Biology subjects

Li, Z.

Publications and source records attributed to Li, Z..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

Engineering Oncolytic Measles Virus with MG53 Couples Pyroptotic Tumor Killing with Immune Microenvironment Remodeling to Enhance Checkpoint Immunotherapy in Non-small Cell Lung Cancer

Lung cancer is the leading cause of cancer-related mortality worldwide, with only approximately 30% of patients benefiting from current immune checkpoint immunotherapy. Oncolytic virotherapy offers a promising strategy to overcome this resistance; however, achieving both potent tumor cytotoxicity and robust antitumor immune activation remains a major challenge. Here, we engineered oncolytic measles virus expressing the tumor suppressor MG53 (TRIM72), designated rMeV-MG53, and evaluated its therapeutic potential against non-small cell lung cancer (NSCLC). rMeV-MG53 retained replication kinetics comparable to parental MeV while driving significantly greater cytotoxicity than an unarmed control in NSCLC cells. Mechanistically, MG53 arming amplified caspase-3-dependent apoptosis and potentiated Gasdermin E (GSDME) cleavage, engaging GSDME-mediated pyroptosis as a key tumor-killing mechanism; pharmacological inhibition confirmed caspase-dependent apoptosis as the initiating event leading to pyroptosis, while excluding necroptosis and ferroptosis as significant contributors to rMeV-MG53-induced cytotoxicity. MG53 overexpression induced an intrinsic pro-inflammatory transcriptional signature enriched for TNF, NF-{kappa}B, and IL-17 signaling, and rMeV-MG53 elicited significantly stronger type I interferon and pro-inflammatory cytokine induction than the unarmed control. In an immunocompetent, MeV-permissive syngeneic NSCLC model, intratumoral rMeV-MG53 achieved superior tumor growth inhibition, amplified caspase-3/GSDME pyroptosis, selectively upregulated Cxcl10, Ifng, and Il1b, and drove robust CD8 T-cell and Granzyme B effector infiltration. This immune remodeling was accompanied by compensatory PD-L1 upregulation, and combining rMeV-MG53 with anti-PD-L1 blockade achieved the strongest tumor suppression of all treatment groups. These findings establish MG53-armed oncolytic MeV as a strategy coupling GSDME-mediated pyroptosis with antitumor immune remodeling to sensitize immune-resistant NSCLC to checkpoint immunotherapy.

immunology↗

bioRxiv2026

Organism-scale annotation with Pan-human Azimuth

Single-cell atlases now span many human tissues, but inconsistent annotations across studies limit their utility as a unified reference. We introduce Pan-human Azimuth, a supervised neural network that maps human cells from diverse tissues and datasets onto a single hierarchical organism-scale typology. Developed through NIH HuBMAP, the model is trained on a uniquely curated corpus designed to maximize diversity across tissues and technologies while enforcing uniform, interpretable annotations and stringent quality control. The use of a single organism-wide reference enables us to map tens of millions of cells in the Tabula Sapiens and scBaseCamp repositories, perform cross-tissue comparisons across thousands of samples, and identify striking tissue specialization among fibroblast states. Pan-human Azimuth naturally extends to annotating spatial transcriptomic data, recovering canonical kidney cortical structures and distinguishing glomerular states consistent with expert pathology. We release Pan-human Azimuth alongside cloud, R, and Python interfaces to facilitate standardized organism-wide single-cell analysis.

genomics↗

bioRxiv2026

VASP Promotes Aortic Valve Calcification by Interacting with FBLIM1 to Activate the Focal Adhesion Pathway

