Biology subjects

Ge, J.

Publications and source records attributed to Ge, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Follow-up availability and the robustness of immune transcriptomic recovery after myocardial infarction

Background: Longitudinal blood transcriptomes describe immune changes after myocardial infarction, but later assays do not necessarily represent the population sampled at admission. We examined whether recovery summaries depend on observable selection and assumptions about unavailable assays. Methods: We reanalyzed official processed data from GSE59867, linking 111 patients with ST-segment elevation myocardial infarction across admission, discharge, one month, and six months. Seven fixed Hallmark programs were scored on a common 17,590-gene vocabulary using a bounded within-sample rank statistic. The primary endpoint was the six-month inflammatory-response score. We separated paired-completer change from the observed follow-up mean minus the entire baseline mean; fitted cross-fitted availability and outcome models; and evaluated full-support completion bounds and prespecified missing-mean scenarios. Artificial deletion tested estimators in the 83 observed six-month participants. GSE123342 provided unlinked marginal comparisons and explicitly conditional completion scenarios. Results: GSE59867 contained 101, 95, and 83 follow-up assays. At six months, inflammatory-response change was -0.00893 among paired completers and -0.00999 for the marginal contrast (95% participant-bootstrap interval -0.01217 to -0.00783). Augmented inverse-probability weighting gave -0.01004 (-0.01556 to -0.00727). The full-support completion interval was [-0.16460,0.08765], but eliminating the negative change required an unavailable-assay mean 4.42 observed-follow-up standard deviations above the observed mean. The primary direction remained negative throughout the prespecified {+/-}2-SD scenarios; interferon and coagulation directions were less stable. Under artificial outcome-dependent deletion, all evaluated estimators retained bias. The unlinked external cohort had 65 admission, 64 day-30, and 37 year-one MI assays; the year-one inflammatory contrast was -0.00459, with a conditional tipping shift of 1.70 SD. Conclusions: The observed inflammatory-response rank-score decline was stable to baseline-score adjustment and the prespecified {+/-}2-observed-SD missing-mean scenarios, while unrestricted completion did not identify its direction. Robustness varied across programs and data settings. These findings concern relative transcriptomic scores and assay availability, not clinical recovery, survival, or intervention efficacy.

bioinformatics↗

bioRxiv2026

Disease-associated amino acid substitutions outside canonical motor motifs impair Myo1e localization and activity

Steroid-resistant nephrotic syndrome (SRNS) is a severe kidney disorder characterized by proteinuria and disruption of glomerular filtration, often driven by genetic defects in genes encoding proteins required for podocyte functions. Among these, MYO1E, encoding the actin- and membrane-associated motor protein Myosin 1e (Myo1e), has been implicated in familial and sporadic forms of SRNS. Here, we investigated two MYO1E missense variants, A92E and G562R, identified in trans in a patient with childhood-onset SRNS and located outside canonical P-loop and switch subdomains of the Myo1e motor domain. Both residues are highly conserved, located within predicted -helices in the motor domain, and replaced by larger charged residues, which may reduce protein stability or folding. In podocyte-derived cells, both mutants failed to localize at intercellular junctions and displayed reduced colocalization with actin. The G562R variant additionally formed cytoplasmic aggregates that were partially expression-level-dependent and exhibited decreased fluorescence recovery after photobleaching, indicating impaired protein dynamics. In vitro motility and ATPase assays indicated that the G562R mutant exhibited a marked loss of ATPase activity while the A92E mutant displayed ATPase activity similar to the WT but was characterized by reduced motility and thermal stability. Together, these results demonstrate that A92E and G562R mutations compromise Myo1e localization and function, supporting their pathogenic role in SRNS.

cell biology↗

bioRxiv2026

A public-data reproducibility benchmark of a 2.5-D U-Net with a slice-level topology term for type-B aortic dissection segmentation

