Biology subjects

Du, X.

Publications and source records attributed to Du, X..

At least 19 recordsLinked to original sources

bioRxiv2026

FLASH X-rays preserve neutrophil chromatin to boost antitumor immunity

Ultrahigh dose-rate FLASH radiotherapy spares normal tissue while preserving antitumor activity, positioning it as a promising technology in radiation oncology, but its immunomodulatory mechanisms remain elusive. Here, using a bilateral subcutaneous tumor model in mice, we show that 8-Gy FLASH X-rays, versus an equal dose of conventional dose-rate (CONV) X-rays, elicit a robust abscopal antitumor effect with anti-PD-1 therapy. Single-cell transcriptome and T cell receptor (TCR) profiling reveal that FLASH X-rays plus anti-PD-1 enhance antitumor immune infiltration and TCR clonal expansion in both irradiated and abscopal tumor lesions. Mechanistically, the ultrashort temporal continuity of FLASH dose delivery conserves chromatin compaction in neutrophils during exposure and inhibits neutrophil extracellular trap (NET) formation, thereby dismantling NET-mediated CD8+ T-cell exclusion within primary tumors. Conversely, CONV or split-dose FLASH X-rays induce marked chromatin modifications prior to dose completion, leading to chromatin hyper-relaxation which promotes NETosis and consequently abrogates systemic antitumor immunity. Notably, this detrimental effect can be reversed by pharmacologically suppressing PARylation-mediated chromatin modification and decondensation in neutrophils. These findings identify radiation-induced aberrant chromatin relaxation in neutrophils as a critical determinant of radioimmunotherapy outcomes, providing a rationale for redefining the FLASH effect and advancing its clinical translation.

cancer biology↗

bioRxiv2026

Spatiotemporal Heterogeneity of HPV Integration Architectures Drive Oncogenic Features of Oropharyngeal Cancer

Viral integration is common in human papillomavirus-positive oropharyngeal squamous cell carcinoma (HPV+ OPSCC), but its structural and clinical significance remains unclear. We integrated targeted capture sequencing of 197 HPV+ OPSCCs with long-read nanopore sequencing of 17 tumors and models to characterize HPV-host rearrangements. We developed a novel quantitative informatics framework that classifies integration structures as Type1 (simple, single/low-copy) or Type2 (clustered, high-copy, rearranged). HPV integration occurred in 83% of tumors, with recurrent hotspots including TP63, MYC, CD274, TRAF2, and KMT2C. Type2 events were enriched for HPV E2 disruption, focal human amplifications, preferential transcription, and noncanonical HPV-host RNA fusion isoforms. Type2 tumors showed increased HPV oncogene expression and activation of MYC, NF-{kappa}B/TNF, PI3K-AKT-mTOR, Hippo/YAP-TAZ, and epithelial stemness programs. Multi-region and longitudinal analyses revealed intratumoral heterogeneity and clonal selection of Type2 architectures during progression, supporting integration structure as a potential marker of aggressive behavior and risk stratification.

bioinformatics↗

bioRxiv2026

Thalamic Dysconnectivity and Negative Symptoms in Schizophrenia Spectrum Disorder

Background and Hypothesis Negative symptoms in schizophrenia spectrum disorder (SSD) are associated with poor functional outcomes and reduced quality of life; however, effective treatments remain limited. A better understanding of the underlying brain mechanisms is needed to develop better treatments. Neuroimaging studies implicate multiple brain networks in negative symptoms, though findings remain heterogeneous, potentially reflecting the multidimensionality of both symptoms and brain networks. Larger, more systematic dissections are required to identify the key hub(s) underlying negative symptoms. Study Design Structural MRI data from 394 participants (210 SSD, 184 healthy controls [HC]) were analyzed to identify cortical thickness and subcortical volume demonstrating both SSD-HC differences and associations with negative symptoms measured by the Brief Negative Symptom Scale (BNSS). Regions meeting both criteria were selected as seeds for resting-state functional connectivity analyses in 143 SSD patients to examine association with negative symptoms and their subdomains. Study Results The thalamus was the only region demonstrating significant structural abnormalities both in SSD and an association with BNSS total score (p-FDR<0.05). Functional-network-defined thalamic subregions were subsequently examined. Several thalamic hypoconnectivities were significantly corresponded with negative symptoms, involving thalamic subregions associated with the cortical default mode, somatosensory, medial temporal, and dorsal attention networks (p=0.001, corrected<0.05). Blunted affect showed the most extensive thalamic connectivity alterations, involving the striatum, cerebellum, and temporoparietal junction/superior temporal sulcus (TPJ-STS). Thalamic hypoconnectivity with TPJ-STS was also associated with overall negative symptoms and anhedonia. Conclusions This study identifies the thalamus as a central hub of negative symptom-related dysfunction in SSD and highlights specific thalamic subnetworks as potential targets for circuit-based interventions.

