Biology subjects

Dong, R.

Publications and source records attributed to Dong, R..

At least 19 recordsLinked to original sources

bioRxiv2026

In situ identification of pre-hematopoietic stem cells and their niche

Definitive hematopoietic stem cells (HSCs) emerge predominantly along the ventral surface of the dorsal aorta in the embryonic aorta-gonad-mesonephros (AGM) region, yet the spatial organization of the niche underlying this developmental asymmetry remains poorly understood. Defining the native niche of pre-HSCs has also been hindered by their rarity, transient nature and lack of a single definitive marker for their identification in situ. Here, we integrated single-cell and spatial transcriptomics to construct a spatiotemporal atlas of the niche in the AGM. Neural cells and chondrogenic mesenchyme predominated dorsally, whereas N-cadherin mesenchymal stromal cells (N-cad+ MSCs) formed a ventral layer between the aortic endothelium and mesonephric cells. BMP and SHH signaling showed overall dorsal enrichment, whereas WNT, NOTCH and KIT signaling were enriched ventrally, with these cellular and signaling patterns dynamically remodeled across HSC ontogeny. Imaging-based spatial transcriptomics validated the findings and further enabled the identification of individual pre-HSCs in situ and revealed a multicellular niche comprising endothelial cells, N-cad+ MSCs, intra-aortic hematopoietic cluster cells and macrophages. TGF{beta} and NOTCH signals were primarily supplied locally, whereas major sources of BMP and WNT were more distant. Functional perturbation identified niche-derived CD200 as an immune-regulatory signal promoting HSC development, validating a spatially predicted niche interaction. Together, our findings link tissue-scale spatial organization with the local multicellular niche supporting the preferential development of HSCs along the ventral aorta.

developmental biology↗

bioRxiv2026

Evolutionary Design of Membrane-Lytic Antimicrobial Peptides with Mixture of Experts

Antimicrobial peptides (AMPs) hold great promise in combating drug-resistant pathogens, yet current design models do not explicitly account for their primary mode of action, membrane disruption. To address this gap, we propose AMPainterV2, a model that designs membrane-lytic AMPs using generative adversarial imitation learning. AM-PainterV2 integrates a Mixture-of-Experts (MoE) policy network to support insertion, deletion, and mutation operations, thereby expanding the evolutionary design space. In vitro experiments demonstrate that all ten top-ranked peptides evolved from random sequences are active membrane-lytic AMPs, with the best candidate achieving a mean minimal inhibitory concentration (MIC) of 1.5 {micro}M and superior membrane-lytic activity compared to polymyxin B. Particularly, a deletion-only version of AMPainterV2 enables membrane-lytic AMP miniaturization, yielding six miniaturized peptides with comparable or improved activity and an average 36% length reduction. Collectively, AMPainterV2 advances mechanism-driven AMP design and offers a valuable tool for cost-effective AMP development.

bioinformatics↗

bioRxiv2026

IL-21-producing peripheral helper T cells associate with autoimmune bile duct injury in biliary atresia

