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Dong, G.

Publications and source records attributed to Dong, G..

At least 19 recordsLinked to original sources

Conflicts and coalitions among selfish toxin-antidote elements shape the evolution of hyperdivergent haplotypes

Genetic conflict drives evolutionary innovation, yet most research has focused on arms races between selfish elements and their hosts. A second layer-competition among selfish elements-remains largely unexplored. Here, we uncover such a conflict between two antagonistic toxin-antidote elements (TAs), loki-1/sgyn-1 and thor-1/sif-1, in Caenorhabditis tropicalis. Each toxin, LOKI-1 or THOR-1, selectively kills progeny homozygous for the opposing haplotype, favoring heterozygotes. Their antidotes, SGYN-1 and SIF-1, evolved from F-box proteins, although SIF-1 subsequently lost its F-box domain. We solved the crystal structure of the THOR-1-SIF-1 complex and used in vivo mutagenesis to validate the binding interface, supporting direct toxin neutralization independently of F-box-mediated degradation. A survey of 676 wild isolates revealed two contrasting evolutionary outcomes of antagonizing TAs: independently evolved loki-1/sgyn-1 and thor-1/sif-1 remain confined to alternative hyperdivergent haplotypes, whereas other homologous TAs can recombine to form composite haplotypes. Altogether, our findings establish competition among selfish elements as a distinct form of genetic conflict, and support models in which antagonistic TAs act as barriers that restrict gene flow between neighboring populations.

evolutionary biology↗

Inferring cascade drivers of VEXAS syndrome by a causal machine learning tool CauNagi

VEXAS syndrome is an adult-onset severe autoinflammatory disease caused by somatic mutations in UBA1, yet the cascade mechanisms linking primitive hematopoietic abnormalities to mature myeloid dysfunctions remain largely unknown. Identifying master regulators of a progressive disease, a black-box process, from complex transcriptomic data also remains challenging. To address this challenge, we developed CauNagi, a computational framework for prioritizing cascade candidate regulators (CCRs). CauNagi integrates a causal representation learning module derived from CausCell with an iterative deep learning backbone adapted from UNAGI; in addition, CauNagi extends these two components with a unique downstream module for CCRs analysis designed to characterize regulatory propagation across hierarchical cellular states. Mechanistically, CauNagi iteratively integrates causal disentangled representation learning with (1) disease-stage cell-state trajectory reconstruction and (2) dynamic regulatory analysis. Benchmarking on single-cell transcriptomic datasets showed that CauNagi preserved cell-type structure in idiopathic pulmonary fibrosis (IPF) and enriched known acute myeloid leukemia(AML)-associated genes among its top-ranked global regulators. When applied to VEXAS syndrome, CauNagi readily revealed inflammatory responses, endoplasmic reticulum stress, and myeloid bias, consistent with the disease features. Furthermore, the CCRs analysis module of CauNagi assisted us in identifying 36 causal drivers, with SPI1, NFKB1, STAT3, and FOS prioritized as high-confidence regulatory hubs linking aberrant myeloid differentiation and inflammatory programs. These findings were further supported by an independent single-cell transcriptomic dataset from a murine VEXAS model. Overall, CauNagi provides a computationally efficient and systematic framework for identifying candidate causal regulators. Beyond hematopoietic diseases, CauNagi may also be applicable to other progressive disorders for which multistage single-cell transcriptomic datasets are available. CauNagi is available at https://github.com/steamed-stuffed-bun/CauNagi.

bioinformatics↗

Palmitoylation calibrates mitochondrial transport of insulin across the endothelium in insulin resistance