neuroscience↗

bioRxiv2026

Multi-omics fine-mapping uncovers a pleiotropic intestinal enhancer variant linking PMAIP1 regulation to pig growth and fatness

Genetic loci influencing multiple complex traits often remain difficult to interpret because the underlying functional variants, target genes and tissue contexts are unresolved. Here, we investigated the regulatory basis of a shared signal for average daily gain (ADG) and backfat thickness (BF) in Yorkshire pigs. By integrating GWAS in 7,972 pigs, targeted capture sequencing, LD-based fine-mapping, porcine epigenomic annotations, three-dimensional chromatin interaction maps and functional assays, we narrowed the shared SSC1 signal to a 1.59-Mb interval and functionally prioritized rs334769214 (T>G) as the leading candidate variant. The T>G substitution produced marked allele-specific differences in enhancer activity and nuclear-protein binding, while transcription-factor co-transfection assays identified FOXL1-responsive, allele-dependent regulatory activity. Chromatin interaction and CRISPRa analyses supported a regulatory connection between the rs334769214-containing enhancer and PMAIP1, and PMAIP1 overexpression promoted apoptosis in porcine intestinal epithelial cells. In the capture-sequenced subset, the G allele was associated with higher ADG and BF, consistent with a relative loss-of-activation model. Together, these findings delineate a candidate FOXL1-enhancer-PMAIP1 regulatory pathway and demonstrate how multi-omics fine-mapping can advance a shared quantitative-trait locus toward a testable molecular mechanism underlying variation in growth and fatness.

genetics↗

bioRxiv2026

INS-fMRI: a novel method for mapping mesoscale connectome networks in vivo in nonhuman primates

Mapping brain connections is paramount in neuroscience. Lacking has been a method that can systematically map mesoscale (<1mm) connections in the brain in vivo at brainwide scale. Mesoscale mapping is particularly important for NHPs in which information is represented in submillimeter clusters (e.g. cortical columns, striosomes, thalamic rods). Here, we present a method called INS-fMRI, which comprises optical stimulation of single sites in the brain using pulsed Infrared Neural Stimulation (INS), coupled with mapping of functionally connected sites in the brain using ultrahigh field fMRI. It is the only method available for mapping mesoscale connections rapidly (multiple networks mapped within single MRI sessions), systematically (allowing comparison of networks within single individuals), in vivo (no animal sacrifice needed), at whole brain scale, and without viral transfection. This method has broad applicability to a wide range of neuroscience questions. It can be used at any brain site, on different animal models, and on different MRI platforms. The ability to probe circuits repeatedly within single individuals also opens doors for studying changes in mesoscale circuits over time (e.g. for development, aging, disease studies). In addition, as this method circumvents the need for viral transfection, there is exciting potential for human clinical application.

neuroscience↗

bioRxiv2026

A multi-tissue epigenomic atlas links the sheep non-coding genome to domestication and complex traits