BackgroundBiliary atresia (BA) is a severe neonatal liver disease characterized by progressive fibrosis and bile duct obliteration. ObjectiveAlthough immune dysregulation is implicated in the pathogenesis of BA, the specific mechanisms driving bile duct injury remain incompletely understood. This study aimed to characterize tertiary lymphoid structures (TLSs) within extrahepatic biliary remnants (EBRs), identify their cellular mediators, and evaluate the therapeutic potential of targeting IL-21 receptor signaling. DesignWe performed integrated bulk RNA sequencing, single-cell RNA sequencing, spatial transcriptomics, multiplex immunohistochemistry, and flow cytometry on clinical samples from BA patients and non-BA cholestatic controls. TLS maturation was assessed by CD23 immunohistochemistry in EBRs from 148 BA patients and correlated with clinical parameters. Anti-IL-21R antibody treatment was evaluated in a rhesus rotavirus-induced BA mouse model, with treatment initiated on day 4 post-infection. ResultsTLSs were identified in BA EBRs with significantly higher prevalence than in matched liver tissues. Mature TLSs containing CD23 germinal centers were associated with elevated serum matrix metalloproteinase-7, more advanced hepatic fibrosis, and localized autoantibody deposition on injured bile ducts. Single-cell profiling revealed expanded CD4+ T peripheral helper (Tph) cells expressing IL-21 and CXCL13 within TLS-containing EBRs. Tph cells were enriched in peripheral blood of BA patients compared to non-BA cholestatic controls (P = 0.0025), and serum IL-21 was significantly elevated (P < 0.0001). Post-infection IL-21R blockade in the mouse model reduced jaundice incidence, improved weight gain, prevented extrahepatic biliary obstruction, and significantly improved long-term survival. ConclusionTLSs in BA extrahepatic biliary remnants harbor expanded Tph cells associated with IL-21-mediated B cell activation and bile duct injury. IL-21R blockade ameliorated disease in a murine BA model, identifying the IL-21/IL-21R axis as a potential therapeutic target warranting further investigation. Key MessagesO_ST_ABSWhat is already known on this topicC_ST_ABSImmune dysregulation contributes to biliary atresia (BA), with documented lymphocyte infiltration and defective B cell tolerance. However, the cellular mechanisms linking local immune activation to bile duct injury are unclear, and the roles of organized lymphoid structures and specific CD4 T cell subsets in orchestrating local humoral responses have not been characterized. What this study addsThis study demonstrates that mature tertiary lymphoid structures in extrahepatic biliary remnants are associated with disease severity markers and localized bile duct injury in BA. We identify T peripheral helper cells as an expanded IL-21-producing CD4 T cell population within these structures, and show that post-infection IL-21 receptor blockade prevents biliary obstruction and improves survival in a murine BA model. How this study might affect research, practice or policyThese findings identify the IL-21/IL-21R signaling axis as a candidate therapeutic target in BA warranting further preclinical and translational investigation. TLS maturation status in biliary remnants and serum autoantibody levels may serve as potential biomarkers of disease severity, meriting prospective evaluation in clinical cohorts.

immunology↗

bioRxiv2026

LDSC regression-based heritability estimates can be biased when summary statistics are obtained from meta-analysis or imputed variants

MotivationLinkage disequilibrium score (LDSC) regression is a popular method to estimate heritability for complex traits using summary statistics and linkage disequilibrium (LD) reference panels, offering a practical alternative to methods requiring individual-level data. Despite its widespread use, LDSC regression can produce biased heritability estimates. The properties of LDSC regression were investigated using summary statistics from several large-scale Alzheimers disease (AD) studies and a variety of LD reference panels. These heritability estimates were compared with those obtained from individual-level data. ResultsWhen LDSC regression was applied to summary statistics obtained from meta-analysis, it led to an underestimation of heritability. This can occur if meta-analysis is used to combine studies of different ancestries leading to the caveat of the lack of an appropriate LD reference panel. Additionally meta-analyses often include studies with different phenotype definitions, that not only impacts heritability estimates but also makes them uninterpretable. Summary statistics generated from imputed variants, even those with high imputation accuracy, can lead to underestimation of heritability. For example, the heritability estimates for AD were reduced from 0.265 (se 0.148) to 0.160 (se 0.041) when imputed variants (INFO>0.9) were included compared to analyzing only genotype array variants. A decrease in heritability estimates was also observed when individual-level imputed variant data were analyzed using GCTA-GREML. Our findings highlight the caveats of estimating heritability using meta-analysis summary statistics or imputed data instead of genotyped or sequence data.

genetics↗

bioRxiv2026

Anatomical Identification and Pressure Myography of the Rat Middle Cerebral Artery: A Comprehensive Protocol for Diverse Genetic Models

