Biology subjects

Xu, Z.

Publications and source records attributed to Xu, Z..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

PAD2 knockout reduces myelin protein aggregates, modulates neuroinflammation and protects motor neurons, axons and neuromuscular junction in a SOD1-ALS mouse model

BackgroundDysregulated peptidyl deiminase 2 (PAD2) and aberrant protein citrullination (PC), a posttranslational modification (PTM), are involved in various inflammatory and neurodegenerative diseases. We previously showed in transgenic mice and postmortem human tissues that PC and PAD2 are altered in amyotrophic lateral sclerosis (ALS), a neurodegenerative disease characterized by motor neurons loss, paralysis, and death. Herein, we investigated the role of PAD2 in ALS by PAD2 knockout in a SOD1-ALS mouse model. MethodsTo investigate the role of PAD2-induced citrullination in ALS pathogenesis, we generated PAD2 knockout (PAD2KO) in SOD1G93A ALS mouse model and investigated the consequent modulation on the neuropathology and clinical symptoms, using molecular biology techniques such as qPCR, Western blotting, confocal microscopy, and electron microscopy. Additionally, we identified C3 as being citrullinated in human ALS using ionFinder. ResultsOur results show that PAD2KO blocked the increased PC and reduced myelin basic protein (MBP) aggregates in the ALS model. PAD2KO also improved motor neuron survival and the integrity of myelin, axons, and neuromuscular junctions, and reduced microgliosis in the white matter and C3 protein levels in astrocytes. Clinically, data from monitoring the body weight changes suggests that PAD2KO modulates the course of the disease in the ALS mouse model, accelerating the onset while slowing the progression after the onset, and modestly extending the survival of male mice. ConclusionThese results show that PAD2 is responsible for the increased PC in ALS and PC contributes to neuroinflammation and degeneration of motor neurons and myelinated axons. The modest modulation of the disease phenotype suggests that the role of PC in ALS is complex, involving altered PC in numerous proteins and in multiple cell types. Future studies are needed to investigate how PC modulates individual protein functions in various cell types to understand the contribution of PC to ALS pathogenesis.

neuroscience↗

bioRxiv2026

Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features

Cancer arises from extensive genetic and epigenetic alterations that reshape chromatin, transcriptional regulation, and malignant cell states. To systematically chart cancer-intrinsic regulatory programs, we constructed a pan-cancer single-cell transcriptomic and epigenomic atlas encompassing 60 human cell lines representing 16 tissue origins and 20 cancer types, comprising 240,957 single-nucleus RNA-seq and 223,347 single-nucleus ATAC-seq profiles. Integrative analyses revealed extensive pan-cancer cell-state heterogeneity, core gene-regulatory networks, and a conserved epithelial-mesenchymal transition (EMT) axis that transcends tissue of origin. Copy-number variation analysis identified transcription factor amplification and downstream hyperactivation as key drivers of cancer cell-state reprogramming. To further examine how regulatory programs diverge within a cancer lineage and contribute to clinically divergent outcomes, we performed a focused comparison of cutaneous melanoma with acral melanoma, a rare, UV-independent subtype underrepresented in existing pan-cancer atlases. The comparison uncovered a universal inflammation-suppressive program in acral melanoma and an inflamed regulatory landscape in cutaneous melanoma, with the JAK-STAT pathway and downstream transcriptional responses as central discriminators. Integration of single-cell and bulk datasets across models and patient cohorts further linked in vitro tumor-intrinsic gene regulations with in vivo microenvironmental composition and immunotherapy responses. Together, by extending single-cell multi-omic profiling to rare alongside common cancer subtypes, this atlas offers a resource for mapping pan-cancer and subtype-specific gene-regulatory programs that shape cancer cell-state plasticity.

genomics↗

bioRxiv2026

High-density Lipoprotein Inspired Lipid Nanoparticles for Systemic RNA delivery to the Brain

