Biology subjects

Dong, X.

Publications and source records attributed to Dong, X..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Arf GTPases Define BST-2-Independent Pathways for HIV-1 Assembly and Release

ADP-ribosylation factor (Arf) proteins are small GTPases that regulate intracellular membrane trafficking and actin cytoskeleton remodeling through cycles of GTP binding and hydrolysis. Arf1, a central regulator of Golgi and endosomal trafficking, and Arf6, which controls plasma membranes and endosomal dynamics, have both been implicated in late stages of the HIV-1 life cycle. However, the precise mechanisms by which these GTPases support HIV-1 assembly and release remain incompletely understood. Here, we provide direct evidence that Arf1 and Arf6 are required for efficient trafficking of the HIV-1 Gag polyprotein, assembly, and virion release. Perturbation of Arf1 function with either a GTP-locked (Q71L) or GDP-locked (T31N) mutant significantly reduced virus release, impaired Gag association with membrane compartments, and blocked Gag targeting to the plasma membrane. Manipulation of Arf1 activity via the GTPase-activating protein AGAP1 further demonstrated that dynamic cycling of Arf1 between GTP- and GDP-bound states is essential for productive Gag trafficking. Similarly, expression of a constitutively active Arf6 mutant (Q67L) misdirected Gag to intracellular membranes and markedly decreased virion production. Importantly, disruption of Arf1 or Arf6 function did not affect the total expression, surface levels, or intracellular distribution of the host restriction factor BST-2. Together, these findings establish that Arf1- and Arf6-mediated trafficking pathways are critical host determinants of HIV-1 assembly and release, functioning independently of BST-2 antagonism. IMPORTANCEThe small GTPases Arf1 and Arf6 control fundamental processes in membrane trafficking and cytoskeletal dynamics, yet their roles in HIV-1 replication are not well defined. We show that both proteins are required for efficient trafficking of HIV-1 Gag polyprotein to the plasma membrane and for subsequent virus release. Disrupting either GTPase reroutes Gag to intracellular membranes and reduces virion production, independently of the antiviral host factor BST-2. These results identify Arf1- and Arf6-dependent trafficking as critical host pathways for HIV-1 assembly and egress, expanding our understanding of the cellular machinery hijacked by retroviruses to support infections.

microbiology↗

bioRxiv2025

Mapping mesenchymal diversity in the developing human intestine and organoids

The organization of diverse mesenchymal populations during human intestinal development is critical for tissue architecture and function yet remains poorly defined. To construct a comprehensive, tissue-scale map of the developing human small intestine, we leveraged single-cell RNA-sequencing data to build a custom Xenium spatial transcriptomics gene panel covering the diversity of cell types in the human intestine. Analysis was focused on the developing mesenchyme populations (also referred to as fibroblasts or stroma) given the lack of spatiotemporal information about these cell populations. We defined 5 broad mesenchymal populations occupying discrete anatomical locations within the lamina propria and submucosa - the subepithelial cells (SEC), lamina propria fibroblasts (LPF), submucosal fibroblasts (SMF), smooth muscle cells (SMC), and CXCL13+ fibroblasts. Our data reveal dynamic spatial remodeling of fibroblast communities during development and establish molecular markers to distinguish these populations. We leverage this high-resolution atlas to benchmark pluripotent stem cell-derived human intestinal organoids and to demonstrate how this foundational resource can be used to dissect intestinal stromal signaling in a spatial manner, with broad implications for modeling development, regeneration, and disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/665939v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@46299borg.highwire.dtl.DTLVardef@55a014org.highwire.dtl.DTLVardef@180a104org.highwire.dtl.DTLVardef@1cb42b2_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA spatial atlas of fibroblast heterogeneity in the human intestine C_LIO_LIPopulations include subepithelial, submucosal, lamina propria, and CXCL13+ fibroblasts C_LIO_LIFibroblast position in the developing intestine is maintained into adulthood C_LIO_LIOrganoids largely recreate the spatial organization of the human intestine C_LI

developmental biology↗

bioRxiv2025

Tissue-Specific Co-Expression Patterns of BAF Complexes Provide Regulatory Insights Across Human Tissues with Implications for Endocrine and Non-Endocrine Functions