The middle cerebral artery (MCA) is critical for cerebral blood flow autoregulation and a primary site of cerebrovascular pathology in stroke, Alzheimers disease, and vascular dementia. Pressure myography enables precise ex vivo quantification of MCA structure and function, but requires accurate anatomical identification and careful vessel handling to ensure reproducibility across diverse rat genetic models. This chapter provides a comprehensive, step-by-step protocol for isolating and cannulating the rat MCA M2 segment for pressure myography. We detail precise anatomical landmarks to ensure consistent vessel selection across strains. The protocol includes optimized solutions, cannulation techniques, and pressure protocols validated across multiple rat models, including transgenic (TgF344-AD), diabetic (T2DN), consomic (SS.5BN, FHH.1BN), and genome-edited strains. Extensive troubleshooting notes address common technical challenges, including vessel viability assessment, pressure integrity, and strain-specific autoregulatory ranges. This methodology bridges molecular genetic findings with fundamental cerebrovascular physiology, enabling researchers to characterize myogenic reactivity, passive mechanical properties, and structural remodeling in rat models of cerebrovascular disease.

physiology↗

bioRxiv2026

Self-supervised Internal Learning Enhances Isotropic Resolution for Three-dimensional Fluorescence Microscopy

Three-dimensional fluorescence microscopy often exhibits anisotropic resolution because axial information is poorly sampled and more blurred than lateral information, which complicates quantitative interpretation of fine 3D structures. Although optical remedies and computational restoration have been explored, many approaches require demanding system calibration or rely on accurate PSF models and assumptions that are difficult to satisfy across all samples and modalities. Here we present DeepIso, a self-supervised isotropy restoration framework that couples supervised pretraining with an internal-learning inference stage to estimate degradation directly from the measured volume. Without explicit PSF specification or enforced lateral-axial structural equivalence, DeepIso recovers axial frequency content and improves the continuity of elongated structures while retaining fine features, with superior performance over existing computational approaches in terms of both visual inspection and quantitative metrics. The method is validated on synthetic benchmarks and experimental datasets, demonstrating isotropy enhancement across confocal, light-sheet, and 3D structured illumination microscopy, thereby supporting downstream volumetric analysis including segmentation and tracking.

bioengineering↗

bioRxiv2026

Inhibition of Soluble Epoxide Hydrolase Rescues Cognitive Deficits by Preserving Neurovascular Integrity and Attenuating Glial- and Neuropathology in Diabetic-Related Dementia

Diabetes mellitus (DM) is a major risk factor contributing to the development of Alzheimers disease-related dementias (ADRD). While one of the early symptoms of both Alzheimers disease (AD) and DM-related ADRD is a reduction in cerebral blood flow, the underlying biological mechanisms driving this decline remain to be fully elucidated. Genome-wide association studies have linked AD/ADRD to single-nucleotide polymorphisms in the gene encoding soluble epoxide hydrolase (sEH), an enzyme we previously reported to be upregulated in the brains of an AD rat model. Our previous work also demonstrated that chronic inhibition of sEH with 1-trifluoromethoxyphenyl-3-(1-propionylpiperidin-4-yl) urea (TPPU) preserves hippocampal-dependent spatial learning and memory and improves cerebral hemodynamics in both AD and DM-ADRD models. In the present study, we found that chronic TPPU treatment (1 mg/kg/day for 9 weeks) reduced brain sEH expression, improved cortical-based long-term non-spatial recognition memory involving both cortical and hippocampal networks, and reduced anxiety in DM-ADRD rats. TPPU improved brain perfusion and normalized impaired whisker-evoked functional hyperemia, an effect linked to upregulation of Kir2.1 expression in cerebral capillaries. Furthermore, TPPU restored tight junction proteins (ZO-1 and OCLN), mitigated capillary rarefaction, and suppressed astrocyte and microglial activation. At the cellular level, TPPU attenuated hippocampal neurodegeneration, restored the expression of synaptic proteins (PSD95 and SY38), and reduced levels of key pro-inflammatory chemokines, including MCP-1, RANTES, and MIP-1, in DM-ADRD. In conclusion, TPPU preserves cognitive function in DM-ADRD by mitigating cerebrovascular dysfunction, neuroinflammation, and gliosis while protecting synaptic integrity and neuronal survival, representing a promising therapeutic strategy for DM-ADRD.

neuroscience↗

bioRxiv2026

Leveraging cis- and trans-variants to improve protein expression level prediction for proteome-wide association studies

