Biology subjects

Gu, H.

Publications and source records attributed to Gu, H..

At least 19 recordsLinked to original sources

bioRxiv2026

CellMethMarker provides an integrated database of human cell- and tissue-type-specific DNA methylation markers

Cell- and tissue-type-specific DNA methylation markers provide epigenetic signatures of cellular identity and are widely used to infer cellular origin from bulk and single-cell methylomes. Existing resources mainly emphasize disease-associated biomarkers, methylome atlases, genomic annotations or RNA-based cell markers, leaving an unmet need for an integrated region-level resource dedicated to such markers. Here we present CellMethMarker (http://gu-zhanglab.hfcas.ac.cn/CellMethMarker), a curated database integrating 347,514 de novo markers derived from uniformly processed whole-genome and reduced-representation bisulfite sequencing datasets, 2,203,507 literature-derived marker records and harmonized metadata for 2,810 samples. CellMethMarker enables cell- and tissue-centered marker retrieval, coordinate-based search, genome-browser visualization, interactive methylation analysis and data download. In an independent single-cell methylome atlas, these markers recover the expected cell-type-associated methylation patterns, and a platform-matched reference built from them lowers the mean deconvolution error from 0.365 to 0.144. CellMethMarker therefore links region-level DNA methylation variation to cellular identity and supports methylome-based cell-type annotation and deconvolution.

bioinformatics↗

bioRxiv2026

OTTER: Orchestrated Transcriptomic, Tumor-xenograft (PDX/CDX), and Epigenomic Reporting Workflow

Summary: Tumor xenograft sequencing libraries inevitably contain infiltrating murine host reads, but conventional deconvolution tools fail on bisulfite sequencing (BS-seq) because chemical C-to-T deamination collapses sequence entropy and destroys graft recall (< 0.015%). We present OTTER, an automated, compiled multi-omics workflow framework that decouples execution into static domain operators, an immutable reference registry, and a native strand-aware edit-distance engine, restoring bisulfite deconvolution (52%-54% recall across a 0%-99% compositional gradient) while preserving complete decision parity on transcriptomics. Availability and implementation: OTTER is implemented in Go and Rust, runs on x86_64 Linux (including CentOS 7 with glibc 2.17), and is freely available open-source under the MIT License at https://github.com/otterlab-bio/otter; test and validation data are provided at https://huggingface.co/datasets/fallingstar10/otter-data.

bioinformatics↗

bioRxiv2026

Xenograft supervision and joint methylation-fragment-end encoding define a reusable molecular scoring layer for cell-free tumor DNA

Circulating tumor DNA is often scarce in plasma, and regional methylation summaries can obscure informative differences between individual molecules. Here we present ctDNA-BERT, a Transformer that scores individual bisulfite reads without predefined differentially methylated regions by jointly encoding CpG methylation state, nucleotide context and the fragment 3' end. Xenografts provide molecule-level tumor supervision. The resulting frozen scorer supported tumor-fraction estimation in synthetic and patient-derived xenograft mixtures and enriched tumor-concordant methylation and chromatin-accessibility signals in independent hepatocellular carcinoma and stage III pan-cancer plasma without cohort-specific retraining. Features derived from selected reads discriminated stage I cancers from healthy controls in a retrospective cohort of 1,477 specimens, achieving an out-of-fold area under the receiver operating characteristic curve of 0.884. By separating molecular scoring from sample-level inference, ctDNA-BERT provides a reusable read-level scoring layer for cell-free DNA methylation analysis.

bioinformatics↗

bioRxiv2026

AMPK-dependent brain-wide norepinephrine release promotes recovery from metabolic coma in mice

Coma is a pathological brain state characterized by loss of consciousness. How the brain recovers from coma remains largely unknown. Using mouse models of metabolic coma, we identified an endogenous neuromodulatory pathway that actively promotes coma recovery. In mice subjected to hypoglycemic coma, hypoglycemia triggered AMPK-dependent excitation of nucleus tractus solitarius (NTS) neurons, which activated locus coeruleus (LC) norepinephrine neurons through a glutamatergic NTS-LC circuit. LC activation drives widespread norepinephrine release across cortical and subcortical regions, thereby promoting post-coma arousal. Notably, coma-associated brain-wide norepinephrine release was unconventional in both scale and duration, with a magnitude approximately 10-fold higher than physiological norepinephrine release during sleep-wake cycles. This neuromodulatory process also operated during hypercapnic coma. Vagus nerve stimulation accelerated coma recovery by engaging this endogenous anti-coma mechanism. Our findings uncover an AMPK-dependent brainstem circuit that actively restores arousal from metabolic coma, revealing a neural defense strategy against profound metabolic stress.

