Biology subjects

Zhao, D.

Publications and source records attributed to Zhao, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Heat-dependent engagement of a buried mitophagy motif in prohibitin 2

Mitophagy receptors are generally switched on by upstream enzymes rather than by the receptor itself. Whether a receptor can instead respond directly to a physical stimulus has not been established. Here we show that a second LC3-interacting region (LIR) in prohibitin 2 (PHB2) is regulated by temperature. It lies in a marginally stable helix that holds its two anchor residues about 5 angstrom apart, whereas a bound LIR spans about 9 angstrom. Replica-scaling simulations showed that this helix, but not a matched control from the same protein under identical scaling, samples that geometry; purified PHB2 bound ATG8-family proteins only at 313 K and above. Substitutions designed from this geometry to stabilise (K253A/R255A) or destabilise (I254G) the helix altered binding, mitochondrial recruitment and respiration in PHB2-null cardiomyocytes. Mice carrying the stabilising substitutions in cardiomyocytes sustained greater cardiac injury during heat stroke despite matched thermal load and comparable systemic injury. Motif accessibility may therefore be a regulated variable rather than a fixed property of a fold.

molecular biology↗

bioRxiv2026

Acetylation of NDUFA13 at K7 Senses OXPHOS Dysfunction to Disrupt Prohibitin Scaffolds and Drive Cristae Remodelling in Heart Failure

Mitochondrial cristae disintegration is a hallmark of heart failure, yet how oxidative phosphorylation (OXPHOS) dysfunction triggers this structural collapse remains unclear. Here we identify acetylation of the complex I subunit NDUFA13 at lysine 7 (K7) as a metabolic sensor coupling OXPHOS dysfunction to cristae remodelling. OXPHOS inhibition drove NDUFA13-K7 hyperacetylation, inducing conformational compaction and translocation to the intermembrane space. Acetylated NDUFA13 competitively engaged PHB2 through its coiled-coil domain, displacing PHB1 and disassembling prohibitin scaffolds. The acetylation-mimetic NDUFA13-K7Q induced cristae fragmentation in vitro, and cardiomyocyte-specific K7Q knock-in mice showed accelerated mortality and cristae loss under pressure overload, accompanied by impaired TCA cycle flux, defective fatty acid oxidation and selective depletion of polyunsaturated cardiolipins. These findings establish NDUFA13-K7 acetylation as a reversible switch converting bioenergetic failure into pathological cristae remodelling and metabolic reprogramming, highlighting therapeutic potential for targeted deacetylation.

cell biology↗

bioRxiv2026

Closing the phenotyping gap: non-invasive electromagnetic induction enables high-throughput screening of crop root function in the field

Crop root systems play a critical role in water uptake and yield improvement under drought. However, a lack of methods to measure root system function at scale, particularly in the field, poses significant challenges to explore them in crop improvement programs. To address this bottleneck, we introduce a novel approach to directly screen water uptake and root activity in the field through integrating electromagnetic induction (EMI) sensing, inversion modelling and machine learning. This study was conducted as an on-farm field experiment comprising a factorial combination of 13 sorghum genotypes and three row spacings with three replications. Time-lapse EMI surveys were conducted from flowering to maturity using a customised DualEM-21S sensing system. Artificial neural network models were developed to predict 3D soil moisture ({theta}) using depth-specific true soil electrical conductivity estimated from EMI inversion algorithms, and the prediction accuracy was evaluated. Crop water use and functional root traits were derived from changes in {theta} profiles between successive EMI surveys using cubic splines fitted within a linear mixed model framework. Results indicate that dynamics of {theta} can be predicted with high accuracy (R2 = 0.83). There was a significant positive correlation between the EMI-derived crop water use and root length density at the depths without water stress. The functional root traits were significantly affected by growth stages, genotypes, row spacings, and their interactions. In general, narrower row spacing resulted in deeper rooting depth by flowering, which was associated with a larger canopy and higher grain number. In contrast, wider row spacing promoted greater post-flowering root growth, leading to increased post-flowering water use and, consequently, larger grain weight. Overall, our approach enables rapid characterisation of variation in crop water use, rooting depth and root growth in the field. It provides a valuable framework for understanding the dynamic interactions between root function and yield traits across variable field environments, with potential to accelerate genotype selection and optimise crop design in breeding and agronomy programs.