Since genetic effects are often mediated through proteins, the analysis of proteomic data can provide insights into disease etiology. However, most studies lack proteomic data. To address this problem, we developed TransCisPredict to perform proteome-wide association studies (PWAS) at a biobank scale. TransCisPredict reduces computational burden through linkage-disequilibrium block selection which facilitates incorporating cis- and trans-variants to predict protein expression and performs protein-phenotype association analyses. To account for differences in protein regulatory architecture, four prediction methods are used for weight estimation, i.e., BayesR, Elastic Net, LASSO, and SuSiE. Five-fold cross-validation (CV) is used to select the optimal method for each protein. Weight estimation was performed using White British UK Biobank study subjects (N=42,644) with proteomic and genotype array data. Of the 2,920 available protein expression levels, 2,339 could be predicted with a CV-R2>0.05 when cis- and trans-variants were used. Since most methods are limited to cis-variation, for comparison only cis-variants were used for prediction yielding 466 proteins with a CV-R2>0.05. A PWAS was performed for 2,339 predicted protein expression levels and type 2 diabetes (T2D) using White British UK Biobank study subjects without proteomic data (N=364,132) followed by two-sample Mendelian randomization using a method that controls for horizontal pleiotropy for validation. Forty proteins were associated with T2D and validated. For the 466 cis-only predicted protein expression levels, three proteins were associated with T2D and validated. Incorporating both cis- and trans-variation using TransCisPredict facilitates the prediction of many more proteins compared to using cis-only variants thereby increasing the power of PWAS.

genetics↗

bioRxiv2026

Size Scaling of the Electrochemical Performance of Ti3C2Tx MXene Microelectrode Arrays for Electrophysiological Recording and Stimulation

Miniaturized neural interfaces for research, diagnostics, and neuromodulation therapies require electrode materials that maintain low impedance and high charge injection capacity as device dimensions shrink to ensure high-quality recordings and safe stimulation. Conventional interfaces rely on metals like platinum (Pt), which are limited by intrinsically high impedance and low charge transfer capacity, reducing their performance in sub-100 {micro}m applications. Ti3C2Tx MXene has emerged as a promising alternative for high-density recording and stimulation interfaces, though the fundamental charge transfer mechanisms governing its performance remain poorly understood. This study evaluates Ti3C2Tx MXene microelectrodes across a range of diameters (25 - 500 {micro}m) and systematically elucidates the mechanisms governing their recording and stimulation capabilities. Electrochemical impedance spectroscopy, cyclic voltammetry, and voltage transient measurements - supported by equivalent-circuit modeling - revealed enhanced recording and stimulation capabilities of the MXene microelectrodes over size-matched Pt microelectrodes, attributed to reduced charge-transfer resistance and increased double-layer capacitance. Finally, varying the volume and concentration of the spray-coated Ti3C2Tx films showed that increased MXene concentration and volume enhanced performance by creating thicker, rougher interfaces. Together, these results establish Ti3C2Tx MXene as a promising electrode material with exceptional performance at the microscale.

bioengineering↗

bioRxiv2026

PepMCP: A Graph-Based Membrane Contact Probability Predictor for Membrane-Lytic Antimicrobial Peptides

MotivationThe membrane-lytic mechanism of antimicrobial peptides (AMPs) is often overlooked during their in silico discovery process, largely due to the lack of a suitable metric for the membrane-binding propensity of peptides. Previously, we proposed a characteristic called membrane contact probability (MCP) and applied it to the identification of membrane proteins and membrane-lytic AMPs. However, previous MCP predictors were not trained on short peptides targeting bacterial membranes, which may result in unsatisfactory performance for peptide studies. ResultsIn this study, we present PepMCP, a peptide-tailored model for predicting MCP values of short peptides. We collected more than 500 membrane-lytic AMPs from the literature, conducted coarse-grained molecular dynamics (MD) simulations for these AMPs, and extracted their residue MCP labels from MD trajectories to train PepMCP. PepMCP employs the GraphSAGE framework to address this node regression task, encoding each peptide sequence as a graph with 4-hop edges. PepMCP achieved a Pearson correlation coefficient of 0. 883 and an RMSE of 0. 123 on th e node-level test set. It can recognize membrane-lytic AMPs with the predicted MCP values for each sequence, thereby facilitating mechanism-driven AMP discovery. Additionally, we provide a database, MemAMPdb, which includes the membrane-lytic AMPs, as well as the PepMCP web server for easy access. Availability and ImplementationThe code and data are available at https://github.com/ComputBiophys/PepMCP. Contactc.song@pku.edu.cn Supplementary InformationSupplementary data are available online.