Background: Type-B aortic dissection requires separation of the true and false lumina in heterogeneous, anisotropic CTA. A topology term may reduce fragmentation, but its reproducibility must be tested under a fixed case split and independent native-grid evaluation. Methods: We used the public Graz type-B aortic dissection CTA collection (40 cases; CC BY 4.0) and froze a 28/6/6 case split for training, development, and held-out testing. A compact 2.5-D U-Net trained with cross-entropy plus multiclass Dice was compared with the identical model augmented by a fixed-weight (0.5) differentiable slice-level soft clDice term. Two training seeds were run for each arm. All 40 cases passed the NRRD audit; predictions for six held-out cases were restored to their native grids and scored with case-level 3-D voxel-grid Dice, voxel-grid morphological clDice, 6-connected component counts, physical-volume error, and 2,000-resample case-level paired bootstrap intervals. Results: With seed 20261007, topology-minus-baseline differences were -0.028 (95% CI -0.053 to -0.004) for true-lumen Dice, +0.032 (-0.006 to +0.096) for true-lumen voxel-grid clDice, +0.071 (+0.037 to +0.103) for false-lumen Dice, and +0.073 (+0.048 to +0.103) for false-lumen voxel-grid clDice. With seed 20261008, the corresponding differences were -0.040 (-0.065 to -0.018), +0.013 (-0.034 to +0.071), -0.099 (-0.187 to -0.004), and -0.058 (-0.124 to -0.001). Descriptive pooled means over 12 case rows per arm were true-lumen Dice 0.577 for topology versus 0.611 for baseline and false-lumen Dice 0.409 versus 0.422; these pooled rows are not independent cases. Conclusions: Under this fixed six-case test split, the corrected slice-level topology term did not produce a consistent benefit. True-lumen Dice was lower in both seeds, while false-lumen effects reversed direction between seeds; topology-clDice changes were small and/or interval-crossing. The benchmark supports an auditable failure-analysis workflow but does not support a general topology benefit, clinical use, external generalization, or a panvascular decision system.

bioinformatics↗

bioRxiv2026

Panvascular-JEPA: Unseen-Structure Evaluation of Factorized Predictive States for Hemodynamic Networks

Predictive representations for vascular simulation should be tested on unseen network structures and compared with the governing equations before being interpreted as general-purpose world models. We constructed a new, dimensioned but uncalibrated nodal resistance-inertance-compliance benchmark containing all 38 connected, non-isomorphic six-node graphs with five to seven edges. Twenty-four structures supplied training, validation, and new-background testing; 14 structures were wholly withheld. Across 648 parameter backgrounds and two prescribed action programs, 1,296 trajectories contained 96 forecast steps over three cycles. Four graph predictors received equal six candidate optimization searches, followed by five fixed-seed fits. Selected configurations and analysis code were locked before test trajectories were generated. Comparators included known-equation numerical integrators, an inertia-free reduction, and a five-coefficient model fitted to training trajectories. Unseen-structure mean standardized RMSE was 8.46 x 109 for four-factor OPF, 329 for single factor OPF, and 1.83 x 1031 for supervised graph prediction, compared with 1.09 x 10-4 for foursubstep known-equation integration and 6.77 x 104 for the fitted mechanism. The primary OPF-4 minus OPF-1 difference was 8.46 x 109, with a paired stratified-graph 95% percentile interval of [2.23 x 105, 2.54 x 1010]. Neural errors were strongly dependent on training seed and network structure, with extreme forecasts dominating the means. All four neural means exceeded persistence; relative performance within this comparison did not establish a usable forecasting model. The study supplies a distinct numerical test of structure transfer, factor-count control, and recursive stability. Its conclusions concern the implemented models, optimization budget, and finite graph catalogue. It establishes neither patient-specific performance nor anatomical transfer, biological remodeling, device efficacy, or clinical readiness.

bioengineering↗

bioRxiv2026

The Dilated Cardiomyopathy E525K Mutation Stabilizes the Cardiac Myosin Interacting-Heads Motif While Activating the Isolated Motor Domain