plant biology↗

bioRxiv2026

Evidence-resolved benchmarks separate biological context recognition from direct-partner specificity in protein interaction models

Sequence-based models enable scalable protein-protein interaction (PPI) prediction, but whether high scores identify direct physical partners or broader biological compatibility remains unclear. Here we show that biological-context recognition and direct-partner specificity are separable prediction capabilities. We introduce ProtNegDB (http://protnegdb.bjmu.edu.cn/), an evidence-resolved resource distinguishing experimentally supported non-binding from coordinate-verified noncontact within PDB biological assemblies. Using context-matched benchmarks, we find that five sequence-based predictors show limited ability to distinguish direct partners from noncontacting members of the same assembly, whereas PLM-Interact readily ranks both above unrelated proteins. Representation analyses reveal that adaptation to PPI prediction can strengthen biological-context encoding without yielding transferable direct-contact specificity. AlphaFold3 shows greater, though still incomplete, direct-partner resolution, suggesting that explicit multimer modeling can help refine partner specificity. In PLM-Interact, negatives defined by reconstituted direct-binding, cellular binary/proximity and co-complex assays occupy distinct score regimes. Across independent datasets and multiple models, experimental direct non-binding and assembly noncontact further show reproducible, model-dependent scoring patterns. High sequence-based PPI scores should not be interpreted as direct-interface probabilities. Mechanistically interpretable evaluation instead requires explicit consideration of interaction-evidence semantics and partner specificity.

bioinformatics↗

bioRxiv2026

Cell Type-Specific Structural and Functional Signatures of APOE4, Age and Sex in the Mouse Anterior Olfactory Nucleus

As the strongest genetic risk factor for late-onset Alzheimer's disease (AD), the human APOE {varepsilon}4 allele alters neuronal physiology before overt pathology. However, how aging and sex modify these effects in the anterior olfactory nucleus (AON), an early AD-affected brain region, remains unclear. Here, we performed whole-cell recordings and post hoc morphological reconstructions of pyramidal cells (PCs) and interneurons (INs) in acute AON slices from adult and aged humanized APOE3 (E3) and APOE4 (E4) knock-in mice of both sexes with identification of context-dependent remodeling across structural, intrinsic, and synaptic domains. In PCs, morphology was broadly susceptible to APOE genotype x age x sex and their interactions. Functionally, aged E4 PCs exhibited a more depolarized resting membrane potential than aged E3 PCs. Additionally, afterhyperpolarization amplitude displayed a marked age x genotype interaction, reversing the direction of the E4 - E3 difference from adulthood to aging. Excitatory synaptic event frequency showed a complex genotype and age and sex interaction, whereas inhibitory synaptic event amplitude was elevated in E4 mice. In contrast, INs displayed far more restricted alterations. Morphological changes were limited to dendritic length, which was modulated by age and sex specifically in E4 mice. Physiologically, genotype effects were confined to action potential amplitude, while aging primarily altered membrane properties and excitatory synaptic inputs. Together, these findings demonstrate that APOE genotype cell-specifically shapes AON neuronal properties through interactions with age and sex, suggesting that APOE4 establishes altered cellular states that influence how this circuit responds to subsequent disease-related stress.

neuroscience↗

bioRxiv2026

Structure-aware deep learning predicts influenza antigenicity and guides vaccine strain recommendation

