Biology subjects

Gu, X.

Publications and source records attributed to Gu, X..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Suppression of Glucosylceramide Synthase Reverses Drug Resistance in Cancer Cells Harbor Homozygous p53 Mutants

Glucosylceramide synthase (GCS) catalyzes ceramide glycosylation in response to cell stress that produces glucosylceramide and other glycosphingolipids. GCS overexpression is a cause of drug resistance and enriches cancer stem cells (CSCs) during cancer chemotherapy. Previous studies showed that GCS modulates expression of p53 mutants and oncogenic gain-of-function (GOF) in heterozygous knock-in cell models (TP53 R273H-/+). However, it is unclear whether GCS can modulate the effects of homozygous p53 mutations, which are common in many cancer cases. We report herewith that inhibition of GCS, via UGCG-knockout and using new inhibitor (Genz-161), effectively re-sensitizes drug resistance and diminishes CSCs in colon cancer cells carrying the homozygous p53 R273H mutation. In aggressive WiDr cells carrying TP53 R273H mutation, knockout of UGCG gene using CRISPR/Cas9 editing or inhibition of GCS with Genz-161 sensitized cancer cells to oxaliplatin, irinotecan and paclitaxel. With decreased ceramide glycosylation in lipidomic profiling, both UGCG-knockout and Genz-161 treatments substantially decreased wound healing, and diminished CSCs and tumor growth under chemotherapy. Interestingly, inhibition of RNA m6A methylation by neplanocin A reactivated p53 function and reversed drug resistance. Mechanistic investigation revealed that GCS inhibition downregulated METTL3 expression and repressed RNA-m6A modification on mutant p53 R273H effects. Altogether, our findings demonstrate that ceramide glycosylation promotes METTL3 expression and RNA m6A methylation in response to drug-induced stress, thereby promoting mutant p53 expression and associated GOF. Conversely, inhibition of GCS can diminish CSCs and drug resistance via reduction of m6A modification and reactivation of p53 function. GCS inhibition is an achievable approach for mutant cancer treatment.

cancer biology↗

bioRxiv2025

Multi-Class Classification of Cannabis and Alcohol Use Disorder: Identifying Common and Substance-Specific Neural Circuits.

Machine learning approaches have advanced the identification of neural signatures of substance use, particularly through case-control comparisons and network-level analyses. However, most studies have focused on single substances in isolation, making it difficult to directly compare shared and distinct network computations and limiting their generalizability, given that many individuals engage in polysubstance use. Here, we introduce an explainable, connectivity-based multiclass classification framework that models distributed brain network organization to delineate both shared and substance-specific mechanisms of addiction. This design enables direct comparison among cannabis users, alcohol users, and controls, revealing network computations that uniquely differentiate each group. Using functional connectivity features from cue-induced craving tasks, we classified cannabis users (n=166), alcohol users (n=101), and healthy controls (n=238), achieving high out-of-sample accuracy (87% for cannabis, 69% for alcohol, and 73% for controls). Functional connectivity-based models consistently outperformed activation-based models, highlighting the importance of inter-regional network properties for biomarker development. Network analysis further revealed dorsal prefrontal, cingulate, and precuneus hubs consistent with meta-analytic craving networks and substance-specific connectivity motifs enhanced prefrontal coupling in cannabis users and greater insular-striatal integration in alcohol users. These results demonstrate that distinct network configurations define different substance-use profiles, advancing interpretable biomarkers for addiction neuroscience.

neuroscience↗

bioRxiv2025

Ribosome remodeling drives translation adaptation during viral infection and cellular stress

The ribosome is the highly conserved molecular machine that decodes mRNAs during protein synthesis. While traditionally thought to consist of a uniform set of proteins, here we discover that ribosome composition is reprogrammed to adapt to intrinsic and external cellular perturbations. During infection by non-segmented negative-sense viruses, viral entry into cells recruits the large ribosomal subunit protein rpL40 to a noncanonical site on the small subunit of 80S ribosomes near the mRNA entry site. These specialized ribosomes preferentially bind viral mRNAs to drive enhanced viral protein synthesis that is critical for replication under host pressures. Unexpectedly, we find that viruses have co-opted this translation pathway from a previously unrecognized endogenous ribosome remodeling program in which metabolic stress alters ribosome structure to promote mRNA translation required for cell survival. Thus, ribosome remodeling is a conserved mechanism enabling dynamic protein synthesis across pathogen and cellular adaptation.

