Biology subjects

Hu, B.

Publications and source records attributed to Hu, B..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

A secreted citrus protease cleaves an outer membrane protein of the Huanglongbing pathogen

Plants secrete a variety of proteases as a defense response during infection by microbial pathogens. However, the relationship between their catalytic activities and antimicrobial functions remains largely unknown. Particularly, few biologically relevant substrates of these proteases have been identified. Huanglongbing (HLB) has been a major threat to the citrus industry worldwide. The HLB-associated bacterium, Candidatus Liberibacter asiaticus (Las), was previously shown to deploy an inhibitor of papain-like cysteine proteases (PLCPs) to promote disease in citrus. In this study, we identified an outer membrane protein (OMP) of Las, LasOMP1, as a substrate of the citrus PLCP CsRD21a. LasOMP1 is one of the most highly expressed genes in Las. CsRD21a cleaves LasOMP1 and produces cleaved peptide products, which could be detected in vitro and in HLB-diseased citrus plants. We found that CsRD21a targets the N-terminal portion of LasOMP1, potentially at an extracellular loop region. Importantly, transgenic sweet orange overexpressing CsRD21a showed reduced Las titers and delayed disease symptoms, highlighting that engineering this protease is a promising strategy to enhance HLB resistance in citrus. Together, our work reveals a pathogen-derived substrate of plant PLCPs and highlights bacterial OMPs as direct targets of plant defense. Significance StatementHuanglongbing (HLB) is the most devastating disease of citrus with no resistance having been identified in commercial cultivars. Previous work implicated papain-like cysteine proteases (PLCPs) as an important hub of defense in citrus; however, their precise role in HLB tolerance remained unclear. Here, we identify and characterize an outer membrane protein (OMP) from the HLB-associated bacterium as a substrate of the citrus PLCP RD21a. We demonstrate a specific cleavage of the bacterial OMP by citrus RD21a, which may impair pathogen growth and/or activate plant immunity. Importantly, overexpression of RD21a enhances HLB tolerance in sweet oranges. This work identifies OMPs as substrates of plant PLCPs and provides insights into protease defense functions.

plant biology↗

bioRxiv2025

Targeting HIF-2α in Colorectal Cancer Reveals a Cholesterol Biosynthesis-Dependent Ferroptotic Vulnerability

Colorectal carcinoma (CRC) remains a major cause of cancer-related mortality, with rising incidence in individuals under 55, highlighting the need for novel therapeutic strategies. Hypoxia-inducible factor 2 alpha (HIF-2) has been genetically validated as a critical driver of colorectal tumorigenesis, with intestinal epithelium-specific deletion in mice markedly reducing tumor formation. PT2385, a selective small-molecule HIF-2 inhibitor applied in renal cell carcinoma treatment, has not been evaluated in CRC. Here, we demonstrate that HIF-2 inhibition with PT2385 alone fails to suppress CRC growth in vitro under normoxic or hypoxic conditions and in xenograft models in vivo. To identify vulnerabilities induced by HIF-2 blockade, we performed an unbiased CRISPR metabolic screen. This revealed cholesterol biosynthesis as a critical dependency. Targeting this pathway with clinically approved statins (atorvastatin, pitavastatin, simvastatin) synergized with PT2385 to suppress CRC cell growth, reduce colony formation, and enhance cell death. Mechanistic studies show that combined HIF-2 and HMG-CoA reductase inhibition with statins promotes ferroptosis, characterized by increased lipid peroxidation and depletion of antioxidant metabolites. These effects are fully reversed by the ferroptosis inhibitor liproxstatin-1. Genetic knockdown of HIF-2 or HMG-CoA reductase recapitulated enhanced sensitivity to combination therapy. In vivo, co-administration of PT2385 and atorvastatin significantly reduced tumor growth and increased ferroptotic cell death in xenografts, confirming the mechanistic link. Collectively, these findings uncover a metabolic vulnerability of CRC to dual HIF-2 and cholesterol biosynthesis inhibition, supporting a clinically actionable strategy that leverages safe, FDA-approved statins to potentiate HIF-2-targeted therapy. SignificanceCombined HIF-2 inhibition and cholesterol biosynthesis inhibition using statins reveals a metabolic vulnerability in colorectal cancer that enhances ferroptosis, thus offering a clinically actionable strategy for therapeutic intervention.