BRG1/BRM-associated factor (BAF) chromatin remodeling complexes are essential for normal endocrine function and are implicated in various metabolic and developmental disorders. However, the full range of chromatin-based regulatory modules in endocrine development remains unclear. We developed a computational pipeline to analyze bulk RNA-seq data from 54 human tissues and constructed tissue-specific co-expression networks for 30 core BAF complex genes. Weighted gene co-expression network analysis (WGCNA) and Louvain clustering identified gene modules for each tissue, which we compared to 46 curated BAF subcomplex gene sets using Jaccard similarity. In metabolically active non-endocrine tissues (kidney, skeletal muscle, vasculature, fibroblasts), we observed strong co-expression with canonical BAF (cBAF) and polybromo-associated BAF (pBAF) modules. Central nervous system tissues were dominated by neuron-specific BAF (nBAF) modules. Endocrine tissues (e.g., thyroid, adrenal) and gastrointestinal epithelia displayed co-expression profiles resembling smooth muscle-like BAF and pBAF modules, suggesting chromatin programs that integrate hormone secretion with contractile and barrier functions. These patterns show that each tissue exhibits a distinct, non-random combination of BAF subcomplexes, potentially reflecting its functional chromatin state. Our results demonstrate that tissue-specific gene expression profiling can reveal differences in protein complex regulation. The modular deployment of BAF chromatin remodeling complexes appears tailored to the functional demands of each organ. This study lays a foundation for further investigation of epigenetic regulation in endocrine development and disease and provides a framework for identifying tissue-specific chromatin remodeling strategies. Plain Language Summary (optional)The US National Institutes of Health have invested in large-scale measurements of how different human body tissues use their genetic material. This study pilots use of these data to understand better how various genes come together to form nanomachines that in turn regulate the same genetic material.

bioinformatics↗

bioRxiv2025

BST-2 inhibits SARS-CoV-2 egress at intracellular membranes and is neutralized by ORF7a

Bone marrow stromal antigen 2 (BST-2, or tetherin) is an interferon-inducible host restriction factor that inhibits the release of enveloped viruses by tethering nascent virions to cellular membranes. While its antiviral function is well established in retroviral systems, its role in SARS-CoV-2 egress remains unclear. Here, we used a virus-like particle (VLP) system composed of SARS-CoV-2 structural proteins M, E, and N to investigate the impact of BST-2 on viral particle release. BST-2 significantly inhibited VLP release in HEK293T and Calu-3 lung epithelial cells. Confocal microscopy revealed that BST-2 colocalizes with viral structural proteins at the endoplasmic reticulum-Golgi intermediate compartment (ERGIC), the main site of coronavirus assembly. We next evaluated the roles of the SARS-CoV-2 accessory proteins ORF3a and ORF7a in overcoming this restriction. ORF3a localized to endolysosomal compartments and promoted VLP release through a BST-2-independent mechanism, without altering BST-2 expression or localization. In contrast, ORF7a colocalized with both BST-2 and ERGIC markers and restored VLP release by promoting BST-2 degradation. Notably, ORF7a also relieved BST-2-mediated restriction of HIV-1 VLP release, suggesting a conserved antagonistic function. These findings identify BST-2 as an intracellular inhibitor of SARS-CoV-2 particle release and establish ORF7a as viral accessory antagonist that neutralizes this host defense.

microbiology↗

bioRxiv2025

EVscope: A Comprehensive Bioinformatics Pipeline for Accurate and Robust Analysis of Total RNA Sequencing from Extracellular Vesicles