molecular biology↗

bioRxiv2025

Beta bursts mediate amygdala gating of hippocampal emotional encoding

The amygdala and hippocampus are key structures in emotional processing, yet the transient neural dynamics coordinating their interaction remain poorly understood. We simultaneously recorded single-neuron activity and local field potentials from these regions in epilepsy patients performing an emotional image-rating task. Neurons in both areas exhibited firing rate changes predictive of subjective emotional valence. While conventional spectral analysis revealed no valence-specific patterns, beta bursts (13-30 Hz)--transient, high-power events-were uniquely modified by task features. In both regions, beta bursts were associated with increased gamma amplitude and enhanced phase coherence, with beta-gamma phase-amplitude coupling capturing emotion-related dynamics. Critically, amygdala beta bursts were associated with strong suppression of hippocampal firing, coinciding with interneuron activation, during negative valence/highest arousal processing, whereas hippocampal bursts showed no reciprocal influence. These findings suggest that beta bursts may represent a temporally precise neural correlate of emotional appraisal and a candidate mechanism for targeted neuromodulation in mood disorders.

neuroscience↗

bioRxiv2025

Heterogeneity in inhibition of genetically diverse dengue virus strains by Wolbachia

The release of Aedes aegypti mosquitoes transinfected with the virus-inhibiting Wolbachia bacterium has the potential to reduce the burden caused by dengue virus (DENV). However, the robustness of this control strategy across the wide genetic diversity of DENV remains unknown. Here, we systematically tested two commonly used Wolbachia strains (wAlbB and wMelM) for their ability to inhibit 60 genetically diverse DENV isolates spanning all four serotypes. We found stronger inhibition by wMelM (median relative dissemination: 0.04) than wAlbB (median relative dissemination: 0.19). Furthermore, while we found substantial heterogeneity in inhibition across DENV isolates, we found that more DENV-3 isolates were weakly inhibited (median relative dissemination: 0.47 for wAlbB and 0.39 for wMelM) compared to the other serotypes (median relative disseminations: 0.10-0.18 for wAlbB and 0-0.11 for wMelM). Using transmission dynamic models, we further showed that differential Wolbachia inhibition results in increased probability of reemergence, particularly in high transmission intensity settings, with strong selection for DENV strains that have higher relative dissemination in mosquitoes. Our work highlights the importance of considering DENV genetic diversity, including the long-term risk of selection, in Wolbachia-based control interventions.

microbiology↗

bioRxiv2025

Curing autoimmune diabetes with islet and hematopoietic cell transplantation after CD117 antibody-based conditioning

Mixed hematopoietic chimerism after allogeneic hematopoietic cell transplantation (HCT) promotes tolerance of transplanted donor-matched solid organs, corrects autoimmunity, and could transform therapeutic strategies for autoimmune type 1 diabetes (T1D). However, development of non-toxic bone marrow conditioning protocols is needed to expand clinical use. We developed a chemotherapy-free, non-myeloablative (NMA) conditioning regimen that achieves mixed chimerism and allograft tolerance across MHC barriers in NOD mice. We obtained durable mixed hematopoietic chimerism in prediabetic NOD mice using anti-c-Kit monoclonal antibody, T-cell depleting antibodies, JAK1/2 inhibition, and low-dose total body irradiation prior to transplantation of MHC-mismatched B6 hematopoietic cells, preventing diabetes in 100% of chimeric NOD:B6 mice. In overtly diabetic NOD mice, NMA conditioning followed by combined B6 HCT and islet transplantation durably corrected diabetes in 100% of chimeric mice without chronic immunosuppression or graft-versus-host disease (GVHD). Chimeric mice remained immunocompetent, as assessed by blood count recovery and rejection of 3rd party allogeneic islets. Adoptive transfer studies and analysis of autoreactive T cells confirmed correction of autoimmunity. Analysis of chimeric NOD mice revealed central thymic deletion and peripheral tolerance mechanisms. Thus, with NMA conditioning and cell transplantation, we achieved durable hematopoietic chimerism without GVHD, promoted islet allograft tolerance, and reversed established T1D. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=197 SRC="FIGDIR/small/673576v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@23fcdorg.highwire.dtl.DTLVardef@1aac97borg.highwire.dtl.DTLVardef@191e06forg.highwire.dtl.DTLVardef@25be2b_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Discovery of an Adaptive Neuroimmune Response Driving Itch and Fast Tick Removal with Implications for Preventing Pathogen Transmission

