Biology subjects

Liu, Y.

Publications and source records attributed to Liu, Y..

At least 271 records · Page 15Linked to original sources

bioRxiv2026

Patient-specific "Physical Twin" artery-on-chip platform reveals complex flow-dependent VWF mechanobiology and guides personalized antithrombotic therapy

Ischemic stroke triggered by carotid atherosclerosis remains unpredictable because the thrombosis embolization is governed by patient-specific vascular geometry and hemodynamics that cannot be recapitulated in conventional models. Here, we engineered "Physical Twin" artery-on-chip platforms that reproduce individualized carotid anatomy with humanized subendothelial matrix composition and arterial endothelial phenotype under physiological flow patterns. We then established thrombotic microenvironments following laser-induced injury. Computational fluid dynamics-guided experiments across distinct patient geometries reveal that local shear dictates a mechanobiological hierarchy: high-shear bifurcations ([~]3,000 s-{superscript 1}) produce von Willebrand factor (VWF) A1-dependent thrombi suppressible by conformationally sensitive inhibitors, whereas low-shear stenoses generate fragile aggregates where VWF-integrin IIb{beta} coupling governs embolization overgrowth. Pulsatile flow suppresses thrombotic growth independent of mean shear. Molecular dynamics simulations reveal why conformationally sensitive nanobodies (caplacizumab) outperform shear-independent aptamers (ARC1172) in high-shear bifurcation flow zones. This Physical Twin platform provides a mechanistic blueprint for geometry-informed, personalized antithrombotic therapy selection.

bioengineering↗

bioRxiv2026

Neuronal secretome from bipolar patient-derived neurons alters network function and contains candidate biomarkers for diagnosis and lithium response

Delayed diagnosis and treatment are a major burden to patients with bipolar disorder. While lithium is the most effective treatment against mania, depressive episodes, and suicide, only 30% of patients respond to it fully. Currently there are no reliable methods to predict lithium responsiveness. To address these challenges, we aimed to identify potential diagnostic and treatment response biomarkers for BD, in addition furthering understanding of BD pathophysiology. Here, we leveraged human induced pluripotent stem cell (hiPSC) derived neurons from lithium responsive (LR), lithium non-responsive (LNR), and healthy age-matched controls (CTL). We found extracellular vesicle (EV) cargos from hiPSC-derived neurons are indicative of disease state and treatment-response. Unbiased proteomic and miRNA profiling identified 10 proteins and 13 miRNAs that were differentially expressed in BD EVs relative to CTL, as well as distinct molecular signatures separating LR ad LNR groups. These differences converged on pathways related to synaptic function, neurotrophic signalling, and cellular stress responses. Additionally, we found the BD neuronal secretome alters activity in non-BD neuronal networks. Chronic treatment of CTL cultures with BD neuron-conditioned media modified the proportion of active neurons and the frequency and amplitude of calcium transients in individual neurons. We demonstrate that neuronal EVs contain molecular signatures of disease state and treatment response in BD and identify the BD secretome as an active regulator of neuronal network homeostasis. This study provides novel insights into the pathophysiology of BD and candidate biomarkers for personalized BD diagnosis and treatment selection.

neuroscience↗

bioRxiv2026

GatorDuo: Global-Consistency Dual-Graph Refinement With Pseudo-Label Agreement for Spatial Transcriptomics