Mutations in {beta}-cardiac myosin are a common cause of inherited cardiomyopathies. The dilated cardiomyopathy E525K mutation alters both thick filament regulation and motor activity, yet the structural basis for these effects has remained unclear. Here, we combined cryo-EM and MD simulations to determine how E525K affects the conformational landscape of cardiac myosin in both its autoinhibited interacting-heads motif (IHM) and isolated myosin head states. E525K-mutated myosin exclusively adopted a single S2 conformation in IHM, in contrast to the conformational heterogeneity observed in wild-type myosin. Structural and electrostatic analyses revealed that the mutation increased positive charge density at the blocked-head (BH) - S2 (subfragment-2) interface, strengthening interactions with negatively charged residues within S2. 3D variability analysis and MD simulations of the E525K IHM demonstrated reduced S2 mobility, consistent with strengthened BH - S2 interactions, and decreased conformational flexibility, providing a structural mechanism for stabilization of the IHM state. To investigate the isolated myosin head, we determined cryo-EM structures of wild-type and E525K subfragment-1 (S1). The mutation induced local conformational rearrangements in the activation-loop and Loop 3 region, the SH3-like domain, and the essential light chain of S1, revealing structural changes that support the enhanced motor activity previously reported for isolated E525K myosin motors. These findings show that E525K stabilizes the autoinhibited IHM through electrostatic stabilization of the BH - S2 interface while inducing structural changes consistent with activation of the isolated motor domain, providing structural insights into how a single DCM mutation differentially regulates cardiac myosin S1 and IHM structure and function.

biophysics↗

bioRxiv2026

PanVasc Research for AI assisted evidence analysis in panvascular intervention

Panvascular intervention research requires evidence workflows that preserve source identity, outcome definitions and observation windows. We developed PanVasc Research, an executable research framework, and evaluated a fixed local Qwen3-4B model using two complementary tasks. Fifty ClinicalTrials.gov records from five vascular query strata generated 200 source-fidelity tests with intact evidence or controlled removal of the requested source, primary outcome or timeframe, plus 50 clean controls. A separate 100-statement sample from the official NLI4CT test set assessed clinical-trial entailment and evidence selection against existing expert labels. Generic and checklist prompts used identical evidence and maximum generation budgets; each output was also evaluated with an input-only deterministic contract. Registry exact accuracy was 51/200 (25.5%) with the generic prompt and 77/200 (38.5%) with the checklist; intact-case agreement was 50/50 and 48/50. The rule baseline recovered 200/200 tuples. NLI label accuracy was 48/100 (48.0%) and 50/100 (50.0%), respectively. The source contract retained 35 and 31 incorrect NLI labels in the two arms. Registry references establish fidelity to a registration snapshot, while NLI4CT concerns breast-cancer trials and does not validate vascular expertise. The framework also retains provenance-recorded literature retrieval, structured research planning and local numerical analysis. These experiments support a bounded assessment of source handling and semantic failure, rather than a new foundation model or autonomous scientific discovery. A proposed endpoint representation identifies the additional domain annotation and independent validation required for a panvascular research model.

bioinformatics↗

bioRxiv2026

Pathogen-associated odor experience induces inherited olfactory avoidance in a parasitoid wasp

Odors allow animals to evaluate resources and risks, but the neural and inherited consequences of experience with ecologically meaningful odors remain poorly understood. Since both parasitoids and entomopathogenic fungi are widely used as agents in integrated biocontrol, we asked whether exposure to pathogen-associated volatiles can reassign odor value in a parasitoid wasp and whether the acquired bias is transmitted to descendants. Adult female Scleroderma guani were exposed, without host contact, to volatiles from Beauveria bassiana-infected hosts or to methyl cinnamate (MC), a representative component of the infected-host odor. Twelve-hour exposure shifted subsequent choices away from infected-host odor and MC, whereas shorter exposure produced different effects, indicating duration-dependent olfactory plasticity. The shift occurred without an explicit reward or punishment and is therefore consistent with non-associative learning. Unexposed F1 and F2 descendants of MC-exposed females expressed the same avoidance bias. MC stimulation elicited stronger calcium responses in mushroom-body regions of trained females and their descendants. Head transcriptomes identified reduced expression of the crustacean cardioactive peptide receptor (CCAPR) as a shared molecular signature, and CCAPR RNA interference phenocopied the odor-avoidance behavior. Finally, maternal treatment with sinefungin, a broad S-adenosylmethionine-dependent methyltransferase inhibitor, left maternal behavioral shift intact but abolished the F1 bias, implicating a methylation-sensitive process in transmission. Together, these results reveal that a pathogen-associated odor can induce durable, cross-generational reweighting of olfactory value in a non-model insect and identify candidate neural and neuropeptidergic mechanisms linking sensory experience to inherited behavior, and providing a new perspective on utilizing training in integrated biocontrol as well.