cancer biology↗

bioRxiv2025

N6-Methyladenine DNA modification regulates pathogen virulence in nematodes

Understanding the global regulatory mechanisms that control pathogen virulence gene expression is essential for elucidating the molecular basis of pathogenicity. N6-methyladenine (6mA) plays a crucial role in regulating gene expression in response to various environmental stresses; however, its role in pathogen virulence remains largely unexplored. Here, we report the widespread occurrence of 6mA across 17 nematode isolates and map its genomic landscape in six notorious agriculturally important pathogen root-knot nematodes (RKNs). We demonstrated that 6mA is characterized by a conserved GAG motif across nematodes, but exhibits species-specific distribution patterns and distinct effects on gene expression. In particular, its enrichment in transposable elements differs between polyploid and diploid nematodes, suggesting lineage-specific epigenetic regulation potentially associated with polyploidy. We further identified two functional 6mA demethylases, MiNMAD-1 and MiNMAD-2, and confirmed their catalytic activity and active sites. Host-induced gene silencing of minmad-1 significantly increased plant resistance to three polyploid RKN species. A detailed functional analysis revealed that minmad-1 knockdown disrupted virulence gene expression during the parasitic stage, thereby reducing nematode infectivity. Together, our findings suggest 6mA demethylase as a key epigenetic regulator of RKNs virulence, providing new insights into nematode biology and offering promising targets for the development of sustainable control strategies. Significance Statement6mA methyltransferase regulates the expression of virulence genes in certain pathogenic bacteria and plays a critical role in their infectivity. However, the regulation of virulence gene expression in eukaryotic pathogens, particularly plant pathogens, remains poorly understood. Most studies on pathogen virulence have focused on individual effectors, with little insight into global regulatory mechanisms. Here, we demonstrate that 6mA broadly shapes virulence gene expression patterns in polyploid RKNs. Moreover, transgenic tobacco, tomato, and rice plants expressing dsRNA against nematode demethylases showed significantly enhanced resistance to RKNs. These findings establish 6mA demethylase as a promising epigenetic target for controlling plant-parasitic nematodes.

molecular biology↗

bioRxiv2025

A cytological framework of female meiosis in Arabidopsis

Female and male meiosis often differ in many aspects, such as their duration and the frequency as well as the positioning of crossovers. However, studying female meiosis is often very challenging and thus, much less is known about female versus male meiosis in many species including plants. To approach this gap, we have developed a live-cell imaging system for female meiocytes in Arabidopsis. This allowed us to obtain a temporally resolved cytological framework of female meiosis in the wildtype that serves as a guiding system for future studies. Here, we have applied this imaging system to study mutants in cyclin- dependent kinase inhibitors, in which a designated female meiocyte undergoes several mitotic divisions before entering meiosis. This enabled us to address when a meiocyte is committed to meiosis, a key question during reproductive development and in particular for the analysis of apomictic species in which meiosis is skipped. HighlightsEstablishment of a live-cell imaging system captures dynamic features of female meiosis. Identification of cytological landmarks ensures robust assignment of meiotic stages. Time-lapse imaging enables quantitative dissection of meiotic phases. Application of the framework reveals great plasticity in the commitment to meiosis.

cell biology↗

bioRxiv2025

Exploring Cerebellar Hippocampal Dynamics in Temporal Lobe Epilepsy: A Multivariable Synthetic Modeling Study of Purkinje Cell Degeneration and Stimulation Timing