Acquired tick resistance (ATR) is well characterized in tick-exposed animals, compromising tick fitness through antibody-mediated activation of basophils. Yet, anti-tick vaccines inducing ATR have had limited success. Here, we describe a neuroimmune event preceding ATR that leads to rapid host-mediated tick removal. Tick-sensitized guinea pigs mechanically remove ticks within 3-6 hours via an acquired neuroimmune-induced itch response that correlates with increased dermal expression of itch-associated genes like OSM and skin infiltration by T cells and macrophages, independently of IgG and IgE antibodies. When we expose humans to ticks, a similar immune response is observed. Blocking T cells before tick sensitization prevents immune cell infiltration to bite sites and abrogates scratching and tick removal. This neuroimmune response is independent of Trpv1 as tick-sensitized guinea pigs treated with resiniferatoxin remove ticks effectively. Itch-induced tick removal or IITR offers a novel approach to tick-borne disease prevention through early tick detection and removal.

neuroscience↗

bioRxiv2025

Population genomics of the endangered scaly-foot snail defines conservation units amid deep-sea mining threats in Indian Ocean vents

Hydrothermal vents in the Indian Ocean face imminent deep-sea mining, yet lack baseline high-resolution connectivity data for their endemic fauna. We present the first population genomic study of the endangered scaly-foot snail (Chrysomallon squamiferum), an iconic species distributed across three vent biogeographic provinces. Analysing 125 individuals from eight vent fields using 14 million single-nucleotide polymorphisms, we identify five genetic groups that warrant recognition as evolutionarily significant units. Demographic modelling reveals critical contributions from extinct or unsampled phantom populations to the contemporary genetic structure. Together with physical ocean modelling, we show that the deep currents drive asymmetric south-to-north gene flows, while transform faults act as dispersal barriers. We propose Longqi-Duanqiao fields on the Southwest Indian Ridge and Wocan field on the Carlsberg Ridge as two isolated populations prioritised for protection. Given its exceptional adaptations, wide distribution, and public recognition, the scaly-foot snail is well-positioned to serve as both a flagship and umbrella species to ensure the survival of a broader suite of vent biodiversity. As the International Seabed Authority finalises its Mining Code in 2025, our findings provide essential genomic evidence to mitigate the impacts of mining on genetic diversity and inform transboundary conservation strategies for this vulnerable ecosystem.

ecology↗

bioRxiv2025

Spiroplasma and heat hardening can buffer insect male fertility loss at high temperatures

Insects upper thermal limits for survival, activity, and fertility have been used to assess vulnerability to climate change, yet heritable endosymbionts - present in over 70% of insect species - are often overlooked. While emerging research suggests some endosymbionts can increase thermal tolerance, their effects on upper lethal and fertility thermal limits has rarely been investigated. Additionally, short-term exposure to sub-lethal high temperatures (heat hardening) can increase insect heat tolerance, but its impact on male fertility is unclear and potential interactions with endosymbionts has not been explored. Here, we investigate whether the endosymbiont Spiroplasma poulsonii and heat hardening influence upper survival and fertility thermal limits in a native widespread host of Spiroplasma (Drosophila hydei) and a novel host (Drosophila birchii), a rainforest-restricted species with low heat tolerance. Heat hardening generally improved survival and fertility following a heat shock. The presence of Spiroplasma increased survival and fertility of D. hydei males following heat-shock, while in D. birchii, it did not enhance survival but protected male fertility after heat-shock and modulated hardening responses at sub-lethal temperatures. While protective effects varied across species, sex, and trait, both Spiroplasma and hardening significantly buffered male fitness loss during heat shock in both host species and halved heat exposure risk under current and predicted climate change in the rainforest restricted D. birchii. These findings highlight that, beyond generating novel phenotypic variation, endosymbionts can interact with plastic responses to heat stress, emphasising the importance of accounting for endosymbiont-mediated effects on thermal tolerance when assessing insect vulnerability to climate change and exploring strategies to manipulate insect thermal tolerance.