Spatial transcriptomics (ST) measures gene expression together with spatial coordinates, enabling spatial domain identification of coherent tissue regions. Many recent approaches rely on graph-based modeling to combine spatial neighborhoods and transcriptomic (gene-expression) similarity, yet neighborhood construction is often unreliable under sparsity and technical noise. As a result, spurious cross-domain shortcut edges can persist in static graphs and propagate misleading signals during message passing, ultimately blurring domain boundaries and weakening cluster separability. In this paper, we propose GatorDuo, a topology-aware dual-graph contrastive self-supervised framework for robust spatial domain identification that couples gene-expression similarity with spatial proximity through complementary neighborhood graphs. GatorDuo introduces global-consistency-based graph refinement that uses a pseudo-label agreement mask to suppress cross-domain shortcut edges in both views, thus stabilizing neighborhood topology for representation learning. To avoid manual tuning of domain resolution, GatorDuo further employs a contextual bandit reinforcement-learning strategy to adaptively select the clustering granularity (the number of clusters) used for refinement. The refined view-specific embeddings are integrated via a hybrid-routing Mixture-of-Experts (MoE) module to generate a unified embedding, optimized with contrastive objectives augmented by an MoE-alignment term. Across eight public benchmarks spanning sequencing- and imaging-based ST at spot and single-cell resolution, and compared with ten representative baselines, GatorDuo consistently delivers strong and robust spatial domain identification performance across multiple clustering metrics, while yielding informative unified embeddings that can support downstream biological analyses.

bioinformatics↗

bioRxiv2026

Causally validated phase-amplitude coupling enables high-fidelity motor decoding for next-generation brain-computer interfaces

Modern Brain-Computer Interfaces (BCIs) face a fundamental performance plateau due to their reliance on broad spectral power reduction (Event-Related Desynchronization, ERD) as the primary decoding feature. ERD acts as a coarse metabolic proxy for cortical activation, discarding the high-frequency temporal syntax necessary for high-dimensional motor control. Here, we demonstrate that Phase-Amplitude Coupling (PAC)--specifically, the phase-locking of high-gamma (70-150 Hz) firing to residual Beta oscillations--provides a high-fidelity temporal feature for decoding motor intent. Using high-density electrocorticography (HD-ECoG) during motor imagery, we show that incorporating Beta-PAC into machine-learning classifiers (LDA/SVM) significantly outperforms traditional power-based features. To definitively validate the causal robustness of this feature against mathematically-derived artifacts, we leveraged a rare in vivo human structural lesion model. In a patient with focal tumor infiltration of the motor tract, the metabolic gate (ERD) was preserved, yet structural uncoupling completely abolished Beta-PAC, collapsing network topology and reducing single-trial decoding accuracy to chance levels. Our findings causally validate Beta-PAC as a robust, independent control signal, establishing a physiological foundation for next-generation, phase-dependent neuroprostheses.

neuroscience↗

bioRxiv2026

A sensitized model of thrombosis validates known multigenic relationships and suggests novel modifiers of hemostasis

BackgroundVenous thromboembolism is a major cause of morbidity and mortality. Despite identification of risk factors, not all individuals with thrombophilia develop thrombosis. Understanding the multigenic factors modifying this incomplete penetrance would help guide patient care. MethodsThe zebrafish has a conserved hemostatic system and is amenable to large genetic studies. Loss of antithrombin III (At3) in zebrafish leads to an early consumptive coagulopathy and lethality in adulthood. Using this genetic background as a sensitized model we performed a dominant unbiased genome-wide N-ethyl-N-nitrosourea (ENU) mutagenesis screen followed by whole genome sequencing (WGS). We used survival studies, laser-mediated endothelial injury, and ex vivo protein assays to validate hits. ResultsENU-treated at3+/- males were crossed with at3+/- females to produce 4,030 total offspring (1.5x genome coverage). Four permanent lines transmitting a survival benefit beyond 7 months were identified and sequenced. A candidate screen of 63 known coagulation-related loci revealed a missense mutation, C504F, in a highly conserved residue of the prothrombin (F2) heavy chain, which was validated through genetic and biochemical studies. Evaluation of UK Biobank electronic health record (EHR) data was underpowered to detect interactions between F2 and AT3 due to minmal deleterious mutations. Mutations produced through genome editing revealed that heterozygosity for factor X and plasminogen also modified at3-/-, resulting in reduced lethality. The three remaining lines had no coagulation-related variants segregating with survival, suggesting the presence of novel modifier loci. ConclusionsUnbiased genome-wide screening identified a modifier of thrombosis. This demonstrated that re-balancing of hemostasis to mitigate thrombosis is conserved in zebrafish, including an unexpected role for fibrinolysis. This interaction was not detected even in a large human dataset, establishing the continued benefit of the zebrafish model. Finally, we found evidence for novel loci outside of the canonical coagulation cascade that may be new targets for diagnosis or treatment.