Impaired insulin transport across the endothelium contributes to insulin resistance, a poorly understood condition implicated in diabetes and many other chronic diseases. Insulin has been reported to undergo non-receptor-mediated endocytosis resembling fluid-phase uptake through unclear mechanisms. Here we show in mice with diet-induced insulin resistance that endothelial-specific deletion of the depalmitoylase acyl-protein thioesterase 1 (APT1) improved glucose tolerance and insulin sensitivity without affecting chronic inflammation or capillary structure. Endothelial APT1 deficiency increased interstitial insulin levels in mice confirmed by in-situ microneedle-based sampling. In cultured human microvascular cells, APT1 inhibition enhanced cell transport of high-dose insulin independent of the insulin receptor and canonical endocytic machinery. Unexpectedly, live-cell imaging revealed insulin rapidly localizing to mitochondria prior to endolysosomal trafficking, even at physiological insulin concentrations. APT1 inhibition delayed mitochondrial discharge of insulin to lysosomes. Cyclosporin A, an immunosuppressant known to affect mitochondrial function, preserved mitochondrial insulin content and promoted insulin transport in cultured cells, and enhanced interstitial insulin delivery in mice. Proteomic analysis revealed two palmitoylated proteins, PACS1 and YTHDF2, required for APT1-mediated mitochondrial-endolysosomal trafficking of insulin. A mitochondrial insulin shuttle in endothelial cells may participate in the physiological adaptation to hyperinsulinemia and its regulation by palmitoylation suggests a novel approach to insulin resistance.

physiology↗

Super-Resolution Visual ProteomEx for Hard Tissues and Clinical Samples

Correlating nanoscale tissue architecture with unbiased molecular composition within the same specimen remains a fundamental challenge in spatial biology. Current spatial proteomics methods either lack the imaging resolution required to resolve nanoscale tissue architecture or achieve only limited proteome coverage, and untargeted approaches capable of deep protein identification have yet to be integrated with super-resolution imaging within a single workflow. Here, we present microProteomEx, an integrated platform that combines hydrogel-assisted tissue expansion with mass spectrometry-compatible fluorescence imaging, laser capture microdissection, and bottom-up proteomics to achieve simultaneous three-dimensional super-resolution imaging (effective lateral resolution down to [~]47 nm on conventional diffraction-limited microscopes) and spatially resolved proteomics at a scalable lateral resolution of 29-100 {micro}m (0.02-0.28 nL volumetric resolution). By optimizing fixation, protein anchoring, and a secondary re-embedding strategy, we extend the method to mechanically resilient tissues, including mouse kidney and heart, as well as to formalin-fixed, paraffin-embedded clinical specimens. We demonstrate single-glomerulus and single-plaque proteomics (450-1,000 proteins per structure), resolve proteomic differences between malignant melanoma and giant congenital melanocytic nevus in a rare pediatric case, and characterize the morphology-resolved molecular heterogeneity of cored versus diffuse amyloid-beta plaques in a mouse model of Alzheimers disease across two disease stages. microProteomEx establishes a broadly accessible framework for correlating tissue ultrastructure with deep spatial proteomics, with direct implications for disease biology, biomarker discovery, and precision medicine.

biochemistry↗

Kinemomics: spatiotemporal morphodynamic mapping of ventricular kinematic subpopulations in organotypic fetal heart slices

Recent advancements in omics technologies have deepened our understanding of complex biological systems and the interplay among gene expression, mechanical cues, and cellular metabolism. However, capturing the spatiotemporal dynamics of live cellular behavior within intact tissue contexts remains a major challenge. Here, we introduce Kinemomics, a framework for spatiotemporal mapping of morphogenetic kinematic states in living tissue. Using a novel fetal cardiac organotypic slice culture system that preserves both beating and morphogenesis, Kinemomics integrates live fluorescent labeling, timelapse imaging, and endpoint immunofluorescence to generate morphodynamic profiles across full-thickness developing myocardium. We validate Kinemomics under controlled Yap-1 signaling perturbations and demonstrate its ability not only to intrinsically decode region- and treatment-specific phenotypes, but also to resolve their spatiotemporal evolution during development and malformation. Kinemomics further reveals localized emergent developmental and malforming fronts that drive system-level behavior, establishing a generalizable platform for investigating computational morphodynamics and cross-scale interactions in complex spatiotemporal systems.

