetaGCN advances neuroimaging-based precision diagnosis and provides new insights into the neural and biological mechanisms of adolescent depression.

neuroscience↗

bioRxiv2026

Transporter-Mediated Uptake of Microcystin-LR in Human Trophoblasts: Regulation By Oxygen Concentration and Cell Fusion

BackgroundRising global temperatures and eutrophication are increasing the intensity and frequency of cyanobacterial harmful algal blooms that release toxins including microcystin-LR (MC-LR). MC-LR inhibits protein phosphatases in the human liver and brain, but its accumulation in the placenta is unclear. Placental transporter expression varies across pregnancy and is influenced by physiological cues, such as low oxygen concentrations which activate HIF1A, and trophoblast cell fusion forming syncytiotrophoblasts that engage CREB-driven transcription. This study examined whether MC-LR accumulates in placental cells, which transporters mediate uptake, and how these transporters are regulated by HIF1A and CREB. MethodsIntracellular accumulation of MC-LR (0.1-10 {micro}M, 3 hour) was measured in human cytotrophoblasts (JAR, BeWo) and extravillous trophoblasts (HTR-8/SVneo) by western blotting for MC-LR-adducted proteins. Organic anion transporting polypeptide (OATP) involvement was tested using cyclosporin A (10 {micro}M), an OATP inhibitor, before exposure to the OATP substrate or MC-LR. Cells were also cultured under 3%, 8%, or 20% O2 to induce hypoxic responses or treated with forskolin (a potent intracellular cAMP inducer) to stimulate cell fusion before MC-LR exposure. ResultsMC-LR accumulated in all three placenta cell lines in a concentration-dependent manner. Cyclosporin A reduced MC-LR uptake by 57% in JAR cells, confirming OATP-mediated transport. Low O2 increased OATP4A1 expression and function but reduced protein phosphatase expression, decreasing MC-LR-bound proteins by 52-72%. Forskolin increased OATP4A1 expression and enhanced MC-LR uptake >2.5-fold. ConclusionMC-LR enters placental trophoblasts via active OATP transport, likely OATP4A1, and uptake increases under hypoxia and trophoblast fusion.

pharmacology and toxicology↗

bioRxiv2026

Association of CRP and synovial fluid HMGB1 with Pain in Oligoarticular and Polyarticular Juvenile Idiopathic Arthritis: a cross-sectional study

BackgroundPain is one of the most prevalent and distressing symptoms in juvenile idiopathic arthritis (JIA) and often persists despite treatment. Damage-associated molecular patterns (DAMPs), such as high mobility group box 1 (HMGB1) and S100A8/A9, have been implicated in inflammatory activation and nociceptive sensitization, but their associations with pain are not fully characterized in JIA. MethodsPlasma and paired synovial fluid (SF) samples were obtained from patients with oligoarticular and polyarticular JIA from the Juvenile Arthritis Biobank (JABBA). A discovery cohort (n = 79) was used to investigate associations between biomarkers and pain, and these associations were subsequently examined in a validation cohort (n = 38). Levels of HMGB1, S100A8/A9, IL-6, IL-8, C2C, and TRAP5b were measured using ELISA. Associations between biomarkers and patient-reported pain scores were assessed using multivariable linear regression analyses. ResultsPlasma and SF levels of most biomarkers did not show significant correlations, except for TRAP5b, which demonstrated a moderate correlation. In the discovery cohort, as multivariable linear regression analyses, both CRP and SF HMGB1 ({beta} = 1.14, 95% CI: 0.21-2.08; {beta} = 1.54, 95% CI: 0.06-3.01 respectively in fully adjusted model) were independently associated with higher pain scores. SF S100A8/A9 ({beta} = 1.00, 95% CI: 0.10-1.89) was additionally associated with pain in fully adjusted models. Sensitivity analyses confirmed the robustness of these findings. These associations were further supported in the validation cohort. ConclusionsPain in JIA is associated with both systemic CRP and local alarmin markers, with SF HMGB1 showing a particularly robust association. These findings highlight the importance of local joint HMGB1 in pain mechanisms and suggest a potential role for DAMP-mediated pathways in persistent pain in JIA.