Non-coding regulatory variation drives complex traits, domestication, and evolutionary adaptation, yet the sheep genome lacks high-resolution functional annotation. Here we present SheepEpimap, a multi-tissue regulatory atlas harmonizing 516 CUT&Tag histone modifications, ATAC-seq, and RNA-seq datasets across 43 adult tissues in sheep. We annotated 2.93 million cis-regulatory elements, yielding 557,441 enhancer-gene pairs and 145,407 variants with allele-specific effects. By training a sequence-to-function deep-learning model, we decoded the base-pair syntax of chromatin accessibility, annotated transcription factor motif instances genome-wide, and constructed 12,210 tissue-specific gene regulatory networks (GRNs). Integrating this resource with multi-tissue expression quantitative trait loci, selection sweeps, and genome-wide association studies prioritized non-coding variants driving domestication and complex traits. Finally, cross-species analysis revealed that sequence-conserved, tissue-matched enhancers were significantly enriched in the heritability of complex traits and diseases in humans. In summary, SheepEpimap (https://genome.ucsc.edu/s/mengzhu/SheepEpimap) provides an open-access foundational ecosystem for sheep functional genomics, precision breeding, and comparative biology.

genetics↗

bioRxiv2026

The Everything Bagel Feature Finder: Ultra-fast automated feature finding for untargeted metabolomics

Metabolomics studies are increasingly being applied with hundreds to thousands, even tens of thousands of samples that demand rapid, automated data processing while maintaining analytical sensitivity or quantitative accuracy. A major computational bottleneck is feature finding, which is the transformation of LC-MS and LC-MS/MS data into a set of analyte signals aligned and quantified across samples. Feature finding can be computationally intensive and often requires manual iterative parameter optimization. To accelerate this process, we present the Everything Bagel (EB) feature finder, an ultra-fast automated feature finding tool that integrates feature detection, retention-time alignment, and gap filling designed for run-time and memory efficiency. We benchmarked EB against two automated feature finding methods on eight benchmarking datasets. Specifically, we evaluated these three feature finding methods by measuring spike-in standard detection coverage, dilution series quantification accuracy, and yeast 12C/13C credentialed features. In this evaluation, the EB feature finder achieved performance comparable to, and often exceeding, existing methods while requiring up to 150-fold lower CPU hours and up to 113-fold lower wall time. We further demonstrated the bioanalytical validity of EB by reanalyzing published datasets used for biomarker discovery and reproduced biologically significant features that matched the published findings using manually tuned feature finding settings. Taken along with the speed improvements, we anticipate EB will enhance the ability to automatically analyze datasets with thousands to tens of thousands of samples for the community.

bioinformatics↗

bioRxiv2026

Phagocytic activity of perivascular cell promotes CNS injury pathology

Injury, stroke, and neurological diseases cause persistent accumulation of cellular debris that deteriorates lesion microenvironment and impedes central nervous system (CNS) repair. Debris clearance in the injured CNS has long been attributed primarily to microglia and infiltrating macrophages. Here, we identify perivascular cells as previously unrecognized phagocytes that expand after injury and exhibit robust phagocytic activity. Perivascular cell phagocytosis is conserved across multiple mouse models of CNS injury and human stroke lesions. These cells exhibit key hallmarks of phagocytosis, including LC3-associated phagocytosis for efficient lysosomal degradation. Mechanistically, phosphatidylserine serves as the eat-me signal and Axl mediates myelin debris uptake. Myelin phagocytosis drives perivascular cell proliferation, fibrosis and lesion progression. Genetic deletion of Axl in perivascular cells or pharmacological inhibition with the FDA-approved Axl inhibitor Gilteritinib reduces pathology and improves functional recovery after spinal cord injury. Together, these findings establish Axl-dependent perivascular cell phagocytosis as a therapeutic target for CNS repair.

neuroscience↗

bioRxiv2026

A biointegrated living brain stimulator evokes specific neural signalling

Implanted brain stimulators play a crucial role in treating various neurological disorders, including Parkinsons disease (PD), Alzheimers disease, epilepsy, and depression. However, none of the existing implanted brain stimulators can realize specific neuromodulation due to fundamental disparities in signal transmission between electrical signal-induced neuronal responses and neurotransmitter-evoked neural signalling in natural neural circuits, leading to persistent challenges in biosafety and therapeutic effectiveness. Inspired by the dopaminergic neural circuit, we report a biointegrated living brain stimulator (BBS) that integrates ferroelectric bioelectronics, dopaminergic cells, and a gelatin hydrogel matrix, enabling dopamine neurotransmitter-evoked neural signalling. In contrast to conventional brain stimulators, the BBS are capable of programmed secretion of physiological-level dopamine, specifically activating nigral dopamine pathways and restoring motor function in a rodent PD model. By integrating the advantages of both bioelectronics and medicine, this lifelike BBS offers a great promise for next-generation bioelectronics, medicine, and brain-machine interfaces.