BackgroundCalcific aortic valve disease (CAVD) is the most prevalent valvular heart disease, yet there is no effective pharmacological therapy to halt or reverse its progression. Focal adhesions (FAs) are dynamic structures that connect cells to the extracellular matrix (ECM), serving not only as mechanical anchors but also as critical signalling hubs that regulate cell adhesion, spreading, migration, differentiation, and mechanotransduction. However, their specific role in CAVD pathogenesis remains largely unknown. MethodsTo identify upregulated hub genes, an integrated analysis of proteomics and RNA sequencing was performed on calcified aortic valves. To investigate functional roles in vitro, we utilized genetic knockdown and overexpression of VASP in valvular interstitial cells (VICs), followed by phenotypic evaluations of osteogenic differentiation, calcification, and elastin (ELN) secretion. Downstream mechanisms were explored using RNA-seq in VASP-overexpressing VICs, alongside pharmacological inhibition of the FA pathway. Finally, protein-protein interaction assays were conducted to map and analyze the physical binding between VASP and the structural domains of FBLIM1. ResultsIntegrated omics analysis identified VASP as a significantly upregulated gene in human calcified aortic valve tissues. Functionally, VASP knockdown inhibited, whereas its overexpression promoted, the osteogenic differentiation of VICs. RNA-seq revealed that VASP overexpression activated the FA pathway, and the pharmacological blockade of this pathway successfully suppressed calcification both in vitro and vivo. Mechanistically, we demonstrated a direct physical interaction between VASP and the third LIM zinc-binding domain of FBLIM1, and knockdown of FBLIM1 effectively reversed the pro-calcific effects of VASP. Finally, VASP overexpression was found to promote the secretion of ELN, which subsequently contributed to the calcification process. ConclusionOur study reveals that the interaction between VASP and FBLIM1 drives CAVD progression by activating the FA pathway, which subsequently leads to excessive ELN secretion. These findings reveal a novel mechanistic pathway and may provide a potential therapeutic target for CAVD intervention. What are the Clinical Implications?We have identified the VASP-FBLIM1-FA-ELN axis as a novel molecular pathway involved in CAVD pathogenesis, greatly enriching our understanding of the complex process of aortic valve calcification. This pathway intricately links cytoskeletal dynamics, cell adhesion signalling, and ECM remodelling, providing a new theoretical framework for pathophysiological research in CAVD. In clinical practice, VASP and its downstream pathway components, particularly FBLIM1 and the FA pathway, may serve as potential biomarkers and therapeutic targets for the early diagnosis and treatment of CAVD. For example, the FA pathway inhibitors PF-573228 and Y15 demonstrated significant anti-calcification effects both in vitro and in vivo, suggesting that targeting this pathway may offer a new nonsurgical intervention strategy for patients with CAVD.

cell biology↗

bioRxiv2026

Multiscale learning and topological analysis across complex postures enable robust nematode size quantification in pharmacological assays

Body size is an important trait that reflects animal development and physiology. In nematodes, precise measurement is valuable for linking variation in body dimensions to biological questions such as developmental timing, genetic regulation, and drug responses. However, robust size measurements can be difficult to obtain because nematodes can vary in curvature, have self-intersecting postures, and overlap with neighboring animals. Current image analysis software, such as CellProfiler, can measure isolated animals in straight postures but struggles with curly or overlapping animals. Here, we present NemaSize, an artificial intelligence (AI)-aided pipeline to measure Caenorhabditis nematode body sizes across complex postures using multi-scale learning and topology-aware skeletonization. Using You Only Look Once (YOLO) models trained at different spatial scales, NemaSize first identifies individual animals in a large field of view (FOV; 6.75 x 6.75 mm) and then performs high-resolution body segmentation in the region of interest (ROI). Next, NemaSize converts segmented body masks into topological graph representations, allowing curly and overlapping animals to be classified and skeletonized according to the body topology. NemaSize achieved less than 4% overall error in length and width measurements across all posture classes. Compared to CellProfiler, NemaSize demonstrated higher robustness for complex postures, including a 48% error reduction in length measurements for curly or self-overlapping animals. Application of NemaSize in high-throughput imaging assays further shows that NemaSize provides accurate quantification of Caenorhabditis briggsae larval development in response to the anthelmintic drug ivermectin, a task that was difficult for CellProfiler because of curly animal postures. Together, NemaSize provides a robust approach for automated body size quantification for Caenorhabditis nematodes and will support broad applications in high-throughput pharmacological and genetic screens. Beyond nematodes, NemaSize introduces a multiscale computational framework for analyzing elongated biological objects with complex topologies.

pharmacology and toxicology↗

bioRxiv2026

A Minimally Invasiveness Hybrid Brain-Computer Interface: A Distributed, Scalable and Evolvable Architecture for Whole Brain Access