ObjectiveTo investigate whether Purkinje cell degeneration precedes or follows seizure onset in temporal lobe epilepsy (TLE), delineate shared cerebello-hippocampal pathways, and assess the influence of stimulation timing on modeled seizure outcomes. MethodsWe developed a comprehensive 50-variable evidence model integrating structural, molecular, and circuit-level variables sourced from existing literature. Utilizing this framework, we created a PASS-validated (see Appendix for details)synthetic cohort comprising 10,000 virtual subjects. Analytical approaches included causal inference via inverse probability of treatment weighting (IPTW), mediation analysis, factorial ANOVA, and equivalence testing using the Two One-Sided Test (TOST). The models predictive fit was intentionally modest (RMSE = 0.499; R2 = -0.010), aligning with its primary role in causal exploration rather than precise outcome forecasting. Statistical evaluations were stratified by timing and circuit integrity factors. ResultsCausal reanalysis indicated that Purkinje cell density exerted a weak, nonsignificant direct effect on seizure burden (average treatment effect [ATE] = +0.0045, 95% CI: -0.0053 to +0.0143) (see Table 1, row 1). Mediation analysis revealed negligible indirect effects through GABAergic modulation pathways. In contrast, stimulation timing proved a pivotal factor: early intervention ([≤]4 days post-onset) resulted in significantly enhanced seizure reduction (p = 0.045, mean {Delta} = -0.020), accompanied by a notable timing x integrity interaction (Table 1, row 3). Factorial ANOVA substantiated this interaction (F = 3.30, p = 0.019, partial 2 = 0.001), with Tukeys honest significant difference (HSD) post-hoc tests identifying timing as the primary differentiator. Equivalence testing via TOST, using a predefined margin of {+/-}0.015 seizures/hour, did not fully establish equivalence for Purkinje effects (p1 = 0.0019, p2 = 0.136), though the confidence interval suggested minimal clinical relevance. Sensitivity analyses, including outlier assessments and biological noise simulations, affirmed the models robustness. O_TBL View this table: org.highwire.dtl.DTLVardef@1df407eorg.highwire.dtl.DTLVardef@3436borg.highwire.dtl.DTLVardef@3f51eaorg.highwire.dtl.DTLVardef@11b1338org.highwire.dtl.DTLVardef@8ae914_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONSummary of Causal Effects Across Model Conditions Average treatment effects (ATEs), confidence intervals, and p-values are shown for key model paths. TOST testing assessed equivalence of Purkinje cell impact using {+/-}0.015 margin. Interaction and robustness outcomes are reported descriptively. C_TABLECAPTION C_TBL Reproducibility and Perturbation TestingFor reproducibility evaluation, the synthetic pipeline was re-run under modified scenarios: (1) DAG perturbation by removing the Thalamus [->] GABAergic Tone edge to examine relay dependency, and (2) parameter shifts by adjusting GABA coefficient priors by {+/-}10% to emulate biological variability. Each perturbation generated a fresh synthetic cohort (n = 10,000), with recomputation of ATEs, mediation estimates, and ANOVA terms. Comparisons to the baseline run confirmed stability in effect directions and significance thresholds. InterpretationThis multivariable modeling approach implies that cerebellar stimulation may mitigate modeled seizure burden predominantly via timely application rather than reliance on baseline Purkinje cell integrity. Recent empirical studies reinforce cerebellar structural alterations in TLE and the potential of non-invasive stimulation techniques, such as repetitive transcranial magnetic stimulation (rTMS), to induce vermis volume changes correlated with seizure reduction (So et al., 2024). Additionally, ongoing clinical trials exploring transcranial alternating current stimulation targeting the cerebellum in refractory TLE align with our timing-sensitive findings. All results stem from biologically informed synthetic cohorts and are positioned to inform empirical validation in translational contexts. ConclusionModel-derived insights highlight the optimization of cerebellar stimulation timing as a promising, testable avenue for modulating hippocampal excitability in TLE, irrespective of underlying Purkinje cell status. These findings underscore the value of synthetic frameworks in hypothesizing dynamic intervention strategies.