bioinformatics↗

bioRxiv2025

A tale of two distinct actin networks underlies the entire life cycle of focal adhesion

Cell assembles focal adhesion (FA) to transmit the stress fiber (SF)-based actomyosin contraction onto the extracellular matrix (ECM) for mesenchymal migration, essential for many physiological processes (e.g., development and wound healing). To transmit force efficiently, both FA and SF contractility are built as "clutches" and in positive feedback with each other; conversely, the SF-engaging FA imposes a strong cell-ECM anchorage and must be disassembled timely to facilitate the cell migration. How the cell balances the two opposing roles of FA in cell migration is an open question. Particularly, it is not well-understood how a cell builds the FA de novo to clutch with SF and disassemble the clutches when needed in a coherent manner. Combining theory and experiments, we show that the entire life cycle of FA is seamlessly orchestrated by the FA-localized spatiotemporal coordination between retrograde actin flow and SF, without destroying the FA constituent molecules. Retrograde actin flow drives the centripetal growth of nascent FA, paving the way for SF engagement. The SF further stabilizes the growing FA into maturation via the positive feedback that clutches the contractility with the FA. Finally, the retrograde actin flow increase, in coupling to the local cell edge retraction, tugs the mature FA in the proximal direction that relaxes the associated SF contractility, turns off the clutching, and triggers the FA disassembly. Our finding sheds light on the organizational principles that cell streamlines the mechanochemical interplay between FA, actin cytoskeleton, and cell edge dynamics for efficient cell migration.

cell biology↗

bioRxiv2025

Mechanism-driven screening of membrane-targeting and pore-forming antimicrobial peptides

The rise of antibiotic resistance has generated an urgent demand for the discovery of new antimicrobial peptides (AMPs), prompting the development of various screening strategies. However, the specific function mechanisms of AMPs are often overlooked during the screening and optimization processes. In this study, we introduce a mechanism-driven screening approach that employs machine learning-based computational models to identify peptide sequences that target membranes and form pores. This approach explicitly considers critical factors such as structural features, membrane ainity, and the ability of peptides to oligomerize. Our method was applied to the metaproteomes of poison frogs, African clawed frogs, and human skin, followed by experimental validation. Seven peptides were successfully screened, each demonstrating antimicrobial activity with minimal hemolysis and cytotoxicity. These peptides exhibited membrane disruption capabilities in liposome leakage assays, with three showing broad-spectrum antimicrobial activity. Furthermore, single-molecule experiments indicated that these peptides can oligomerize on membranes, while electrophysiological measurements detected pore formation, confirming the effectiveness of our screening strategy. Therefore, our screening approach can effectively identify AMP sequences that act through membrane-targeting and poreforming mechanisms, offering a promising, mechanism-driven strategy for the discovery of new antimicrobial agents to combat antibiotic resistance.