Brain-computer interfaces face a fundamental trade-off between the signal fidelity and stimulation precision of noninvasive systems and the surgical burden and scalability of invasive systems. Non-invasive BCIs suffer from low signal quality and poor stimulation accuracy due to the skull barrier and the variability introduced by the scalp and skull. Existing invasive BCIs rely on traumatic surgical procedures or brain-penetrating electrodes, which limits their spatial extensibility, application, and patient acceptance. Here, we introduce a minimally invasive hybrid BCI architecture that uses the skull as a distributed interface layer rather than treating it solely as a barrier. The hybrid BCI comprises four integrated components: (1) the safe and smart micro-hole craniotomy; (2) distributed microelectrodes subcutaneously implanted in micro-holes in the skull with the distal end in contact with the dura; (3) an external bi-directional wearable headset for coupling, recording, stimulation, and channel selection; and (4) an AI-assisted planning and control agent. Animal studies have shown that micro-holes with a diameter of 300-800 m can be safely and conveniently prepared at any predefined locations across the skull without impairing the dura. In vivo experiments on rats demonstrate that the hybrid BCI with skull-implanted microelectrodes evidently increases resting-state spectral power and improves the signal-to-noise ratio of somatosensory and steady-state visual evoked responses compared to the scalp EEG; the computational modelling shows that distributed skull-dura microelectrodes can increase the intracranial electrical field strength and steer focused temporal-interference fields towards predefined deep brain targets. These findings will lay a solid foundation for future endeavors in wireless integration, safety evaluation and clinical benefits of the hybrid BCI. In summary, we propose the hybrid BCI as a distinct minimally invasive BCI paradigm with the great potential as a distributed, scalable, and upgradable neural interface that can expand the clinical application of minimally invasive BCI techniques.

bioengineering↗

bioRxiv2026

The basal cell state maintains pancreatic cancers by controlling an immunosuppressive circuit

Intra-tumoral heterogeneity is a cardinal feature of solid tumors, yet how distinct cancer cell states functionally contribute to malignant and stromal diversity in situ remains poorly understood. Using mouse models to lineage-trace or genetically ablate the two predominant cancer cell states in autochthonous pancreatic ductal adenocarcinoma (PDAC), we discover that basal cancer cells are highly plastic, whereas classical cancer cells exhibit limited plasticity. Strikingly, ablation of the basal, but not the classical, state induced rapid and durable tumor collapse, driven by loss of immunosuppressive cancer-associated fibroblasts, macrophage repolarization, and reprogramming of the tumor cytokine milieu, culminating in tumor destruction by cytotoxic lymphocytes. Knockout of a single cytokine, GM-CSF, specifically in basal cells recapitulated macrophage repolarization and lymphocyte recruitment observed upon basal state ablation and shrank tumors. These results reveal the basal cell state controls an immunosuppressive cell circuit critical for PDAC maintenance, motivating therapeutic targeting of the basal cells.

cancer biology↗

bioRxiv2026

Prior Context Scaffolds Sentential Semantic Integration during Noisy Speech Comprehension

Understanding speech in noise is a central challenge of everyday communication, yet listeners often succeed by using prior context. How the brain uses such context remains debated: it may refine predictions about upcoming words, or it may provide a higher-level framework that helps degraded speech cohere into meaning. Here we combined simultaneous EEG-fNIRS recording with hierarchical multivariate encoding models to track how prior context shapes speech processing from acoustics to words and sentential meaning. Participants listened to natural spoken narratives under clear speech, noisy speech, and context-supported noisy speech conditions. Context brought comprehension of noisy speech close to clear-speech levels. EEG revealed that contextual support reduced neural encoding of lexical surprisal and entropy, indicating weaker tracking of local word-level prediction demands. In contrast, when context was available, fNIRS showed enhanced encoding of sentence-level semantic integration across frontal regions and the right angular gyrus, and stronger angular gyrus encoding predicted better comprehension. By combining EEG and fNIRS to capture complementary electrophysiological and hemodynamic signals, this multimodal approach reveals a hierarchical shift in degraded speech comprehension: prior context does not simply improve word-by-word prediction, but scaffolds the integration of noisy input into coherent discourse.

neuroscience↗

bioRxiv2026

Bidirectional communication between neurons in the mesentery and ileal myenteric neurons

The intestinal mesentery has been recently classified as a new organ and contains various cell types including adipocytes, preadipocytes, endothelial cells, and immune cells. In addition, neuronal cell bodies are found in the small intestinal mesentery and are situated either individually or clustered together with glial cells in small ganglion structures close to the gut wall. However, little is known about the origin or function of these extra-intestinal mesenteric neurons. The aim of this study was to better these characterize mesenteric neurons and to examine their connectivity with the ENS using calcium imaging in adult mouse ileum with the mesentery attached. Here we show that neurons in the mesentery express typical ENS neurochemical markers, respond to 5-HT, ATP and the nicotinic agonist DMPP, and receive nicotinic synaptic inputs. Furthermore, using labeling with the neuronal tracer DiI, some mesenteric neurons were found to project into the gut wall and can provide functional excitatory inputs to myenteric neurons. By contrast, we did not find evidence for mesenteric neurons providing inputs to other extrinsic neuronal targets, suggesting that they preferentially interact with the ENS. We also demonstrate that mesenteric neurons can be activated by intestinal distension and that the mesentery provides a source of inhibition to the myenteric plexus. Taken together, we show that the ENS not only interacts with vagal and spinal afferents, and sympathetic and parasympathetic nerves, but also neurons situated in the mesentery. Finally, our data suggest that these neurons may provide a form of negative feedback to the myenteric plexus such as in the event of intestinal distension. These findings have important implications for the regulation of intestinal motility in physiological and pathophysiological conditions.