cell biology↗

bioRxiv2026

A graph-based pangenome reveals the genetic basis of climate-resilient and horticultural traits in pear

Climate change poses an increasing threat to the cultivation of deciduous fruit trees, placing greater demands on modern pear breeding. Using pear germplasm adapted to diverse environments, we assembled 11 chromosome-level genomes. In combination with 13 publicly accessible pear genomes, we analyzed presence-absence variations (PAVs) and constructed a graph-based pangenome for pear. By performing a PAV-eQTL analysis of the fruit of 123 pear accessions, we identified PAVs significantly associated with expression levels of genes that may be involved in regulating agronomic traits. Population analysis of 268 pear accessions revealed two stop-gained variants in DAM1 of independent origin, which may function in advancing the blooming date and reducing the chilling requirement. We detected complex PAVs at the NOR1 locus, including two copy-number variations and one deletion. These PAVs contributed to the rapid diversification of the NOR1 locus and the fruit development period through regulating ARF5 and other ripening-related genes. We revealed the selection history of the NOR1 locus and developed novel pear individuals that accumulated alleles for low chilling requirement, early blooming date, and short fruit development period. The results provide valuable resources for pear genomics research and offer a guideline for breeding modern pears with climate resilience.

plant biology↗

bioRxiv2026

Single-type neuron transcriptomics uncovers cell-type-specific regulators of host defense in Caenorhabditis elegans

Understanding how the nervous system regulates immune responses requires insight into how individual neurons respond to infection. In Caenorhabditis elegans, sensory neurons such as ASH play important roles in modulating innate immunity; however, the molecular mechanisms operating within these neurons remain poorly defined. Previous transcriptomic studies have relied on whole-animal RNA sequencing, which lacks the cellular resolution needed to detect neuron-specific signaling programs. Here, we performed single-type neuron transcriptomic profiling to characterize gene expression in ASH neurons from infected and uninfected animals. We found that ASH neurons undergo extensive transcriptional remodeling in response to pathogen exposure, with enrichment of genes associated with G protein-coupled receptor signaling, neuropeptide activity, and sensory transduction. Notably, we identified genes, including zig-3 and F36F2.8, that are strongly induced in ASH neurons but are not detected in whole-animal transcriptomic datasets. Functional analysis using ASH-specific RNA interference demonstrated that knockdown of either gene significantly reduces survival during Pseudomonas aeruginosa infection, whereas whole-animal RNAi produces no detectable phenotype. Together, these findings reveal that cell-type-resolved transcriptomics can uncover functionally important regulators of host defense that are masked in bulk analyses and provide new insight into neuron-intrinsic mechanisms of neuroimmune regulation.

molecular biology↗

bioRxiv2026

A Beta-Binomial Model for Estimating Zero- or One-inflated Pain Trajectories

Chronic pain is a widespread public health issue that imposes substantial health, emotional, and economic burdens on individuals and communities. Because pain is subjective and lacks objective biomarkers, it is typically measured using patient-reported scores, often on a numerical scale from zero to ten. Increasingly, pain studies use ecological momentary assessment, with multiple daily assessments over days and across study phases (e.g., a series of baseline and post-intervention assessments). These data frequently show many ratings at the extremes (i.e., at minimum or maximum pain scores), commonly referred to as zero- and one-inflation in the statistical literature, along with considerable within-person variability both within and across days. These phenomena present challenges for statistical analyses, as they violate assumptions of most commonly used statistical techniques (e.g., the normality assumption of linear mixed models). We propose a Bayesian beta-binomial mixed-effects model for modeling potential zero- or one-inflated pain scores while accounting for variability using random effects on the mean and variance parameters across subjects. A simulation study demonstrates that the method accurately estimates model parameters across realistic sample sizes, time points, and zero- and one-inflation levels. An application to data from two longitudinal pain studies demonstrates that the model fits the data better and, when correctly specified, yields accurate uncertainty intervals for longitudinal changes in pain compared to existing models, especially for zero- and one-inflated outcomes. Additionally, the model directly estimates the probability of clinically meaningful pain events. The proposed method provides a powerful statistical framework for studying the patient-reported pain trajectories.