neuroscience↗

bioRxiv2025

TPClust: Temporal Profile-Guided Subtyping Using High-Dimensional Omics Data

Clustering is widely used to identify subtypes in heterogeneous populations, yet most approaches rarely integrate longitudinal phenotypic trajectories with high-dimensional molecular profiles, limiting their ability to resolve biologically and clinically meaningful heterogeneity in progressive diseases. We developed TPClust, a supervised, semi-parametric clustering method that integrates high-dimensional omics data with longitudinal phenotypes including outcomes and covariates for outcome-guided subtyping. TPClust jointly models latent subtype membership and longitudinal outcome trajectories using multinomial logistic regression informed by molecular features selected via structured regularization, along with spline-based regression to capture subtype-specific, time-varying covariate effects. Simulations demonstrate valid inference for time-varying effects and robust feature selection. Applied to transcriptomic profiles and longitudinal cognitive data from 1,020 older adults in the Religious Orders Study and the Rush Memory and Aging Project, TPClust identified four aging subtypes including intermediate subtypes not captured by unimodal approaches with distinct cognitive trajectories, time-varying risk profiles, clinical and neuropathological features, and multimodal molecular signatures.

bioinformatics↗

bioRxiv2025

Procrastination partly reflects an evolutionary byproduct of non-planning impulsivity

Procrastination has immediately visible repercussions on health and survival resilience, yet shows stably heritable and remains increasingly pervasive across human societies. Despite a paradox, this behavior is theoretically explained to represent a byproduct of evolutionary advantages underlying impulsivity, yet not deciphered well by scientific evidences. After adjusting psychometric endogeneity, we demonstrate the unique predictive roles of non-planning impulsivity (NPI) during late adolescence and early adulthood uniquely predicts procrastination in later adulthood in a twin cohort (N = 154). This association was further replicated in two independent cohorts (N = 327, N = 1,543). Using AE models, in conjunction of single-paper meta-analytic synthesis (N = 3,656 twin pairs), we observed significant shared genetic contributions underlying this NPI-procrastination association (rg = 0.51, 95% CI: 0.18 - 0.84). Beyond to the phenotypic heritability, employing a Genome-Wide-Association Study (GWAS), six NPI-procrastination overlapping SNPs are identified, functionally accounting for neural dysregulation. Thus, leveraging neurodevelopmental normative modelling (N = 37,407), online meta-analytic estimations (k = 198, loci = 5,855) and seed-based d mapping estimates (N = 893), cortical deviations in the left dorsolateral prefrontal cortex (DLPFC) - the brain region showing highest probabilistic overlap mapping NPI to procrastination, partly explains their shared genetic variants, but are substantially independent in genetic contribution. Mendelian Randomization analysis finally indicates causal roles of NPI and procrastination both, to DLPFC deviations. Our findings empirically clarified this theory that procrastination partly derives from NPI as an evolutionary byproduct indeed, but is still unique in neurogenetic entities. Brief summaryProcrastination is a puzzling human behavior that compromises survival-relevant outcomes yet remains both widespread and heritable. Although theorized as a byproduct of impulsivitys evolutionary advantages, empirical support for this account has been limited. Here, we provide converging evidence across psychometric, genetic, and neuroimaging modalities to show that non-planning impulsivity during late adolescence and early adulthood uniquely predicts later procrastination, and that the two traits share significant genetic overlap. We further identify specific genetic variants and morphological deviations in the DLPFC that link, but also partially dissociate, their biological pathways. These findings clarify the evolutionary and neurogenetic architecture of procrastination and underscore its partial derivation from impulsivity alongside distinct developmental origins.

neuroscience↗

bioRxiv2025

NERVE GROWTH FACTOR IS SUFFICIENT TO CAUSE MULTIPLE OSTEOARTHRITIS-RELEVANT PATHOLOGICAL FEATURES IN NAIVE MURINE KNEE JOINTS