The continuous accumulation of genetic mutations in influenza A viruses (IAVs) drives antigenic drift, necessitating precise antigenic prediction for optimal vaccine strain selection. While sequence-based methods have advanced antigenic surveillance, they neglect the three-dimensional structural context that fundamentally dictates viral antigenicity. Here, we introduce Vir3D, which leverages ESMFold-derived structural information from amino acid sequences to precisely predict viral antigenicity and guide vaccine strain selection. Across both human H3 and highly pathogenic avian H5 subtypes, Vir3D not only accurately discriminates antigenic variants and infers pairwise antigenic distances, but also mechanistically delineates key structural residues driving viral immune evasion. In a decade-long retrospective analysis, Vir3D-prioritized vaccines consistently achieve broader antigenic coverage of circulating strains than World Health Organization (WHO) recommendations. Crucially, Vir3D successfully predicts that the emerging U.S. dairy cattle H5N1 virus (TX/24) remains antigenically stable relative to clade 2.3.4.4b vaccine strains, and subsequent wet-laboratory validation of hemagglutination inhibition (HI) assays definitively corroborates this finding. Overall, Vir3D establishes a powerful, structure-driven framework for proactive influenza surveillance and pandemic preparedness.

bioinformatics↗

bioRxiv2026

Isoflurane and surgery aggravate APOE4-dependent lipid dysregulation and neural dysfunction, leading to neurological impairment in male mice

PurposePerioperative exposure to the volatile anesthetic isoflurane (ISO) has been associated with cognitive and olfactory deficits and may increase the risk of Alzheimers disease (AD). Apolipoprotein E4 (APOE4), the strongest genetic risk factor for AD, contributes to disease pathogenesis through disrupted lipid homeostasis. However, whether and how isoflurane interacts with APOE genotype to influence neurological vulnerability remains unclear. MethodsYoung adult, presymptomatic humanized APOE4 and APOE3 knock-in mice underwent laparotomy under 2 h of isoflurane anesthesia. Microglia and astrocytes were isolated from the olfactory bulb (OB) and hippocampus (HI) by magnetic-activated cell sorting. Lipid composition, transcriptional responses, and functional outcomes were assessed using lipidomic, bulk RNA-seq, and longitudinal behavioral testing. In vivo and ex vivo electrophysiological recordings evaluated neuronal excitability and synaptic transmission in both regions. ResultsBy day 7 post-anesthesia, cell type-specific lipidomic profiling of both OB and HI revealed more pronounced lipid perturbations in microglia and astrocytes from APOE4/ISO mice than from APOE3 mice, characterized by elevated free fatty acids, increased lipid peroxidation, triglyceride depletion, and reduced hippocampal hexosylceramides and cardiolipins. Electrophysiological recordings showed greater olfactory circuit dysfunction in APOE4/ISO mice, accompanied by persistent odor memory deficits, transient olfactory sensitivity loss, early motor coordination impairments, and delayed cognitive deficits. RNA sequencing of the OB identified downregulated lipid metabolism and atherosclerosis-related pathways. ConclusionThese findings establish a mechanistic link between APOE4-dependent glial lipid dysregulation, olfactory circuit dysfunction, and delayed cognitive impairment following isoflurane anesthesia and surgery, highlighting lipid homeostasis as a potential therapeutic target.

neuroscience↗

bioRxiv2026

Genetically informed single-cell and spatial mapping of metabolic programs in human health and disease

Defining cell-type-specific endogenous metabolic features, the spatial distribution of cell-level metabolic states and cellular responses to exogenous metabolites is very important for understanding disease mechanisms. However, existing transcriptome-based metabolic models primarily infer intracellular reaction or pathway-level activities, and therefore cannot directly assess associations between individual metabolite levels and cellular states, particularly for metabolites that act extracellularly as signalling molecules rather than entering cells as metabolic substrates. To overcome this problem, we introduce the gmMAP (Genetically informed metabolite trait mapping across single-cell and spatial tissues), a framework that integrates metabolite GWAS summary statistics with single-cell and spatial transcriptomes to map metabolic programmes at cellular and spatial resolution. Notably, the gmMAP enables the prediction of endogenous metabolic process activation while also revealing intrinsic associations between exogenous metabolites and diverse cellular functional states. To further capture the connectivity of cellular metabolic networks, we incorporated a constraint-based metabolic flux model to evaluate global metabolic activity. To evaluate the accuracy and generalizability of gmMAP, we applied the framework across representative biological contexts spanning human development, physiological homeostasis, inflammation and cancer. In human kidney development, the gmMAP captured dynamic metabolic programmes, which was validated using paired transcriptomic and metabolomic reference datasets, supporting its reliability in metabolite identification and metabolic-flow inference. At the organ level, the gmMAP reconstructed spatial metabolite distribution patterns across 17 mouse organs under homeostatic and autoimmune inflammatory conditions, and further extension of gmMAP to 24 normal human tissues generated a multi-scale metabolic atlas at both organ and cellular resolutions. In disease settings, gmMAP revealed metabolic reprogramming across 29 pan-cancer cell populations, and identified potential links between exogenous metabolites and inflammation-associated stromal metabolic remodelling in ulcerative colitis. Together, gmMAP can consistently connect genetically informed metabolite traits with cell states, spatial tissue organization and disease pathology.