MotivationExtracellular vesicle (EV) RNA sequencing has emerged as a powerful approach for studying RNA biomarkers and intercellular communication. Nevertheless, the extremely low abundance, fragmented nature and ubiquitous tissue origin of EV RNAs, alongside potential contamination from co-isolated materials, such as free DNA and bacterial RNA, pose substantial analytical challenges. These complexities highlight a pressing need for a standardized, computational workflow that ensures robust quality control and EV RNA characterization. ResultsHere, we present EVscope, an open-source bioinformatics pipeline designed specifically for processing EV RNA-seq datasets. EVscope employs an optimized genome-wide expectation-maximization (EM) algorithm that significantly improves multi-mapping read assignment at single-base resolution by effectively leveraging alignment scores (AS) and local read coverage, specifically tailored for fragmented and low-abundance EV RNAs. Notably, EVscope uniquely generates EM-based BigWig files for downstream analysis, a capability currently unavailable in existing EM-based BigWig quantification tools. The pipeline systematically integrates 27 major steps, including quality control, analysis of library structure, contamination assessment, read alignment, read strandedness detection, UMI-based deduplication, RNA quantification, genomic DNA (gDNA) contamination correction, cellular and tissue source inference and visualization with a comprehensive HTML report. EVscope incorporates a comprehensive, updated annotation covering 19 distinct RNA biotypes, encompassing protein-coding genes, lncRNAs, miRNAs, piRNAs, retrotransposons (LINEs, SINEs, ERVs), and additional non-coding RNAs (tRNAs, rRNAs, snoRNAs). Furthermore, it leverages two highly balanced circRNA detection algorithms for robust circular RNA identification. Notably, a downstream module enables the inference of the tissue/cellular origins of EV RNAs using bulk and single-cell RNA-seq reference datasets. EVscope is implemented as a convenient, single-command Bash pipeline leveraging Conda-managed standard software packages and custom scripts, ensuring reproducibility and straightforward deployment. Availability and implementationCode, documentation, and tutorials are available at GitHub (https://github.com/TheDongLab/EVscope) and archived on Zenodo (https://zenodo.org/records/15577789).

bioinformatics↗

bioRxiv2025

Salicylic Acid Engages Central Metabolic Regulators SnRK1 and TOR to Govern Immunity by Differential Phosphorylation of NPR1

Immunity is a delicate balance between combating infection and preserving the metabolic functions vital for host survival. However, the mechanisms by which immune responses are coordinated with cellular metabolism remain largely unknown. Here, we show that NONEXPRESSER OF PR GENES 1 (NPR1), the central plant immune regulator of salicylic acid (SA)-mediated defense responses, is controlled by a cascade of posttranslational modifications (PTMs) involving two master nutrient-sensing kinases. Under normal growth conditions, TARGET OF RAPAMYCIN (TOR) inhibits NPR1 through phosphorylation at Ser-55/59. During defense responses, elevated SA enhances SNF1-RELATED KINASE 1 (SnRK1) activity, which in turn inhibits TOR signaling and phosphorylates NPR1 at Ser-557. This phosphorylation event activates NPR1 and facilitates its subsequent PTMs. Together, our results reveal an integral role of SA (the active metabolite of aspirin) in controlling central metabolic regulators SnRK1 and TOR to coordinate immune responses and growth through antagonistic modifications of NPR1.

plant biology↗

bioRxiv2025

A high-throughput immunopeptidome platform for MHC II alleles to characterize antigen-specific CD4 + T cells

CD4+ T cells play a pivotal role in adaptive immunity, recognizing peptide antigens presented by MHC II molecules during infections and tumor development. Identifying immunodominant MHC II epitopess is essential for understanding CD4+ T cell responses; however, current methods such as mass spectrometry, suffer from low sensitivity and throughput, while computational algorithms show variable accuracy. To overcome these challenges, we developed EliteMHCII, a high-throughput immunopeptidome profiling platform that identifies antigen-derived MHC II epitopes and measures peptide binding affinity across 24 globally common MHC II alleles. Using EliteMHCII, we assessed the immunodominant epitopes of the SARS-CoV-2 RBD protein. Validation in vaccinated individuals and humanized mouse models revealed a strong correlation between high-affinity peptides and robust CD4+ T cell responses, while low-affinity peptides failed to elicit responses. Therefore, our immunopeptidome profiling platform, EliteMHCII, serves as a rapid, high throughput, feasible platform for CD4+ T cell epitope discovery at a global populational level in the context of infectious diseases and cancer immunotherapy.