biophysics↗

bioRxiv2025

VPS35/Retromer-dependent MT1-MMP regulation confers melanoma metastasis

Retromer is a conserved endosomal trafficking complex responsible for recycling transmembrane protein cargoes. Membrane-type I matrix metalloproteinase (MT1-MMP), a well-studied membrane-type metalloprotease, is highly expressed in metastatic melanomas. Previously, we reported that inducing MT1-MMP perinuclear localization and inhibiting MT1-MMP membrane localization significantly reduce melanoma metastasis. However, the regulation of MT1-MMP subcellular localization and recycling is still largely unknown. Here, we performed target gene shRNA screening and found that shRNA targeting the retromer complex subunit vacuolar protein sorting 35 (VPS35) inhibited MT1-MMP membrane localization and induced its perinuclear localization. We found that inhibiting VPS35/retromer decreased MT1-MMP recycling and increased MT1-MMP-lysosome localization, which significantly affected the stability of MT1-MMP. Furthermore, our results indicated that VPS35/retromer regulates the transcription of MT1-MMP through the activation of the IL6/STAT3 inflammatory signaling pathway. Tissue microarray analysis indicated that VPS35/retromer positively correlated with MT1-MMP levels and distant metastasis. Xenograft experiments showed that targeting VPS35/retromer significantly inhibited melanoma lung metastasis, which is dependent on MT1-MMP. Our results implicate the importance of VPS35/retromer in metastatic dissemination. Our study suggests that targeting the VPS35/retromer-MT1-MMP axis will contribute to inhibiting the metastasis of melanoma.

cancer biology↗

bioRxiv2025

Painting Peptides with Antimicrobial Potency through Deep Reinforcement Learning

In the post-antibiotic era, antimicrobial peptides (AMPs) serve as ideal drug candidates for their lower likelihood of inducing resistance. Computational models offer an efficient way to design novel AMPs. However, current optimization and generation approaches are tailored for different application scenarios. To address this challenge, we propose a novel AMP design model named AMPainter. Based on deep reinforcement learning, AMPainter integrates both optimization and generation tasks in a unified framework. We apply AM-Painter to three types of peptides, including known AMPs, signal peptides (SPs), and random sequences. AMPainter outperforms ten related models in enhancing the activity of known AMPs, and evolves effective AMPs from membrane-active SPs with a success rate of 80%. Furthermore, several de novo designed AMPs from random sequences are validated along with their evolutionary paths. Therefore, AMPainter contributes to paint antimicrobial potency to diverse peptides, assisting in expanding the AMP sequence space and discovering novel antimicrobial agents.

bioinformatics↗

bioRxiv2024

Leveraging Drosophila Models to Explore AI-generated Synthetic Peptide's Potential in Boosting Honeybee Health and Resilience

The integration of artificial intelligence (AI) and machine learning (ML) in peptide design has revolutionized the development of antimicrobial peptides (AMPs), which are essential components of innate immunity. In this study, we identified a novel synthetic peptide, PAN4 (GAYTFKIRRK), through genetic screening of AI-generated candidates in Drosophila melanogaster. PAN4 demonstrated robust antimicrobial activity, stress tolerance, and antitumor effects, significantly enhancing survival rates following bacterial infections and improving locomotor behaviors without adversely affecting lifespan. Furthermore, PAN4 expression in intestinal stem cells completely suppressed RasV12-induced tumor progression, indicating its potential role in cancer prevention. The peptide also mitigated gut barrier dysfunction associated with sleep deprivation and reduced inflammation in a dextran sulfate sodium (DSS)-induced colitis model. Mechanistically, PAN4s antimicrobial activity was linked to its interaction with specific peptidoglycan recognition proteins (PGRPs), particularly PGRP-SC1a, while the Tak1-mediated immune signaling pathway was found to be non-essential for its efficacy. PAN4 showed promising effects on honeybee health, enhancing survival rates under bacterial stress. Furthermore, PAN4 expression demonstrated significant anti-tumor activity in the Drosophila gut tumor model. Our findings suggest that PAN4 serves as a versatile agent with significant implications for enhancing immune responses and combating diseases in honeybee populations, paving the way for future applications in agriculture and medicine.