neuroscience↗

bioRxiv2026

Hidden grassland productivity from overlooked herbivore impacts

Grasslands cover approximately 40% of Earth's land surface and contribute substantially to terrestrial primary production. Despite widespread grazing, field estimates of grassland aboveground net primary productivity commonly overlook two grazing-related processes: biomass consumed by herbivores and post-grazing compensatory growth. The magnitude and direction of the resulting biases remain unclear. Here we quantified these biases using a 3-year yak grazing experiment on the Tibetan Plateau, a meta-analysis of 152 grazing experiments across China, and a global synthesis of 212 paired observations from 58 studies. Overlooking biomass consumed by herbivores consistently underestimated productivity by 34-51%. By contrast, overlooking grazing-induced compensation generated smaller but more variable biases, ranging from 29% underestimation to 19% overestimation, mainly reflecting contrasting compensatory responses under rotational versus continuous grazing. These findings show that overlooking grazing-mediated processes introduces substantial, process-dependent biases in grassland productivity estimates, underscoring the need to incorporate these processes into ecosystem and climate assessments.

ecology↗

bioRxiv2026

The microbial soy metabolite S-equol mitigates cadmium neurotoxicity in mice

Environmental exposures are major but understudied determinants of chronic disease. Cadmium is a pervasive toxic metal encountered through diet and tobacco smoke that has been associated with cognitive impairment and Alzheimer's disease mortality, yet strategies to mitigate its neurotoxicity remain limited. S-equol is a gut microbial metabolite of soy daidzein that crosses the blood brain barrier and preferentially activates estrogen receptor beta. Here, we show that cadmium disrupts an axis linking the equol producing gut bacterium Adlercreutzia equolifaciens to circulating S-equol and hippocampal estrogen receptor expression in mice, that S-equol attenuates cadmium-induced cytotoxicity and restores neuronal, glutamatergic and synaptic transcriptional programs in mouse neural progenitor cells, and that circulating S-equol in older humans is lower in apolipoprotein E4 carriers and covaries with body mass index, identifying S-equol as a microbiome-derived, host-modulated candidate countermeasure against cadmium neurotoxicity.

neuroscience↗

bioRxiv2026

Loss of DNA Demethylase Enhances Arsenic Resistance Via Reducing of PIN2 Antisense Long Noncoding RNA

DNA methylation dynamics regulate diverse plant stress responses, but the mechanisms governing arsenic (As) tolerance through epigenetic pathways remain largely unknown. Here we report that Arabidopsis mutants lacking the DNA demethylase, REPRESSOR OF SILENCING (ROS1), show substantially enhanced As resistance. Integrating transcriptome and methylome data, we found that PIN-FORMED 2 (PIN2), encoding an auxin efflux carrier that also transports As out of cells, represents a key ROS1 target. In ros1, we observed increased methylation in the last exon of PIN2, a region functioning as the promoter for an antisense long non-coding RNA (lncRNA). Hypermethylation of the promoter suppresses the antisense lncRNA, which follows reduction of sense PIN2 transcription. As a result, PIN2 expression increases in ros1 mutants during As exposure, enhancing As tolerance. Analysis of ros1 pin2 double mutants confirmed that PIN2 acts downstream of ROS1 in As tolerance. Our study demonstrates an epigenetic pathway in which ROS1 regulates As tolerance by controlling PIN2 expression through antisense lncRNA-mediated transcriptional interference, offering new epigenetic strategies using plants in heavy metal contaminated environments.

plant biology↗

bioRxiv2026

Controlled near-space exposure induces community restructuring in an ocean water microbiome