biochemistry↗

bioRxiv2025

The mutational dynamics of the Arabidopsis centromeres

Centromeres are specialized chromosomal regions essential for sister chromatid cohesion and spindle attachment during cell division. Although many centromeres consist of highly variable tandem repeat arrays, the mutational processes driving this variability remain poorly understood. Here, using replicated genome assemblies of Arabidopsis thaliana mutation accumulation (MA) lines, we define the centromeric mutation spectrum. We find that point mutations occur at an almost tenfold higher rates than in chromosome arms, largely driven by non-allelic gene conversion between closely linked repeat units. Large kilobase-scale indels are also frequent and consistently preserve the tandem repeat array by adding or removing only complete repeat units. Analysis of MA lines deficient in the helicase RTEL1 supports the involvement of homology-directed DNA repair in these mutational processes. Moreover, simulations of sequence turnover using the centromere-specific mutation spectrum recapitulate the emergence of homogenized repeat blocks characteristic of natural centromeres. Together, our results show that centromere evolution is driven by a distinct mutational spectrum shaped by homology-directed DNA repair, providing a quantitative framework for how local mutational processes generate and maintain the large-scale architecture of centromeric DNA.

genomics↗

bioRxiv2025

High-Codon: A Deep Learning-Based Codon Optimization Tool for Enhanced Heterologous Protein Expression in Escherichia coli

High-Codon is a deep learning-based codon optimization tool designed to enhance the expression levels of heterologous proteins in Escherichia coli. This approach employs a BERT pre-trained model to construct a sequence labeling framework for predicting optimal codons. Additionally, an expression-level weighted loss function is introduced to strengthen the models ability to learn from highly expressed proteins. Evaluation using 100 protein sequences from 34 species demonstrates that High-Codon outperforms traditional optimization methods.

bioinformatics↗

bioRxiv2025

Xcr1+ type 1 conventional dendritic cells are essential mediators for atherosclerosis progression

BackgroundAtherosclerosis is characterized by lipid accumulation within plaques, leading to foam cell formation and an inflammatory response within the aortic lesions. Lipid disorders have been extensively investigated, however the cellular and molecular mechanisms that trigger the inflammatory response in atherosclerotic plaques remain far from being fully understood. Xcr1+ cDC1 cells are newly identified antigen-presenting cells in activating immune cells. However, the role of cDC1 cells in the development of atherosclerosis remains highly controversial. ResultsWe first confirmed the presence of cDC1 within human atherosclerotic plaques and discovered a significant association between the increasing cDC1 numbers and atherosclerosis progression in mice. Subsequently, we established Xcr1Cre-Gfp Rosa26LSL-DTA ApoE-/- mice, a novel and complex genetic model, in which cDC1 was constitutively depleted in vivo during atherosclerosis development. Intriguingly, we observed a notable reduction in atherosclerotic lesions in hyperlipidemic mice, alongside suppressed T cell activation of both CD4+ and CD8+ subsets in the aortic plaques. Notably, aortic macrophages and serum lipid levels were not significantly changed in the cDC1-depleted mice. Single-cell RNA sequencing revealed heterogeneity of Xcr1+ cDC1 cells across the aorta and lymphoid organs under hyperlipidemic conditions. As Xcr1 is the sole receptor for Xcl1, we next explored to target Xcr1+ cDC1 cells via Xcl1 by establishing Xcl1 and ApoE deficient mice. Xcl1 knockout mice exhibited decreased atherosclerotic plaque formation and reduced aortic cDC1 accumulation, indicating that Xcl1 contributes to cDC1-mediated atherosclerotic lesion development. ConclusionsOur results reveal crucial roles of cDC1 in atherosclerosis progression and provide insights into the development of immunotherapies by targeting cDC1 through Xcl1.

immunology↗

bioRxiv2025

ROMO1 loss in cholinergic neurons induces mitochondrial ultrastructural damage and ALS-like neuromuscular degeneration

