Biology subjects

Liu, Y.

Publications and source records attributed to Liu, Y..

At least 253 records · Page 14Linked to original sources

bioRxiv2026

Transgenic human dipeptidyl peptidase-4 Syrian hamsters support MERS coronavirus infection and contact transmission

Middle East respiratory syndrome coronavirus (MERS-CoV) is a global health concern due to a high fatality rate associated with human infections and no approved vaccines or therapeutics. While Syrian hamsters are a value animal model for coronavirus research, including SARS-CoV-2, MERS-CoV does not infect wild-type hamsters. Here, we generated transgenic Syrian hamsters expressing human dipeptidyl peptidase-4 (hDPP4), the cellular receptor for MERS-CoV., MERS-CoV replicated efficiently in the respiratory tract tissues of hDPP4 hamsters, causing lethal disease. Treatment with the 3CLpro inhibitor nirmatrelvir significantly reduced viral titers in the lower respiratory tract of infected hDPP4 hamsters. While airborne transmission was not observed, direct contact transmission was observed in all contact hDPP4 hamsters cohoused with infected cage mates. Immunization with purified MERS receptor-binding domain protein reduced virus replication and disease severity but did not prevent direct contact transmission. Collectively, our findings demonstrate that hDPP4 transgenic Syrian hamsters are useful for studying MERS-CoV pathogenesis, transmission, and countermeasure efficacy.

microbiology↗

bioRxiv2026

First evaluation of a human DPP4 transgenic hamster model for MERS-CoV pathogenesis and transmission

MERS-CoV poses a constant pandemic risk, as its viral lineages continue evolving, and zoonotic spillover events could lead to random viral polymorphisms that might lead to human adapted variants. Currently, no small animal model reliably recapitulates both disease progression and transmission dynamics, which are critical aspects for counter-viral measures like vaccine development. Although the Syrian hamster is an optimal animal model for SARS-CoV-2 infection and transmission, it is naturally resistant to MERS-CoV infection. Dipeptidyl peptidase-4 (DPP4) is the functional receptor for MERS-CoV infection, and is highly expressed in human kidney, intestine, liver, and lung tissues. Here, we evaluated the suitability of a human DPP4 (hDPP4) transgenic Syrian hamster model for MERS-CoV research. We used two different MERS-CoV strains (EMC/2012 and D10540/2023) for intranasal inoculation of hamsters. Both strains replicated efficiently, led to comparable severe clinical outcomes, and had similar viral transmission efficiencies. MERS-CoV RNA and nucleoprotein antigen were mainly detected in the brain and the respiratory tract. In summary, we validated a novel hDPP4-transgenic hamster as a suitable model for MERS-CoV infection enabling vaccine and transmission research.

microbiology↗

bioRxiv2026

Efficient and accurate near telomere-to-telomere haplotype reconstruction of diploid genomes

Telomere-to-telomere (T2T) and haplotype-resolved assembly are crucial for understanding eukaryotic genomes. For diploid species, this resolution is critical to uncover allelic variations, inheritance patterns, and functional genomic traits. Current scaffolding methods typically employ either sequence-based or graph-based strategies. Sequence-based approaches rely on proximity signals to yield high contiguity, but underutilize assembly graph information, resulting in more structural errors and chromosomal misassignments. Graph-based methods leverage graph topology for higher accuracy but frequently struggle to achieve chromosome-scale contiguity. However, neither strategy alone can overcome its inherent limitations to simultaneously achieve high contiguity and accuracy. To address these challenges, we introduce HapFold, the first hybrid scaffolding framework that synergistically leverages the complementary strengths of both graph-based and sequence-based approaches. By integrating the topological accuracy of assembly graphs with the proximity-guided contiguity of sequence models, HapFold achieves highly accurate, chromosome-scale or near-T2T haplotype reconstructions for diploid genomes. Compared to existing methods, HapFold achieves superior assembly quality while accelerating computation by an order of magnitude. Furthermore, in the haplotype reconstruction of diploid genomes using standard Oxford Nanopore Technologies simplex reads, HapFold enables the reconstruction of a greater number of near-T2T assemblies. Our approach provides a robust and scalable solution for the high-fidelity reconstruction of haplotype-resolved diploid genomes.