bioinformatics↗

bioRxiv2026

Organoid modeling of tumor-associated macrophages reveals phagocytosis checkpoint blockade-induced conversion to an immunosuppressive SPP1+ phenotype

Tumor-associated macrophages (TAM) exert essential functions during the immune response to cancer. However, investigations of TAM within a native human tumor microenvironment (TME) have been impeded by a lack of appropriate model systems. Here, patient-derived organoids (PDO) from air-liquid interface (ALI)-grown tumor fragments, containing a human TME that encompassed stroma and immune subsets, robustly preserved TAM that were maintained by endogenous CSF-1 and appropriately responded to polarization signals. Antibody blockade of the CD47 regulatory checkpoint in organoids stimulated phagocytosis and remodeled TAM cytokine secretion profiles that were confirmed in anti-CD47 phase I trial patients. Amongst PDO histologies screened, anti-CD47 tumor killing was notable in clear cell renal cell carcinoma (ccRCC) which was associated with increased TAM infiltration. PDO contained diverse previously described TAM subsets; however, anti-CD47 reprogrammed organoid TAM toward an immunosuppressive SPP1+ phenotype, highlighting a negative feedback mechanism. Our findings uncover a resistance circuit engaged by macrophage checkpoint blockade and position ALI PDO as a robust translational platform for dissecting human macrophage biology and informing precision immunotherapy.

cancer biology↗

bioRxiv2026

Know Your Alphabet: Conformational Noise, Latent-Space Encodings, and the Future of Structural Phylogenetics

Structural alphabets have transformed protein phylogenetics by enabling sequence-style alignment and maximum-likelihood inference to be applied directly to structural data. However, a coordinate-explicit alphabet, in which character states are derived from three-dimensional atomic positions, encodes not only evolutionary signal but also the conformational variability inherent to protein structure. This source of noise has not previously been quantified in a phylogenetic context, and no framework exists for comparing alphabets with respect to their conformational sensitivity. Here, we introduce the Normalised Noise Index (NNI), a Shannon entropy-based metric for quantifying conformational sensitivity in structural alphabet encodings, and apply it alongside ensemble-wide Robinson-Foulds (RF) variance as a framework for characterising the impact of conformational noise on phylogenetic inference. Across 3,749 single-chain NMR ensembles from the Protein Data Bank, we show that 3Di character variability is a pervasive feature of experimentally observed conformational spread, with NNI negatively correlated with within-ensemble structural stability. A 100 ns molecular dynamics simulation of myoglobin confirmed that thermal fluctuations alone are sufficient to generate comparable 3Di character variation and, in 2.9% of cases, to redirect maximum-likelihood tree search away from the expected topology in a 4-taxon globin benchmark with independently established relationships. Exhaustive enumeration of 4,800 conformational replicates across three NMR ensembles revealed that topological variance under 3Di encoding is approximately 1.7-fold greater than under structural distance, based on 11,517,600 pairwise RF comparisons, a source of uncertainty invisible to standard bootstrap analysis. By contrast, TEA, a sequence-derived structure-aware alphabet inferred from ESM-2 embeddings rather than directly from atomic coordinates, is insulated from conformational sampling by construction and yields zero topological variance across all conformational replicates, serving here as a noise-insulated reference rather than a proposed replacement for 3Di. Together, these results demonstrate that alphabet choice is a methodological variable in structural phylogenetics, and that the NNI metric and RF variance frame-work introduced here provide a practical basis for principled noise characterisation as new structural alphabets continue to emerge.

bioinformatics↗

bioRxiv2026

Selective Elimination of TP53 Mutant Cells by Transcript-Activated Chromatin Shredding