developmental biology↗

Evolution of an Aurora Kinase A Inhibitor from an Essential tRNA Synthetase

Gene duplication is a major driver of evolution, yet how it generates fundamentally new molecular functions remains poorly understood. Here, we show how such novelty arose in KLMT-1, a selfish toxin that causes genetic incompatibilities in Caenorhabditis tropicalis. KLMT-1 evolved via duplication of an essential tRNA synthetase but, strikingly, lost its ancestral role in tRNA biology and translation. Instead, KLMT-1 localizes to centrosomes, where it targets Aurora kinase A (AIR-1). This innovation is mediated by a three-amino acid insertion that extends a {beta}-hairpin loop, enabling electrostatic interaction with a regulatory interface on the kinase. Our results demonstrate how changes in selective pressure, combined with minimal modifications in neutrally evolving regions, allow duplicated proteins to access new functional space and evolve entirely new molecular activities.

evolutionary biology↗

Integrated Metagenomics and Metabolomics Studies Reveal Core Bacterial Guild Regulating Carbohydrate Metabolism in Pediatric MASLD

BackgroundMetabolic dysfunction-associated steatotic liver disease (MASLD) is a prevalent pediatric disorder with limited treatment options, primarily due to an incomplete understanding of its molecular drivers. Recent research underscores the role of microbial guilds in metabolic health, but the mechanisms by which dysbiosis driven by core species and co-abundant symbionts disrupt metabolic homeostasis in pediatric MASLD remain unclear. ResultsHere, we conducted integrated metagenomic and metabolomic analyses on 285 pediatric subjects including MASLD patients, obese and healthy controls. The gut dysbiosis in MASLD was characterized by a depletion of Phocaeicola vulgatus, Bacteroides uniformis, Parabacteroides distasonis, and Bacteroides thetaiotaomicron. Co-abundance network analysis, integrating our cohort with four public datasets, identified these species as core guild members associated with MASLD. Microbial enrichment analysis showed significant disruptions in carbohydrate metabolism, particularly the downregulation of the tricarboxylic acid (TCA) cycle, fructose and sucrose metabolism, and pentose and glucuronate interconversions. P. vulgatus and B. uniformis were identified as dominant species linked to the downregulation of KEGG orthologs (KOs) in these disrupted pathways that were inversely correlated with hepatic injury biomarkers. CAZyme database analysis further emphasized P. vulgatus as the primary contributor to glycoside hydrolases involved in monosaccharide utilization. Finally, both untargeted and targeted metabolomics analysis validated a disrupted metabolic network centered on the TCA cycle and monosaccharide metabolism in pediatric MASLD. ConclusionOur findings suggest the core guild species P. vulgatus and B. uniformis may serve as critical regulators of carbohydrate metabolism in pediatric MASLD, offering potential mechanistic targets for gut microbiome-based interventions.

microbiology↗

Flu Virus Infection in Juvenile Mice Leads to Lifelong Multi-Organ Damage and Parkinsonian Pathological Changes in Aging