Systemic delivery of nucleic acids to the central nervous system (CNS) remains fundamentally limited by the blood-brain barrier (BBB) and the lack of cell-type specificity. Inspired by endogenous high-density lipoproteins (HDLs) that naturally traverse the BBB, we engineered a library of 112 HDL-inspired lipid nanoparticles (HLNPs) to deliberately program protein corona composition and direct nanoparticle trafficking across the BBB. High-throughput in vivo screening identified HLNPs with robust brain accumulation and preferential enrichment within distinct neural cell populations. Quantitative proteomic analysis revealed that elevated apolipoprotein A-I/apolipoprotein E and vitronectin/apolipoprotein E ratios correlate with enhanced BBB transport. We further demonstrated that neuron-targeted HLNPs delivering PTEN siRNA produced functional recovery and lesion reduction in a murine traumatic brain injury model, while microglia-targeted HLNPs carrying interleukin-10 mRNA potently suppressed neuroinflammation. Together, these findings establish HLNPs as a versatile RNA delivery platform that leverages protein corona programming for enhanced brain delivery and cell-type-selective targeting.

bioengineering↗

bioRxiv2026

Combinatorial screening of nanoparticles for nose-to-brain RNA delivery to modulate neuroinflammation after traumatic brain injury

Traumatic brain injury (TBI)-induced neuroinflammation can evolve over weeks or months, contributing to ongoing secondary damage and worsening neurological recovery. RNA-based therapeutics hold great potential to regulate inflammatory signaling, but delivery to the brain remains challenging because of the blood brain barrier. Intranasal administration offers a direct non-invasive route for brain access but is often limited by low delivery efficiency. Here we constructed a combinatorial library of DNA-barcoded 103 lipid nanoparticles by varying lipid components with diverse headgroup chemistries and bioreactive moieties. A high throughput screening of these nanoparticles in vivo following intranasal administration led to the identification of top candidates with highest brain accumulation. Intranasal delivery of an antagomir targeting microRNA-9-5p loaded nanoparticle effectively reduced cerebral microRNA-9-5p levels, suppressed inflammatory markers, and improved neurological outcomes in TBI. These results demonstrate a systematic approach for optimizing intranasal lipid nanoparticle design and support the feasibility of RNA delivery to modulate neuroinflammation after brain injury.

bioengineering↗

bioRxiv2026

Circadian misalignment underlies immune escape in breast cancer

Circadian regulation shapes tissue physiology, yet how it organizes cellular and molecular dynamics within the tumor microenvironment (TME) and influences tumor immunity remains unclear. Using temporal single-nucleus multiomic profiling of mouse breast tumors, we uncovered extensive circadian programs that are both cell-type-specific and shared across the TME, governing proliferation and immune responses. Notably, cancer epithelial cells exhibited global acrophase misalignment relative to immune populations. This intercellular desynchrony manifests as temporal decoupling between tumor proliferation and immune activation, discordant antigen presentation and T cell recognition with intrinsic activation-exhaustion overlap in T cells, and asynchronous PD-1/PD-L1 oscillations that sustain checkpoint-mediated suppression. Similar patterns were observed in human triple-negative breast cancer (TNBC). Together, these findings establish intercellular circadian misalignment as a mechanism of tumor immune evasion and position the circadian architecture of the tumor-immune ecosystem as a previously underappreciated determinant of tumor development and therapeutic response. HIGHLIGHTSO_LISingle-cell multiomics maps circadian regulation of tumor-immune programs. C_LIO_LICircadian regulation in cancer epithelial cells is misaligned with immune cell populations. C_LIO_LITumor-immune temporal misalignment undermines antitumor immunity. C_LIO_LICircadian misalignment in human TNBC suggests relevance for immunotherapy timing. C_LI

cancer biology↗

bioRxiv2026

HESTA: a curated and reusable database for the human early organogenesis spatiotemporal transcriptome atlas