Genetic mutations that drive cancer often occur in tumor suppressor proteins, including the p53 transcription factor which is altered in [~]40-50% of cases1,2. However, current therapies fail to target most such mutations because the mutant proteins typically lack defined drug-binding pockets, and restoring the endogenous function has proven challenging. Here, we programmed CRISPR-Cas12a2, an RNA-guided nuclease with trans-nucleolytic cleavage activities3,4, to selectively kill cancer cells by targeting cancer-specific transcripts. This approach eliminates cells by inducing trans chromatin cleavage, triggering DNA damage and cell death. Unlike existing methods, RNA-guided Cas12a2 senses cellular RNA signatures to shred chromatin, enabling precise targeting of undruggable mutations. Transcript-activated chromatin shredding provides an innovative paradigm to develop precision disease treatments for undruggable targets.

cell biology↗

bioRxiv2026

Spatial imprints of emergent cardiomyocyte states in the pressure-overloaded heart

Resilience to cardiac stress is essential for health, yet the relationship between cardiomyocyte (CM) stress response and local microenvironment remains unclear. Here, we combined MERFISH spatial transcriptome profiling with Cellouette, an improved cell segmentation method, to determine CM-microenvironment relationships in a mouse model of ventricular pressure overload. We report the shape, transcription profile, spatial organization, and physical connectivity for >400,000 cells across stressed and healthy tissues. Under stress, CMs adopted a spectrum of emergent transcriptional states, with advanced states marked by a metabolic and pro-fibrotic shift. To discover CM-environment relationships, we performed a network analysis of physical cell connectivity combined with cell-type-specific profiling. We found that pro-fibrotic CM progression was tightly linked to distinct local microenvironments, and CM metabolic shifts could be inferred from transcriptional patterns in neighboring non-CM cells, revealing microenvironmental imprints of disease. We thus provide a resource for understanding the heterogeneity of outcome during cardiac pressure overload. HighlightsO_LICellouette provides accurate segmentation for single-cell spatial transcriptomics in cardiac tissue. C_LIO_LIPressure overload creates spatial gradients of cardiomyocyte pro-fibrotic states. C_LIO_LICardiomyocyte pro-fibrotic progression is linked to changes in local cell composition and gene expression. C_LIO_LITranscriptional states of non-muscle cells predict metabolic state of adjacent cardiomyocytes. C_LI

genomics↗

bioRxiv2026

Helminth-remodeled microbial indole-3-lactic acid drives AhR-dependent disease tolerance

Helminths systemically suppress host immunity, yet whether they impose immune tolerance by rewiring host-associated microbial metabolism remains unclear. Here we show that Trichinella spiralis infection remodels intestinal tryptophan metabolism to generate an AhR-dependent regulatory immune state. T. spiralis infection enriched the commensal bacterium Ligilactobacillus murinus, which converted tryptophan into indole-3-lactic acid (ILA), a microbial metabolite that directly engaged the aryl hydrocarbon receptor. Antibiotic-mediated microbiota depletion abolished infection-induced ILA accumulation, AhR activation and Treg/Th17 rebalancing, whereas fecal microbiota transplantation from infected donors or supplementation with L. murinus or ILA restored these effects. Pharmacological blockade or genetic deletion of AhR eliminated the ability of T. spiralis, L. murinus and ILA to restrain LPS-induced cytokine-storm-like lung inflammation, establishing AhR as an essential host node in this circuit. Extending these findings to viral inflammatory disease, oral ILA improved survival and reduced pulmonary immunopathology in SARS-CoV-2-infected K18-hACE2 mice. Re-analysis of human COVID-19 metabolomic data further revealed reduced circulating ILA in severe disease. These findings define a helminth-remodeled microbial tryptophan metabolic pathway that promotes disease tolerance and identify the ILA-AhR axis as a candidate postbiotic strategy for limiting hyperinflammatory tissue injury.

immunology↗

bioRxiv2026

Methionine Deprivation-induced Reprogramming of Hepatic Rhythms Is Mediated by Glucocorticoid Receptor