bioengineering↗

bioRxiv2026

A sequence-based proactive intelligence for influenza antigenic profiling improves vaccine strain selection

Seasonal influenza viruses accumulate antigenic changes, eroding population immunity and necessitating recurrent vaccine updates. Hemagglutination inhibition (HI) assays are the standard for measuring antigenic relationships between circulating and vaccine strains; however, their limited throughput constrains the scale and timeliness of surveillance. Here, we present fluProfiler, a foundation-model-based framework that learns a stable mapping from viral sequences to antigenic space and uses this representation to support influenza antigenic prediction, vaccine strain evaluation, and diversity-driven sampling. fluAgPredictor aligns hemagglutinin (HA) and neuraminidase (NA) sequence representations with HI-derived antigenicity, enabling accurate and consistent inference of pairwise antigenic distances across surveillance-aligned evaluation settings. Without prior annotation of antigenic sites, it identifies key residues in immunodominant epitopes and reveals the cooperative contributions of HA and NA to antigenic variation. Building on this antigenic-space representation, fluVacSelector provides antigenic coverage scores that are concordant with World Health Organization (WHO) vaccine recommendations while also flagging potential candidates that may offer broader coverage ahead of formal consultations. fluAgEnhancer further leverages the same representation to prioritize antigenically informative and diverse strains for experimental characterization, achieving comparable predictive accuracy with approximately 25% fewer HI measurements than random sampling. Together, these modules provide a high-throughput and interpretable complement to HI testing, converting routine genomic surveillance into a more proactive, data-driven support system for antigenic monitoring and vaccine strain selection.

bioinformatics↗

bioRxiv2026

A Lightweight Dual-Attention Neural Network for In-Situ Hyperspectral Classification of Microalgae

Accurate monitoring of microalgae is essential for assessing marine ecological health and preventing harmful algal blooms in ocean engineering. Current in situ identification methods often suffer from limited discriminative feature extraction and inadequate adaptation to complex underwater imaging conditions. This study introduces a lightweight dual-attention neural network, termed ANMM, designed for real-time, in situ hyperspectral classification of microalgae within integrated underwater monitoring systems. The model strengthens a deepened AlexNet backbone with multi-head latent attention (MLA) and multi-head self-attention (MSA) mechanisms, which jointly enhance local feature refinement and global spectral dependency modeling. An early-stopping strategy is further incorporated to prevent overfitting and ensure robust generalization. Evaluated on a custom dataset of field-collected fluorescence spectra, the model achieves a classification accuracy of 98.91%, outperforming several state-of-the-art deep-learning counterparts. With a compact parameter size of 16.34 M and low-latency inference on edge hardware, the system demonstrates strong potential for deployment on embedded underwater sensing platforms. This work provides a practical and efficient AI-driven solution for continuous marine microalgae monitoring, supporting advances in ocean observation technology and ecological engineering.

microbiology↗

bioRxiv2026

Automating the Construction of Contextualized Biomedical Knowledge Graphs for Scientific Inference

Biomedical interactions are inherently dynamic, often shifting or even reversing under specific physiological states. However, existing extraction methods simplify these complex mechanisms into context-agnostic binary associations, resulting in semantic loss and contradictory evidence. Here, we present AutoBioKG, an end-to-end framework that constructs context-aware knowledge graphs by leveraging composite triples to encode environmental conditions and entity attributes alongside core relationships. Powered by an open information extraction model trained on BioOpenIE and further refined through self-training with pseudo-labels from unlabeled literature, the framework exhibits broad generalization. Notably, AutoBioKG achieved the highest zero-shot F1 across DDI, ChemProt, and BioRED, outperforming the best-performing baseline on each benchmark by 3.6-17.8 percentage points. Furthermore, AutoBioKG-derived graphs outperformed existing approaches on yes/no, factoid, and list questions in the BioASQ biomedical question-answering evaluation, particularly for queries requiring fine-grained contextual information. Together, these results support AutoBioKG as a scalable framework for transforming unstructured literature into structured, context-aware biomedical knowledge.