BackgroundHuman organogenesis is orchestrated by precise spatiotemporal gene expression. Mapping these dynamic processes requires transcriptomic data that preserve native anatomical context across continuous developmental stages. FindingsWe present a spatiotemporal transcriptome database of human embryogenesis, profiling 77 sagittal sections from 13 euploid embryos (CS12-CS23) using Stereo-seq, yielding 14,708,858 bin50 spots. The atlas annotates 50 organs and maps 198 molecularly distinct substructures, complemented by 607,093 snRNA-seq cells. The database features a Spatial Exploration module for locating sections and visualizing spatial distributions of organs and substructures, and an Organ Atlas module for visualizing gene expression, regulon activities, and pathway enrichment at the single-organ level across stages. ConclusionsThis database provides an interactive resource to access spatial gene expression, substructures, and regulatory networks across 50 developing human organs, supporting further research into the mechanisms of human organogenesis.

bioinformatics↗

bioRxiv2026

A User-Friendly Ear-EEG-Based Brain-Computer Interface Using Text Sequence Stimulation

BackgroundEar-EEG-based brain-computer interfaces (BCIs) provide improved wearability and comfort compared to traditional scalp-EEG systems. However, their performance is constrained by low signal-to-noise ratios (SNRs) and high rates of BCI illiteracy under conventional luminance-modulated steady-state visual evoked potential (SSVEP) paradigms. MethodsThis study introduces a text-sequence stimulation paradigm to address these limitations by leveraging ventral visual pathway responses that are more accessible to electrodes near the ear. Using offline frequency-sweeping experiments across 4-8 Hz, we identified optimal stimulus parameters (4.6-6.8 Hz with 0.25{pi} phase shifts) and integrated them into a 12-target BCI system. We further conducted online experiments to compare the response characteristics and real-time spelling performance between the proposed text-sequence paradigm and conventional luminance stimulation. ResultsComparative experiments with 14 participants demonstrate that text sequence stimuli achieve an average information transfer rate (ITR) of 44.59 {+/-} 10.50 bits/min, outperforming luminance modulation by 76.18% in ITR. Notably, text sequence stimulation effectively mitigated BCI illiteracy, with all participants achieving near or above 70% accuracy (mean: 86.37 {+/-} 9.61%). This represents a significant improvement over luminance modulation, where 50% of users fell below 70% accuracy. ConclusionsBy reducing the flicker area by 14% and mimicking the natural luminance variations that occur during reading, the proposed method enhanced visual comfort. The online results further validate text-sequence stimulation as a high-performance and user-friendly paradigm for ear-EEG BCIs, supporting their practicality for assistive applications.

neuroscience↗

bioRxiv2026

Astrocytic D1 Dopamine-Signaling Regulates Synaptic Remodeling and Cocaine Seeking

D1-type receptor (D1R)-mediated dopaminergic signaling within the nucleus accumbens shell (NAcSh) is essential for forming adaptive circuit changes that embed persistent memories associated with drug seeking and craving. While D1R is expressed in both NAcSh neurons and astrocytes, the specific contribution of astrocytic D1R to drug-related circuit plasticity remains poorly understood. Here, we demonstrate in mouse NAcSh slices that D1R agonists increase astrocytic Ca2+ activity, an effect that is attenuated by astrocyte-specific D1R knockdown. Furthermore, selective knockdown of astrocytic D1R in the NAcSh prior to cocaine self-administration inhibits cocaine-induced generation of silent synapses, therefore hampering the associated remodeling of NAcSh circuits. Behaviorally, knockdown of NAcSh astrocytic D1R expedites the extinction of cocaine seeking and reduces cue-induced reinstatement. These results identify astrocytic D1R as a fundamental component of NAcSh dopamine signaling during cocaine experience that remodels synaptic connections and neural networks underlying drug seeking and relapse.

neuroscience↗

bioRxiv2026

Molecular and Morphological Evidence Reveals Cryptonema producta in Shui Hau, Hong Kong, Previously Misidentified as Anomalocardia flexuosa

For over four decades, the bivalve Anomalocardia flexuosa has been recorded in Hong Kong coastal waters. However, the known native distribution of this heavily exploited commercial species is restricted to the Atlantic coast of South America, raising questions about the biogeographical validity of the Hong Kong populations. By employing an integrative taxonomic approach combining morphological re-evaluations and molecular phylogenetic analysis of the COI gene, we confirm that the species in Shui Hau, Hong Kong, China, has been historically misidentified. The population belongs to Cryptonema producta (syn. Anomalocardia producta).