genomics↗

bioRxiv2026

The Origin and Evolution of Protein Synthesis: A Co-Adaptation Flexible-Rigid Docking Model Based on First-Principles Reasoning

Although the "RNA world" hypothesis suggests that RNA played a crucial role in the origin of life [7], the functional framework of RNA in prebiotic protein synthesis and the mechanisms of genetic code formation during the prebiotic period remain poorly understood. Here, using the prebiotic "primordial soup" as a model, we reconstructed the detailed steps that would yield a protein with a stable ordered amino-acid sequence in the "primordial soup" at the prebiotic period. In the "primordial soup", a large number of medium- to large-sized biomolecule-like substances--such as RNA-like and protein-like molecules of various sizes and shapes, as well as related polymers like amino-acid-RNA-like etc.--did generate and accumulate. Moreover, protein-like and RNA-like molecules formed even more intricate complexes. These complexes bound free mRNA-like molecules through complementary base pairing. Subsequently, with an extremely low probability, two adjacent amino-acid-RNA-like molecules became bound to this free mRNA-like molecule, and their amino acids underwent a condensation reaction by the complexes, producing peptides and eventually proteins or polypeptides. This free mRNA-like molecule exhibits a certain flexible structure, whereas the super-large complexes formed by protein-like and RNA-like molecules (which possess certain activities) and the amino-acid-RNA molecules exhibit relatively rigid structures. Long-term evolution and mutual selection led to the emergence of proteins with stable amino acid sequences and moderate catalytic activity. In this way, the nucleotide information embedded in such mRNA-like molecules indirectly express through protein synthesis--a process we term the "A Co-Adaptation Flexible-Rigid Docking Model", where flexible mRNA-like molecules dock onto rigid complexes to enable ordered peptide formation. Finally, we show how trinucleotide codons emerge naturally from the flexible-rigid docking constraints.

evolutionary biology↗

bioRxiv2026

Spatiotemporal Cascade of AP1/CCA1-TOC1 Module Gates Stem Development

Stem development is crucial in plant vertical architecture and overall crop improvement. The molecular mechanisms underlying the initiation and circadian growth of stem remain still enigmatic. Here, we demonstrate that APETALA1 (AP1) spatially initiates circadian stem growth through a noncell-autonomous role of TIMING OF CAB EXPRESSION1 (TOC1) emanating from the floral meristem to inflorescence meristem in Arabidopsis thaliana. Mechanistically, AP1 interacts with and recruits CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) to associate TOC1. Dynamic formation of the AP1-CCA1 complex is crucial for maintaining the circadian rhythmicity and expression of TOC1. Tissue-specific expression of TOC1 in floral meristems rescues the developmental defects of toc1 mutants at both functional and transcriptional levels. Furthermore, TOC1 directly activates the circadian expression of pectin methylesterase gene family, which is critical for its role in stem development. AP1 homologs regulate circadian stem elongation and plant height in wheat and rice, underscoring the conserved mechanism across flowering plants. Our findings uncovered a spatiotemporal regulatory cascade gating stem development and identified candidate genes for crop improvement.

plant biology↗

bioRxiv2026

Cholangiocyte RUNX1 Orchestrates Fibrogenic and Inflammatory Signaling to Drive Biliary Fibrosis

