Biology subjects

Fu, H.

Publications and source records attributed to Fu, H..

At least 19 recordsLinked to original sources

bioRxiv2026

NIH's dedicated K23 trial pathway was associated with more K-trial leadership but no detectable gain in new trials

Research funders often train investigators by funding a project, expecting the experience to produce leaders of the next one. Delivering the funded project and leading new work are different outcomes. In 2018 the US National Institutes of Health (NIH) created a dedicated clinical trial pathway for its K23 mentored career development awards. Using registry records for 1,847 K23 awardees and a language-model measurement corrected against blinded human review, we compared awardees whose awarded plans proposed their own trial with those whose plans did not, before and after the change. The pathway was followed by more leadership of the award-supported trial (difference in differences, 13.7 percentage points; 95% confidence interval, 5.7 to 21.2) but no detectable gain in leadership of distinct new trials (-3.8; -14.4 to 6.9), including over seven years. The K-trial estimate exceeded the new-trial estimate by 17.4 points (5.3 to 29.7) under every measurement correction. The additional supported trials were registered with the awardee as principal investigator and started at rates similar to earlier ones, whereas whether more awardees led any trial depended on the correction. Because groups were defined by awarded plans, the design cannot fully separate changes in behaviour from changes in who was funded. A training pathway can raise delivery of the work it funds without a detectable increase in leadership of further trials. As NIH consolidates its career awards and ends K support for trial conduct, evaluations should measure both outcomes.

scientific communication and education↗

bioRxiv2026

Bacterial Peptidoglycan Extends Lifespan by Activating Lysosomal Activity through V-ATPase Binding

Lysosomal dysfunction is a hallmark of aging, yet whether microbial components actively regulate this organelle to influence longevity remains unknown. Here, we identify bacterial peptidoglycan (PGN), a major cell wall component degraded by host lysozyme, as an evolutionarily conserved activator of lysosomal function that extends lifespan in both C. elegans and mice. We show that aging leads to an intestinal decline in lysozyme expression, which impairs bacterial cell-wall digestion and results in systemic PGN deficiency. Late-life PGN supplementation (starting at 18 months of age) significantly prolongs mouse lifespan and improves healthspan. Mechanistically, PGN localizes to lysosomes and directly binds V-ATPase subunits, enhancing ATP hydrolysis activity and promoting lysosomal acidification. This effect is abolished by V-ATPase inhibition (bafilomycin A1) or genetic disruption of lysosomal components (cup-5 and vha-12 mutants), confirming that functional V-ATPase is strictly required for lysosomal function and the longevity benefit. Importantly, PGN restores lysosomal acidification in aged cells, alleviates cellular senescence markers, and improves multiple hallmarks of aging including locomotion and muscle integrity. Collectively, these findings reveal an evolutionarily conserved mechanism whereby hosts exploit bacterial cell wall components to maintain cellular homeostasis, establishing a gut microbiome-lysosome-longevity axis with implications for microbiome-based anti-aging interventions.

physiology↗

bioRxiv2026

TR-107, a novel mitochondrial ClpP agonist, induces robust antitumor activity against preclinical models of adrenocortical carcinoma