bioinformatics↗

bioRxiv2026

Genos-m: a foundation model for human-associated microbial genomes

Human-associated microbial genomes encode extensive strain-level diversity and niche-specific gene repertoires that are critical to host health. However, these complex sequence features remain difficult to capture using general-purpose DNA foundation models, highlighting the need for dedicated representation learning tailored to the human microbiome. Here, we introduce Genos-m, an open-source foundation model for human-associated microbial genome representation. Genos-m was pretrained on approximately 1.2 trillion nucleotide tokens from a curated microbial genome corpus, including human-associated prokaryotic isolates, high-quality metagenome-assembled genomes (MAGs) and bacteriophages, supplemented with GTDB species-level representative genomes to broaden prokaryotic taxonomic breadth. The model uses a sparsely activated Mixture-of-Experts (MoE) Transformer architecture, with 4.7 billion total parameters, approximately 330 million activated parameters per forward pass and a maximum context length of one million base pairs. We evaluated frozen Genos-m representations across short-sequence and gene-level tasks, biosynthetic gene cluster (BGC)-based regional sequence tasks, whole-genome strain phenotype prediction, and zero-shot transfer on prokaryote-related RNAfitness assays. Across these benchmarks, Genos-m consistently ranked among the leading comparison models, with the best performance in five of eight gene-fitness regression tasks and in BGC type classification. Using sparse autoencoders, we identified sparse features in Genos-m hidden activations that aligned with annotated ORFs, intergenic regions, and tRNA and rRNA loci. In downstream applications, Genos-m-derived genome-informed species representations in-corporated into a human microbiome self-supervised learning model improved colorectal cancer (CRC)-control classification over conventional species-abundance random forest models. Genos-m also generated stable sample-level embeddings from as few as 10,000 metagenomic reads, retaining gut microbial community structure that distinguished geographic origin and aligned with enterotypes defined from full-depth taxonomic profiles. Together, these results support Genos-m as a reusable representation model for microbial genomes and metagenomes, with conclusions bounded by the reported datasets, task definitions and evaluation protocols. Genos-m model weights, inference code, and usage documentation are publicly available on GitHub (https://github.com/BGI-HangzhouAI/Genos-m) and Hugging-Face (https://huggingface.co/BGI-HangzhouAI/Genos-m).

bioinformatics↗

bioRxiv2026

Ferrous Iron Accumulation Is a Hallmark and Therapeutic Vulnerability of Therapy-Induced Senescence

Chemotherapy and radiation reduce tumor burden but leave behind residual cells that survive via therapy-induced senescence (TIS). These cells constitute a latent reservoir fueling recurrence, yet strategies for their selective elimination are lacking. Here, we identify lysosomal ferrous iron accumulation as a conserved hallmark and actionable vulnerability of TIS tumor cells. Across diverse models, senescent tumor cells exhibit marked hypersensitivity to ferroptosis induction. In breast cancer PDX models, sequential ferroptosis induction following chemotherapy significantly delays recurrence, while dual inhibition of GPX4 and FSP1 produces durable, often complete, eradication of residual tumors without overt toxicity. Mechanistically, activation of the TFEB-HO-1 axis in TIS tumor cells drives ferrous iron accumulation, thereby priming cells for ferroptosis. Together, these findings establish ferrous iron accumulation as a defining feature of TIS and position ferroptosis induction as a potent senolytic strategy to eliminate therapy-refractory residual disease. Statement of significanceSenescent tumor cells remaining after treatment can drive cancer recurrence yet remain poorly understood and therapeutically intractable. Here, we identify lysosomal ferrous iron accumulation as a universal hallmark of therapy-induced senescence and demonstrate that ferroptosis induction functions as an effective senolytic strategy. Our findings provide mechanistic and translational support for the "one-two punch" therapeutic paradigm.

cancer biology↗

bioRxiv2026

Structures of Cas9-Bound Double-Stranded DNA Mini-Circle Reveal Impacts of DNA Shape on Cas9 Target Interrogation