The widespread prevalence of Long COVID underscores the potential for viral infections to exert prolonged effects on hosts long after initial recovery. Despite this recognition, the long-term and even lifelong consequences of viral infections remain poorly understood. In this study, we infected juvenile mice with influenza viruses and systematically examined the lifelong effects (from 4 to 450 days post-infection) of these infections. Pathological analysis revealed persistent lifelong damage in multiple organs, including chronic lung inflammation and fibrosis, along with significant cardiac and renal pathology. Viral infection led to substantial neuronal loss in key brain regions of mice (hippocampal CA1, CA3, and striatum) during middle and old age. Strikingly, we identified two hallmark pathological features of Parkinsons disease - dopaminergic neuron degeneration and Lewy body-like -synuclein inclusions - in middle and aged infected mice. Transcriptomic profiling demonstrated sustained upregulation of inflammation-related genes in both lung and blood tissues, correlating with observed pathological changes. Lung-derived secreted proteins, encoded by differentially expressed genes, may mediate cross-organ communication affecting cardiac, renal, and neurological function. Brain transcriptome analysis at three months post-infection revealed downregulation of neurodevelopmental genes, potentially contributing to subsequent neuronal loss and Parkinsonian pathology. These findings collectively suggest that pulmonary influenza infection can induce systemic multi-organ effects through both secretory pathways and chronic inflammatory responses. The study offers crucial insights for developing more effective strategies to prevent and manage infectious diseases and their long-term sequelae.

microbiology↗

Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes

Detecting somatic mutations in normal tissues is challenging due to sequencing errors and the low allele fractions of post-zygotic variants. Duplex sequencing greatly reduces errors and can detect mutations at any allele fraction, but systematic, cross-platform comparisons are lacking. We present a comprehensive benchmarking of six duplex sequencing technologies used by the SMaHT Network: CODEC, CompDuplex-seq, HiDEF-seq, NanoSeq, ppmSeq, and VISTA-seq. We evaluated their performance using cord blood DNA, a tumor-normal cell line mixture, and homogenates from six human tissues. Each method shows distinct profiles in genomic footprint, sensitivity, and cost. Despite differences in library construction and sequencing platforms, estimates of mutation rates and mutational signatures are highly concordant. Integration with ultra-deep whole-genome sequencing shows that duplex approaches sensitively capture mutations and signatures beyond embryonic or clonally expanded variants. These results provide a foundation for selecting duplex methods and interpreting their data, enabling scalable single-molecule analyses of somatic mutation landscapes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/692823v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@123b221org.highwire.dtl.DTLVardef@83ba0aorg.highwire.dtl.DTLVardef@2b0ab0org.highwire.dtl.DTLVardef@1cae35e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

Widespread Epistasis between Cancer Driver Mutations and Allele-Specific Copy Number Variations

Cancer driver mutations alone are often insufficient to fully explain tumorigenesis. We demonstrate that these mutations cooperate with somatic copy number variations (CNVs) in a tissue-specific pattern of genomic epistasis. Analyzing 93,462 tumors, we identified 54 gene-cancer type pairs with significant co-occurrence of somatic mutations and CNVs. Our new Binoculars algorithm, which resolved phased DNA/RNA reads, revealed frequent preferential amplification in oncogenic mutation alleles, including AKT1 p.E17K, BRAF p.V600E, KRAS p.G12C/D/V, NRAS p.Q61K, and a fraction of gain-of-function TP53 p.R175H. Conversely, deletions selectively targeted the reference alleles, leading to loss of heterozygosity of IDH1 p.R132H and tumor suppressor mutations, including CDKN2A and TP53 truncations. Lung cancer patients carrying co-occurrences of somatic mutation-CNVs in TP53 and KRAS showed poorer survival than those carrying the same gene mutations. These findings reveal epistasis of cancer mutations and CNVs at an allelic resolution, suggesting specific genomic events to enhance patient stratification and therapeutic targeting.

genomics↗

Differential Alterations of Gut Microbiota in Girls with Isolated Obesity, Isolated Precocious Puberty, and Their Comorbidity