IntroductionBiliary fibrosis and inflammation are central to the pathogenesis of cholangiopathies such as primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC). Inflammatory and fibrogenic stimuli, such as transforming growth factor-{beta} (TGF{beta}) and lipopolysaccharide (LPS) signaling, drive these processes, but their underlying transcriptional mechanisms in cholangiocytes remain incompletely defined. We investigated the role of Runt-related transcription factor 1 (RUNX1) as a transcriptional co-regulator of fibroinflammatory signaling in cholangiocytes. MethodsHuman PSC-derived cholangiocytes (PSC-Cs) and mouse large biliary epithelial cells (MLEs) were subjected to RUNX1 knockdown or pharmacologic inhibition (Ro5-3335 or AI-10-104). Cytokine secretion was profiled by Luminex multiplexing; RUNX1 genomic binding and protein interactome were assessed by ChIP-qPCR, ChIP-seq, and LC-MS/MS. In vivo, Mdr2-/- mice received Ro5-3335, and cholangiocyte-selective Runx1 knockout mice (Krt19-CreERT) were challenged with a DDC diet, followed by evaluation of fibrosis and inflammation. ResultsRUNX1 expression was significantly increased in cholangiocytes from PSC and PBC patients, and Mdr2-/- mice. RUNX1 knockdown or inhibition reduced IL6, TNF, and other proinflammatory cytokines in PSC-Cs and attenuated TGF{beta}-, LPS-, and TNF-induced Il6 and Ccl2 expression in MLEs. ChIP-qPCR and ChIP-seq revealed TGF{beta}-induced RUNX1 binding to the Il6 promoter and 727 additional genomic sites enriched for fibrosis and inflammatory pathways; predicted upstream regulators included TGF{beta}, TNF, and NF{kappa}B signaling. Proteomic analysis identified TGF{beta}-induced RUNX1 interactions with SMAD2 and NF{kappa}B2. In vivo, Ro5-3335 treatment in Mdr2-/- mice reduced hepatic collagen, ECM gene expression, immune cell infiltration, and serum liver injury markers and bile acids. Similarly, cholangiocyte-specific Runx1 deletion mitigated fibrosis, inflammation, and liver injury in DDC-fed mice. ConclusionRUNX1 is a central transcriptional hub integrating TGF{beta} and inflammatory signals in cholangiocytes. Its inhibition attenuates biliary fibrosis and inflammation in cholestatic models, supporting RUNX1 as a potential therapeutic target in fibroinflammatory cholangiopathies.

physiology↗

bioRxiv2026

Cell Type-informed Characterization of Spatial Niches from Spatial Multimodal and Multi-omics Data

Cell niches play critical roles in tissue organization and orchestrate homeostasis, development, and disease progression. Advances in spatial omics technologies now allow diverse molecular and image-derived data to be jointly captured while preserving spatial context, but deciphering cell niches from such spatial multimodal and multi-omics data remains challenging. Existing computational methods are still limited in their flexibility across variable combinations of spatial modalities and omics data. Here we introduce SpaNECT, a unified and flexible framework designed to accommodate spatial multimodal and multi-omics data for cell niche characterization. SpaNECT further incorporates reference-informed cell-type information to support biologically interpretable niche analysis. Systematic evaluations across diverse tissues, disease conditions, and developmental stages showed that SpaNECT consistently outperformed representative methods in resolving cell niches. In mouse brain spatial multi-omics data, SpaNECT uncovered niche-associated molecular and regulatory programs; in developing chick heart, it tracked cross-stage niche reorganization and progressive remodeling of ventricular-associated cell states during maturation. Overall, SpaNECT establishes a general and robust framework for characterizing cell niches across spatial multimodal and multi-omics data.

bioinformatics↗

bioRxiv2026

Improve the Efficacy of B7-H3-Targeting Antibody-Drug Conjugate DS-7300a in TP53-deficient Tumors by Inducing Ferroptosis