bioinformatics↗

bioRxiv2025

Early blood-spinal cord barrier stabilization preserves peri-lesional tissue and improves recovery after SCI

Vascular disruption is an early and critical event in spinal cord injury (SCI), but its contribution remains poorly understood. Using novel in vivo two-photon dual-dye imaging, we found simultaneous blood-spinal cord barrier (BSCB) leakage and venous dilation in both the injury epicenter and adjacent transitional segment after cervical SCI in rats. Notably, vascular permeability in the transitional zone preceded axonal and neuronal loss, revealing a therapeutic window. Systemic delivery of ferulic acid-glycol chitosan (FA-GC) nanoparticles, a membrane-sealant, rapidly stabilized the compromised vasculature, reduced neuronal loss in the transitional region, and improved forelimb muscle strength. These findings identified acute vascular leakage beyond the injury epicenter as a driver of secondary pathology and highlight early vascular stabilization as promising therapeutic strategy.

pathology↗

bioRxiv2025

Planar cell polarity-directed cell crawling drives polarized hair follicle morphogenesis

During epithelial morphogenesis, cell polarity aligns individual cell behaviors into collective motions that shape developing tissues. Here, we combine experiments with computational modeling to investigate how cell-scale forces oriented by Planar Cell Polarity (PCP) direct the collective, counter-rotational cell flows that occur during hair placode morphogenesis. We rule out that PCP directs apical neighbor exchanges, as junctional myosin and PCP protein localization are not co-correlated with junction shrinkage. Instead, we find that PCP directs anterior-directed crawling of placode cells along the basal surface of the tissue through a mechanism that requires cell crawling regulator Rac1. Modeling the placode as a continuum viscoelastic fluid, we find that active forces from cell crawling at the basal surface is sufficient to generate the experimentally observed counter-rotational cell motion at the apical surface. Our results show an unexpected role for PCP in epithelial morphogenesis, centering the basal surface as the site of force generation.

developmental biology↗

bioRxiv2025

A multi-tissue atlas of genetic regulatory effects in sheep

Characterizing the impact of genomic variants on genome function and ultimately complex traits in livestock is essential for the development of sustainable precision agriculture and comparative genomics. Here, as part of the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we present the pilot phase of the SheepGTEx resource through analyzing 6,761 RNA-sequencing samples of 51 primary tissues in a multi-breed population of sheep. We identify millions of regulatory variants associated with seven types of molecular phenotypes, and fine-map 322,468 primary and 114,017 non-primary effects, revealing a high degree of regulatory allelic heterogeneity. We systematically characterize the pleiotropic effects of these variants on molecular phenotypes, assess their context-specific regulatory patterns across tissues, breeds, sexes, and developmental stages, as well as explore their evolutionary constraints across mammals. Finally, we demonstrate the substantial potential of the SheepGTEx resource (https://sheepgtex.farmgtex.org), by providing examples of regulatory mechanisms underpinning 34 complex traits, population divergence between European and Asian breeds, and adaptive evolution in sheep over the past ten millennia.

genomics↗

bioRxiv2025

Exploring the Restoration of Memory Post-NeuronalRegeneration from Induced ALS-FTD in Dugesia tigrina

Amyotrophic lateral sclerosis-frontotemporal dementia (ALS-FTD) is a neurodegenerative disease characterized by progressive neuronal loss and motor decline. Recovery remains beyond therapeutic reach, and even complete neurogenesis does not ensure preservation of memory capacity (defined as the strength of synaptic connections). Freshwater planarians, capable of whole-body regeneration and associative learning, provide a tractable model to study the relationship between neuronal damage and behavior. Their "single-circuit" centralized nervous systems allow evaluation of oxidative stress, a key driver of ALS-FTD pathology, which was induced via hydrogen peroxide. In this study, 180 planaria underwent three phases. Phase 1 established baseline memory using a 28-day operant conditioning protocol with a light-based training device. Success was determined by the proportion of planaria in concentric circles defined as zones (A-C) with a respective gradient descent of light concentration. Phase 2 determined hydrogen peroxide (H2O2) concentrations sufficient to induce oxidative stress that triggered regenerative signaling and neuronal damage without lethality. Phase 3 applied the optimal concentration, allowed regeneration, and retested memory. The optimal concentration of hydrogen peroxide was 5 ppm, triggering blastema formation and neuronal damage while preserving viability. Zone occupancy analyses utilizing prior found concentration revealed measurable post-exposure shifts: Zone A increased initially but trended lower post-exposure, Zone B increased, and Zone C decreased significantly. These results indicate that while memory capability persists after neurogenesis, the quality of memory decreases. In accordance with this study, current treatments for ALS-FTD that focus solely on neurogenesis will not fully restore cognitive function.