AbstractAdrenocortical carcinoma (ACC) is a rare and highly aggressive endocrine malignancy originating from the adrenal cortex with limited effective treatment options. The underlying pathophysiology of ACC is uniquely characterized by abnormal steroid production and increased metabolic activity, highlighting the critical role of mitochondria in adrenal steroid hormone biosynthesis and tumor metabolism. In this study, we investigated the therapeutic potential of TR-107, a novel and highly selective small-molecule agonist targeting the mitochondrial protease ClpP. Pharmacologic hyperactivation of ClpP disrupts mitochondrial proteostasis and bioenergetics and has shown promising antitumor activity in various preclinical models. Our results demonstrated that TR-107 induces potent dose-dependent cytotoxic effects at nanomolar concentrations in ACC cell lines NCI-H295R and mACC3 as well as short-term ACC patient-derived organoid (PDO) models, markedly reducing cell viability and confluency in vitro. Metabolic analyses revealed that TR-107 significantly impaired oxygen consumption, indicating a disruption of oxidative phosphorylation and substantial attenuation of basal cellular respiration. Mechanistic studies showed dose-dependent increases in reactive oxygen species (ROS) levels and upregulation of proteins involved in mediating the ferroptotic rheostat. Pharmacokinetic assessment uncovered that TR-107 was not a substrate of the ABCB1 (MDR1/P-glycoprotein) efflux transporter, suggesting potential to overcome common multidrug resistance mechanisms. Given the importance of IGF-2 signaling in ACC, we further explored the combinatorial effects of TR-107 with IGF-1 receptor (IGF-1R) inhibitors and discovered that co-treatment produced synergistic reductions in cell viability across NCI-H295R, mACC3, and ACC PDOs. Collectively, these findings support the potential of mitochondrial ClpP hyperactivation as a promising therapeutic strategy for ACC and demonstrate that TR-107 exhibits significant antitumor activity as a monotherapy or in combination with IGF-1R inhibitors. These findings provide a strong rationale for advancing ClpP agonists into clinical development for the management of ACC.

cancer biology↗

bioRxiv2026

An end-to-end framework for single-cell-resolution, whole-transcriptomic spatial profiling in post-mortem human brain

Single-cell resolution spatial transcriptomics enables transcriptome-wide molecular profiling within intact tissue architecture, providing unprecedented opportunities to investigate cellular organization and disease-associated molecular states in the human brain. However, applying these technologies to post-mortem human brain tissue remains challenging due to RNA degradation, heterogeneity in tissue preservation, and a lack of standardized analytical workflows. These challenges are particularly pronounced for whole-transcriptome platforms, where successful implementation requires optimization of both experimental and computational procedures. Here, we present an end-to-end framework for single-cell-resolution, whole-transcriptome spatial transcriptomics of fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) post-mortem human brain tissue. The framework combines an optimized experimental workflow with a preservation-agnostic bioinformatics pipeline for data processing, integration, and annotation. Experimentally, we show that a condensed two-day Visium HD workflow provides improved library quality, lowered qPCR cycle thresholds, and more consistent fragment size distributions. Sequencing saturation analyses further identified cost-effective sequencing depths that maximize transcript recovery while minimizing redundant sequencing. Computationally, we established a scalable workflow incorporating DAPI-based nuclear segmentation, transcript assignment, quality control, reference-guided integration, clustering, and cell-type annotation. We implemented a reference-based highly variable gene selection strategy to enable robust cross-sample harmonization independent of tissue preservation method. Application of this framework to seven Alzheimers disease frontal cortex specimens (five FF and two FFPE) generated a unified single-cell spatial transcriptomic atlas comprising more than 530,000 spatially resolved cells. The integrated dataset resolved major neuronal, glial, and vascular cell populations, recapitulated expected cortical architecture, and enabled direct comparison of FF- and FFPE-derived spatial transcriptomic profiles. Together, this work provides a practical experimental and computational framework for single-cell resolution, whole-transcriptome spatial transcriptomics in post-mortem human brain tissue and delivers a publicly available resource that expands the utility of archived and frozen specimens for studies of neurodegeneration and other neurological disorders. ImportanceSpatial transcriptomics of human post-mortem brain tissue is limited by RNA degradation, preservation variability, and lack of standardized workflows. Here, we present an end-to-end framework combining an optimized two-day Visium HD protocol with a preservation-agnostic bioinformatics pipeline. This approach improves library quality, defines efficient sequencing strategies, and enables robust spatial profiling across both FF and FFPE samples. Applied to Alzheimers disease brain tissue, it generates high-resolution single-cell spatial data and expands the utility of archived and frozen specimens for studying neurodegenerative diseases.

neuroscience↗

bioRxiv2026

Group size and activity influence shoal choice in Goldfish: Replication of zebrafish findings using a drift-diffusion model