CRISPR-Cas9 is an RNA-guided endonuclease that cleaves double-stranded DNA at specific sites and has been adapted as a powerful tool for genome manipulation. Cas9 recognizes its target through multiple conformational transitions coordinated between the Cas9 ribonucleoprotein and the DNA duplex. Such transitions, and consequently Cas9 targeting specificity, are expected to be significantly influenced by the collective duplex physical properties referred to as DNA shape. To advance our currently limited understanding of the interplay between DNA shape and Cas9 target interrogation, we solved two cryo-EM structures of SpyCas9 bound to a cognate target embedded in a relaxed 95-base-pair DNA double-stranded minicircle. The Cas9-bound DNA segment engages in similar interactions involved in PAM-binding and R-loop initiation as those observed in Cas9-bound linear DNA. However, R-loop is limited to less than three base-pairs, thus interfering with Cas9 cleavage. The minicircle DNA, which is fully resolved, retains its global shape. As Cas9 locally unwinds the protospacer, the closed-ring topology constrains the movement of the paired PAM-distal DNA duplex, thus interfering with R-loop propagation. These data provide detailed insight into the interplay between DNA shape and Cas9 structure and function, and may shed light on genome-editing and manipulation in environments with varied DNA topologies.

biophysics↗

bioRxiv2026

Conserved bacterial genes for biosynthesis of the algal morphogen thallusin span land and sea

Bacterial signals control the development of marine algae, yet the molecular basis of these cross-kingdom interactions remains largely unknown. Thallusin is the paradigmatic case: isolated in 2005, it induces rhizoid and cell wall formation in the green seaweed Ulva at picomolar concentrations, but its biosynthesis has remained elusive for two decades. Comparative genomics across five bacterial phyla identifies a conserved set of genes - the eustigmatophyte bacterial operon (ebo) - as determinants of thallusin biosynthesis. Isotope labeling, heterologous expression, and gene deletion in Stieleria maiorica show that the aromatic scaffold derives from a cyclitol precursor and L-aspartate, with subsequent prenylation and cyclization. Searching 124,295 prokaryotic genomes identifies producers in eleven bacterial lineages, including soil cyanobacteria, establishing thallusin as a widespread cross-kingdom signal reaching beyond the ocean.

microbiology↗

bioRxiv2026

Comprehensive Complete-Genome Analysis of Lactobacillaceae and Bifidobacteriaceae Reveals Strain-Specific Metabolic Interactions in Chinese Gut Microbiota

Bifidobacteriaceae and Lactobacillaceae are key probiotic families and widely used in food production, yet a comprehensive understanding of strain functions and their gut microbial interactions based on complete genomes remain understudied. Here we constructed a complete-genome dataset of 3,300 strains from these two families, including 1,151 newly isolated from China. Compared with draft assemblies, complete genomes substantially recovered a gene functional landscape encompassing stress tolerance, surface exopolysaccharide synthesis, nutrient utilization, and mobile genetic elements. Major species from both families exhibited a prevalence >60% in the Chinese population, far higher than that in US/Dutch cohorts. Notably, as a core probiotic species with remarkable genomic plasticity and gut-adaptive potential, Lactiplantibacillus plantarum stood out in our dataset for its enriched functional profile and was particularly abundant in the Chinese population. Moreover, compared with non-Chinese genomes, our isolates of key species displayed less metabolic complementarity and stronger competition with potentially pathogenic keystone species in the gut, thereby linking strain origin to enhanced probiotic potential and ecological fitness to benefit human gut health.