zoology↗

bioRxiv2026

Myelin basic protein is an RNA chaperone in microglial nuclear retro-transport

CNS oligodendrocytes generate myelin, an RNA-containing proteolipid substance that enhances axonal transmission. In multiple sclerosis (MS), myelin debris is phagocytosed by microglia (MG), and prior studies have detected myelin-derived mRNA in MG nuclei, suggesting a retrograde transport pathway. We report myelin basic protein (MBP) is a nucleic acid-binding and trafficking protein. We found that retro-transport of myelin RNA into the MG nucleus was phagocytosis and importin-dependent. Transcriptomic and proteomic analyses of MG nuclei revealed enrichment of myelin mRNAs and proteins, with MBP singularly detected in soluble and chromatin-associated fractions. MBP bound mRNA with high affinity (Kd {approx} 0.30 nM) and was sufficient to facilitate MG RNA nuclear import in vitro and in vivo. Functionally, MBP mediated the delivery of small interfering RNAs for targeted knockdown of toll-like receptor 4. These findings indicate MBP as an RNA-binding protein capable of MG nuclear import, providing insight into neuroinflammatory pathology of MS.

neuroscience↗

bioRxiv2026

Centromeric origin of Arabidopsis interstitial telomeric repeat domains

The mechanisms underlying the emergence of new DNA repeat classes remain poorly understood. One such example is the formation of interstitial telomeric repeat (ITR) domains commonly viewed as telomere-fossil byproducts of chromosome rearrangements. Here, we report that in Arabidopsis thaliana, ITRs arise from centromeres as centromeric-telomeric mosaic satellites that expand into higher-order structures via in situ amplification. Long-read sequencing of mutation accumulation lines and forward simulations of mutational processes confirmed the propensity of centromeres to form telomeric motifs. During establishment, ITRs adopt an atypical chromatin state that excludes CENH3 incorporation, thereby enabling escape from the functional constraints of centromere identity. Accordingly, a pangenomic survey of natural accessions showed that ITRs vary abruptly and independently of telomere length, notably through transposon-associated block duplications. These findings identify centromeres as major sources of telomeric sequences and an original route for the emergence of new DNA satellite types.

genomics↗

bioRxiv2026

LongAllele: a joint inference framework for allele-specific analysis on long-read bulk and single-cell RNA sequencing

Allele-specific analysis from RNA-seq is a powerful approach to characterize cis-regulatory effects. However, existing methods remain limited in both haplotype inference and allelic testing. Their haplotype-inference workflows separate variant calling, haplotype phasing, and read-haplotype assignment into sequential steps, failing to fully exploit within-read single-nucleotide variant (SNV) linkage information and propagating errors into downstream allelic analysis. At the testing stage, they ignore non-phasable reads lacking heterozygous SNVs, biasing calls and inflating false positives, and remain incomplete across gene-, isoform-, and local-event-level variant effects. Here, we present LongAllele, a statistical framework that employs an expectation-maximization algorithm to jointly infer heterozygous variants, haplotype structure, and read-haplotype assignments from long-read bulk and single-cell RNA sequencing. LongAllele further introduces phasability-aware testing that explicitly accounts for non-phasable reads, avoiding inflated false-positive calls when haplotype information is incomplete. It also enables comprehensive allelic testing across gene-level allele-specific expression (ASE), isoform-level allele-specific transcript usage (ASTU), and local-event-level haplotype-associated exon and junction usage (HAEU and HAJU), providing a multi-scale view of cis-regulation across biological contexts. We applied LongAllele to long-read RNA-seq datasets spanning GTEx (multi-tissue bulk), peripheral blood mononuclear cells (single-cell), human hippocampus (single-nucleus), and human cortex from two Alzheimers disease (AD) case-control cohorts (bulk, Oxford Nanopore and PacBio). LongAllele consistently revealed greater context dependence in expression-level than isoform-level allelic regulation across tissues, cell types, and disease states, and pinpointed high-impact regulatory variants including rare splice-site mutations missed by standalone variant callers. It further showed that purifying selection constrains allelic imbalance at both gene and isoform levels and resolved AD-associated variant effects in individual transcriptomes across long-read platforms.

