Biology subjects

Moon, Y.

Publications and source records attributed to Moon, Y..

9 recordsLinked to original sources

bioRxiv2026

Single-Cell and Spatial Analysis Reveals Retention of FCRL4⁺ Memory B Cells in Pediatric Tonsillar Hypertrophy

Pediatric tonsillar hypertrophy is a leading cause of sleep disordered breathing in children, yet the immune mechanisms sustaining tonsillar enlargement remain unclear. Using integrated single cell and spatial profiling of pediatric tonsils in a discovery cohort (n = 45) and independent validation cohort (n = 32), we identify a selective expansion and follicular retention of FCRL4+ memory B cells within the mantle zone of hypertrophic tonsils. These cells exhibit a quiescent, tissue-adapted phenotype characterized by NFATC1 repression and reciprocal RUNX1/RUNX2 regulation. Their accumulation is orchestrated by follicular type 1 regulatory T (Tr1) cells, which engage CTLA-4/CD86 checkpoint interactions to suppress plasma cell differentiation and reinforce a local immune tolerance program. Together, these interactions establish a persistent follicular niche enriched in regulatory FCRL4+ memory B cells. Our findings delineate a mechanistic Tr1/FCRL4+ B cell axis underlying follicular hypertrophy and highlight potential immunomodulatory targets for nonsurgical management of pediatric sleep-disordered breathing.

immunology↗

bioRxiv2026

The m6A methyltransferase complex protein VIRMA engages hepatitis C virus RNA through a WTAP-independent mechanism

Cellular proteins in the m6A methyltransferase protein complex (m6A-MTC) work together to modify both cellular and viral RNAs with N6-methyladenosine (m6A), an RNA modification that regulates viral infection. We previously showed that hepatitis C virus (HCV), a cytoplasmic positive-sense RNA virus, has an m6A-modified RNA genome. We also found that m6A deposition on HCV RNA requires WTAP, which promotes association of the METTL3-METTL14 catalytic heterodimer to the viral RNA. However, the factors that directly recognize HCV RNA and recruit the m6A-MTC to the viral genome are unknown. Here, we identify the cellular m6A-MTC component VIRMA as an HCV RNA-targeting factor required for METTL3 association with the viral genome. We show that endogenous VIRMA can associate with both HCV and cellular RNAs independently of WTAP. Further, we define distinct domains of VIRMA involved in WTAP interaction and RNA binding and show that the regions of VIRMA involved in WTAP-interaction are required for cellular but not HCV RNA association. Together, these results establish that VIRMA uses distinct molecular determinants to engage viral and cellular RNAs and define VIRMA as a substrate-recognition factor required for m6A-MTC association with HCV RNA.

molecular biology↗

bioRxiv2026

Infant gut microbiomes contribute to metabolic states that impact brain function

Alterations in the gut microbiome are associated with neurodevelopmental disorders, but causal mechanisms and therapeutic strategies remain undefined. Here, we demonstrate that human infant microbiomes isolated during the first six months of life drive behavioral impairments in mice and that microbiota-based interventions restore mice to normal behavior. Early-life microbiomes from twelve infants who later exhibited cognitive deficits at 2 years old (low-scoring) transferred adverse metabolic, brain, and behavioral phenotypes to mice, in contrast to microbiomes from twenty-three cognitively typical or high-scoring infants. Deficits in mice were rescued by fecal microbiota transplant from high-scoring infants or a rationally designed consortium that promoted amino acid levels. We confirmed lower fecal amino acid concentrations in low-scoring infants and replicated the association between early-life microbiome composition and cognitive outcomes in a second geographically independent infant cohort. Altogether, we discovered an early-life microbiome-mediated metabolic state causally linked to cognitive deficits and amenable to microbial intervention.

microbiology↗

bioRxiv2025

Allosteric deimmunisation of a Salmonella phosphatase enhances catalytic function

Genetically engineered Salmonella strains are promising vectors for cancer therapy, but their clinical use is limited by host immune responses. A key immunogenic antigen, the phosphatase PhoN, is metabolically essential for bacterial survival in the vitamin B6-depleted tumour microenvironment and thus cannot be simply deleted. While conventional deimmunisation targets surface residues, we present a strategy of allosteric deimmunisation by mutating non-surface, buried residues within the dominant h2 helix T-cell epitope. We hypothesised that the epitope is allosterically coupled to the distal active site gate, allowing for the simultaneous modulation of immunogenicity and enzymatic function. Using a computational pipeline, we designed deimmunised variants and used molecular dynamics (MD) simulations to predict their functional effects. The simulations revealed that mutations in the h2 helix allosterically controlled the gates flexibility. The enzymatic activities of the deimmunized variants were correlated with the MD predictions: two of the five designed variants exhibited 2[~]3-fold increases in catalytic function. This work demonstrates that non-surface epitopes can be rationally engineered to not only ablate immunogenicity but also to allosterically enhance protein function.

biophysics↗

bioRxiv2025

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

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

immunology↗

bioRxiv2024

Evaluation of false positive and false negative errors in targeted next generation sequencing