Mitochondrial dysfunction is strongly associated with the pathogenesis of amyotrophic lateral sclerosis (ALS), a neurodegenerative disorder characterized by progressive motor neuron degeneration. However, it remains obscure whether mitochondrial abnormities are sufficient to drive ALS development. Here, we show that selective depletion of reactive oxygen species modulator 1 (ROMO1), an inner mitochondrial membrane-delimited protein, in cholinergic neurons leads to adult-onset, progressive locomotor deficits in mice that closely resemble ALS pathology. ROMO1 ablation in cholinergic neurons induces ALS-like neuromuscular degeneration, as evidenced by age-dependent motor neuron loss, axon degeneration, disrupted cholinergic transmission, neuromuscular junction denervation, and the resultant muscle atrophy. Notably, ROMO1 loss induces early and progressive mitochondrial cristae deformation in motor neurons, preceding the onset of ALS-like syndromes. Our findings support that mitochondrial impairment in vulnerable motor neurons is a sufficient contributor to ALS etiology, positioning mitochondria as a potential therapeutic target.

neuroscience↗

bioRxiv2025

Amino acid sensing by the α-cell mitochondrial phosphoenolpyruvate cycle regulates intracellular Ca2+ levels without impacting glucagon secretion

Pancreatic islet -cells are increasingly recognized as amino acid sensors for the organism. Building on our prior work in {beta}-cells, we sought to determine whether the mitochondrial phosphoenolpyruvate (PEP) cycle is involved in -cell amino acid sensing. Three different methods were used to probe the PEP cycle, including pyruvate kinase activators (TEPP-46), and mice with -cell specific deletion of pyruvate kinase (PKM1/2-KO) or mitochondrial PEP carboxykinase (PCK2-KO). The mitochondrial fuels glutamine/leucine antagonized alanine/arginine-stimulated Ca2+ influx and glucagon secretion under hypoglycemic conditions. Both PKM1/2 and PCK2 were required for glutamine/leucine to close KATP channels and limit amino acid-stimulated membrane depolarization. The Ca2+ response to amino acids was suppressed by pyruvate kinase activation with TEPP-46, and enhanced by -cell deletion of pyruvate kinase or PCK2 - all without changing glucagon secretion. Finally, using diazoxide/KCl to probe the pathways downstream of membrane depolarization, we identified an essential role of the PEP cycle in homeostatically restoring intracellular Ca2+ levels. In sum, the -cell mitochondrial PEP cycle senses glutamine/leucine and inhibits KATP channels similarly to {beta}-cells, while restricting amino acid-stimulated membrane depolarization and Ca2+ influx. However, defying expectations, none of the amino acids tested, including alanine/arginine, regulate glucagon secretion by modulating membrane depolarization or intracellular Ca2+. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/656009v2_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@18a29f0org.highwire.dtl.DTLVardef@1c77041org.highwire.dtl.DTLVardef@9adc1dorg.highwire.dtl.DTLVardef@e91407_HPS_FORMAT_FIGEXP M_FIG Graphical abstract-cells as amino acids sensors. Arginine, alanine, and glutamine potentiate glucagon secretion, while leucine has a suppressive effect (left). Independently of glucagon secretion, glutamine and leucine suppress alanine and arginine-stimulated Ca2+ influx via the phosphoenolpyruvate (PEP) cycle, which closes KATP channels and suppresses Vm depolarization (right). C_FIG HighlightsO_LIOur studies identify a role for the -cell PEP cycle in sensing amino acids under hypoglycemic conditions. C_LIO_LIPyruvate kinase and PCK2 are required for glutamine/leucine to close -cell KATP channel and limit membrane depolarization and Ca2+ influx. C_LIO_LIGlutamine/leucine oppose alanine/arginine-stimulated Ca2+ influx and glucagon secretion. C_LIO_LIAll of the amino acids tested regulate glucagon secretion, but none do so by modulating membrane depolarization or intracellular Ca2+ levels. C_LI

cell biology↗

bioRxiv2025

A First-in-Class Therapy Targeting Transcription-Replication Conflicts Drives Synthetic Lethality in Homologous Recombination Deficient Cancers