immunology↗

bioRxiv2026

Hippocampal Neuroinflammation and Altered Peripheral Neurobiological Protein Profile in Experimental Arthritis and Systemic Juvenile Idiopathic Arthritis

BackgroundChildren with juvenile idiopathic arthritis (JIA) are reported to exhibit increased rates of symptoms affecting emotional regulation and behavior. However, underlying biological mechanisms remain unclear. Neuroinflammation in the central nervous system (CNS) can be triggered by peripheral immune effects and may contribute to these observations. In this study, we aimed to investigate if neurobiological alterations are present in systemic JIA (sJIA), and if CNS neuroinflammation occurs during arthritis, and to explore the potential mechanisms involved. MethodsPlasma samples from patients with active sJIA (n = 16) and sex- and age-matched healthy controls (HCs, n = 16), together with paired samples from the same sJIA patients during inactive disease (n = 12), were analyzed using Olink proteomics to determine the peripheral neurobiological and inflammation protein profiles. Clinical data was retrieved from the Swedish Pediatric Rheumatology Register and medical charts. CNS Neuroinflammatory responses and underlying mechanisms were further explored through in vivo and in vitro experiments. FindingsActive sJIA patients exhibited altered neurobiological protein profiles compared with HCs. These alterations correlated with higher scores of pain and life impact in patients, suggesting that the altered profiles may reflect neurofunctional changes in the patients. Notably, the neurobiological protein profile remained altered even during the inactive phase of the disease. In chronic arthritic mice, microglial activation and impaired neurogenesis were observed in hippocampus, with no significant cortical changes. RNA-seq analysis implicated mitochondrial dysfunction and oxidative stress in mediating neuroinflammation during chronic arthritis in mice. Heme oxygenase 2 (HMOX2) was identified as a peripheral biomarker indicating hippocampal microglia activation. Combined neurobiological and inflammation profiling in sJIA patients implicated Interleukin-6 (IL-6) and Interleukin-18 (IL-18) as key drivers of hippocampal microglia activation during arthritis. InterpretationChronic arthritis is associated with neuroinflammation and altered neurobiological protein profiles in sJIA. HMOX2 emerges as a promising plasma biomarker of CNS changes. IL-6 and especially IL-18 are indicated as key drivers of neuroinflammatory processes. These findings offer insights for clinical monitoring and targeted therapies. FundingThis study was funded by grants from the Swedish Research Council and The Swedish Rheumatism Association. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSChildren with juvenile idiopathic arthritis (JIA) have increased rates of emotional and behavioral disturbances compared with healthy peers. Systemic inflammation and chronic arthritis are suspected to affect the central nervous system, but biological mechanisms in systemic JIA (sJIA) are poorly understood. Added value of this studyIn this study, we demonstrate patients with sJIA have a distinct plasma neurobiological protein profile compared with healthy controls, which correlate with higher pain and life impact scores. In chronic arthritic mice, hippocampal microglial activation, impaired neurogenesis, and mitochondrial dysfunction with oxidative stress are presented. By combining patient and mouse data, we identify heme oxygenase 2 (HMOX2) as a candidate plasma biomarker of hippocampal neuroinflammation and implicate IL-6, and especially IL-18, as key mediators linking chronic arthritis to neurobiological changes. Implications of all the available evidenceThis study provides molecular evidence that neurobiological alterations in sJIA patients and supports incorporating neurobiological and neuropsychiatric monitoring into the clinical follow-up of children with sJIA. We highlight the mechanistic targets and measurable biomarkers (e.g. HMOX2) for future studies and trials aiming to modulate neuroinflammation in chronic arthritis. This study may inform the development of personalized treatment strategies, including IL-18-directed therapies, for patients at risk of neurological or psychosocial complications.