BackgroundChildhood obesity and precocious puberty (PP) are escalating public health concerns with a significant comorbidity. Emerging evidence implicates gut microbiota dysbiosis in both conditions, yet microbial associations with their co-occurrence remain unexplored. MethodsA total of 68 girls (18 normal, 25 PP-only, 18 obesity-only, and 7 obesity-PP comorbidity) were enrolled. 16S rRNA sequencing was applied to determine gut microbiota of girls. Microbial diversity, composition, and differential abundant taxa were analyzed. ResultsWhile overall microbial diversity and community structure were similar across groups, obesity-only subjects exhibited significantly increased microbial richness (Chao1 index, P<0.01 vs. all groups), characterized by a higher Firmicutes/Bacteroidota ratio (P<0.001 vs. normal/PP), increased Proteobacteria (P<0.001 vs. normal), and enrichment of genera including Blautia, Faecalibacterium, Roseburia, Anaerostipes, Haemophilus, and Lachnospiraceae_NK4A136_group (P<0.05 vs. other groups). PP-only subjects showed reduced Verrucomicrobiota (P<0.001 vs. normal/obesity) and elevated Escherichia_Shigella (P<0.05 vs. normal). Most strikingly, the obesity-PP comorbid group exhibited a unique gut microbiota profile characterized by a dramatic depletion of Firmicutes compared to the obesity-only group (P<0.001) and a remarkable nearly 100-fold increase in Verrucomicrobiota abundance (P<0.001 vs. other groups), suggesting a distinct microbial ecotype potentially contributing to the pathophysiology of this comorbidity. ConclusionThis study delineated unique gut microbiota alterations associated with isolated obesity, isolated PP, and their comorbidity in girls. The distinct dysbiotic pattern in comorbid obesity-PP suggested complex microbiota-host interactions, providing a new microbiological perspective for understanding the mechanism of comorbidity between obesity and precocious puberty.

microbiology↗

IgG-Bridging-Seeded Synergistic Aggregation of SARS-CoV-2 Spikes Underlies Potent Neutralization by A Low-Affinity Antibody

Mechanistic studies of viral neutralization typically prioritize high-affinity antibodies, relegating low-affinity binders to the sidelines. We report P5-1C8, a Class 1 SARS-CoV-2 antibody that exemplifies this underexplored "low-affinity yet high-potency" phenotype, retaining strong neutralization of Omicron JN.1 despite markedly weakened trimer binding (KD = 225 nM; IC50 = 0.06 nM). Structural and biophysical analyses reveal that P5-1C8 engages WT and BA.1 spikes through canonical intra-spike bivalency, but with JN.1 it induces aggregation. Using virion-like nanoparticles displaying multiple spikes, we show that IgG remains bound with no detectable dissociation and triggers pronounced aggregation. Coarse-grained molecular dynamics delineate the stepwise pathway in which weak IgG-spike contacts seed aggregation via transient inter-spike bridging. Together, these findings establish the first mechanistic framework demonstrating how weak-binding antibodies can nonetheless achieve potent neutralization through higher-order aggregation, thereby expanding the conceptual landscape of antibody function and opening new directions for antibody evaluation and design. Graphical AbstractLow-affinity antibodies are frequently disregarded in discovery pipelines. This work reports P5-1C8, a Class 1 SARS-CoV-2 antibody with weak trimer binding (KD-to-IC50 > 3,700-fold) yet potent neutralization of Omicron JN.1. Structural, biophysical, functional and coarse-grained simulations collectively demonstrate that transient inter-spike IgG bridging seeds higher-order aggregation, which in turn drives neutralization and provides a mechanistic framework. O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/691454v1_ufig1.gif" ALT="Figure 1000"> View larger version (79K): org.highwire.dtl.DTLVardef@1d4f132org.highwire.dtl.DTLVardef@1274400org.highwire.dtl.DTLVardef@e186a6org.highwire.dtl.DTLVardef@4f1870_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Longitudinal Live Imaging Derived 4D Hemodynamics and Dynamic Tissue Mechanics Across Outflow Tract Morphogenesis