Marine microbiomes may experience extreme environmental stress during atmospheric transport, yet how near-space conditions reshape natural microbial communities remains poorly understood. Here, we investigated the effects of controlled near-space exposure on a seawater microbiome using high-altitude balloon experiments and 16S rRNA amplicon sequencing. While alpha diversity remained relatively stable across exposure conditions, weighted UniFrac and PERMANOVA analyses revealed reproducible shifts in microbial community composition associated with flight exposure. Taxonomic profiling demonstrated coordinated restructuring across multiple microbial lineages rather than dominance of a single taxon-specific response. Comparable beta-dispersion among groups supported the robustness of these compositional differences. Together, these findings demonstrate that near-space exposure was associated with reproducible restructuring of microbial community composition without substantial loss of overall diversity. Raw sequencing data have been deposited in the NCBI Sequence Read Archive under BioProject accession PRJNA1479017.

ecology↗

bioRxiv2026

Cyclic-thiourea ionizable lipids program multilamellar mRNA-LNPs for sustained expression, frozen-storage stability and potent vaccine immunotherapy

Lipid nanoparticles (LNPs) are the leading delivery vehicles for mRNA therapeutics, yet transient expression and limited formulation stability constrain their broader therapeutic application. Here we report the phenotype-driven discovery of an ionizable lipid (HI-62) bearing a 1,3,5-triazinane-2-thione (cyclic-thiourea) headgroup that reproducibly assemble mRNA into onion-like multilamellar nanoparticles. Cryogenic electron microscopy revealed ordered internal lamellae, while molecular-dynamics simulations supported a cooperative assembly model involving pH-responsive electrostatics, headgroup preorganization and short-range directional interactions. The lead HI-62 formulation maintained greater than 95% mRNA encapsulation across N/P ratios of 3-7, prolonged reporter expression for substantially longer durations than benchmark formulations following intravenous and intramuscular delivery, and retains physicochemical integrity and in vivo potency after repeated freeze-thaw cycles and 18 months of storage at -20. In the tumor models, HI-62 elicits robust cellular responses and achieved significant inhibition of tumor growth. These findings establish cyclic-thiourea headgroup chemistry as a design principle for programming lipid-RNA organization into multilamellar architecture, and provide a design principle for next-generation LNPs platform with durable protein expression and superior stability. The HI-62-based formulation has been utilized in mRNA cancer vaccine program which will enter clinical development in months.

bioengineering↗

bioRxiv2026

ApoE4 impairs astrocyte lipid droplet formation via endolysosomal dysfunction

An important component of neuron-glia coupling is the transport and delivery of neuron-derived lipids to glial lipid droplets. This pathway is important as failure to store incoming lipids in glial lipid droplets exacerbates neurodegeneration. ApoE4, a risk factor for Alzheimer's disease, impairs this transport pathway. But how ApoE4 affects lipid trafficking in glia and whether these alterations can be restored is poorly understood. Here, we demonstrate that ApoE4 particles impair endolysosomal function and promote lipofuscin formation in cultured primary astrocytes, thereby disrupting the trafficking of lipids for storage into lipid droplets. Lipid droplets, however, can be recovered by preventing lysosomal impairment with PCSK9, a secreted protein that prevents LDLR recycling and reduces ApoE4 internalization. Lipid droplets are similarly recovered in the presence of ApoE4 by repairing endolysosomal function. Our findings reveal new insight into how ApoE4 dysregulates lipid storage while uncovering new mechanisms to correct these defects.

neuroscience↗

bioRxiv2026

Mechanosignaling Promotes Macrophage Apoptosis Resistance in Pulmonary Fibrosis via Metabolic Reprogramming