bioinformatics↗

bioRxiv2026

Rhythmic motor activity alleviates auditory attentional blinks

Effective sensory processing relies on both attention and the motor system, yet whether motor activity could provide attention-like functions to regulate perception remains unknown. We hypothesized that rhythmic motor signals could provide phasic regulation of prioritizing and sampling perceptual targets. Using an auditory attentional blink paradigm that created a temporal deficit in selective attention, we found that temporally aligned finger tapping improved the probe detection during the attentional blink window but impaired performance when attentional resources were abundant. Furthermore, transcranial alternating current stimulation (tACS) over the right sensorimotor cortex alleviated attentional blink when the probe was close to the peak of the stimulation, whereas stimulation over the left aggravated attentional blink when the probe was close to the trough. These results suggest that the motor system is a resource-dependent rhythmic regulator of attentional sampling. Motor signals can override attentional bottlenecks, suggesting the motor system as an active shaper of cognitive processes.

neuroscience↗

bioRxiv2026

ExMODE: A Multi-Omics Repository for Extremophile Adaptation and Bioprospecting

Extreme environments, though hostile to most life forms, host specialized extremophile communities that have redefined biological cognition and emerged as vital biotechnological resources, with their unique adaptive traits and bioactive molecules driving advances in multiple scientific and industrial fields. However, research on extremophiles is hindered by limitations in culture-based methods, fragmented multi-omics data with non-uniform annotation standards across repositories, the lack of cross-extreme comparative research in existing resources, and the singularity of data dimensionality that neglects key structural information, all of which restrict the functional interpretation of extremophile microbes and the exploitation of their bioprospecting potential. To tackle these challenges, we developed ExMODE (https://db.genomics.cn/exmode/), a comprehensive multi-omics database platform dedicated to extremophiles. It centrally integrates multi-omics data from diverse extreme habitats with a standardized annotation framework, resolving data fragmentation and enabling systematic cross-environment comparative analyses to elucidate extremophile adaptive mechanisms. Moreover, ExMODE aggregates multi-dimensional datasets including genes, genomes, secondary metabolite sequences and protein structures, overcoming the constraints of single-dimensional data and significantly improving the efficiency of biotechnological resource discovery from extreme microorganisms.

microbiology↗

bioRxiv2026

Generation of High-Affinity Anti-GIPR Antagonist Antibodies with Sustained and Non-rebound Weight Loss in DIO Mice by AlfaBodY

The glucose-dependent insulinotropic polypeptide receptor (GIPR) is an attractive therapeutic target for metabolic disorders, with GIPR antagonism emerging as a promising strategy for obesity and type 2 diabetes. However, developing functional antibodies against GPCRs remains challenging due to their complex architecture and conformational dynamics. Here, we employed AlfaBodY, an iterative active learning platform integrating structural and sequence information, to in silico design human anti-GIPR antibodies. Through four rounds of optimization, we generated antibodies with high binding affinities. Lead candidates AB106-131 (KD 1.2 nM) and AB106-156 (KD 1.7 nM) exhibited 7 to 10-fold higher affinity than 2G10 (KD 12 nM) while maintaining comparable antagonistic activity in a cAMP reporter assay (IC50 4[~]5 nM). In diet-induced obese mice, AB106-156 alone induced weight loss comparable to that of semaglutide ([~] -15%), while preserving lean mass and achieving sustained weight control after treatment withdrawal. Co-administration with the GLP-1 receptor agonist semaglutide produced synergistic weight reduction (-25.4%) and markedly attenuated the fat-mass rebound observed with semaglutide alone. Our results demonstrate that AI-driven design can generate potent anti-GIPR antibodies with favourable in vivo efficacy, supporting further development of GIPR antagonist for obesity and related metabolic disorders. The AlfaBodY platform enables faster development of more efficacious biologic drugs.

pharmacology and toxicology↗

bioRxiv2026

Aligned recordings of neural spiking activity and licking behavior in thirsty mice