BACKGROUNDNerve growth factor (NGF), a key mediator of pain and inflammation, is increased in joints with osteoarthritis (OA). Neutralizing NGF with monoclonal antibodies has shown analgesic effects in painful knee OA, but clinical development was stopped due to side effects in the joints. Knowledge about the biological effects of long-term exposure of joint tissues to NGF is limited. Therefore, we aimed to explore the effects of repeated intra-articular (IA) injections of NGF into the knee joints of healthy mice on pain and sensitization, as well as joint innervation and structure. METHODSWe conducted five experiments in male C57BL/6 mice. In Experiment 1, NGF (50ng or 500ng) or vehicle was injected IA into the knee of naive wildtype (WT) mice, twice a week for 4 weeks. We assessed knee swelling, knee hyperalgesia and histopathology. In Experiment 2, mice were injected with 500ng NGF or vehicle, twice a week for 4 weeks and microCT of the knee was performed. In Experiment 3, NaV1.8-tdTomato reporter mice were injected with 500ng NGF or vehicle, twice a week for 4 weeks, and joint innervation was assessed. In Experiment 4, WT mice received 500ng NGF or vehicle twice a week for 4 weeks and were used for single cell RNA sequencing (scRNAseq) of the synovium. In Experiment 5, L3-L5 DRGs of mice that received 3 IA injections of 500ng NGF or vehicle twice a week were used for bulk RNA sequencing. RESULTSRepeated bi-weekly IA injections of NGF caused knee hyperalgesia in naive mice. NGF caused dose-dependent knee swelling, synovial pathology, increased bone mineral density and trabecular bone thickness in the medial subchondral bone, growth of pre-osteophytes in the medial compartment, but no cartilage degeneration. NGF injection caused sprouting of NaV1.8+ neurons in the medial but not the lateral synovium. ScRNAseq of the synovium revealed upregulated genes related to neuronal sprouting, synovial fibrosis and ossification, confirming histopathological findings. Bulk RNA seq of DRG showed upregulated pathways related to axonal growth. CONCLUSIONSIn healthy mouse knees, NGF induced mechanical sensitization, synovitis, neoinnervation in the medial synovium, subchondral bone changes and pre-osteophyte growth in the medial compartment, thus capturing many pathological changes observed in OA, except cartilage damage.

neuroscience↗

bioRxiv2025

Secondary structure transitions and dual PIP2 binding define cardiac KCNQ1-KCNE1 channel gating

The KCNQ1+KCNE1 potassium channel complex forms the slow delayed rectifier current (IKs) critical for cardiac repolarization. Loss-of-function variants in KCNQ1 and KCNE1 cause long QT syndrome types 1 and 5 (LQT1/LQT5), accounting for over one-third of clinical LQTS cases. Despite prior structural work on KCNQ1 and KCNQ1+KCNE3, the structural basis of KCNQ1+KCNE1 remains unresolved. Using cryo-EM and electrophysiology, we determined high-resolution (2.5-3.4 [A]) structures of human KCNQ1+KCNE1 in both closed and open states. KCNE1 occupies a pivotal position at the interface of three KCNQ1 subunits, inducing seven "helix-to-loop" transitions in KCNQ1 transmembrane segments. These structural rearrangements: 1) stabilize the closed pore and the conformation of the intermediate voltage-sensing domain, thereby determining channel gating, ion permeation, and single channel conductance; 2) enable a dual-PIP2 modulation mechanism, where one PIP2 occupies the canonical site, while the second PIP2 bridges the S4-S5 linker, KCNE1, and the adjacent S6, stabilizing channel opening; 3) create a fenestration capable of binding compounds specific for KCNQ1+KCNE1 (e.g., AC-1). Together, these findings reveal a previously unrecognized large-scale secondary structural transition during ion channel gating that fine-tunes IKs function and provides a foundation for targeted LQTS therapy development.

biophysics↗

bioRxiv2025

Developmental dynamic transcriptomics reveals multiple effectors and transcription factors critical for Ditylenchus destructor parasitism