The mechanisms underlying the progression of pulmonary fibrosis in idiopathic pulmonary fibrosis (IPF) and other interstitial lung diseases remain unclear. Increased extracellular matrix stiffness is a hallmark of fibrotic lung diseases. Monocyte-derived macrophages can promote fibrosis progression. However, there is limited understanding of how the mechanical properties of the fibrotic microenvironment influence macrophage phenotypes. Profibrotic macrophages are apoptosis-resistant, and this phenotype is modulated by enhanced mitochondrial bioenergetics. The objective of the study was to determine how lung tissue stiffness impacts macrophage phenotypes and fibrotic progression. We demonstrate that mechanoactivated macrophages exhibit apoptosis-resistance, increased expression of the antiapoptotic protein Bcl-xL and increased mitochondrial oxidative phosphorylation. Critically, the metabolic reprogramming observed in mechanoactivated macrophages is dependent on increased glutaminolysis. Inhibition of glutaminolysis attenuated apoptosis resistance in mechanoactivated macrophages. Moreover, inhibition of Bcl-xL in vivo protected mice against experimental pulmonary fibrosis. Lastly, mechanoactivated primary IPF macrophages produce more profibrotic cytokines and promote extracellular matrix production in precision-cut lung slices. We describe a mechanism for acquired macrophage apoptosis resistance dependent on metabolic reprogramming regulated by extracellular matrix stiffness. Our results identify mechanoactivated apoptosis-resistant macrophages as pro-fibrotic mediators, suggesting a novel therapeutic target in IPF and related fibrotic disorders.

molecular biology↗

bioRxiv2026

Akkermansia muciniphila prevents cadmium-induced cognitive impairment through gut microbiome mediated mechanisms

Akkermansia muciniphila has emerged as a promising next-generation probiotic with beneficial effects on learning and memory, but whether and how it can protect against environmental toxicant-induced cognitive impairment remains unknown. Cadmium (Cd) is a widespread environmental neurotoxicant that disrupts the gut-brain axis and impairs hippocampus-dependent learning and memory, yet effective preventive interventions are lacking. In this study, we discovered that oral supplementation with human fecal microbiome-derived A. muciniphila prevented Cd-induced cognitive impairment in mice throughout 9 weeks of oral Cd exposure at a human body burden-relevant concentration. Notably, brain Cd concentrations were not affected by A. muciniphila supplementation, indicating that cognitive protection was mediated through gut-brain signaling rather than affecting metal accumulation in the brain. Multi-omics characterization identified coordinated gut-brain pathways underlying this protective effect. A. muciniphila preserved Cd-suppressed Lactobacillus taxa (L. crispatus, L. intestinalis, L. taiwanensis), which positively correlated with cognitive performance, and restored intestinal tight-junction integrity across multiple intestinal sections, particularly the ileum. A. muciniphila also normalized Cd-induced cytokine dysregulation in the serum. In addition, colonic branched-chain fatty acids (BCFAs) emerged as candidate gut-brain mediators, with 2-methylpentanoic acid showing a robust negative correlation with cognitive performance. These A. muciniphila-mediated changes across gut microbiome, intestinal barrier, systemic cytokines, and microbial metabolites coincided with reversal of Cd-induced hippocampal transcriptional alterations regulating synaptic and vascular signaling. Together, this study identified A. muciniphila as a preventive microbiome-based strategy against environmental Cd neurotoxicity in mice, demonstrated that the gut microbial homeostasis can confer cognitive resilience independently of brain toxicant burden, and revealed distinct BCFAs as potential gut-brain mediators of heavy-metal-induced cognitive decline.

pharmacology and toxicology↗

bioRxiv2026

Acute Aerobic Exercise in Individuals with Obesity Abolishes Amino Acid-Stimulated Muscle Protein Synthesis in the Immediate Postexercise Period

BackgroundIn healthy individuals, exercise and amino acid availability act synergistically to stimulate muscle anabolism. However, this interaction may be impaired in individuals with obesity. ObjectiveWe examined whether acute aerobic exercise alters amino acid-stimulated muscle protein synthesis during immediate postexercise recovery in adults with obesity. MethodsSixteen sedentary adults with a body mass index >30 kg/m2 underwent a stable-isotope tracer infusion to measure mixed-muscle protein fractional synthesis rate (FSR) in the basal/fasted state and during an amino acid infusion, either with or without prior aerobic exercise. Participants were randomly assigned to receive either amino acid infusion alone (AA) or 45 min of cycling exercise at [~]65% heart rate reserve immediately before amino acid infusion (EX + AA). ResultsAmino acid infusion increased muscle protein FSR in the AA group (P < 0.0001) but not in the EX + AA group (P > 0.05), and the amino acid-stimulated increase in FSR was 78% lower in EX + AA than in AA (P < 0.01). The amino acid infusion increased (P < 0.05) plasma amino acid concentrations in both groups. However, during the amino acid infusion, plasma concentrations of essential and branched-chain amino acids, including leucine, were lower in EX + AA than in AA (P < 0.05). Moreover, across participants, absolute changes in muscle protein FSR were positively associated with plasma leucine concentrations during the amino acid infusion (P < 0.05). ConclusionsThese findings show that, in individuals with obesity, acute aerobic exercise markedly attenuates amino acid-stimulated muscle protein synthesis during early postexercise recovery. These findings have important implications for designing nutritional strategies to optimize muscle anabolism in this population.