Hidden beneath the layer of tumor malignancy lies unchecked proliferation driven by hyperactive transcription, which fosters the formation of RNA:DNA hybrids. These structural intermediates precipitate collisions between the transcription and replication machineries. Central to mitigating this genomic threat is interleukin enhancer-binding factor 2 (ILF2), which orchestrates the recruitment of RNA:DNA helicases to resolve R-loops and, in doing so, reveals cancer cells dependency on stress-mitigating mechanisms to avert genome catastrophe. Our discovery of Molephantin and its lead derivative, NYH0002 is the outcome of delineating ILF2s function. NYH002 exerts direct binding to the ILF2 complex and disrupts RNA:DNA helicase activity to elicit genome-wide DNA breakages. Tumors with elevated cyclin E and E2F1 expression are sensitive to NYH002, while those deficient in homologous recombination repair exhibit lethality. Collectively, these findings position ILF2 as a key regulator of R-loop homeostasis and reveal a therapeutic vulnerability that NYH002 exploits to suppress tumor malignancy.

cancer biology↗

bioRxiv2025

Divergent MIC of Clarithromycin and Azithromycin Against Clinical Isolates of Mycobacterium abscessus Complex

Current treatment guidelines for Mycobacterium abscessus complex (MAB) infections recommend macrolides (clarithromycin/CAM and azithromycin/AZM) as cornerstone therapies, considering them clinically interchangeable without distinction. This study evaluated the comparative in vitro activity of clarithromycin (CAM) and azithromycin (AZM) against 146 clinical isolates of Mycobacterium abscessus complex organisms. MIC distributions revealed significantly higher resistance to AZM (94.5% resistant at [≥]8 g/mL) compared to CAM (77.4% resistant at [≥]8 g/mL), with only 4.8% of isolates susceptible to both drugs. Notably, 26 strains (17.8% of total) showed AZM resistance despite being non-resistant to CAM (MIC <8 g/mL) among 146 clinical isolates. Among the 33 CAM-non-resistant isolates (including susceptible and intermediate strains), 78.8% (26/33) were AZM-resistant, demonstrating frequent discordance in susceptibility profiles. These findings contrast with current treatment guidelines that recommend using CAM and AZM interchangeably without distinction. Subspecies analysis showed three distinct susceptibility profiles: isolates susceptible to both antibiotics (n=3, M. massiliense), isolates resistant to both antibiotics (n=3, M. massiliense), and M. bolletii with CAM-susceptible/AZM-resistant phenotypes (n=2). This differential resistance pattern suggests that while both drugs face substantial resistance challenges, CAM retains meaningful activity against certain strains that are AZM-resistant-particularly in M. bolletii. These findings indicate that AZM and CAM should not be used interchangeably to treat MAB infections and emphasize the need to prioritize CAM over AZM in treatment regimens.

microbiology↗

bioRxiv2025

Longitudinal single-cell analysis reveals RUNX1T1 as an early driver in treatment-induced neuroendocrine transdifferentiation

Treatment-induced neuroendocrine prostate cancer (t-NEPC) is a lethal form of advanced prostate cancer that can emerge from adenocarcinoma under androgen receptor pathway inhibition, but the tumor-cell states and regulators underlying this transition remain incompletely defined. Here, we analyzed longitudinal single-cell RNA sequencing data from the LTL331/331R patient-derived xenograft model across seven disease stages, comprising 32,269 tumor-cell transcriptomes from treatment-naive adenocarcinoma, post-castration regression, and relapsed NEPC. We identified an AR-low/NE-low intermediate state that emerged after castration and before overt relapse, as well as two transcriptionally distinct terminal NEPC states marked by ASCL1high/FOXA2low and ASCL1low/FOXA2high programs. RUNX1T1 was induced in the intermediate state and remained elevated across both terminal states. RUNX1T1 enhanced NE-associated features and cell viability during enzalutamide treatment in adenocarcinoma cells, whereas its knockdown in NCI-H660 cells reduced NE-associated transcriptional programs, proliferation, and survival and shifted the transcriptome toward an intermediate-like state. Chromatin interactome analysis and co-immunoprecipitation linked RUNX1T1 to G9A/LASP1-containing chromatin repressor complexes. These findings define a temporal framework for treatment-induced NEPC progression and identify RUNX1T1 as an early-induced and sustained regulator of NE lineage transition and maintenance of established NEPC.