neuroscience↗

bioRxiv2025

Standardizing the mouse MCAO Stroke Model: Distinguishing Internal Carotid vs Pterygopalatine Artery Occlusion

BackgroundThe intraluminal middle cerebral artery occlusion (MCAO) model is widely used in preclinical stroke research, but outcomes remain inconsistent because of variable occlusion times and inadvertent filament placement into the pterygopalatine artery (PPA). MethodsWe applied a modified version of the Koizumi method to directly visualize the internal carotid artery (ICA)-PPA bifurcation and systematically compare targeted ICA versus PPA occlusion. We combined multiple complementary methods - survival studies, neurological scoring, 2,3,5-Triphenyltetrazolium chloride (TTC) infarct staining, Evans blue blood brain barrier (BBB) permeability assays, laser speckle cerebral blood flow imaging, small-animal magnetic resonance imaging (MRI), and evaluation of inflammatory gene expression through qPCR - to rigorously characterize injury patterns, survival, and inflammatory responses. ResultsICA occlusion approximately caused a rapid 70% reduction in cerebral blood flow, progressive infarction (15 min: smaller infarct with approximately 50% 7-day survival; 30 min: moderate infarct but >50% mortality), and cortical edema. In contrast, PPA occlusion produced only a gradual 44% decline in blood flow, small infarcts at 60 min) and preserved survival (80% at 7 days). Finally, magnetic resonance imaging in 15-minute ICA occluded mice identified the development of cortical edema which was not observed in sham, 15-minute PPA, or 60-minute PPA mice. ConclusionThese findings identify 15-minute ICA occlusion as the most practical balance between reproducible infarction and survival for long-term studies, while 30 minutes is best reserved for short-term infarct induction when survival is less critical. By resolving two critical sources of MCAO variability, occlusion duration and vascular targeting, this study provides a standardized protocol and evidence-based occlusion benchmarks that will improve reproducibility in preclinical stroke studies

physiology↗

bioRxiv2025

Comparative transcriptomics reveals an extracellular worm argonaute as an ancestral regulator of LTR retrotransposons.

Safeguarding the genome from non-self elements is essential for reproduction, development, and ageing. One of the major threats to genome integrity is Transposable Elements (TEs), which can be post-transcriptionally silenced through small RNAs (sRNAs) and argonaute proteins. Recent work suggests TE-derived sRNAs may also act as virulence factors in host-pathogen interactions. During infection, the intestinal parasite Heligmosomoides bakeri secretes a single argonaute protein (exWAGO) and a wide variety of TE-derived sRNAs. Although exWAGO is highly expressed, conserved, and secreted by parasitic nematodes, its function and sRNA guide preference remain unclear. Using comparative transcriptomics of the sRNAs bound to exWAGO within parasites of rodents, livestock and humans, and its orthologs in C. elegans, we found that exWAGO is capable of loading sRNAs produced from all classes of TEs in addition to some protein-coding and non-coding transcripts. However, our results suggest that the ancestral endogenous function of exWAGO was likely linked to LTR retrotransposon regulation. To understand how this relates to potential extracellular functions of exWAGO we also examined the sRNAs bound to exWAGO secreted by H. bakeri in both vesicular and non-vesicular forms. Extracellular exWAGO preferentially loads sRNA guides derived from non-autonomous and fragmented LTRs, suggesting the existence of adaptable reservoirs of regulatory sRNAs with potential roles in cross-species RNA communication. Together, our results show that exWAGO is part of an evolutionarily conserved pathway for LTR retrotransposon regulation, while preferentially utilising degenerated elements as sources of secreted sRNAs.

genomics↗