Growth and remodeling of the cardiac outflow tract (OFT) is poorly understood but associated with serious congenital heart defects (CHD). While only a minority of CHDs have identifiable genetic causes, the functional roles of mechanical forces in OFT remodeling are far less characterized. A key barrier has been the lack of longitudinal investigations examining the interplay between dynamic blood flow and wall motion across clinically relevant stages. Here, we developed a live high-frequency ultrasound derived 4D moving-domain computational fluid dynamics (CFD) simulation approach, enabling longitudinal quantification of OFT hemodynamics and tissue mechanics in the same embryos across Hamburger-Hamilton (HH) stage 21 to HH27. We found that rising wall shear stress (WSS) strongly correlates with tissue extension in the distal OFT, whereas the proximal OFT experiences increasing expansive strains and higher hydrostatic stress with heartbeats. Additionally, we identified a double-helical flow pattern in the OFT lumen, possibly reflecting an evolutionary legacy for directing oxidized and non-oxidized blood flow before great vessel septation. Together, our results advanced insights in how hemodynamic forces and tissue stress contribute to OFT remodeling and septation.

developmental biology↗

Cell-type-specific patterns and consequences of somatic mutation in development and aging brain

Elucidating the role of somatic mutations in cancer, healthy tissues, and aging depends on methods that can accurately characterize somatic mosaicism across different cell types, as well as assay their impact on cellular function. Current technologies to study cell-type-specific somatic mutations within tissues are low-throughput. We developed Duplex-Multiome, incorporating duplex consensus sequencing to accurately identify somatic single-nucleotide variants (sSNV) from the same nucleus simultaneously analyzed for single-nucleus ATAC-seq (snATAC-seq) and RNA-seq (snRNA-seq). By introducing strand-tagging into the construction of snATAC-seq libraries, duplex sequencing reduces sequencing error by >10,000-fold while eliminating artifactual mutational signatures. When applied to 98%/2% mixed cell lines, Duplex-Multiome identified sSNVs present in 2% of cells with 92% precision and accurately captured known sSNV mutational spectra, while revealing unexpected subclonal lineages. Duplex-Multiome of > 51,400 nuclei from postmortem brain tissue captured sSNV burdens and spectra across all major brain cell types and subtypes, including those difficult to assay by single-cell whole-genome sequencing (scWGS). This revealed for the first time that diverse neuronal and glial cell types show distinct rates and patterns of age-related mutation, while also directly discovering developmental cell lineage relationships. Duplex-Multiome identified clonal sSNVs occurring at increased rates in glia of certain aged brains, as well as clonal sSNVs that correlated with changes in expression of nearby genes, in both neurotypical and autism spectrum disorder (ASD) individuals, directly demonstrating that somatic mutagenesis can contribute to gene expression phenotypes. Duplex-Multiome can be easily adopted into the 10X Multiome protocol and will bridge somatic mosaicism to a wide range of phenotypic readouts across cell types and tissues.

genomics↗

Neurons accumulate disease-specific somatic genomic changes across taupathologic states in Alzheimer's disease

Tau deposition within neurons marks Alzheimers disease (AD) neuropathology, suggesting that tau may contribute to cellular dysfunction and death. In AD, somatic mutations accumulate in neurons, with features that suggest deleterious effects on cellular function. To examine the relationship between tau and somatic mutation, we isolated neurons according to tau pathology and performed single-cell whole-genome sequencing on tau+, tau-, and tau-agnostic neurons from 13 individuals with AD, as well as neurons from 15 control individuals. We found that AD neurons, regardless of tau status, exhibited an increased burden of somatic single-nucleotide variants (sSNVs) and insertions and deletions (sIndels). Mutational signature analyses revealed disease-specific patterns, including sIndels characterized by two-basepair (2bp) deletions, indicating shared mutagenic mechanisms in AD neurons across tau pathologic cell states. Somatic mutations are associated with tissue-wide tau pathology, suggesting that tangles do not confer cell-autonomous genotoxicity to neurons and that non-tangle components drive somatic mutation in AD.

genomics↗

Gut Microbiota Dysbiosis and Short-chain Fatty Acid alterations in Pediatric New-Onset Type 1 diabetes with Ketoacidosis