Immune checkpoint B7-H3 is an emerging target for immunotherapy. DS-7300a is an advanced B7-H3-targeting antibody-drug conjugate (ADC) warheaded with the topoisomerase I inhibitor DXd. DS-7300a has demonstrated clinical activity, but molecular biomarkers to predict its therapeutic response remain elusive. TP53 is one of the most mutated tumor suppressor genes across cancers, and effective therapies are urgently needed for TP53-deficient cancers. Using prostate cancer (PCa) as a model system, we reported that DS-7300as anti-tumor efficacy is highly dependent on functional p53 in cancer cells, and TP53 defects confer resistance to DS-7300a. Mechanistically, we found that DS-7300a and its payload, DXd, induce DNA damage and activate the ATM/ATR/CHK signaling cascade, thereby stabilizing p53 and inducing a pro-apoptotic and senescence-associated transcriptome. In contrast, TP53-deficient cells fail to detect DXd-induced DNA damage, maintain a high proliferation rate, and exhibit low levels of apoptosis and senescence, thereby conferring resistance to DS-7300a. Ferroptosis is an iron-dependent form of regulated cell death triggered by lipid peroxidation, which is mechanistically and morphologically distinct from apoptosis. Interestingly, DS-7300a treatment elevates lipid peroxidation in TP53-deficient cancer cells and upregulates glutathione peroxidase 4 (GPX4), an antioxidant enzyme that mitigates lipid peroxidation. Using isogeneic xenograft models and a newly developed humanized B7-H3 PCa model, we demonstrated that inducing ferroptosis by pharmacological inhibition of GPX4 enhances DS-7300as efficacy in TP53-deficient tumors. Our studies demonstrate that TP53 status dictates anti-tumor responses to DS-7300a, and ferroptosis induction represents a promising therapeutic approach to overcome resistance to DS-7300a in malignancies harboring TP53 defects.

cancer biology↗

bioRxiv2026

Pyruvate-driven hydrogen production promotes polyphenol bioconversion by gut bacteria

Gut microbial biotransformation of poorly absorbable polyphenols into bioactive, bioavailable metabolites is increasingly recognized as a key mechanism underlying their health benefits of polyphenols. Microbial ellagic acid (EA)-to-urolithin conversion represents a typical example, but the environmental factors that facilitate such metabolism remain underexplored. We discovered that urolithin production by a gut commensal bacterium, Gordonibacter urolithinfaciens (G. uro), is metabolically repressed by arginine. To overcome such limitations, we developed PhenolBoost Medium (PBM) that induces a metabolic shift by suppressing the arginine deiminase pathway while activating pyruvate metabolism and hydrogen production in G. uro, thereby driving urolithin dehydroxylation. Transcriptomic profiling and 13C-isotopic tracing analysis revealed that pyruvate metabolism in PBM upregulates hydrogenase expression, facilitating the dehydroxylation of EA. PBM also promoted the complete conversion of EA to urolithin A in G. uro-Enterocloster bolteae co-culture, and other polyphenol biotransformations. In addition, co-culturing G. uro with hydrogen-producing Bacteroides species significantly increased urolithin production. Furthermore, an arginine-limited, pyruvate-enriched dietary regimen proved effective in vivo, resulting in significantly higher urolithin production and bioavailability in a mouse model. Our findings reveal the critical role of hydrogen in facilitating polyphenol dehydroxylation, and offer a viable nutritional strategy for boosting microbial production of beneficial metabolites from polyphenols.

microbiology↗

bioRxiv2026

RUNX1-deficiency drives immune-active ER+ mammary tumorigenesis through activation of interferon signaling

AbstractRecurrent loss-of-function mutations in RUNX1 occur in estrogen receptor-positive (ER+) breast cancers, yet how RUNX1-loss contributes to breast tumorigenesis remains unclear. Here we used genetically engineered mouse models with luminal mammary epithelial cell (MEC)-restricted gene disruption to investigate its role in breast cancer initiation. Loss of RUNX1 alone, or together with RB1, was insufficient to drive tumor formation. In contrast, combined loss of RUNX1 and p53 induced mammary tumors with full penetrance. These tumors contained ER+ cancer cells and exhibited extensive T cell and macrophage infiltration, indicative of an immune hot microenvironment. Mechanistically, RUNX1-deficiency activated interferon signaling in luminal MECs, associated with derepression of RUNX1 target STAT1 and enhanced inflammatory responses. Consistent with these findings, human ER+ breast cancers with low RUNX1 expression displayed elevated immune signatures and poorer patient survival. Together, our results identify RUNX1-loss as a driver of an immune-active subtype of ER+ breast cancer.

cancer biology↗

bioRxiv2026

Sleeve gastrectomy protects lean mice from future obesity.