The circadian clock tightly interacts with cellular metabolism, and nutritional challenges can profoundly remodel its function. Dietary methionine restriction has been shown to improve metabolic health and extend lifespan. However, whether and how dietary methionine restriction impacts the circadian clock is unclear. Here, we demonstrate that methionine deprivation (MD) in the mouse induces alterations in multiple signaling systems, inducing rhythmic biological events in liver that are entrained by feeding time rather than day/light cycles. Alteration in growth factor signaling leads to loss of activation of a pioneer transcription factor, STAT5, which normally directs rhythmic chromatin localization of the glucocorticoid receptor (GR). Loss of active STAT5 leads to reprogramming of the epigenome and of the GR-directed transcriptome in a manner abolished by liver-specific deletion of GR. These results demonstrate that dietary methionine restriction remodels the circadian biological program directed by glucocorticoid receptor.

genomics↗

bioRxiv2026

Nonclinical pharmacokinetics and relative efficacy of the first 25 novel tuberculosis drug combinations from the PAN-TB consortium: Use of the BALB/c relapsing mouse model and combination pharmacokinetics within a modeling-based framework

The Project to Accelerate New Treatments for Tuberculosis (PAN-TB) aims to accelerate development of shorter, simpler and safer pan-TB combinations, effective for use in both Drug Susceptible (DS)- and Drug Resistant (DR)- TB patients. Towards this aim, bactericidal and sterilizing activity of 25 priority 4-drug combinations was evaluated at doses targeting clinically relevant exposures, in the BALB/c relapsing mouse model of TB. The combinations comprised 8 PAN-TB drugs and candidates: bedaquiline (B), pretomanid (Pa), delamanid (Del), quabodepistat (Q), sutezolid (Sut), GSK2556286 (286), GSK3211830 (830) and ganfeborole (GSK3036656, (656)). Combination PK studies in infected mice enabled dose selection and a population-PK approach guided dosing so that compounds should achieve mean AUC0-24 within 2-fold of their clinical target exposures during the efficacy studies. All test combinations showed time-dependent bactericidal activity, with six regimens reducing lung bacterial burdens below the limit of detection with 8 weeks treatment, similar to the comparator BPaMZ (M is moxifloxacin and Z as pyrazinamide). Cure/Relapse data were modelled to derive population time to cure 90% mice (T90) values. Fifteen PAN-TB combinations had T90s of less than 5 months, sterilizing mice faster than the standard of care for drug susceptible TB, RHZE/RH. The best-performing PAN-TB combinations, BPa830Sut, BPa286Sut and BQSut286, cured 90% of mice in less than 3 months. These 3 top-ranked 4-drug combinations are all centered on a diarylquinoline (B)/oxazolidinone (Sut) core, together with the nitroimidazole (Pa) or a DprE1 inhibitor (Q) plus a novel agent such as the LeuRS inhibitor (830) or the Rv1625c agonist (286).

microbiology↗

bioRxiv2026

Reactivation of a TAL1 progenitor cell enhancer region by non-coding somatic variants in T-lineage acute lymphoblastic leukemia

Aberrant activation of TAL1, a key oncogenic driver, defines a major subgroup comprising [~]30% of childhood T-lineage acute lymphoblastic leukemias (T-ALLs). We and others have shown that somatic non-coding mutations within upstream and intronic cis-regulatory regions of TAL1 contribute to transformation by creating binding sites for MYB and other transcription factors. Here we investigated cis-regulatory mechanisms mediated by somatic mutations occurring in an intergenic region located 29 kilobase pairs downstream of the canonical TAL1 transcription initiation site, implicated in 6% of TAL1-expressing T-ALLs. These somatic variants include i) complex indels resulting in de novo MYB transcription factor binding sites (TFBSs) and ii) internal tandem duplications (ITDs) encompassing canonical MYB TFBSs. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed binding of the TAL1 core regulatory circuit (CRC) transcription factors MYB, GATA3, and RUNX1, resulting in enhancer activity mediated by sequences with the mutant allele. Strikingly, ChIP-seq peaks for the repressive H3K27me3 mark and the active H3K27ac mark co-existed across TAL1 regulatory sequences but enriched for different haplotypes. TAL1 transcription from the mutant haplotype initiated from a promoter located within exon 4 of the canonical TAL1 transcript, resulting in a short isoform normally expressed by hematopoietic stem cells (HSC). Interestingly, neither the isoform expression nor the enhancer activity could be predicted by the sequence-to-function deep learning artificial intelligence (AI) model AlphaGenome, emphasizing the importance of experimental validation. Our findings indicate that selection for cis-regulatory, non-coding variants leads to reactivation of enhancers normally active in HSC but silenced in differentiated lineages during normal hematopoietic cell development.