Plant-parasitic nematodes (PPNs) pose a major threat to global agricultural production, yet fundamental research on their biology remains limited. The origin and evolutionary trajectory of PPNs remain elusive, largely due to the scarcity of chromosome-level genomic data. Among them, migratory PPNs are considered a key transitional form between free-living and obligate parasitic lifestyles, as they exhibit both plant parasitism and fungal feeding behaviors. In this study, we assembled a chromosome-level genome of the sweet potato rot nematode Ditylenchus destructor and confirmed the presence of four chromosomes through Hi-C scaffolding and karyotype analysis. Comparative genomic analysis with two other migratory PPNs, Bursaphelenchus xylophilus and Aphelenchoides besseyi, revealed that the Nigon elements in B. xylophilus are largely conserved with those of the model organism Caenorhabditis elegans, while D. destructor and A. besseyi exhibit extensive Nigon element rearrangements. These rearrangements were strongly correlated with patterns of protein sequence collinearity. Moreover, transcriptomic profiling across five developmental stages of D. destructor identified numerous stage-specific effectors and transcription factors. Functional analysis via RNA interference demonstrated that many of these genes play essential roles in embryogenesis and parasitic activity. Together, our results provide valuable genomic and transcriptomic resources for studying PPNs, uncovering critical insights into their genome evolution and parasitism-related gene functions, and laying a crucial foundation for advancing the understanding of PPN biology and their impact on agricultural systems.

genomics↗

bioRxiv2025

CD14 plays a critical role in pain and inflammation across multiple models of post-traumatic osteoarthritis

Inflammation is a primary driver of osteoarthritis (OA), and no therapies exist to halt or delay disease progression or substantially ameliorate the chronic pain, inflammation and disability that are characteristic of disease. Soluble CD14 (sCD14), a co-factor that enhances inflammatory toll-like receptor signaling, is present in synovial fluid in patients with OA and positively associates with joint space narrowing, synovial macrophage content, and pain. In this study, we show that increased sCD14 within human synovial fluid correlates with joint effusion volume and increased knee hyperalgesia. Next, we evaluated CD14 as a potential therapeutic target in three pre-clinical models of post traumatic OA (PTOA), using both genetic deficiency and pharmacologic blockade to modulate its activity. We demonstrate that deficiency or blockade of CD14 results in significant protection from increased evoked pain behaviors and from OA driven mobility impairments (i.e. decreased cage activity) across models that differ in severity, and across male and female cohorts. Using flow cytometry, single cell transcriptomics, and spatial proteomics, we further show that CD14-deficiency drastically influences the local synovial inflammatory landscape post-injury, reducing monocyte and macrophage populations and modulating local fibroblast populations. Targeting CD14 via genetic deficiency or therapeutic blockade revealed no substantial protection, but no worsening, of cartilage degeneration. Ultimately, our results provide strong support that targeting synovial inflammation through blockade of CD14 can safely ameliorate OA pain and disability after a pre-disposing injury. One Sentence SummaryThe study demonstrates the key role of CD14 in pain, mobility loss, and inflammation in PTOA, and demonstrates the therapeutic potential of CD14 blockade for OA pain relief.

immunology↗

bioRxiv2025

Old mice have a functionally distinct contractile reserve from obese mice

BackgroundCardiovascular disease (CVD) is the leading cause of global mortality, with recent increases attributed to demographic shifts in age and rising rates of obesity. Diminished contractile reserve is a hallmark of a diseased heart; assessing contractile reserve is pivotal in prognosticating and monitoring CVD progression. The Frank-Starling mechanism and sympathetic stimulation are key to enhance contractile reserve but have not been explored in vivo in old and obese mouse models of CVD. This project aims to use speckle tracking echocardiography (STE) to characterize the function of the heart at baseline, with increased preload, and with sympathetic stimulation. We hypothesize that along with blunted systolic function, diastolic function, and contractility, old and obese mice will have a blunted contractile reserve. MethodsSTE was obtained for control (4- month-old), aged (24-month-old), and obese mice (high fat diet-induced). Mice received an intravenous injection of 150L saline to increase preload to assess the Frank-Starling response, followed by injection of {beta}1adrenergic receptor agonist dobutamine to assess sympathetic response. ResultsAt baseline, aging and obese mice demonstrated blunted systolic, diastolic function, and contractility. Endocardial and epicardial wall displacement differed between aging and obese mice with contractile reserve, indicating that they have functionally distinct cardiac phenotypes. ConclusionsThis study is the first to demonstrate blunted systolic function, diastolic function, and contractility through STE in aging and obese mice. Our novel method for investigating the contractile reserve of mice demonstrated aging and obese mice have dissimilar responses when assessing contractile reserve, which could contribute to their distinct functional phenotypes.

physiology↗

bioRxiv2025

Prevalence, Production and the Role of Staphylococcus aureus Superantigens in Cystic Fibrosis Lung Disease.