neuroscience↗

bioRxiv2026

Multilayered specificity of transcription factor binding at cytokine promoters

Transcription factors (TFs) regulate gene expression through sequence-specific DNA binding, and their genomic occupancy is further influenced by TF expression, activation state, and protein-protein interactions. How these mechanisms determine context-specific gene regulation remains incompletely understood, particularly for tightly controlled immune genes such as cytokines. Here, we use paired yeast one-hybrid (pY1H) assays to systematically examine DNA binding of 236 TFs and 392 TF-pairs across 106 cytokine gene promoters. Of the 1,619 TF-promoter interactions identified, 555 required TF cooperativity and 410 were antagonized by at least one TF partner, suggesting that TF-DNA binding is highly dependent on TF partners. Usage of different partners can drastically alter a TFs target repertoire and may result in the recruitment of different transcriptional cofactors. Integration with existing data on TF expression and activation further showed that cooperativity and antagonism provide additional, underappreciated layers of DNA-binding specificity.

systems biology↗

bioRxiv2026

Cysteine-mediated bortezomib resistance is governed by α-ketoacid availability

Dissecting how metabolite availability impacts drug sensitivity is critical for understanding therapy resistance. While proteasome inhibitors like the boronic acid proteasome inhibitor bortezomib are cornerstones of therapy for multiple myeloma, the clinical utility of these drugs is often limited by development of resistance, the metabolic drivers of which remain poorly understood. In this study, we find that -ketoacids, including pyruvate, increase sensitivity to boronic acid proteasome inhibitors independent of their conventional roles in metabolism. Instead, -ketoacids directly react with intracellular cysteine to form thiazolidines, sequestering cysteine away from forming conjugates with boronic acid proteasome inhibitors and detoxifying these drugs. Preventing cysteine-mediated detoxification through -ketoacid supplementation increases the efficacy of boronic acid proteasome inhibitors, leading to greater proteasome inhibition and cytotoxicity that is reversed by cysteine supplementation. These findings suggest that modulating available cysteine through -ketoacid interactions can impact effective levels of some drugs in cells, and represent a potential strategy to overcome resistance and maximize the efficacy of boronic acid proteasome inhibitors.

cancer biology↗

bioRxiv2026

HLiCA: An integrated cell atlas of the healthy human liver

The human liver is composed of a heterogeneous mix of cell types. How these distinct populations contribute individually and collectively to liver function remains poorly understood. Although single-cell technologies have advanced our understanding of liver biology, individual studies have often been limited by small donor cohorts and inconsistent cell type annotations. Integrating multiple datasets can overcome these challenges and better capture biological variability. We present the Human Liver Cell Atlas (HLiCA), an integrated reference of non-disease liver cells assembled from eight datasets across six research centers, encompassing more than 525,000 cells from 110 donors. Developed in collaboration with the Human Cell Atlas Liver Bionetwork, the HLiCA incorporates expert-curated cell annotations refined through community feedback and dedicated cell type annotation meetings. The HLiCA classifies cells into six lineages and expands the cell type resolution to include 47 distinct cell types. Starting from raw sequencing reads, we realigned all data and performed rigorous benchmarking to ensure robust integration across technical and biological variables. Genetic ancestry was inferred for all samples to evaluate the range of ancestral backgrounds represented in the atlas. The expanded cell type annotation enabled identification of previously unrecognized liver cell types, including NRXN1+ stromal cells. Their presence was validated using spatial transcriptomics, which localized NRXN1+ stromal cells to periportal regions. With the number of donors included in the HLiCA we were able to examine cell type specific associations with demographic covariates. In hepatocytes, drug metabolism genes showed differential expression between sexes, and in cholangiocytes, mucus-production genes varied with age. As the largest and most genetically diverse human liver cell atlas to date, the HLiCA provides a comprehensive, well-annotated reference for the field, annotated by expert consensus. This resource will enable deeper interrogation of liver cellular diversity, architecture, and function in the healthy human liver and serve as a reference to understand changes that occur with disease.