microbiology↗

bioRxiv2026

SnoRNA Expression and RNA 2'-O-Methylation in Drosophila melanogaster S2 Cells

Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs that play critical roles in guiding 2-O-methylation (Nm) and pseudouridylation modifications of RNAs. In Drosophila melanogaster, snoRNAs undergo dynamic changes in expression during development. In this study, we identified 239 snoRNAs that are robustly expressed in Drosophila S2 cells, representing 87% of all annotated Drosophila snoRNAs. Given that box C/D snoRNAs guide site-specific 2-O-methylation (Nm) of RNA, we next characterized the Nm landscape of S2 cells using RibOxi-seq2, a high-throughput approach capable of detecting Nm modifications with single-nucleotide resolution. RibOxi-seq2 revealed 17 Nm sites in 18S rRNA with a 94% concordance to previously reported RiboMeth-Seq data. In 28S rRNA, 30 Nm sites were identified, corresponding to an 71.4% overlap with established references. Additionally, we detected both a known Nm site (Gm74) and a novel site (Um66) in 5.8S rRNA, further validating the sensitivity and specificity of the approach. RibOxi-seq2 further identified Nm sites in small nuclear RNAs (snRNAs), expanding the annotation of modified non-coding RNAs. Additionally, the method revealed Nm modifications within internal regions of mRNAs. In total, we detected Nm modifications in 2,057 unique mRNAs, underscoring the widespread presence of this epitranscriptomic modification in coding transcripts. Strikingly, although we could not identify any snoRNAs predicted to guide the mRNA 2-O-methylation modifications by canonical mechanisms, we identified strong consensus sequences surrounding many of these mRNA sites. Together, our findings not only expand the known landscape of Nm-modified RNAs but also highlight the robustness of RibOxi-seq2 for transcriptome-wide RNA modification profiling. Collectively, this study presents a comprehensive atlas of snoRNA expression and 2-O-methylation sites in Drosophila S2 cells, offering valuable insights into the epitranscriptomic landscape orchestrated by snoRNAs.

genomics↗

bioRxiv2026

Heterogeneity-driven adaptive scale graph learning for subcellular spatial transcriptomics

MotivationSpatial transcriptomics enables gene expression profiling within intact tissue sections, providing an important basis for analyzing tissue organization, cellular heterogeneity, and microenvironmental interactions. However, existing spatial structure identification methods often integrate spatial information using fixed neighborhoods or predefined smoothing scales, which limits their ability to adapt to region-specific structural heterogeneity. In homogeneous regions, broader spatial smoothing can help preserve continuous tissue structures, whereas in regions with complex boundaries or mixed cell populations, excessive smoothing may obscure local expression differences and fine-scale structural changes. Therefore, it is necessary to develop an adaptive graph learning framework that can adjust the range of spatial information integration according to tissue structural heterogeneity. ResultsIn this study, we propose HAST, a heterogeneity-driven adaptive-scale graph learning framework for spatial transcriptomics. HAST adaptively determines graph filtering scales according to spatial structural heterogeneity, enabling flexible information aggregation across different tissue regions. It further decomposes gene expression signals into low-frequency structural components and high-frequency residual components, thereby jointly modeling global spatial continuity and local expression variations. Experiments on high-resolution spatial transcriptomics datasets show that HAST improves spatial structure identification and cross-section generalization. Tumor-enriched cluster identification and neighborhood enrichment analysis further demonstrate its ability to characterize tumor-associated spatial regions and microenvironmental organization.

bioinformatics↗

bioRxiv2026

A long-chain heparan sulfate capture mechanism directs paracrine GDNF-GFRα1 signalling through RET

The receptor tyrosine kinase RET is activated by GDNF and GFR1 together as a bipartite ligand, driving receptor activation and signalling in developmental and neuroprotective contexts. Evidence from developmental and cell models has suggested that heparan sulfate (HS) functions as a fourth component in RET signalling by binding to GDNF, but the molecular details remain unclear. Here, we present the cryo-EM structure of the heterohexameric RET:GDNF:GFR1 complex with a fully resolved heparin ligand, revealing an unexpected extended HS binding site spanning all three proteins. The architecture of the complex and binding mode of the HS chain in this complex enables the formation of a higher order 4:4:4 assembly bound to a single 30-saccharide HS chain which bridges two intimately bound complexes. This multi-protein interface selectively binds the highly sulfated domains of HS over other GAG classes, and is essential for RET activation in trans with soluble GFR1, but not in cis when GFR1 is membrane-bound. Our data suggest that HS shapes the dynamics of RET signalling at every stage, from ligand diffusion to signalling complex formation. Thus, GDNF-GFRa1 paracrine signalling reveals a surprising dependence for long-chain GAG function in which the glycan engages in both receptor complex assembly and clustering.

biochemistry↗

bioRxiv2026

Cryo-EM Structure of a 95-Basepair Double-Stranded DNA Minicircle at 5.3 A Resolution