Staphylococcus aureus (SA), the most common cystic fibrosis (CF) lung pathogen, is uniquely capable of producing superantigen (SAg) exotoxins, which are the most potent activators of the immune system. Although the proinflammatory roles of SA-SAgs is well-established, their role in the immunopathogenesis of CF lung disease is unexplored. Herein, we demonstrate that 60-80% of pediatric and adult CF SA isolates carried at least one SA-SAg gene, with the former harboring potent SA-SAgs (Staphylococcal enterotoxin A and B) more frequently (30-60%). Biofilms of clinical SA isolates readily produced biologically active SA-SAgs in artificial sputum medium and purified SA-SAgs retained their bioactivity in human CF sputum in vitro. Repeated intratracheal challenge with purified SA-SAgs induced a robust pulmonary inflammatory response in CF mouse models ({beta}ENAC and CFGC transgenic mice) expressing HLA-DR3 in a dose-dependent manner, with the low dose favoring a type 2 eosinophilic lung inflammatory response, and a high dose eliciting a type 1 inflammatory response with neutrophilic lung inflammation and higher mortality. In vivo neutralization of IFN-{gamma} also promoted SA-SAg-driven type 2 inflammation. Intratracheal infection with sub-lethal dose of a clinical SA isolate producing SEB, but not the SEB-deficient mutant isogenic SA strain, also elicited an eosinophilic inflammatory response.

immunology↗

bioRxiv2025

Network-Based Kidney Allocation Simulation: Evaluating Organ Matching Strategies in Variable Hospital Networks

Kidney allocation is a complex and high-stakes process shaped by various factors. Although existing simulations have improved our understanding of transplant policies, they often stem from the perspectives of medical urgency and biological compatibility. Hence, they often fail to account for the geographic and structural variability of hospital networks that heavily influence organ distribution. In this paper, we present a modular network-based kidney allocation simulation designed to function as a standardized benchmark to evaluate organ matching strategies in more realistic hospital networks. Our simulation models hospitals as nodes in a dynamic network that incorporates detailed donor-recipient compatibility criteria and provides an intuitive interface for testing custom matching policies. Then, through two case studies, we demonstrate how varying network structures and matching strategies affect patient outcomes, quantified through transplant success rates and the percentage of positive patient outcomes. Through these case studies, we derive results that closely resemble real-world observations and identify clear biological explanations for the observed trends, aligning with established empirical knowledge. Our results highlight the importance of geography-/network-aware benchmarks and allocation strategies and provide a standardized platform for future research on optimizing kidney distribution in healthcare networks.

synthetic biology↗

bioRxiv2025

Andrographolide prevents necroptosis by suppressing generation of reactive oxygen species

Andrographolide (Andro), a natural product extracted from the Chinese traditional medicine herb Andrographis paniculata, has been applied for the treatment of diverse inflammatory diseases. However, its effects on necroptosis, a lytic form of cell death implicated in various inflammatory diseases, remain uncharacterized. In the current research, we investigate whether Andro and its derivatives can suppress necroptosis. The results demonstrate that Andro notably inhibits the necroptosis in in vitro cellular models induced by either lipopolysaccharide (LPS) plus IDN-6556 or a combination of TNF-, LCL-161 (Smac mimetic) and IDN-6556. In these cellular models, Andro exhibits inhibitory effects on the phosphorylation of receptor-interacting protein kinase 1 (RIPK1), RIPK3, and mixed lineage kinase domain-like protein (MLKL), as well as on the formation of necrosomes. Specifically, Andro reduces intracellular reactive oxygen species (ROS) and mitochondrial superoxide (mtROS), preserves mitochondrial membrane potential during necroptotic induction, and activates the antioxidant transcription factor nuclear factor E2-related factor 2 (Nrf2). Upon the necroptotic stimulation, some mitochondrial proteins such as Bcl-2 and Bak oligomerize and colocalize with RIPK1, RIPK3, and phosphorylated MLKL (p-MLKL) in necrosomes. However, such a process of necrosome formation can be prevented by Andro. In contrast, derivatives including dehydroandrographolide, neoandrographolide, 14-deoxy-11,12-didehydroandrographolide, and 14-deoxyandrographolide show no anti-necroptotic effects and fail to upregulate Nrf2. Collectively, our findings demonstrate that Andro specifically inhibits the RIPK1/RIPK3/MLKL signaling axis to suppress necroptosis, highlighting its therapeutic potential against necroptosis-related disorders.