Animals often rely on social information when making movement decisions. In zebrafish, classic work showed that shoal size and shoal activity both bias shoal choice. Here we extend these effects in Goldfish (Carassius auratus) and extend them with a drift-diffusion model (DDM) account of individual evidence accumulation under dynamic social cues. Using a three-chamber linear arena, we quantified a focal fishs position for 10 minutes while manipulating (i) numerical differences between flanking shoals and (ii) their activity (swimming speed) via temperature manipulation. ANOVA on time-proportion choices confirmed robust attraction to larger shoals; when shoal sizes were equal, the more active shoal was preferred. In combined manipulations, activity effects dominated at small numbers but saturated as group size increased, indicating a threshold-like integration where activity dominates at small shoal sizes (<3 fish) but saturates at larger sizes. We formalize these processes with a bounded DDM in which a sigmoidal stimulus function maps shoal size and average speed to momentary evidence, subject to random perturbations. The model reproduces the observed psychometric relations between relative numerosity, velocity differences, and choice. Our results (i) generalize zebrafish findings to a carp species with distinct ecology and physiology, and (ii) provide a compact mechanistic link between social cues and individual decision trajectories in dynamic social contexts.

animal behavior and cognition↗

bioRxiv2026

Distinct functions of PBRM1 and BAP1 reconcile the course of kidney cancer evolution and disease progression

Clear cell renal cell carcinoma (ccRCC) progresses along two predominant evolutionary trajectories, defined by PBRM1 ([~]40%) or BAP1 ([~]15%) mutations on a VHL-inactivated background. They have distinct patterns of evolutionary tempo and mode, and vastly different clinical outcomes, yet the underlying genotype-specific molecular phenotypic programmes are unknown. We established a patient-derived preclinical model biobank that captures the genetic diversity of ccRCC. Through integrative analyses of preclinical models and tumour bulk and single cell profiling, we identified transcriptional and epigenetic changes specific to PBRM1- and BAP1-driven ccRCC. Modelling PBRM1 loss in vitro demonstrates that it reinforces renal lineage identity and maintains progenitor-like cell state. In contrast, BAP1 loss drives inflammatory signalling and chromosomal instability. These insights reconcile the distinct evolutionary modes (branched versus punctuated), tempo (slow versus fast) and clinical outcomes associated with PBRM1 and BAP1 mutations, respectively, establishing a framework for patient stratification and genotype-directed therapeutic development.

cancer biology↗

bioRxiv2026

Generation and long-term expansion of human pancreatic islet organoids in vitro

The scarcity of expandable, functional human islet cells remains a major barrier to diabetes therapy. Here, we identify PROCR+ cells within adult human islets and establish a defined culture system to generate pancreatic islet organoids. These organoids self-organize into -, {beta}-, {delta}-, and PP cells at near-native ratios, exhibit regulated insulin and glucagon secretion, and support exponential in vitro expansion. Single-cell transcriptomics reveals a unique progenitor-like cell population that is transcriptionally primed for endocrine differentiation but shares molecular features with fetal trunk cells and endocrine progenitors. When transplanted, the organoids rapidly ameliorate hyperglycemia in diabetic mice. Importantly, in a non-human primate model, intraportal transplantation of these organoids reduced exogenous insulin requirements, restored glucose-stimulated C-peptide secretion, and achieved sustained glycemic control-representing a critical step toward clinical translation. This study provides a strategy for expanding human islet organoids, offering a scalable platform for diabetes treatment, disease modeling, and regenerative medicine.