evolutionary biology↗

bioRxiv2025

IL-33 promotes transcriptional and metabolic adaptations of tissue-resident Th2 cells

The polarization of naive CD4+ T cells into Th2 cells is initiated in lymphoid organs and completed as the cells become tissue resident, where they express ST2, the receptor for the alarmin IL-33, which may be a key signal for tissue integration. Cellular metabolic requirements associated with this transition remain poorly understood. To address this, we compared the response of lymphoid tissue (LT) Th2 cells from helminth parasite-infected mice to stimulation by IL-33 versus through the T cell receptor via anti-CD3/CD28. We found that IL-33, but not anti-CD3/CD28, induced the development of tissue-resident like Th2 cells expressing ST2. This was associated with IL-33 induced changes in arginine metabolism linked to mTORC1 activation and polyamine synthesis, which were required for the development of tissue-resident like Th2 cells. Futhermore, IL-33 induced transcriptional changes in genes involved in chemotaxis and cell adhesion that may be critical for tissue integration. Our findings provide insights into adaptations of Th2 cells responding to tissue-integration cues. SummaryIL-33 promotes development of tissue-resident-like Th2 cells in vitro from lymphoid tissue Th2 cells. This requires arginine-dependent mTORC1 activation and polyamine synthesis, and is marked by transcription of genes associated with chemotaxis and cell adhesion linked to tissue integration.

immunology↗

bioRxiv2025

O-GlcNAcylation-Ubiquitin Crosstalk of METTL1 Drives m7G Epitranscriptomic Collapse and Lipid Metabolic Reprogramming in Diabetic Cardiomyopathy

BackgroundMetabolic remodelling and memory in cardiomyocytes is a pivotal mechanism underlying cardiomyopathy pathogenesis. Clinical observations demonstrate persistent progression of hyperglycaemia-induced multiorgan damage following blood glucose stabilization, which is predominantly mediated through epigenetic regulation. While prior studies have identified epigenetic contributions to hyperglycaemic myocardial injury, the involvement of RNA methylation-particularly N7-methylguanosine (m7G) modification-in this regulatory network remains undefined. MethodsClinical specimens were collected from diabetic patients, and cardiomyocyte-specific METTL1 and ob/ob knockout murine models were established in parallel. Multiomic profiling (proteomics, glycoproteomics, ubiquitinomics, m7G-MeRIP sequencing, and metabolomics) was systematically conducted. The molecular mechanisms governing METTL1 regulation via O-GlcNAcylation and ubiquitination were elucidated through integrated in vitro and in vivo assays. A DUB siRNA library and computational strategies combining molecular docking with molecular dynamics simulations were employed for screening drugs targeting METTL1 O-GlcNAcylation, followed by in vivo therapeutic validation. ResultsComparative analysis of diabetic murine and human samples revealed strong METTL1 downregulation in cardiomyopathy contexts. Tamoxifen-inducible METTL1 knockout mice presented exacerbated diabetic cardiomyopathy phenotypes, confirming its cardioprotective function. Multiomic integration demonstrated that METTL1-mediated m7G modification critically regulates cardiomyocyte fatty acid metabolism. Mechanistically, hyperglycaemia was found to induce O-GlcNAcylation at the METTL1-T268 residue, suppressing m7G methyltransferase activity by 38% (p < 0.01). Subsequent investigations revealed that USP5 deubiquitinase activity is impaired under hyperglycaemic conditions, leading to accelerated METTL1 degradation. Notably, administration of the first-in-class small drug HIT106265621 significantly attenuated cardiomyopathy-associated pathological alterations in ob/ob mice in vivo. ConclusionHyperglycaemia promotes METTL1 O-GlcNAcylation, which impedes USP5-mediated deubiquitination, consequently reducing cardiomyocyte METTL1 protein levels and m7G modification. METTL1 deficiency drives diabetic cardiomyopathy progression through fatty acid metabolic dysregulation, inflammatory activation, and myocardial hypertrophy. Pharmacological inhibition of the OGT-METTL1 interaction using HIT106265621 has therapeutic potential for metabolic cardiomyopathy intervention.