animal behavior and cognition↗

bioRxiv2026

Single genome analysis of normal cells identifies the early steps of kidney cancer.

Whole genome analyses have shown that every cell of the body accumulates thousands of genetic changes during a lifetime, with implications for cancer initiation. We have analyzed normal kidney cells from both healthy individuals and patients with the Von Hippel Lindau (VHL) syndrome, which predisposes to kidney cancer. Using a clonal-expansion method that enables the collection of high confidence genetic and gene expression data from the same cell, we define a new mutational signature that marks a specific subset of damage-activated proximal tubule cells, as well as 96% of clear cell renal cell carcinomas. The underlying mutational process is specifically active in highly transcribed DNA and impacts the occurrence of cancer driver variants in the VHL gene. Our data from normal cells, supported by in vitro experiments, point to perturbations of oxygen availability as a causative factor. These findings link hypoxia, a frequent endogenous stress in the normal renal tissue, to excessive mutation and cancer initiation.

cancer biology↗

bioRxiv2026

BBBP_Atlas: Unified Interpretable Modeling of Blood Brain Barrier Permeability across Small Molecules and Peptides

Accurate prediction of blood-brain barrier permeability (BBBP) is essential for central nervous system drug discovery, yet existing models are often limited by their reliance on predefined physicochemical descriptors, small-molecule-centered training sets, or conformation-dependent representations, which restricts their transferability across chemically diverse modalities especially peptides. In addition, publicly available BBBP datasets remain fragmented, inconsistently standardized, and weakly controlled for molecular redundancy, increasing the risk of data leakage and overestimated model performance. In this study, we propose BBBP-Atlas, a structure-aware BBB permeability prediction model designed for unified modeling of small molecules and peptides with the first cross-modal dataset OmniBBBP. Designed to bypass descriptor and conformation dependencies, our model represents standardized molecular structures as atom-level graphs to capture local atom-bond environments and long-range topological dependencies associated with BBB transport. This design enables direct learning of structure-permeability relationships from molecular topology. For model training and evaluation, we curated a cross-modal, redundancy-filtered database OmniBBBP that seamlessly unifies small molecules and complex peptides, containing 10,218 unique compounds with 9,316 small molecules and 902 peptides. BBBP-Atlas achieved an accuracy of 0.8914 and an MCC of 0.7678 on the independent test set. On a balanced external benchmark of 200 compounds, our model reached an AUC of 0.9108, an accuracy of 0.8500, and an MCC of 0.7000, outperforming LightBBB by an absolute MCC gain of 6%. Case studies further showed that BBBP-Atlas captured clinically meaningful BBB permeability patterns, correctly identifying lorlatinib as BBB-permeable and vancomycin as BBB-impermeable with high confidence. The OmniBBBP-backed BBBP-Atlas offers a versatile and cross-modal approach for single-compound prediction, batch screening, and dataset exploration for CNS drug discovery. BBBP-Atlas is available at https://cadd.drugflow.com/bbbp/.

bioinformatics↗

bioRxiv2026

Seeing the world in a grain of sand: Fine global and local representations in foveal and parafoveal vision