cell biology↗

bioRxiv2026

An autonomous system for multi-objective continuous evolution at scale

Natural evolution is high-dimensional; organisms adapt to many pressures at once, across substrates, environments, and genetic backgrounds. Yet most directed evolution methods flatten this landscape to a single selection axis, hiding tradeoffs, and limiting what can be learned. Phage-assisted continuous evolution (PACE) is uniquely suited for multivariate selection because horizontal gene transfer couples genotype to propagation and allows the same phage lineage to traverse different selection environments. In practice, implementing this at scale has been prohibitive because each selection demands its own host culture, and every culture must be held for days to weeks within a narrow, infectable density window using continuously responsive bioreactors. In this work, TurboPRANCE is presented as an open-source, queueable robotic platform that integrates [~]200 independently controlled turbidostats with 96 parallel PACE lagoons under closed-loop control. Each turbidostat operates as a fully separate unit that can be equilibrated and initiated on its own schedule, enabling asynchronous starts and sustained operation without intervention. Automated media formulation, programmable dosing, on-deck sterilization, and adaptive scheduling coordinate growth control with the changing needs of the robotic workflow, dynamically adjusting dilution and transfer timing around formulation, sampling, and handling steps to keep each culture at consistent infectable densities despite unpredictable method demands. Cultures can be multiplexed and titrated into lagoons at defined ratios, swapped in and out on a schedule, or kept fully separate across experiments, creating a combinatorial space of selection pressures and programs that is effectively unbounded. Additionally, to enable high-throughput evolutionary tracking that scales with TurboPRANCE, Nanopore long-read sequencing was combined with DeepVariant, a deep learning-based variant caller, enabling population-level tracking of evolving variants. The result is a system that generates high-resolution time-resolvable evolutionary trajectories and large parallel datasets spanning diverse selection regimes, yielding dense, multivariate training data to map and engineer complex fitness landscapes at scale. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/709196v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@b0f8daorg.highwire.dtl.DTLVardef@a1d57eorg.highwire.dtl.DTLVardef@c771aeorg.highwire.dtl.DTLVardef@1f8729a_HPS_FORMAT_FIGEXP M_FIG Turbidostat, Phage, and Robotics-Assisted Near Continuous Evolution (TurboPRANCE) In phage-assisted continuous evolution (PACE), biomolecular activity is coupled to pIII expression, linking function to phage propagation. By altering the host strain, distinct selection pressures can be imposed on the same evolving phage population. In TurboPRANCE, [~]200 selection programs can vary over time, including periodic "drift" (mutagenesis), alternation between pressures, or rotational reassignment of host sources, enabling a combinatorial space of selection pressures. C_FIG

bioengineering↗

bioRxiv2026

On the sensitivity of qPCR diagnostics for the canola clubroot pathogen Plasmodiophora brassicae

Clubroot, caused by Plasmodiophora brassicae, is an important disease of canola and other Brassica crops. Polymerase chain reaction (PCR), particularly probe-based quantitative PCR (qPCR), is widely used for the detection of P. brassicae in soil samples. To improve consistency in clubroot detection while maintaining efficiency, diagnostic laboratories would benefit from adopting a single, highly efficient qPCR system for routine testing. In this study, we analyzed the primer and probe sequences of all published PCR and qPCR systems for P. brassicae detection. Based on these analyses, three independently developed probe-based qPCR systems were selected and their performance was evaluated using synthesized target DNA (gBlock). One probe-based qPCR system exhibiting superior sensitivity on gBlock was subsequently evaluated on P. brassicae genomic DNA. This system consistently detected DNA equivalent to four resting spores per reaction, corresponding to a soil sample containing 1,000 spores per g soil when the DNA extraction protocol was considered as a component of the qPCR system. The sensitivity of the system was further validated using DNA extracted from soil samples collected from multiple locations across Alberta, where P. brassicae was detected at levels below those associated with visible clubroot symptoms. Based on these results, we recommend this qPCR system for routine clubroot diagnostics in laboratories across Canada.

microbiology↗

bioRxiv2026

Asymmetric Division in a Two-Cell-Like State Rejuvenates Embryonic Stem Cells

A fundamental question in biology is whether cellular aging is inevitable. Embryonic stem cells (ESCs) challenge this paradigm as rare normal cells capable of indefinite in vitro passage. However, the mechanisms underlying ESC lineage immortality remain unresolved. Using long-term live-cell imaging to follow fates of single ESCs, we show here that ESC lineage renewal is achieved through sporadic entry into a state characterized by the expression of two-cell embryo-specific markers. During this state, cells undergo asymmetric divisions, segregating accumulated DNA damage into one daughter lineage destined for elimination, while producing a second lineage that reverts to the pluripotent state. Importantly, the latter lineage exhibits signs of rejuvenation, including reduced DNA damage and enhanced chimeric efficiency. These findings underscore the crucial role of asymmetric cell division in maintaining the long-term health of the ESC lineage against mounting damage within individual cells, a potential model for studying cellular aging and rejuvenation in mammalian cells.