ObjectiveDiabetic ketoacidosis (DKA) stands as the most common acute hyperglycaemic complication with a relatively high mortality rate among children diagnosed with type 1 diabetes (T1D). Previous studies have shed light on gut dysbiosis in newly-onset T1D children, but research targeting the gut microbiota and microbial metabolites in patients with DKA remains scarce. MethodsShotgun metagenomic analysis was conducted on fecal samples from 96 newly diagnosed T1D children, including 32 patients who presented with DKA upon admission. Short-chain fatty acids (SCFAs) were quantified using gas chromatography/mass spectrometry (GC/MS). Comparative analyses were performed on the gut microbiome and SCFA levels between DKA and non-DKA subgroups. ResultsGut microbiota composition differed between DKA and non-DKA groups. While alpha-diversity remained consistent, beta-diversity showed marked differences between the two groups, and the phyla Firmicutes and Bacteroidetes exhibited predominance in the DKA group. DKA was associated with increased potential pathogens and a significant depletion of SCFA-producing genera (Anaerobutyricum, Dialister, Ruminococcus, Roseburia, Dorea, and Butyricicoccus), accompanied by reduced SCFA levels. Further correlation analysis revealed strong associations between SCFAs, SCFA-producing microbiota, and disease severity indicators. Propionic acid and butyric acid mediated the association between SCFA-producing bacteria and DKA. ConclusionThis study first reported reductions in SCFAs and SCFA-producing bacteria in the fecal samples of T1D children at DKA onset. Our findings highlight SCFAs and their producers as protective biomarkers of DKA and suggest that targeting gut microbiota and SCFA metabolism may offer a potential therapeutic strategy for DKA. ImportanceWhile gut microbiota imbalances have been linked to type 1 diabetes (T1D), little is known about the role of gut microbes and their metabolites during acute diabetic ketoacidosis (DKA), an acute and life-threatening complication. This study examined the gut microbiome and levels of short-chain fatty acids (SCFAs) in fecal samples from children with new-onset T1D with and without DKA. DKA was characterized by distinct microbial signatures, including increased potential pathogens, a loss of beneficial SCFA-producing bacteria, and consistently lower SCFA levels. These changes closely correlated with indicators of disease severity, and further mediation analysis revealed the role of SCFAs in linking gut microbiota to DKA. These findings suggest that SCFAs and their producers may serve as protective markers for DKA, highlighting the potential of microbiome-based interventions to improve outcomes in children facing this critical complication.

microbiology↗

Loss of transcriptional factor Zbtb33 fails to induce clonal hematopoiesis in mice but plays a role in tumor immunity

Clonal hematopoiesis (CH) is an early indicator of hematologic malignancies, driven by mutations in hematopoietic stem cells (HSCs) such as TET2 or TP53. Mutations in ZBTB33 have been implicated in MDS and suggested as a potential driver of CH. However, the role of ZBTB33 in hematopoiesis and its involvement in CH remains unclear. We generated a Zbtb33-knockout mouse strain to elucidate its role in hematopoiesis and the immune system. Our findings indicate that hematopoiesis in Zbtb33-defecient mice appeared grossly normal, and competitive bone marrow transplantation assays demonstrated that loss of Zbtb33 in HSCs did not confer expansional advantage. Introducing the Zbtb33 mutation into Tet2- or Tp53-mutation background yielded no synergistical effects. Tumor challenging assays suggested that Zbtb33 influences cancer immunity response, rather than directly driving CH or myeloid malignancies. In summary, ZBTB33 deficiency was insufficient to induce clonal hematopoiesis but may have a regulatory role in tumor microenvironment. Statement of significanceClonal hematopoiesis (CH) is linked to mutations in hematopoietic stem cells, but the role of Zbtb33 in CH remains unclear. To investigate this, we examined the function of Zbtb33 under physiological conditions and in response to external stimuli. Additionally, we explored whether Zbtb33 mutations cooperate with other genetic mutations to drive clonal hematopoiesis. Key pointsO_LILoss of Zbtb33 fails to induce clonal hematopoiesis and does not synergize with Tet or Tp53 mutations. C_LIO_LIHowever, it plays a significant role in regulating cancer immunity and the tumor microenvironment. C_LI

immunology↗

Disturbing immune homeostasis by neutrophil loss of Uba1 induces VEXAS-like autoinflammatory disease in mice