Double-stranded DNA minicircles have been observed in a variety of biological settings and are also widely employed in biotechnology, therapeutic applications, and basic research. Here, we report a cryo-EM structure of a 95-basepair minicircle (dsMC95) at a 5.3 [A] resolution. dsMC95 forms a closed ring as designed and no local deformation is observed. The two DNA strands are fully resolved, with the major and minor grooves clearly distinguishable. Analysis reveals a nine-fold periodicity in the helical twist, which corresponds to approximately 10.56 base pairs per turn. Together with groove width analysis, the data indicate that dsMC95 maintains a B-DNA configuration. The dsMC95 ring exhibits an in-plane ellipticity of 1.13 and an out-of-plane displacement of 15{degrees}, with differences in out-of-plane displacements observed between the two half-segments. The dsMC95 structure, which is the only free DNA cryo-EM structure with a resolution better than 6 [A] to date, allows comparison to other structures to better understand DNA physical features such as bending. The findings advance our understanding of DNA structure under topological constraints and may inform studies of naturally occurring small circular DNA as well as the manipulation of DNA in nanotechnology applications.

biophysics↗

bioRxiv2026

Targeting THOC2-Mediated mRNA Export Induces PARP Inhibitor Vulnerability in DNA Repair-Competent Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) remains a lethal malignancy with limited therapeutic options. While Poly (ADP-ribose) polymerase inhibitors (PARPi) exploit synthetic lethality in tumors with DNA repair defects, their clinical utility in HCC is hindered by the low prevalence of canonical repair gene mutations and the enhancing DNA repair capacity. Through proteomic analysis of two independent cohorts (n=260), we identified the THO complex component THOC2 as a master regulator of DNA damage response (DDR) via mRNA nuclear export control. Clinically, THOC2 overexpression predicted poor survival (HR=2.68-6.84, P<0.001) and correlated with enhanced DDR gene expression. Mechanistically, THOC2 chaperones mRNA nuclear export of DDR effectors (MDC1, PRKDC, MSH6) and proliferation drivers (TOP2A), thereby establishing a dual pro-repair/pro-growth program. Targeting this vulnerability, THOC2 knockdown induced synthetic lethality with PARPi, reducing Olaparib IC50 by up to 61% and suppressing tumor growth by 76% (P<0.001). Our study illuminates mRNA transport as a druggable DDR modulator and establishes THOC2 as both a prognostic biomarker and a therapeutic target to overcome PARPi resistance in HCC. This work pioneers a strategy to expand synthetic lethality beyond genetic defects by targeting post-transcriptional regulation.

cancer biology↗

bioRxiv2026

Estimating Daily Taxon-specific Tree Pollen at a 1-km Resolution in Atlanta, GA from 2020 to 2024

While tree pollen is a major trigger of allergic respiratory conditions and different taxa exhibit varying allergenic potentials, the lack of high-resolution, taxon-specific exposure metrics have limited our ability to identify which local pollen taxa are primarily responsible for respiratory illness. Traditional pollen monitoring networks, which have an intermittent sampling schedule, are not ideal for examining the delayed effects of pollen exposure due to the missing days. In this study, we developed a modeling framework integrating atmospheric dispersion effects, taxa-specific phenology, and machine learning to predict daily counts of 13 tree taxa in the five-county Metro Atlanta area, Georgia at a 1-km resolution from 2020 to 2024. Machine learning model performance was validated with daily pollen counts collected by a multi-site monitoring network equipped with automated pollen sensors. Findings showed that Betula and Quercus pollens exhibited higher predictive performance than other taxa, with R2 values ranging from 0.69 to 0.92 and from 0.71 to 0.89, respectively. Our 1-kilometer prediction data provides gapless exposure metrics to understand the spatial and temporal variability in pollen exposure, can facilitate investigation of urban pollen hotspots and support epidemiologic studies of pollen-related respiratory outcomes.

plant biology↗

bioRxiv2026

Orally Bioavailable SARS-CoV-2 Protease Inhibitors Bearing a Hydroxymethyl Ketone Warhead