cell biology↗

bioRxiv2025

The biochemical nature of senile plaques: intracellular destabilized-lysosome-enriched neural processes catabolizing extracellular hemorrhagic amyloid materials

The pathological mechanism of senile plaque formation in Alzheimers disease remains a challenging unresolved problem for over one hundred years. In this study, we investigated senile plaque pathogenesis based on immunohistochemistry, fluorescence imaging and quantitative analysis of AD front brain sections with multiple senile plaque related markers such as A{beta}, MAP2, phos-Tau, Cathepsin D, Sortilin 1, Ceruloplasmin and Hemin. Firstly, we confirmed that senile plaque A{beta} deposition mostly happened in MAP2-positive but degenerative neuritic processes. Secondly, we found an interesting dual-component granular or diffusive staining pattern of all of these senile plaque related markers, matching to two states of lysosomes, relatively-stable granule lysosomes and destabilized diffusive lysosomes as shown by lysosome-related marker Cathepsin D or Sortilin 1 staining. Thirdly, dystrophic senile plaque neural processes contain hemorrhage-related markers such as Ceruloplasmin and Hemin. In addition, A{beta} deposition, Tau phosphorylation, lysosome destabilization are all enriched at the sites of microaneurysm formation. Moreover, senile plaques are also characterized by a widespread binary phos-Tau staining pattern with difference in term of staining intensity. We concluded that senile plaques are formed by destabilized-lysosome-enriched neural processes catabolizing extracellular hemorrhagic amyloid materials, with microaneurysm as an important intermediate stage.

cell biology↗

bioRxiv2025

PRSNet-2: End-to-end genotype-to-phenotype prediction via hierarchical graph neural networks

The emergence of large-scale biobanks has opened unprecedented opportunities for the development of data-driven approaches, especially deep learning-based methods, for genotype-to-phenotype (G2P) prediction. However, designing an end-to-end framework capable of directly leveraging extremely high-dimensional genotypic data while simultaneously mitigating overfitting and ensuring robust prediction remains a significant challenge. In this study, we introduce PRSNet-2, an interpretable end-to-end deep learning framework designed to predict complex phenotypes directly from large-scale genotypic data. PRSNet-2 proposes a novel hierarchical graph neural network (GNN) architecture, which first employs a multi-kernel aggregator to map high-dimensional genotypic features to gene-level representations. Next, it models gene-gene interactions through message-passing operations and uses an attention-based readout module to generate interpretable phenotypic predictions. We further introduce significance-guided regularization strategies to boost models generalizability based on prior genetic associations. Extensive empirical evaluations across multiple complex traits and diseases demonstrate that PRSNet-2 consistently outperforms a variety of baseline methods and exhibits superior capabilities in overcoming overfitting, even when modeling around half a million single nucleotide polymorphisms (SNPs). Moreover, PRSNet-2 is shown to be easily extendable to integrate multiple genome-wide association study (GWAS) datasets into a single model, thereby enhancing predictive performance for both single-phenotype and multi-phenotype prediction tasks. The inherent interpretability of PRSNet-2 further facilitates the identification of disease-relevant genes, functional gene modules, and potential therapeutic targets. In summary, PRSNet-2 offers a powerful, versatile tool for both genetic risk stratification and the discovery of biological insights.

genetics↗

bioRxiv2025

The emerging contaminant Cl-PFESA/F-53B is toxic to meiotic cell division and reproduction in Arabidopsis thaliana