immunology↗

bioRxiv2026

Inhibitory Control, Shifting, and Working Memory Updating Domains form Cognitive Phenotypes in Non-human Primates

Executive functions comprise at least four major subdomains: Inhibitory Control, Updating, Shifting, and Working Memory. Cognitive abilities in these subdomains are partially separable and partially unified in a common cognitive control factor in humans, but how these functions are organized in the nonhuman primate (NHP) is largely unknown. Here, we used a multi-task assessment approach and found that NHPs show within single sessions reliable cognitive markers of Inhibitory Control in an antisaccade task, (ii) Updating abilities in a multidimensional continuous updating task, (iii) Working Memory in a delayed matching task, and (iv) Shifting abilities in a feature-based rule learning task. First, we found that subjects performance fell into three separable cognitive phenotypes with unique strengths and weaknesses across cognitive subdomains. Second, beyond individual tasks cognitive metrics gave rise to four latent cognitive factors separating abilities for shifting/learning and working memory updating, and distinguishing abilities in inhibitory control of exogeneous versus endogenous interference. These results document four separable latent cognitive factors underlying executive control performance in this NHP sample, with inter-subject differences of these factors forming cognitive phenotypes.

animal behavior and cognition↗

bioRxiv2026

Non-canonical function of the splicing activator U2AF2 in promoting intron retention in the lncRNAs PURPL and MALAT1

Intron retention (IR) is increasingly recognized as a feature of long noncoding RNAs (lncRNAs), yet the mechanisms that shape IR in lncRNAs and the functional consequences of this process remain largely unexplored. To investigate how IR contributes to lncRNA regulation, we performed a genome-wide screen to identify factors controlling IR in the lncRNA PURPL. This approach uncovered a prominent role for U2AF2, which promotes retention of a specific intron in PURPL through a weak polypyrimidine tract. IR of this intron drives nuclear enrichment of PURPL and enhances cell proliferation, revealing biological relevance. Transcriptome-wide analyses showed that although U2AF2 broadly supports canonical splicing consistent with its well-established function in promoting splicing, it also facilitates IR within a distinct subset of RNAs, including the nuclear speckle-associated lncRNA MALAT1. Loss of U2AF2 disrupts MALAT1 speckle localization and using MALAT1 knockout cells reconstituted with wild-type or intron deleted variants, we identified a single intron critical for MALAT1s speckle localization. Deletion of this intron from endogenous MALAT1 impaired speckle localization and reduced cell migration, phenocopying the loss of MALAT1. Together, these findings reveal IR as a key regulatory mechanism governing lncRNA localization and function and uncover an unexpected role for U2AF2 in promoting IR within specific lncRNA contexts.

cell biology↗

bioRxiv2026

Lacticaseibacillus rhamnosus GR-1 attenuates Escherichia coli-induced endometritis in mice, accompanied by modulation of uterine microbiota and metabolite profiles

ObjectiveEndometritis in dairy cows is a highly prevalent infectious disease in cattle farming, which can cause persistent inflammatory responses in the uterus. This study aimed to evaluate the therapeutic efficacy of Lacticaseibacillus rhamnosus (L. rhamnosus) GR-1 against Escherichia coli (E. coli)-induced endometritis in mice and investigate its regulatory effects on uterine microbiota and metabolites. MethodsA total of 36 female BALB/c mice aged 7-8 weeks were randomly divided into 4 groups: CONT group, ECOL group (1.0x108 CFU/mL E. coli), AMP group (0.1 mg/kg ampicillin), and GR-1 group (1.0x109 CFU/mL L. rhamnosus GR-1). Uterine morphological characteristics were observed, and the expression of uterine inflammatory cytokines, oxidative apoptosis-related genes and proteins, as well as related reproductive indices were detected. 16S rRNA sequencing and metabolomic sequencing were performed to evaluate the profiles of uterine microbiota and metabolites. ResultsL. rhamnosus GR-1 effectively alleviated E. coli-induced uterine edema and inflammatory infiltration, and modulated the levels of inflammatory factors (MPO, IL-6, IL-1{beta}, TNF-, IL-10 and MDA) in the uterus. Meanwhile, this strain elevated the levels of antioxidant factors (GSH-Px and SOD), inhibited the expression of the oxidative apoptosis-related factors Keap1, Bax and caspase-3, and upregulated that of Nrf2, HO-1, NQO1 and Bcl-2. Furthermore, treatment with L. rhamnosus GR-1 increased the abundance of beneficial uterine microbiota, promoted the accumulation of L-isoleucyl-L-proline and N-acetylcysteine, and ameliorated the pregnancy status of mice. ConclusionL. rhamnosus GR-1 enhanced uterine anti-inflammatory and antioxidant stress capacity to alleviate E. coli-induced endometritis in mice. It modulated uterine microbiota and metabolites, and also improved the reproductive capacity of mice. Thus it may provide a potential antibiotic alternative for the treatment of dairy cow endometritis.