physiology↗

bioRxiv2026

Multifaceted regulations of HSV-1 ICP0 on the Anti-Viral Restrictions Imposed by the Host Hippo Kinases Reprogramming

The Hippo pathway is conserved across eukaryotes and controls key biological processes, including cell growth and organ development. Notably, humans with biallelic loss-of-function mutations in the Hippo kinase gene MST1 suffer from combined immunodeficiency, including recurrent infections of herpes simplex virus (HSV), implicating the pathway in host immune regulation. We investigated the role of MST1 and its homolog MST2 in HSV-1 infection. We found that human epithelial cells HEp-2 proteolytically converted full-length MST1/2 into smaller N-terminal fragments (MST1/2-NT) to enhance cell apoptosis in response to the HSV-1 infection. Moreover, while infection by mutants lacking ICP0 or US3 elevated the production of MST1/2-NT and apoptosis, the overexpression of MST1-NT significantly reduced HSV-1 replication, revealing anti-viral properties of MST1/2 cleavage and the viral counteractions by ICP0 and US3. Consistently, we discovered that MST1/2-NT production, which was high in {Delta}ICP0-infected HEp-2 cells, was completely diminished in cells permissive to the {Delta}ICP0 infection, linking the counteraction against host MST1/2 cleavage to ICP0 functions. In addition, host caspases cleaved MST1/2 with differential preferences toward MST1 or MST2 in different infection contexts, indicating multiple regulations on the MST1/2-NT production during HSV-1 infection. While double-knockouts of MST1/2 in HEp-2 cells had marginal effects on wild type HSV-1 replication, it substantially reduced the early intake of {Delta}ICP0 DNA, suggesting a role of full-length MST1/2 in early infection. Altogether, these results uncover the novel and distinct roles of full-length and cleaved Hippo kinases during HSV-1 infection and their multifaceted interactions with ICP0. ImportanceHSV poses serious threats to human health, ranging from cold sores to fatal brain infection. As a successful human pathogen, it deploys various viral proteins to counteract host defenses and subjugate host machinery, but mechanisms underlying these complex HSV-host interactions are not fully understood. For the first time, we report multifaceted interactions between the Hippo kinases and viral proteins during HSV-1 infection. We show that the Hippo kinases are converted to smaller fragments through protein cleavage in HSV-1 infected cells, and the cleaved Hippo fragments are accompanied by host cell death to execute their anti-viral activities. Moreover, multiple viral proteins contribute to counteracting this host defense, including ICP0, which executes a complex interplay with the Hippo kinases to promote infection. Understanding this new layer of virus-host interaction may pave the road to developing novel treatments for herpetic diseases.

microbiology↗

bioRxiv2026

Relief of allosteric inhibition, redox imbalance, and transport limitations enables high-yield L-malate production in Escherichia coli

Malic acid is a C4 dicarboxylic acid traditionally produced from petroleum and widely used in the food industry. As a sustainable alternative, it can also be produced as a value-added platform chemical from biomass. Previously, the Escherichia coli strain XZ658 was engineered to produce L-malate via the carbon-fixation reductive branch of the TCA cycle. In this study, we further improved this system by relieving allosteric regulation of citrate synthase, addressing redox imbalance, and enhancing malate export. These modifications approximately doubled the L-malate titer in the final strain MO128 compared to XZ658 under simple batch fermentation conditions. The process achieved a high mass yield of 1.2 g malate g-{superscript 1} glucose, highlighting the carbon-fixation capacity of the reductive TCA pathway for fermentative malate production.