The use of covalent warheads targeting the catalytic cysteine has been a cornerstone in coronavirus main protease (Mpro) inhibitor development, where various electrophilic motifs have been used including aldehydes, nitriles, ketoamides, and hydroxymethyl ketones (HMKs). Recent efforts have been mostly centered around nitrile warheads, given the success of compounds like Nirmatrelvir and Ensitrelvir in the clinic. However, finding and advancing alternative chemotypes with differentiating chemical and pharmacological profiles is essential for future pandemic preparedness. Among such alternatives, HMKs hold special interest because they balance reduced intrinsic electrophilicity with an excellent selectivity profile. Nevertheless, early HMK-based compounds, such as the clinical-stage Mpro inhibitor PF-00835231, suffered from poor oral bioavailability and therefore required intravenous administration, with or without prodrug derivatization of the hydroxyl group. Here, we describe our efforts in advancing the HMK field via the discovery of mCMX110, a lead that has superior potency, increased unbound exposure in vivo, and favorable oral bioavailability in preclinical studies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/725542v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@40222aorg.highwire.dtl.DTLVardef@831b88org.highwire.dtl.DTLVardef@184a910org.highwire.dtl.DTLVardef@779095_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

CAD rewires nucleotide metabolism to drive oxidative stress in myocardial ischemia/reperfusion injury

Myocardial ischemia/reperfusion (I/R) injury is a major determinant of infarct size and clinical outcome, yet effective therapies remain limited. Although metabolic remodeling is central to I/R pathology, the contribution of nucleotide biosynthesis remains unclear. Here, we identify CAD, the multifunctional rate-limiting enzyme of de novo pyrimidine biosynthesis, as a previously unrecognized regulator of myocardial reperfusion injury. CAD activation exacerbated cardiomyocyte death during simulated I/R, whereas CAD knockdown or pharmacological inhibition was protective in vitro. Mechanistically, CAD enhanced dihydroorotate dehydrogenase (DHODH)-dependent electron transfer, increased the CoQH2/CoQ ratio, and promoted complex I reverse electron transport (RET), thereby amplifying mitochondrial ROS. In parallel, CAD suppressed de novo purine synthesis, causing purine insufficiency, DIS3L-dependent RNA decay, and cytosolic ROS. Importantly, cardiomyocyte-specific CAD deletion protected against cardiac I/R injury in vivo. Together, these findings establish CAD as a metabolic hub linking nucleotide flux to dual-compartment ROS signaling and identify nucleotide metabolism as a therapeutic vulnerability in myocardial I/R injury. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC="FIGDIR/small/725578v1_ufig1.gif" ALT="Figure 1"> View larger version (87K): org.highwire.dtl.DTLVardef@14c4fedorg.highwire.dtl.DTLVardef@1138ed2org.highwire.dtl.DTLVardef@1057d8borg.highwire.dtl.DTLVardef@17546bd_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Identification of Reductases Catalyzing Benzyl Alcohol Formation during Salicylic Acid Biosynthesis in Plants

Salicylic acid (SA), a central hormone in plant immunity, is biosynthesized via a recently elucidated phenylalanine-derived pathway in most seed plants. This pathway requires benzyl alcohol as a key substrate for the formation of the SA precursor benzyl benzoate. However, how benzyl alcohol is produced in plants was unclear. Here, we identify a two-step conversion of benzoyl-CoA to benzyl alcohol via benzaldehyde in Nicotiana (N.) benthamiana. From a forward genetic screen for SA-deficient mutants, the and {beta} subunits of heterodimeric benzaldehyde synthase (BalS) involved in the conversion of benzoyl-CoA to benzaldehyde were found to be required for SA biosynthesis in N. benthamiana. Further reverse genetic analysis revealed that the NADPH-dependent benzaldehyde reductase (BalR1) acts downstream of BalS to convert benzaldehyde to benzyl alcohol. Interestingly, OsBalR1, but not OsBalS or OsBalS{beta}, is required for maintaining high basal SA levels in rice, suggesting the presence of redundant benzoyl-CoA-reducing activities or alternative biosynthesis routes for benzyl alcohol production. Together, this work defines the missing enzymatic steps in phenylalanine-derived SA pathway and provides insights into the evolutionary diversification of SA production strategies in plants.

plant biology↗

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↗