BackgroundObesity and metabolic disease drive premature aging and reduced lifespan. While metabolic interventions like calorie restriction, protein restriction, and time restricted feeding have been shown to improved lifespan, they are either not effective or sustainable for most humans. Bariatric surgery is the most efficacious metabolic intervention available and is associated with increased lifespan. However, whether its longevity benefits derive solely from weight reduction or reflect surgery-specific metabolic reprogramming remains unknown. MethodsWe employed a lean mouse model of sleeve gastrectomy (SG) in which young, lean male C57BL/6J mice underwent SG or sham operation while maintained on low-fat chow, then were challenged with high-fat diet (HFD) in midlife. We assessed glucose metabolism, body composition, energy expenditure, hepatic histology, adipose tissue inflammation, and cecal microbiome composition. ResultsDespite identical weight and food intake on low-fat chow, SG mice demonstrated improved glucose tolerance and insulin sensitivity prior to HFD challenge. Upon HFD exposure, SG animals exhibited enhanced metabolic flexibility with greater capacity for fat oxidation, increased energy expenditure, attenuated weight gain, and reduced adiposity compared to sham controls. SG further reduced hepatic lipid accumulation and attenuated visceral adipose tissue inflammation, marked by decreased pro-inflammatory cytokine expression and reduced macrophage infiltration. These metabolic benefits occurred independently of caloric intake. Cecal microbiome profiling revealed surgery-specific remodeling characterized by Lactobacillus enrichment and reductions in Verrucomicrobia and Clostridia -- a pattern distinct from caloric restriction and consistent with prior SG studies. ConclusionsEarly-life SG confers durable, weight-loss-independent protection against midlife metabolic deterioration. Gut microbiome remodeling, particularly enrichment of Lactobacillus species, represents a candidate mediating mechanism and a potential therapeutic target for aging and metabolic disease.

physiology↗

bioRxiv2026

Estradiol modulates neuronal network hyperexcitability in select NDD risk genes

Sex hormone signaling during neurodevelopment may act as a modulator of risk for neurodevelopmental disorders (NDDs), including autism spectrum disorders (ASDs). By conducting a systematic and multi-modal evaluation of estradiol effects across loss-of-function deletions in 36 functionally diverse, large-effect ASD/NDD genes in human induced pluripotent stem cell-derived neurons and larval zebrafish, we uncover convergent and divergent gene-by-estradiol interactions at the transcriptomic, circuit, and behavioral levels. Whereas estradiol partially ameliorates dysregulated expression signatures across all ASD/NDD gene knockouts examined, it selectively and rapidly dampens network hyperexcitability phenotypes in only a subset of ASD/NDD gene knockouts. Two genes, ASH1L and SCN2A, are particularly responsive to estradiol treatment, with dramatic rescue of molecular and cellular effects in human knockout neurons, coupled with behavioral phenotypes in larval zebrafish mutants. The seven most estradiol responsive genes show enhanced protein-protein interaction network connectivity, strong co-expression in specific postnatal time periods, and enrichment in upper-layer mature excitatory neurons. Altogether, we describe distinct estradiol rescue in different modalities, elucidating shared transcriptomic effects as well as gene-specific cellular and behavioral rescue in the context of loss of function mutations of select ASD/NDD genes.

genomics↗

bioRxiv2026

Lmna deficiency promotes EPHX2 nuclear translocation to ameliorate cardiac dysfunction in mice