The emerging contaminant Cl-PFESA/F-53B damages vegetative development in plants and has been evidenced to be toxic to both mitotic and meiotic cells in animals. We have recently reported that F-53B induces nuclei unviability in meristematic cells leading to disrupted root development in Arabidopsis (Arabidopsis thaliana). However, the toxicity of F-53B to reproductive system in plants remains unelucidated. In this study, by using cytogenetic and microscopic approaches, we analyzed embryo and anther development and multiple meiosis processes in Arabidopsis exposed to 50 or 100 M F-53B. We showed that F-53B disrupts embryo development which results in reduced seed setting in Arabidopsis. Histochemical staining of anthers and a live-imaging assay using a reporter line that expresses GFP-tagged Aborted Microspores (AMS), a key regulator of the tapetum, demonstrated that F-53B impairs anther development. Moreover, we showed that F-53B interferes with chromosome segregation and/or distribution and alters microtubule organization during male meiosis. Quantification of the chiasmata and immunolocalization of the Human Enhancer of Invasion 10 (HEI10) protein on diakinesis chromosomes suggested that F-53B reduces crossover rate. Furthermore, F-53B reduced the number of DNA Meiotic Recombinase 1 (DMC1) protein foci on zygotene chromosomes in Arabidopsis wild-type Columbia-0 (Col-0), and it partially promoted meiotic chromosome integrity in Arabidopsis depleted with Ataxia Telangiectasia Mutated (ATM), a central regulator of DNA double-strand break (DSB) repair, which suggested that F-53B reduces meiotic DSB formation. Taken together, our study reveals the toxicity of F-53B to meiotic cells and reproduction in Arabidopsis, which highlights its potential threats to agricultural safety and ecological diversity. HighlightO_LIF-53B impairs embryo and anther development in Arabidopsis. C_LIO_LIF-53B interferes with chromosome segregation and distribution during male meiosis. C_LIO_LIF-53B interferes with meiotic microtubule organization. C_LIO_LIF-53B reduces meiotic crossover formation. C_LIO_LIF-53B reduces DNA double-strand breaks in meiocytes. C_LI

plant biology↗

bioRxiv2025

Integrated phenotypic and proteomic screening identifies top-tier Alzheimer's disease therapeutic targets

IntroductionAlzheimers disease (AD) is a complex neurodegenerative disorder. Hundreds of therapeutic targets have been nominated through genetic and multi-omic studies, but effective prioritization remains a major bottleneck. MethodsWe applied an integrative screening framework to assess 29 candidate targets from risk-enriched biological domains. Using disease-relevant murine BV2 microglial cell lines with stable Psen2 knockdown, we performed siRNA-mediated perturbations followed by cellular phenotypic assays and quantitative proteomics. ResultsTwenty-five candidate targets significantly altered at least one phenotype, with stronger effects in Psen2 knockdown cells. Integrated proteomic analyses identified several perturbations that reversed AD-associated molecular patterns. Five targets--Ap2a2, Pdhb, Pdha1, Dlat, and Psmc3-- impacted both phenotypes and related proteomic responses. DiscussionWe established a scalable platform for target functional validation that bridges unbiased systems-level assessments of AD risk with experimental evidence. The ESSJ TREAT-AD center will prioritize further resource development for these validated targets.