bioengineering↗

bioRxiv2026

Early Visual Cortex Represents Sensory and Mnemonic Orientations in Separate Subspaces with Preserved Geometry

How early visual cortex (EVC) represents working memory (WM) content while continuing to process incoming sensory input remains unclear. Using fMRI with prolonged delays to isolate mnemonic activity, together with analyses of cross-decoding, low-dimensional subspace structure, and representational geometry, we examined the relationship between sensory and mnemonic orientation representations in human EVC. Cross-decoding generalized poorly between sensory and mnemonic epochs, but this did not imply unrelated codes. Rather, the two occupied separable low-dimensional subspaces while preserving representational geometry across epochs. During discrimination and estimation, sensory- and mnemonic-trained decoders yielded dissociable readouts of concurrent sensory and mnemonic information from the same EVC measurements. Mnemonic coding showed little dependence on the retinotopic radial bias that characterized sensory coding, and trial-by-trial variability in mnemonic representation predicted both discrimination choices and estimation reports. Our findings support a population-level account in which mnemonic information in EVC is re-expressed in a separable but geometrically preserved format.

neuroscience↗

bioRxiv2026

O-GlcNAcylation regulates PPAR-driven metabolic programming in intestinal stem cells

Diet deeply influences health and disease risk by reshaping cellular metabolism. In the intestine, dietary nutrients directly affect intestinal stem cell (ISC) behavior, yet the regulatory mechanisms linking metabolism to transcriptional control remain poorly defined. Because mitochondria function as central metabolic hubs, we focused on mitochondrial signaling to understand how nutrient utilization governs ISC function. Using the MITO-Tag mouse, we isolated metabolites specifically from ISC mitochondria and found that the sugar-derived metabolite UDP-GlcNAc was reduced in ISCs from mice fed a high-fat diet. Moreover, we identified that reducing O-GlcNAcylation (OGN) rapidly increased stem cell frequency, proliferation, regenerative capacity, and the abundance of PPAR target proteins. Mechanistically, these effects depend on PPAR signaling, as genetic loss of Ppar-d/a blocks the ISC phenotypes induced by reduced OGN. These results reveal an OGN-PPAR signaling axis that translates dietary metabolic cues into transcriptional programs governing fuel utilization and ISC behavior in the intestine. Collectively, our findings highlight that OGN is a previously unrecognized regulator of PPAR signaling in intestinal stem cells.

cell biology↗

bioRxiv2026

Erythropoietin Mediates Glycerophospholipid Remodeling During Human Early Erythropoiesis

The unique biconcave morphology and deformability of mature red blood cells (RBCs) require a specific membrane lipid composition. Disruption of this special lipid profile is seen in multiple types of anemia and bone marrow (BM) failure diseases, yet molecular mechanisms regulating lipid metabolism during normal erythroid differentiation remain poorly defined. Here, we identify a previously undescribed role for erythropoietin (Epo) in contributing to the appropriate lipid composition of differentiating human erythroid cells. Using single-cell transcriptomic profiling of ex vivo cultures of human BM-derived hematopoietic stem and progenitor cells cultured with or without Epo, we delineated transcriptional dynamics across differentiation stages, identifying the Epo-dependent transition of burst-forming unit erythroid (BFU-E) to colony-forming unit erythroid (CFU-E) progenitors. Comparative analysis revealed the activation of canonical erythroid programs involving heme biosynthesis, globin expression, and iron regulation, and additionally, uncovered a transient upregulation of lipid metabolic pathways during the BFU-E to CFU-E transition. Complementary untargeted lipidomics demonstrated Epo-dependent alterations in specific glycerophospholipid (GPL) species, consistent with differential expression of GPL biosynthesis genes in the single cell dataset. Intracellular flow cytometry further confirmed the requirement of Epo for maintaining enzymes critical for phosphatidylcholine and phosphatidylethanolamine synthesis in erythroid cells. Together, these multiomic findings reveal a new role for Epo in modulating lipid metabolism during early erythropoiesis and provide mechanistic insight into how membrane lipid composition is dynamically regulated to support normal red cell development.

cell biology↗