cancer biology↗

bioRxiv2025

The sensitising effect of IgG in fibromyalgia syndrome is mediated by Mrgprb2 in mast cells

Fibromyalgia syndrome (FMS) is characterized by elevated levels of immunoglobulin G (IgG), altered bowel habits, and increased pain sensitivity, suggesting immune dysregulation, but the exact mechanism remains unclear. Here, we found that FMS-IgG binds to mast cells in a MRGPRX2/b2-dependent manner, leading to mast cell recruitment and IL-6 secretion. Transferring serum-IgG from FMS patients to mice induced FMS-like symptoms and increased skin mast cells, indicating that FMS-IgG acts through mast cell activation. The ablation of mice Mrgprb2 mast cells or deleting Mrgprb2 receptors prevented IgG-induced heightened sensitivity to mechanical and cold stimuli. Stimulating human LAD2 cells with FMS IgG elicited MRGPRX2-dependent IL-6 production. Consistent with mice findings, mast cell density and tryptase levels increased in human FMS skin samples compared to healthy controls. Taken together our results suggests that FMS IgG mediates hypersensitivity via activation of mast cells bearing the MRGPRX2 receptor and that these cells are a potential therapeutic target.

immunology↗

bioRxiv2025

Divergent Minimum Inhibitory Concentrations of Clarithromycin and Azithromycin Against Clinical Isolates of Mycobacterium abscessus Complex

Current treatment guidelines for Mycobacterium abscessus complex (MAB) infections recommend macrolides (clarithromycin/CAM and azithromycin/AZM) as cornerstone therapies, considering them clinically interchangeable without distinction. This study evaluated the comparative in vitro activity of clarithromycin (CAM) and azithromycin (AZM) against 146 clinical isolates of Mycobacterium abscessus complex organisms. MIC distributions revealed significantly higher resistance to AZM (94.5% resistant at [≥]8 g/mL) compared to CAM (77.4% resistant at [≥]8 g/mL), with only 4.8% of isolates susceptible to both drugs. Notably, 26 strains (17.8% of total) showed AZM resistance despite being non-resistant to CAM (MIC <8 g/mL) among 146 clinical isolates. Among the 33 CAM-non-resistant isolates (including susceptible and intermediate strains), 78.8% (26/33) were AZM-resistant, demonstrating frequent discordance in susceptibility profiles. These findings contrast with current treatment guidelines that recommend using CAM and AZM interchangeably without distinction. Subspecies analysis showed three distinct susceptibility profiles: isolates susceptible to both antibiotics (n=3, M. massiliense), isolates resistant to both antibiotics (n=3, M. massiliense), and M. bolletii with CAM-susceptible/AZM-resistant phenotypes (n=2). This differential resistance pattern suggests that while both drugs face substantial resistance challenges, CAM retains meaningful activity against certain strains that are AZM-resistant--particularly in M. bolletii. These findings indicate that AZM and CAM should not be used interchangeably to treat MAB infections and emphasize the need to prioritize CAM over AZM in treatment regimens.

microbiology↗

bioRxiv2025

PIBE: Parallel ion beam etching of sections collected on wafer for ultra large-scale connectomics

We developed a parallel ion beam etching device that simultaneously thins hundreds of sections on a whole 4-inch wafer at 20 nm steps, enabling sub-centimeter volumetric imaging with high axial resolution. Compared with traditional volume electron microscopy, PIB preserves in-situ continuity within sections and simplifies inter-section registration. Its high axial resolution facilitates reliable neuron segmentation and tracing with reduced proofreading, providing an efficient route toward ultra-large-scale connectomics, such as whole-mouse-brain reconstruction.

neuroscience↗