pathology↗

bioRxiv2025

A nucleation distance sets the cell size-dependent P-body assembly

Cells rely on diverse intracellular structures, including phase-separated granules, to regulate biological processes. Processing body (P-body) is a type of membraneless condensate in the eukaryotic cytoplasm that mediates mRNA degradation and storage. While their molecular composition is well studied, the relationship between their spatial organization and cell geometry, particularly cell size and organelle distribution, remains unclear. Here, we develop a conceptual framework that models phase-separation nucleation and validates the nucleation distance of P-bodies in living yeast cells. Using microfluidic cell sorting and quantitative fluorescence microscopy, we find that small cells contain fewer but larger P- bodies, whereas large cells form more but smaller granules. Monte Carlo simulations of P- body nucleation accurately recapitulate these cell size-dependent patterns and reveal a nucleation distance of 2.2 {micro}m. Furthermore, we demonstrate that increasing vacuolar volume reduces the effective cytoplasmic space and correspondingly raises P-body number, although cell size remains the dominant determinant. Our findings establish nucleation distance as a key parameter that links cell geometry to the biophysical regulation of condensate formation.

cell biology↗

bioRxiv2025

A Compact Two-Photon Module for Simultaneous Dual-Depth, Multi-Region in vivo Brain Imaging

Understanding how distributed brain regions interact across cortical depths is crucial for uncovering the neural basis of behavior and cognition. Two-photon microscopy (2PM) excels at imaging the superficial layer, while three-photon microscopy (3PM) penetrates deep tissues but lacks sufficient speed for capturing fast superficial dynamics. Here, we present a compact two-photon imaging module (2PIM) that seamlessly integrates with existing 3PM to achieve simultaneous, high-speed imaging of superficial and deep brain regions, while preserving the deep tissue penetration of 3PM. This dual-modality system allows for remote and independent control of imaging planes in both axial and lateral dimensions. Leveraging this technology, we discovered context-dependent modulation of hippocampal CA1 and visual cortex responses to identical tactile stimuli, layer-specific temporal dynamics in sensory cortex during air puff stimulation, and depth-divergent neuronal activity patterns in motor cortex across acute-to-chronic pain. These results highlight the systems potential for dissecting the spatiotemporal coordination of distributed brain circuits.

bioengineering↗

bioRxiv2025

Cortex-Wide, Cellular-Resolution Volumetric Imaging with a Modular Two-Photon Imaging Platform

Mapping cortex-wide neuronal activity at single-cell resolution has been limited by the physical trade-off between numerical aperture and field-of-view (FOV) in two-photon microscopes. We present Meso2P, a modular two-photon platform that decouples excitation and detection by introducing a lateral paraboloid fluorescence collector. The design sustains an effective NA 0.87 over a contiguous 6 x 6 mm2 FOV at high speed (2,048 x 2,048 pixels at 7.67 Hz). The modular platform can be upgraded with optional modules for simultaneous multi-plane imaging (1-4 planes at full resolution and speed), volumetric imaging (6 x 6 x 0.5 mm3, 2,048 x 2,048 x 28 voxels at 1 Hz capturing> 210,000 neurons), and holographic two-photon optogenetic stimulation for targeted perturbations. To handle the resulting large-scale data, we provide an open-source deep-learning pipeline that automates motion correction, segmentation, and spike inference. We demonstrate cortex-wide sensory responses, layer-specific network synchrony during anaesthesia, and in-vivo tracking of micro and nanoplastic distribution. Meso2P therefore provides a reproducible route to high-throughput volumetric imaging across almost the entire cortex with high detection efficiency.

neuroscience↗

bioRxiv2025

Improved conditioning for hematopoietic chimerism induces islet tolerance to cure diabetes