Electrophysiological data, which serve as a biological signal that bridges neural activity and behavioral tasks, provide an innovative approach to neuroscience research. In this study, we constructed a dataset that contains over 2000 neurons across 117 days recorded in 20 mice containing 28,573 trials. Data for 5 mice were collected from the Secondary Motor Cortex (M2) region 8 mice was derived from the Ventrolateral Striatum (VLS) and 7 mice were from Substantia Nigra pars Reticulata (SNR). We induced licking behavior in head-fixed mice by periodically delivering water through a spout while simultaneously recording spiking activity from three brain regions and behavior related electrical signals. This dataset ensures precise temporal alignment between neural activity and behavioral events, offering a robust foundation for investigating neural encoding mechanisms and simulation of neural activities. This dataset establishes a precise spike-to-event mapping, which enables high decoding accuracy using Multilayer Perceptron (MLP) and Support Vector Machine (SVM). It can serve as a high-quality benchmark for developing encoding and decoding algorithms in neural networks, particularly Spiking Neural Networks (SNNs).

neuroscience↗

bioRxiv2026

Learning latent conformational landscapes encoded in cryo-EM

A protein populates a landscape of structural states, abundant snapshots of which are sampled in every cryo-EM experiment. Current analysis averages these snapshots into single density maps or partitions them into discrete classes, discarding the continuous dynamics encoded in the data. Continuous latent-space methods offer a promising alternative, yet whether their learned representations are physically grounded remains unresolved. Here, we realize cryo-EM as structural landscape microscopy, in which latent density directly reflects the probabilistic distribution of molecular states. A central question is whether such a landscape reflects physical reality. For integrin v{beta}8, the learned landscape shows strong agreement with independently derived molecular dynamics simulations, supporting its physical plausibility. We then apply the landscape to structural states that conventional cryo-EM cannot resolve. For LIS1-mediated dynein activation, the landscape reveals a spectrum of states from dominant conformations to low-population intermediates defined by distinct binding modes, including a previously unresolved state. For the KCTD5/CUL3NTD/G{beta}{gamma} complex, the landscape resolves continuous conformational pathways directly from experimental data. Probability-guided particle selection further improves reconstruction quality.

molecular biology↗

bioRxiv2026

Genetic interaction between Adgrg6 and Sox9 reveals a feedforward mechanism for postnatal spinal stability

Adolescent idiopathic scoliosis (AIS) is the most common spinal disorder in children and is best understood as a complex polygenic condition. Genome-wide association studies (GWAS) have identified several AIS risk loci, including regions near ADGRG6 and SOX9, yet the functional mechanisms underlying AIS heritability remain poorly defined. Here, we use spatial transcriptomics to characterize altered gene expression in the spine of a conditional Adgrg6 mutant mouse model of AIS (Adgrg6-cKO), revealing reduced expression of Sox9 and several components of extracellular matrix organization in the intervertebral disc. We further show that SOX9 occupies regions of open chromatin within the Adgrg6 locus in cells isolated from the mouse intervertebral disc. Finally, we demonstrate a strong genetic interaction between Adgrg6-cKO and a hypomorphic Sox9 allele that increases both the penetrance and severity of AIS-like pathology in mice. Collectively, these findings support a self-reinforcing feedforward regulatory circuit, where Adgrg6 and Sox9 are co-regulated to maintain extracellular matrix gene expression in the annulus fibrosus and paraspinal tissues. These findings provide mechanistic insight into the functional significance of AIS-associated GWAS loci near ADGRG6 and SOX9 and establish combined Adgrg6-Sox9 insufficiency as a tractable model of polygenic scoliosis susceptibility. O_LIAdgrg6 maintains Sox9 and extracellular matrix gene expression in the intervertebral disc C_LIO_LISOX9 directly occupies open chromatin at the Adgrg6 locus in SOX9 skeletal cells C_LIO_LIAdgrg6 and Sox9 genetically interact to increase scoliosis incidence and severity C_LIO_LICombined loss of Adgrg6 and Sox9 drives ectopic cartilage formation and reduced vertebral bone mineral density in the thoracic spine C_LI

developmental biology↗