genetics↗

bioRxiv2024

IGF2 mediates Hippo signaling to control liver size

The Hippo pathway is a central mechanism in organ size control, but the mediator for its function remains elusive. Here, we show that the expression of insulin-like growth factor II (IGF2) is directly induced by YAP/TAZ transcription cofactors of the Hippo pathway in a developmental stage- and cell type-specific manner. In mouse livers, Igf2 expression is sustained by YAP/TAZ in hepatoblasts and immature hepatocytes at fetal and neonatal stages, coupling with rapid cell proliferation and liver size expansion, whereas turned off in matured hepatocytes following YAP/TAZ inactivation to prevent liver overgrowth. In contrast, YAP/TAZ fails to regulate Igf2 expression in cholangiocytes and diverse liver mesenchymal cells where epigenetic barriers, including DNA and histone methylation, are implanted near Igf2 promoters. Furthermore, IGF2 activates IGF1R signaling and promotes normal and neoplastic liver growth, while the inactivation of IGF2 or IGF1R effectively blocks YAP/TAZ-induced hepatomegaly and hepatoblastoma. In conclusion, our findings reveal that IGF2 is a bona fide mediator of the Hippo pathway, indicating a fundamental role of the Hippo-IGF2-IGF1R signaling axis in organ size regulation and malignancies.

cell biology↗

bioRxiv2024

Investigating the antimicrobial and immunomodulatory effects of honeybee venom peptide apamin in the Drosophila genetic platform.

Apamin, an 18-amino acid peptide neurotoxin, constitutes a significant portion of honeybee venom. Although traditionally recognized for its neurotoxic effects, our research demonstrates that apamin exhibits potent antimicrobial properties when genetically expressed in Drosophila. The antimicrobial efficacy of apamin is independent of its disulfide bonds and is enhanced when the peptide is membrane-tethered. This expression selectively targets and inhibits specific harmful bacterial species, such as Pseudomonas aeruginosa, Enterococcus faecalis, and Escherichia coli, while promoting beneficial bacteria like Lactobacillus plantarum thereby improving the gut microbiome. The antimicrobial activity of apamin is localized to the gut and is associated with increased proliferation of intestinal stem cells, acidification of the midgut pH, and activation of enteroendocrine cell calcium signaling. Furthermore, apamins antimicrobial function is dependent on specific peptidoglycan recognition proteins, with PGRP-LA and PGRP-SCs being essential. Apamin expression alone is sufficient to restore the integrity of the gut barrier compromised by stressed conditions. Ultimately, apamin supplementation enhances honeybee gut health, particularly in the presence of ingested bacteria. The expression of other honeybee antimicrobial peptides also significantly reduces bacterial infection in flies. Overall, our study provides a comprehensive understanding of the molecular function and regulation of honeybee venom peptides and antimicrobial peptides, utilizing the Drosophila model system to unravel their mechanisms of action and therapeutic potential.

immunology↗

bioRxiv2024

Characterization of Multicellular Niches Supporting Hematopoietic Stem Cells Within Distinct Zones

Previous studies of hematopoietic stem cells (HSCs) primarily focused on single cell-based niche models, yielding fruitful but conflicting findings1-5. Here we report our investigation on the fetal liver (FL) as the primary fetal hematopoietic site using spatial transcriptomics. Our study reveals two distinct niches: the portal-vessel (PV) niche and the sinusoidal niche. The PV niche, composing N-cadherin (N-cad)HiPdgfr+ mesenchymal stromal cells (MSCs), endothelial cells (ECs), and N-cadLoAlbumin+ hepatoblasts, maintains quiescent and multipotential FL-HSCs. Conversely, the sinusoidal niche, comprising ECs, hepatoblasts and hepatocytes, as well as potential macrophages and megakaryocytes, supports proliferative FL-HSCs biased towards myeloid lineages. Unlike prior reports on the role of Cxcl12, with its depletion from vessel-associated stromal cells leading to 80% of HSCs reduction in the adult bone marrow (BM)6,7, depletion of Cxcl12 via Cdh2CreERT (encoding N-cad) induces altered localization of HSCs from the PV to the sinusoidal niches, resulting in an increase of HSC number but with myeloid-bias. Similarly, we discovered that adult BM encompasses two niches within different zones, each composed of multi-cellular components: trabecular bone area (TBA, or metaphysis) supporting deep-quiescent HSCs, and central marrow (CM, or diaphysis) fostering heterogenous proliferative HSCs. This study transforms our understanding of niches by shifting from single cell-based to multicellular components within distinct zones, illuminating the intricate regulation of HSCs tailored to their different cycling states.

developmental biology↗