BackgroundCardiovascular diseases are often associated with altered protein subcellular localization. As a major cause of inherited cardiomyopathy, LMNA deficiency could trigger nuclear envelope rupture and broadly impair the localization of nuclear and cytoplasmic proteins. Systemic approaches to identify, dissect and manipulate the localization of endogenous proteins are important for mechanistic and therapeutic investigation. MethodProximity proteomics of the nuclear lamina was performed specifically in cardiomyocytes in Lmna-deficient murine models. AAV-mediated Cas9-based gene silencing and subcellular gene upregulation were conducted via the nuclear localization signal (NLS) and nuclear export signal (NES). Cas9-based somatic mutagenesis was supplemented with the single-strand DNA templates of AAV to achieve robust homology-directed repair (HDR) and targeted NLS knock-in, which translocated cytoplasmic proteins into nuclei. ResultIn vivo proximity proteomics detected increased epoxide hydrolase 2 (EPHX2) in cardiomyocyte nuclei in mice carrying germline or cardiac-specific Lmna truncating variants. This phenotype was associated with ruptured nuclear envelope. Cas9-mediated Ephx2 knockout in cardiomyocytes ameliorated cardiac dysfunction in Lmna-deficient mice. Strikingly, overexpression of NLS-EPHX2, but not NES-EPHX2, also mitigated cardiac dysfunction. The cardiac protective EPHX2 substrates, epoxyeicosatrienoic acids (EETs), did not alter upon NLS-EPHX2 overexpression. By contrast, the Lmna-related DNA damage marker {gamma}-H2AX was reduced. The EPHX-D333A mutant lacking hydrolase activity recapitulated the effects of wildtype EPHX2 in nuclei. AAV-Cas9-based HDR achieved efficient NLS knock-in and EPHX2 nuclear translocation in more than 60% cardiomyocytes, which improved cardiac function. ConclusionLmna deficiency leads to the nuclear translocation of EPHX2, which ameliorated cardiac dysfunction in a hydrolase-independent manner. AAV-HDR-mediated somatic gene editing provides an efficient approach to manipulate the subcellular localization of endogenous proteins in cardiomyocytes in vivo. What is Known?O_LICardiovascular diseases are regulated by the changes in protein subcellular localization. In particular, LMNA-related cardiomyopathy is associated with nuclear rupture and impaired separation between nuclear and cytoplasmic proteins. C_LIO_LIEpoxide hydrolase 2 (EPHX2) is a cytoplasmic hydrolase that catalyzes the hydrolysis of cardioprotective epoxyeicosatrienoic acids (EETs) and aggravates an array of heart diseases including myocardial infarction and heart failure. C_LIO_LICRISPR/Cas9-mediated homology-directed repair (HDR) exhibits uniquely high gene editing efficiency in cardiomyocytes with an AAV-based DNA donor, which is suitable for somatic genetic knock-in of small DNA fragments in vivo. C_LI What New Information Does This Article Contribute?O_LILamin-targeted proximity proteomics specifically in cardiomyocytes uncovers novel proteins undergoing subcellular localization changes upon Lmna deficiency. C_LIO_LILmna deficiency leads to EPHX2 nuclear translocation that ameliorates cardiac dysfunction by both mechanisms of cytoplasmic reduction and nuclear induction. C_LIO_LIAAV-HDR-mediated knock-in provides a robust platform to manipulate subcellular localization of endogenous proteins specifically in cardiomyocytes in vivo. C_LI Cardiovascular diseases are often associated with altered protein subcellular localization, but systemic approaches to identify, study and manipulate subcellular localization remain incomplete. This study established an in vivo proximity proteomics approach to identify novel proteins undergoing localization changes relative to the nuclear lamina. In murine models of LMNA-related cardiomyopathy, this approach uncovered EPHX2, a classic cytoplasmic hydrolase that aggravates cardiovascular diseases, as a new protein that translocated into cell nucleus and exerted a cardiac protective effect. CRISPR/Cas9-based cardiomyocyte gene editing with an AAV-based DNA donor efficiently achieved NLS knock-in into the Ephx2 gene, promoted EPHX2 protein nuclear translocation and mitigated cardiac dysfunction with Lmna deficiency. These findings indicated a novel avenue to identify and manipulate the subcellular localization changes of endogenous proteins for basic and translational cardiology.

pathology↗