cancer biology↗

bioRxiv2026

Molecular basis of quorum-sensing signal transduction by CqsS and its inhibition by CqsA the autoinducer synthase

Vibrio bacteria possess multiple quorum-sensing systems, each of which conveys information into the cell concerning the cell density and species composition of the vicinal community. Germane to the present work is the CqsA-CqsS quorum-sensing pathway that vibrios use for intra-genus communication. CqsA is the synthase for the autoinducer (S)-3-hydroxytridecan-4-one (CAI-1), and CqsS, a bi-functional two-component kinase-phosphatase, is the CAI-1 receptor. Here, we determine the cryo-EM structures of the full-length Vibrio harveyi CqsS dimer in the apo- and ATP{gamma}S-bound states. Our structures reveal the molecular basis for the initiation of the phosphorylation cascade, which we support through biochemical and genetic analyses. Autophosphorylation of CqsS occurs in cis at the conserved histidine residue (H1), whereas phospho-transfer to the conserved aspartate residue (D1) in the C-terminal receiver domain occurs in trans. By co-expressing CqsS and CqsA to capture CqsS bound to CAI-1, we unexpectedly discover a tight interaction between the CqsS intracellular domain and CqsA. In the complex, the CqsS H1 residues are positioned away from the catalytic cavity, and CqsS kinase activity is inhibited. Cryo-EM analysis, focused on the transmembrane domain of CqsS in this complex, reveals the presence of two CAI-1 molecules. CAI-1 binding induces an obvious movement of transmembrane helix 6, disrupting its extension into the cytosol, providing a structural basis for how CAI-1 binding in the periplasm is coupled to signal transduction into the cytoplasm. Together, our findings advance the understanding of CqsS-CAI-1-mediated quorum-sensing signal transduction, an activity that underpins the coordination of group behaviors in vibrios.

microbiology↗

bioRxiv2026

Structure-guided reinterpretation of a disease-associated CWH43 residue-533 truncation identifies internal disruption of a conserved C-terminal module in idiopathic normal pressure hydrocephalus

Idiopathic normal pressure hydrocephalus (iNPH) is a chronic neurological disorder characterized by ventricular enlargement together with gait impairment, cognitive decline, and urinary dysfunction. Disease-associated CWH43 variants have emerged as genetic clues in iNPH, but the molecular consequences of truncating variants remain poorly defined. Here, we used structure-guided analysis to reinterpret the disease-associated human CWH43 variant c.1596del, annotated as p.Leu533Ter and referred to here as the residue-533 truncation. AlphaFold-based modeling of the full-length 699-amino-acid protein supported a conserved C-terminal D3 module spanning residues 407-699. Within this framework, the residue-533 truncation is best interpreted as an internal interruption of D3 rather than deletion of a poorly constrained terminal tail. Pocket analysis identified a dominant candidate surface site within D3 containing 18 pocket-lining residues, 55.6% of which (10/18) are removed by truncation. Independent cavity mapping further showed that the affected region is better understood as a broader cavity-bearing architecture rather than a single local pocket. Cross-boundary contact analysis, multi-model reproducibility, and representative local geometry supported structural coupling between retained and deleted D3 segments, indicating that truncation is predicted to cause retained-side decoupling in addition to direct residue loss. Together, these findings support a model in which the disease-associated residue-533 truncation disrupts a structurally integrated C-terminal module and its associated cavity-bearing architecture. This framework refines interpretation of CWH43-associated iNPH variants and provides a mechanistic bridge between human genetic association and architecture-level loss of function.

genetics↗