Foveal vision enables primates to perceive small objects with remarkable precision by resolving both fine-global form and fine-local detail. Yet current coarse-to-fine and local-to-global frameworks, derived largely from parafoveal recordings and large-object representations, posit that V1 encodes local detail whereas IT represents global form, leaving the neuronal basis of foveal object representation unresolved. Here we show that fine-global form and fine-local detail are encoded parallelly as early as V1 and preserved across V2, V4 and IT at both foveal (1{degrees}-2{degrees}) and parafoveal (2{degrees}-6{degrees}) retinal eccentricities. Coarse-global features dominate parafoveal vision and higher cortical areas. Response latencies revealed a rapid processing sequence, with 2-6 ms separating coarse-global, fine-local, and fine-global processing within parafoveal V1, V2 and V4. These findings establish a cortical neuronal framework to resolve fine-global form of small objects in foveal vision along primate ventral visual stream, supporting fine-scale perception during reading and fine object recognition. Highlights O_LIFoveal two-photon imaging across V1, V2, V4, and IT C_LIO_LIGlobal and local processing examined across eccentricity C_LIO_LIFine and coarse global representations emerge as early as V1 C_LIO_LIFine global and local representations are preserved from V1 up to IT C_LIO_LITightly timed coarse-to-fine-to-fine processing within each cortex C_LIO_LIFast coarse-global dominates parafoveal and higher cortical areas C_LI

neuroscience↗

bioRxiv2025

Cryo-EM Reveals How Cardiomyopathy Therapeutic Drugs Modulate the Myosin Motors of the Heart

Genetic mutations in myosin, the motor protein that powers the heartbeat, are linked to inherited hypertrophic and dilated cardiomyopathies. Mavacamten and omecamtiv mecarbil are therapeutic, myosin-targeted drugs designed to treat these myopathies, but their mechanism of action has remained unclear. Using single-particle cryo-EM, we determined near-atomic resolution structures of wild-type, mavacamten-bound, and omecamtiv mecarbil-bound myosin molecules. Across all conditions, two conformations of myosin were observed. We show how mavacamten stabilizes one conformation by reinforcing key electrostatic interfaces in the molecule, whereas omecamtiv mecarbil weakens these interfaces, favoring the second structure. This remodeling elucidates previously unclear allosteric mechanisms through which these drugs either inhibit or enhance myosin activity, countering the deleterious impacts of disease. These findings reveal how drugs modulate myosin structure to control cardiac contractility.

biophysics↗

bioRxiv2025

QuickStainer: a rapid negative staining device for improved preservation of molecular structure

Negative staining is a widely used technique for observing macromolecules and their assemblies by transmission electron microscopy. It is commonly employed to optimize specimens for cryo-EM. The stain, typically a uranyl salt, surrounds the structure, providing an outline view at about 20 [A] resolution. Many macromolecules are relatively stable and rigid, and negative stain images provide a good representation of their structure. However, some are labile or flexible and their structure or assembly state is altered by binding to the carbon substrate on the grid before specimen staining. In these cases, the negatively stained appearance does not faithfully represent the structure in solution. This problem is reduced when samples are incubated on the carbon surface for short times (5 s) rather than typical times (30-60 s) before staining. To reduce disruption to a minimum, we have developed a rapid negative staining device (QuickStainer) using 3D-printed components, a stepper motor for precisely timed movements, and an Arduino-controlled interface to execute commands. QuickStainer produces consistent, reproducible results, achieving sample incubation times as low as 10 ms before staining. Tests show rapid adherence of molecules to the grid and greatly improved structural preservation of labile specimens compared with standard preparation protocols. The design of QuickStainer can accommodate inclusion of additional steps, such as timed incubation with enzyme substrate, before staining.

biophysics↗

bioRxiv2025

Biodegradation of the endocrine-disrupting compound bisphenol F by Sphingobium yanoikuyae DN12