microbiology↗

bioRxiv2025

Mitochondrial membrane junction-mediated ATP channeling drives activity-dependent glucose metabolism

Neurons and brown adipocytes rely on rapid ATP production from accelerated glucose metabolism to sustain bursts of activity upon stimulation, a process known as activity-dependent glucose metabolism. The first committed step in this pathway, the hexokinase I (HK1)-catalyzed phosphorylation of glucose, consumes ATP, raising the question of how this reaction can be accelerated when cytosolic ATP becomes limiting during stimulation. We identify Cell Cycle Exit and Neuronal Differentiation protein 1 (CEND1), expressed in both cell types, as a critical regulator of this process. Loss of CEND1 impairs activity-dependent glucose utilization, ATP generation, and stimulation-evoked activity both in vitro and in vivo. Mechanistically, CEND1 assembles a complex with HK1, voltage-dependent anion channel 1 (VDAC1), and adenine nucleotide translocase 1 (ANT1) at hemifusion-like membrane junction between the outer/inner mitochondrial membrane, channeling mitochondrially derived ATP directly to HK1. These findings uncover a previously unrecognized mechanism that sustains activity-dependent glucose metabolism, with broad implications for energy homeostasis in specialized cell types.

physiology↗

bioRxiv2025

RAFTER: a releasing factor tethered RNA editing system for quantifying mRNA translation

Measurement of mRNA translational efficiency has heavily relied on quantifying the amount of polysome-associated RNAs which would not always reflect the efficient translation. To address this, we developed RAFTER, which combined RNA editing enzyme with translation releasing factor to selectively label successfully translated RNAs. The translational efficiency estimated based on RAFTER correlated well with that by Ribo-seq and Polysome-seq, but with greatly simplified workflow, which enables it for single-cell analysis.

genomics↗

bioRxiv2025

A dopamine circuit regulates locomotor initiation and persistence in Drosophila

Decisions to initiate or terminate locomotion reflect the commitment of an animal to expend energy and thus must be appropriately regulated. Dopaminergic system has been implicated in locomotor regulation but how it controls these decisions remains unclear. Here we show that a dopamine circuit in Drosophila mushroom body regulates cue-induced locomotor initiation and termination by integrating locomotor history and current motivation. This circuit consists of the locomotor-initiator mushroom body output neurons, MBON09, and the locomotor-terminator MBON21. Previous locomotor initiation by default suppresses the propensity of future initiation through depression of MBON09 activity by locomotion-sensitive dopamine afferents, preventing redundant action. Locomotor persistence is promoted through combined inhibition of MBON21 by MBON09 and by distinct dopamine afferents that receive fluctuating motivational signals. Persistent locomotion under high motivational state, in turn, causes dopamine-dependent MBON09 facilitation, reinvigorating locomotor initiation program. Our results revealed a dopaminergic mechanism to transform recent behavior and current motivation into a moment-by-moment internal state that in turn regulates locomotor decisions.

neuroscience↗