systems biology↗

bioRxiv2025

Molecular mechanism of the key dormancy regulator DosR-dependent transcription activation in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) is the etiological agent responsible for the worldwide disease Tuberculosis. DosR is recognized as the key dormancy regulator of Mtb due to its global transcriptional regulation in intracellular adaptation and long-term persistence prevailing in latent infection. However, the molecular mechanism regarding DosR-dependent transcription activation remains inadequately defined. Here, we successfully determined the cryo-EM structure of an intact DosR-dependent transcriptional activation complex (DosR-TAC), comprising Mtb RNA polymerase (RNAP), DosR, and the hypoxic promoter DNA. In DosR-TAC, two DosR monomers symmetrically dimerize through their N-terminal receiver domains (DosR_RECs) and the distinct 10 helices of the C-terminal DNA-binding domains (DosR_DBDs). Unlike its inhibitory configuration, the DosR dimer undergoes significant conformational changes within the original linker, isomerizing DosR_REC into a canonical ({beta})5 fold. This extended linker affords the DosR_DBDs and DosRI_REC to contact promoter DNA, while concurrently interacting with the conserved domains of RNAP ({sigma}AR4, CTD, and NTD). Additionally, RT-qPCR and growth curve assays of the wild-type and DosR mutant strains, also unravel the physiological importance of this divergent linker. These findings, together with prior hypotheses regarding DosR, support an allosteric activation-recruitment model for DosR. Altogether, these results highlight the molecular mechanism of DosR-dependent transcription activation critical for dormancy survival of Mtb, and offer potential targets for developing anti-dormancy strategies against persistent tuberculosis.

microbiology↗

bioRxiv2025

An activated wheat CCG10-NLR immune receptor forms an octameric resistosome

Nucleotide-binding and leucine-rich repeat (LRR) receptors (NLRs) are widespread intracellular immune sensors across kingdoms. In plants, the G10-type coiled-coil (CCG10)-NLRs form a distinct phylogenetic clade that remains poorly characterized. Here, we identified a gain-of-function (GOF) mutant of Wheat Autoimmunity 3 (WAI3), designated WAI3GOF, which encodes a constitutively activated CCG10-NLR protein due to an amino acid substitution. Cryo-EM structural analysis revealed that activated WAI3 assembles into a distinctive octameric resistosome. Arabidopsis RPS2, another CCG10-NLR, also forms an octamer, indicating a conserved structural property across monocot and dicot plants. The WAI3 resistosome mediates a prolonged and sustained increase in cytosolic calcium influx, facilitated by a unique channel architecture arising from its divergent CC domain configuration. Notably, this domain arrangement may be shared by many plant NLRs that lack the conserved EDVID motif in their CC domains. Our findings uncover a previously uncharacterized resistosome structure and provide insights into plant immune receptor plasticity.

plant biology↗

bioRxiv2025

KICDB: A Causality-Oriented Multi-Omics Database for Kinase Inhibitor-Induced Cardiotoxicity

BackgroundKinase inhibitors (KIs) are mainstays of targeted cancer therapy, but their clinical utility is frequently limited by cardiotoxicity. A systematic resource to explore the underlying causal mechanisms is urgently needed. MethodsWe present the KICDB (Kinase Inhibitor Cardiotoxicity Database), a comprehensive and interactive web server. KICDB is built upon a framework integrating large-scale transcriptomics meta-analysis with causal inference. ResultsThis database centralizes the findings from a comprehensive meta-analysis of 26 kinase inhibitors (KIs) across 7 studies (n=5291) identified 8,907 significant gene expression changes in human cardiomyocytes. To establish causality, we performed a two-pronged Mendelian randomization (MR) analysis testing hundreds of downstream genes and a panel of 43 key kinase proteins against 46 cardiovascular outcomes. This large-scale analysis revealed 26 significant causal associations, implicating novel molecular mediators in KI-induced cardiotoxicity. ConclusionsKICDB serves as a valuable and accessible platform for the cardio-oncology community. By integrating transcriptomic signatures with causal inference data, the database empowers researchers to formulate mechanistic hypotheses, accelerate biomarker validation, and guide the design of future cardioprotective strategies. URL: https://zhang-lab-database.shinyapps.io/KICDB/ Key PointsO_LIWe developed KICDB, a comprehensive and publicly accessible web server, to systematically investigate the causal mechanisms of KI-induced cardiotoxicity. C_LIO_LIKICDB integrates a large-scale meta-analysis of transcriptomic data from 26 KIs with a robust Mendelian randomization (MR) framework to move beyond correlation and infer causality. C_LIO_LIThe analysis identified 8,907 significant gene expression changes and 26 significant causal associations between KI-associated genes and 46 cardiovascular outcomes. C_LI

bioinformatics↗

bioRxiv2025

Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes

Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labeling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions.

biophysics↗