Bisphenol F (BPF) is an emerging environmental pollutant widely present in surface water and wastewater systems. Microbial activity is crucial in driving its degradation, offering a potential avenue for mitigating its environmental impact. Although the degradation pathway for BPF has been identified in various bacteria, the biodegradation mechanisms remain unclear. In this study, we isolated a highly efficient BPF-degrading strain of Sphingobium yanoikuyae DN12, which could utilize BPF as the sole carbon source and energy source for growth, from a river sediment in Anhui Province China. Through Ultra performance liquid chromatography high-resolution mass spectrometry (UPLC-HRMS) analysis, we found that oxidation and hydrolysis are key steps for BPF biodegradation. Utilizing whole-genome sequencing, comparative transcriptomics analysis and biochemical identification, a gene cluster bpf was identified to be involved in BPF degradation. BpfAB is a two-component oxidoreductase responsible for converting BPF to 4,4-dihydroxybenzophenone (DHBP). BpfC is a Baeyer-Villiger monooxygenase (BVMO) responsible for converting DHBP to 4-hydroxyphenyl-4-hydroxybenzoate (HPHB). Isotope tracing demonstrated that the oxygen atom incorporated by BpfAB originates from water, whereas that incorporated by BpfC derives from molecular oxygen (O2). BpfD is an /{beta} hydrolase responsible for converting HPHB to 4-hydroxybenzoate (4HB) and 1,4-hydroquinone (HQ). Analysis of the taxonomic and habitat of 325 prokaryotic genomes revealed that BpfA-like homologs are predominantly found in the phylum Pseudomonadota, primarily inhabiting soil and aquatic environments. This study enhances our understanding of the biodegradation mechanism of BPF, and provides guidance for the effective remediation of BPF-contaminated environments. IMPORTANCEBPF is a widely used alternative to bisphenol A and poses a growing threat to ecosystems and human health due to its environmental persistence and endocrine-disrupting effects. Although microbial degradation pathways for BPF have been reported, the key enzymes involved and their catalytic mechanisms remain unclear. This work reports the isolation of a Sphingobium strain capable of mineralizing BPF and the genetic basis for the catabolic pathway. Three enzymes--a two-component oxidoreductase, a Baeyer-Villiger monooxygenase, and an /{beta} hydrolase--were biochemically characterized and shown to catalyze the three critical steps in BPF degradation. These findings provide insights into the biochemical processes involved in the microbial degradation of BPF.

microbiology↗

bioRxiv2025

Impact of Inactivation Methods on Biosafety and Antigen Reactivity of Brucella melitensis from the Perspective of Astral-DIA Proteomics Based on Antibody Immunoprecipitation Mass Spectrometry

Effective Brucella inactivation is imperative for safe vaccine development, diagnostics, and sample handling, particularly in resource-limited regions lacking high-level containment facilities. This study investigated inactivation methods using the Rev.1 vaccine strain and three Brucella melitensis field isolates from Gansu (GS-XG, GS-SN, GS-MQ). Heat (80{degrees}C/95{degrees}C, 10-20 min) and formaldehyde (0.4%/0.6%, 48-72 h) inactivation were evaluated for biosafety and antigenicity. Rev.1 was completely inactivated by 80{degrees}C/95{degrees}C for 20 min or 0.6% formaldehyde for 48-72 h. Superior antigenicity, compared to phenol inactivation, was confirmed by ELISA and Western Blot. However, field isolates demonstrated greater resistance, surviving 80{degrees}C for 20 min and 0.4% formaldehyde for 72 h, necessitating stricter conditions (95{degrees}C, 20 min; 0.6% formaldehyde, 72 h) for their complete inactivation. Astral-DIA proteomics analyzed approximately 60% of the proteome ([~]2000/3300 proteins), revealing 256, 311, and 318 differentially expressed proteins between 80{degrees}C/95{degrees}C heat, 48-h/72-h formaldehyde, and heat/formaldehyde methods, respectively. Gene Ontology and KEGG analyses indicated heat inactivation upregulated cellular structure proteins but downregulated metabolic pathways, with 95{degrees}C potentially damaging conformational epitopes. Formaldehyde treatment (48 h) stabilized soluble antigens, preserving ribosomal and regulatory protein epitopes, while 72-h treatment induced organelle disintegration. Protein-Protein Interaction networks suggested heat inactivation enhanced immunogenicity of membrane and stress proteins, suitable for targeted studies, whereas formaldehyde preserved broader epitopes, beneficial for whole-cell vaccines and multi-epitope screening. Inactivation methods must be tailored to specific strain characteristics and applications. Astral-DIA provides molecular insights into antigenicity loss, guiding future research on protein functions and epitope dynamics for precise brucellosis control.