BackgroundAlthough next generation sequencing (NGS) has been adopted as an essential diagnostic tool in various diseases, NGS errors have been the most serious problem in clinical implementation. Especially in cancers, low level mutations have not been easy to analyze, due to the contaminating normal cells and tumor heterozygosity. ResultsIn targeted NGS (T-NGS) analyses for reference-standard samples containing mixtures of homozygote H. mole DNA with blood genomic DNA at various ratios from four certified NGS service providers, large differences in the lower detection limit of variants (16.3 times, 1.51[~]24.66%) and the false positive (FP) error rate (4280 times, 5.814 x 10-4 [~]1.359 x 10-7) were found. Employment of the commercially available Dragen system for bioinformatic analyses reduced FP errors in the results from companies BB and CC, but the errors originating from the NGS raw data persisted. Bioinformatic conditional adjustment to increase sensitivity (less than 2 times) led to a much higher FP error rate (610[~]8200 times). In addition, problems such as biased preferential reference base calls during bioinformatic analysis and high-rate FN errors in HLA regions were found in the NGS analysis. ConclusionT-NGS results from certified NGS service providers can be quite various in their sensitivity and FP error rate, suggesting the necessity of further quality controls for clinical implementation of T-NGS. The present study also suggests that mixtures of homozygote and heterozygote DNAs can be easily employed as excellent reference-standard materials for quality control of T-NGS.

genomics↗

bioRxiv2022

Identification and characterization of a dlx2b cis-regulatory element both sufficient and necessary for correct transcription during zebrafish tooth development

Despite growing recognition of the importance of cis-regulatory elements in vertebrate development, the mechanisms by which enhancers control gene expression during organogenesis remain incompletely understood. To address this gap, we investigated the regulation of the transcription factor dlx2b during zebrafish larval tooth formation. Using CRISPR/Cas9-mediated genome editing, we generated a GFP knock-in line that recapitulates dlx2b expression in developing tooth germs. Through targeted manipulation of enhancer sequences, we identified a minimal tooth enhancer (MTE), which is sufficient to drive most of the endogenous dlx2b tooth germ expression pattern in vivo. Functional dissection of the MTE revealed that four evolutionarily conserved transcription factor binding sites are essential for enhancer activity. Mutating these sites within a transgenic reporter abolishes enhancer-driven expression, while deletion of the same sequences at the endogenous dlx2b locus causes a dramatic shift in the genes expression pattern. These findings suggest that loss of MTE function permits alternative cis-regulatory elements to gain control of the promoter, highlighting the dynamic nature of enhancer-promoter interactions during development. Together, these results uncover fundamental principles of enhancer function during vertebrate organogenesis and demonstrate the power of empirical dissection in decoding cis-regulatory architecture. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/477116v3_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@5a5909org.highwire.dtl.DTLVardef@18b79bforg.highwire.dtl.DTLVardef@1e61eaeorg.highwire.dtl.DTLVardef@e845f8_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2020

Chemogenetic activation of astrocytes in the hippocampus and cortex changes the transcriptome of microglia and other cell types.

Astrocytes are the most common glial cell type in the brain, yet, it is unclear how their activation affects the transcriptome of neighboring cells. Engineered G protein-coupled receptors (GPCRs) called Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) enable selective activation of specific cell types, such as astrocytes. Here, we combine activation of astrocytes in the hippocampus and cortex of healthy mice with single-cell RNA sequencing. Our data show that long-term activation of astrocytes dramatically alters the transcriptome of astrocytes and microglia. Genes that were differentially expressed in Gq-DREADD-activated astrocytes are involved in neurogenesis and low-density lipoprotein particle biology, while those in the microglia were involved in lipoprotein handling, purinergic receptor activity, and immune cell migration and chemotaxis. Furthermore, network analysis showed that Gq-DREADD-mediated activation in astrocytes resulted in an upregulation of genes involved in the GPCR signaling pathways and calcium ion homeostasis, confirming astrocyte activation. This dataset will serve as a resource for the broader neuroscience community, and our findings highlight the importance of studying transcriptomic alterations in microglia after astrocyte activation in vivo.

neuroscience↗

bioRxiv2020

Acoustofluidic Assembly of 3D Neurospheroids to Model Alzheimer's Disease

Neuroinflammation plays a central role in the progression of many neurodegenerative diseases such as Alzheimers disease, and challenges remain in modeling the complex pathological or physiological processes. Here, we report an acoustofluidic 3D cell culture device that can rapidly construct 3D neurospheroids and inflammatory microenvironments for modeling microglia-mediated neuroinflammation in Alzheimers disease. By incorporating a unique contactless and label-free acoustic assembly, this cell culture platform can assemble dissociated embryonic mouse brain cells into hundreds of uniform 3D neurospheroids with controlled cell numbers, composition (e.g. neurons, astrocytes, and microglia), and environmental components (e.g. amyloid-{beta} aggregates) in hydrogel within minutes. Moreover, this platform can maintain and monitor the interaction among neurons, astrocytes, microglia, and amyloid-{beta} aggregates in real-time for several days to weeks, after the integration of a high-throughput, time-lapse cell imaging approach. We demonstrated that our engineered 3D neurospheroids can represent the amyloid-{beta} neurotoxicity, which is one of the main pathological features of Alzheimers disease. Using this method, we also investigated the microglia migratory behaviors and activation in the engineered 3D inflammatory microenvironment at a high throughput manner, which is not easy to achieve in 2D neuronal cultures or animal models. Along with the simple fabrication and setup, the acoustofluidic technology is compatible with conventional Petri dishes and well-plates, supports the fine-tuning of the cellular and environmental components of 3D neurospheroids, and enables the high-throughput cellular interaction investigation. We believe our technology may be widely used as in vitro brain models for modeling neurodegenerative diseases, discovering new drugs, and testing neurotoxicity.

bioengineering↗