Mixed hematopoietic chimerism after hematopoietic cell transplantation (HCT) can modulate the immune system and induce tolerance to allogeneic tissues. However, bone marrow conditioning-related toxicities preclude wider adoption of HCT for transplant allotolerance. We sought agents that reduced conditioning intensity, while promoting durable mixed chimerism after HCT across complete major histocompatibility complex (MHC) mismatch in diabetic mice, permitting islet allotransplantation and diabetes reversal. We systematically tested baricitinib (JAK1/2 inhibitor), venetoclax (Bcl2 inhibitor), and CD47 antibody, agents in current clinical use, and quantified hematopoietic chimerism after HCT. Combined with CD117 antibody, transient T cell depletion, and just 10 centigray (cGy) total body irradiation (TBI), these agents enabled durable mixed chimerism and matching allo-islet tolerance, to cure diabetes without evidence of GVHD. Thus, we have developed a conditioning regimen to promote allogeneic mixed hematopoietic chimerism and transplanted islet allotolerance that minimizes conditioning radiation and cures diabetes, a significant achievement.

immunology↗

bioRxiv2025

Structural innovations and neurogenic continuity define avian brain development and evolution

Understanding how neurogenic diversity and brain architecture emerge is crucial for deciphering the mechanisms of brain plasticity and cognitive evolution. Here, we present a comprehensive single-cell and spatial transcriptomic atlas of the budgerigar brain, a highly cognitive avian species. We uncover a striking dorsoventral symmetry in excitatory neuron distribution, precisely organized along the lamina mesopallialis intermedia (LMI), a key boundary structure. Cross-species comparisons further reveal the origins of this unique avian pallial organization, offering new insight into avian brain evolution. Our study also highlights distinct developmental trajectories and asynchronous maturation patterns between telencephalic and optic tectum excitatory neurons, underscoring their contribution to innate circuit assembly. Furthermore, we identify adult neural stem cells (NSCs) with evolutionarily conserved transcriptomic signatures across avian species, emphasizing their role in brain plasticity and adaptation. These findings refine fundamental models of avian brain development and elucidate conserved principles of cognitive plasticity.

evolutionary biology↗

bioRxiv2025

Neuropeptidergic transmission shapes emergent properties of prefrontal cortical circuits underlying learning

The prefrontal cortex (PFC) is essential for top-down control of affect and its dysfunction is implicated in many psychiatric disorders. Inhibitory interneurons expressing somatostatin have been implicated in cognition, affect, and disease. However, somatostatins function as a neuropeptide transmitter remains unclear. Here, we investigated the contribution of somatostatin neurotransmission in differentiating between salient (rewarding or aversive) and neutral outcomes. Monitoring somatostatin release and somatostatin receptor antagonism revealed time-dependent regulation of outcome-specific associative learning during acquisition. We found that somatostatin transmission enables configural representations incorporating a salient, aversive outcome in prefrontal cortical neurons, and a threat-driven shift in population-level network activity in-vivo. These findings show a novel role for somatostatin, an interneuron "cellular marker", signaling in shaping learning and emergent network dynamics. Further this framework revealed that reduced somatostatin neuropeptidergic transmission may impair top-down control of affective behaviors observed in mental health disorders, suggesting potential new avenues for therapeutic intervention.

neuroscience↗

bioRxiv2025

13C tracing in synaptosomes reveals that SGLT2 inhibition with dapagliflozin prevents metabolic deficits in the 5X-FAD model of Alzheimer's Disease

Metabolic dysfunction is linked to several forms of age-related neurodegeneration including Alzheimers Disease (AD), and targeting brain energy metabolism is an increasingly attractive mode of therapeutic intervention. However, commonly used in vitro methods to identify specific metabolic pathways of interest in preclinical models of neurodegenerative disease have considerable limitations. They are prone to subselection of sample material, unable to identify cell type-specific effects, or cannot identify metabolic defects upstream of mitochondria. Here we address these challenges by validating a method for stable isotope tracing with isolated synaptic nerve terminals, or synaptosomes. We further applied this approach to study glucose metabolism in synaptosomes isolated from the 5X-FAD mouse model of AD treated with the antidiabetic sodium-glucose linked transporter-2 (SGLT-2) inhibitor Dapagliflozin. Treatment with Dapagliflozin preserved steady-state levels of synaptosomal metabolites and enrichment from labeled glucose into citrate that was reduced in the 5X-FAD model. These changes correlated with trends towards improved spatial working memory but not amyloid burden. The results highlight the utility of stable isotope tracing in synaptosomes to identify precise sites of metabolic dysfunction and mechanisms of action for metabolic drug candidates in preclinical models of neurodegeneration.

biochemistry↗