pharmacology and toxicology↗

bioRxiv2025

A Single-Cell Atlas of RNA Alternative Splicing in the Glioma-Immune Ecosystem

Single-cell analysis has refined our understanding of cellular heterogeneity in glioma, yet RNA alternative splicing (AS)--a critical layer of transcriptome regulation--remains underexplored at single-cell resolution. Here, we present a pan-glioma single-cell AS analysis in both tumor and immune cells through integrating seven SMART-seq2 datasets of human gliomas. Our analysis reveals lineage-specific AS across glioma cellular states, with the most divergent AS landscapes between mesenchymal- and neuronal-like glioma cells, exemplified by AS in TCF12 and PTBP2. Comparison between core and peripheral glioma cells highlights AS-redox co-regulation of cytoskeleton organization. Further analysis of glioma-infiltrating immune cells reveals potential isoform-level regulation of protein glycosylation in regulatory T cells and a link between MS4A7 AS in macrophages and clinical response to anti-PD-1 therapy. This study emphasizes the role of AS in glioma cellular heterogeneity, highlighting the importance of an isoform-centric approach to better understand the complex biological processes driving tumorigenesis.

genomics↗

bioRxiv2025

High-Quality Cell Capture Reveals Transcriptomic Changes After Single-Axon Injury of Mauthner Cells

In vivo single-cell capture methods based on micropipettes are essential for correlating morphological characteristics with transcriptomic profiling under physiological conditions. However, they often suffer from significant contamination of off-target cells. Consequently, we developed Hip-seq, which significantly reduces heavily contaminated cells, decreases contamination levels, improves cell reproducibility, and enhances data analysis accuracy compared to patch-seq. Using Hip-seq, we found that axon regeneration failure could be due to abnormal activation of translation and the circadian clock. Axon-regenerable central neurons reactivated axon development-related genes during regeneration. And one-to-one associated analysis helped identify pro-regenerative genes.

neuroscience↗

bioRxiv2025

Regulation of alternative polyadenylation events by PABPC1 affects erythroid progenitor cell expansion

Erythropoiesis is precisely regulated by multilayer networks and is crucial for maintaining steady-state hemoglobin levels and ensuring effective oxygen transport. Alternative polyadenylation (APA) is a post-transcriptional regulatory mechanism that generates multiple mRNA isoforms from a single gene, based on specific 3-untranslated region sequences. While APA plays a vital role in various cellular processes, its mechanism in erythropoiesis remains unexplored. Here, we employed an integrative approach combining bioinformatics and experimental validation to systematically analyze APAs role in erythropoiesis. We mapped the APA landscape during erythroid differentiation, discovering notable APA shifts crucial for the maturation from burst-forming unit erythroid to colony-forming unit erythroid. Notably, our findings highlighted PABPC1 as the primary APA regulator of these stages. Functional investigations revealed that knocking down PABPC1 disrupts erythroid progenitor cell proliferation and differentiation, implicating the proteins essential role in modulating cell fate through APA regulation. We further identified that decreased PABPC1 levels led to the increased usage of the proximal polyA site of TSC22D1 and gene overexpression, revealing a novel mechanism through which APA affects erythroid progenitor expansion and differentiation. These insights uncover a novel dimension of APA regulation in early erythropoiesis, providing new strategies for the treatment of diseases associated with erythropoiesis disorders.

developmental biology↗