ObjectiveVEXAS (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) syndrome is an identified haemato-rheumatoid disease caused by somatic UBA1 mutations in hematopoietic stem cells. We report Uba1 loss in various mouse hematopoietic cell types leads to diverse effects, with approximately 70% Uba1 depletion in neutrophils inducing non-lethal VEXAS-like symptoms. MethodsUsing nine different Cre/flox-mediated conditional-knockout (CKO) models, we interrogated the phenotypes caused by hematopoietic loss of Uba1. Neutrophil-specific depletion of Uba1 were validated and VEXAS-like phenotypes were examined. ResultsUba1 loss in HSCs induces extensive hematopoietic cell death while in B or T cells, or megakaryocytes induces corresponsive cell death but these mutants appear normal. Uba1 loss in monocytes and neutrophils failed to induce cell death and the mutants are viable. Among the models, only Uba1 loss in neutrophils manifests autoinflammatory symptoms including increased counts and percentage of neutrophils, increased proinflammatory cytokines, vacuoles in myeloid cells and dermatitis. Residual Uba1 is about 30% in the mutant neutrophils, which manifest disturbed cellular hemostasis. Genetic loss of Morrbid partially mitigated the VEXAS-like symptoms. ConclusionOur study reveals diverse effects of Uba1 loss in hematopoietic cells and establishes a VEXAS-like murine model, facilitating understanding and potential treatments for this syndrome prevalent in aged men. HIGHLIGHTSO_ST_ABSWHAT IS ALREADY KNOWN ON THIS TOPICC_ST_ABSVEXAS syndrome is a recently identified hematological and immunological disease prevalent in adult man but rarely in adult woman. Somatic mutations in the E1-enzyme encoding gene UBA1 in hematopoietic stem cells is the driver on the top of the genetic etiology of the disease. However, the major pathogenic cell type(s) for VEXAS syndrome has not been experimentally examined and mouse models recapitulating the disease are lacking. WHAT THIS STUDY ADDSO_LIUsing nine different conditional-knockout (CKO) murine models, we interrogated the pleiotropic phenotypes caused by loss of the ubiquitin activation enzyme Uba1 in different hematopoietic cell types; C_LIO_LIOur results demonstrated that among the nine tested CKO mutants, only neutrophil loss of Uba1 results in VEXAS-like autoinflammatory disease; C_LIO_LIThe VEXAS-like symptoms in the S100a8Cre-CKO mutant mice include: increased counts of white blood cells and neutrophils, increased percentage of neutrophils, increased serum level of proinflammatory cytokines (IL-1{beta}, IL-6 and TNF), observation of vacuoles, increased survival, and increased phagocytosis in mutant neutrophils; C_LIO_LIPharmacological treatments with IL-1 inflammatory pathway inhibitors Anakinra or Canakinumab or genetic loss of the myeloid pro-survival regulator Morrbid partially mitigated the VEXAS-like symptoms in the S100a8Cre-CKO mutants; C_LI HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYThe study reports a technical strategy of developing the murine models for VEXAS syndrome. In addition, the study dissects cellular and molecular mechanisms, especially the cell-type-dependent tolerance and pathogenicity of loss of function of Uba1, for the occurrence of the autoinflammation diseases in mice. The study provides translational implications in etiology and potential treatment choices for the newly-identified haemato-rheumatoid syndrome in clinical management.

immunology↗