microbiology↗

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

Mechanisms of resistance to VHL loss-induced genetic and pharmacological vulnerabilities

The von Hippel-Lindau tumor suppressor (VHL) is a component of a ubiquitin ligase complex that normally controls cellular responses to hypoxia. Endogenous VHL is also utilized by proteolysis-targeting chimera (PROTAC) protein degraders, a promising class of anti-cancer agents. VHL is broadly essential for cell proliferation, yet it is a key tumor suppressor in renal cell carcinoma. To understand the functional consequences of VHL loss, and to identify targeted approaches for the elimination of VHL null cells, we have used genome-wide CRISPR-Cas9 screening in human renal epithelial cells. We find that, upon VHL loss, the HIF1A/ARNT complex is the central inhibitor of cellular fitness, suppressing mitochondrial respiration, and that VHL null cells show HIF1A-dependent molecular vulnerabilities that can be targeted pharmacologically. Combined VHL/HIF1A inactivation in breast and esophageal cancer cells can also provide resistance to ARV-771, a VHL-based bromodomain degrader that has anti-cancer activity. HIF1A stabilization can thus provide opportunities for early intervention in neoplastic VHL clones, and the VHL-HIF1A axis may be relevant for the development of resistance to the emerging class of PROTAC-based cancer therapies.

cancer biology↗

bioRxiv2025

Group 2 Innate lymphoid cells promote allograft survival by constraining and inducing anergy in alloreactive CD4+ T cells

Although solid organ transplant outcomes have dramatically improved over the last several decades, incomplete understanding of the immune interface between the donor organ and the recipients immune system has impaired our ability to induce immune tolerance in most transplant recipients. Since group 2 innate lymphoid cells (ILC2s) reside in all transplanted solid organs, participate in wound healing, and coordinate other immunoregulatory cell populations, we investigated their role in the alloimmune response. Using a mouse heterotopic cardiac transplant model, we show that recipient ILC2s replace donors ILC2s, upregulate MHCII without expressing costimulatory molecules. In addition, recipient derived ILC2s process and present alloantigen, inducing CD4+ T cell anergy via Caspase-3 pathway. When recipient-derived ILC2s are not present, we observed a significant increase in infiltrating donor reactive CD4+ T cells and worsened allograft survival. Additionally, expansion of ILC2s in vivo through IL33 administration prolonged the survival of murine heart allografts. Overall, these data highlight a critical and novel immunoregulatory role of host-derived ILC2s in solid organ transplant, where they induce anergy in alloreactive CD4+ T cells, promoting the induction of alloimmune tolerance.

immunology↗

bioRxiv2025

Developing a versatile technology for agroinfiltration in multiple plants

Agrobacterium-mediated transient transformation methods are widely used in plant science and molecular pharming. However, plant immune response and post-transcriptional gene silencing (PTGS) can compromise gene expression, limiting the adaptability of these methods across plant species. The lack of a robust reporter system further hinders advancements in agroinfiltration technology. To address these challenges, we developed a fungal bioluminescence pathway (FBP)-based reporter system that utilizes caffeic acid to generate self-sustained luminescence. By incorporating NahG and P19, our FBP assay enhances transient transformation efficiency in over 20 plant families, including major crops, vegetables, ornamental plants, and trees. Furthermore, we demonstrate its utility for assessing protein localization, interactions, and transcriptional regulation in multiple plant species, thereby broadening our understanding of gene function throughout the plant kingdom.

plant biology↗