genomics↗

bioRxiv2026

Multi-omics, organoid-based modeling reveals an SRC/mTOR-dependent fetal-like stem cell trajectory in colorectal cancer

BackgroundSingle-cell atlases have described diverse stem cell states in colorectal cancer (CRC), however, the overarching trajectories of those states and the underlying functional mechanisms, including their relevance for drug sensitivity, need better understanding. MethodsWe established 64 patient-derived organoids from microsatellite-stable colorectal cancers, characterized their transcriptomes and genomes, and performed drug screening with 62-140 clinically approved substances. We analyzed additional published transcriptome data from patient-derived organoids (72 patients from three independent datasets), TCGA-CRC data (466 patients), and single-cell transcriptomes of tumor biopsies (123,000 cells from six independent cohorts) to establish a functional and molecular landscape of CRC stem cells. We performed mechanistic follow-up analyses by mass-spectrometry-based proteomics, large-scale kinase inhibition assays and immunofluorescence analyses. ResultsWe find a continuous landscape of CRC stem cells that is characterized by distinct developmental programs: adult stem cell-to fetal-like regenerative states and transition between differentiation programs. By large-scale drug perturbations and multi-omics modeling, we identify a regenerative/fetal-like stem cell trajectory characterized by PI3K/mTOR dependency. We find the identified developmental axes conserved in organoid, clinical, as well as single-cell data, and the fetal-like PI3K/mTOR-dependent state to be associated with poor clinical prognosis. Mechanistically, PI3K/mTOR vulnerability is linked to a lack of adaptive capability due to suppressed mRNA translation and associated with an upregulated SRC signaling network. ConclusionsOur work moves beyond a molecular CRC landscape by combined functional perturbation analyses in organoids. This enables mechanistic modeling of stem cell state regulation and identifies an SRC/mTOR-dependent regenerative state in CRC, which might allow improved therapeutic targeting in the future.

cancer biology↗

bioRxiv2026

A CSF Proteomic Clock Reveals Opposing Brain-Aging Programs and Predicts Neurological Disease Progression

Aging is the risk factor for neurological disease, yet the molecular architecture of human brain aging remains poorly defined. Here, we analyzed more than 10,000 cerebrospinal fluid (CSF) proteomes across multiple cohorts and proteomic platforms to developed a 249-protein CSF aging clock that accurately predicts age and generalizes across independent datasets. CSF brain-age acceleration was increased across diverse neurological diseases, associated with blood-brain barrier (BBB) dysfunction, and predictive of longitudinal cognitive decline, neuroimaging progression, and dementia conversion. A simplified 30-protein panel retained similar prognostic performance. Biologically, clock proteins resolved two opposing programs: pro-aging activation of immune, vascular/BBB, ECM and coagulation pathways marked by CHI3L1, CD14, VWF, LRG1 and LTBP2, and anti-aging collapse of neuronal, synaptic, axonal and structural-maintenance programs marked by NPTX2, COL1A2, NID1, CDH8 and PENK. Brain-wide single-cell and regional mapping linked these programs to disease-vulnerable compartments. These findings establish a molecular framework for biological brain aging and neurological disease vulnerability.

neuroscience↗

bioRxiv2026

Phylogenetic Mosaic of an Arms Race with Asymmetrical Sexual Conflict and Its Macroevolutionary Consequences in a Lineage of Small Water Striders

Sexual conflict has been hypothesized as a driver of speciation, though its effects are likely heterogeneous across phylogenies and between sexes. The Gerromorpha (semi-aquatic bugs), which inhabits water surfaces across diverse aquatic environments, long served as a model for studying sexual conflict. While previous studies have focused on rapid antagonistic coevolution and the genetic basis of sexually antagonistic traits, the macroevolutionary consequences of asymmetrical sexual conflict-particularly male-dominated grasping traits versus female resistance-remain largely unexplored. Within the subgenus Pseudovelia, males exhibit pronounced phenotypic diversification in grasping structures, whereas females show modest, clade-specific resistance traits, suggesting male-biased asymmetric conflict. This system presents a valuable opportunity to examine how sexual conflict influences diversification and asymmetrical trait evolution across lineages. Using 204 individuals, representing over half of the subgenus's species diversity, we reconstructed a time-calibrated phylogeny, quantified diversification rates, assessed sexual conflict intensity across clades, and analyzed correlations between sexual trait evolution and diversification. Our results reveal extensive phylogenetic conflict, particularly within the East Asian clade, driven by introgression and incomplete lineage sorting (ILS). Furthermore, we observe significant phylogenetic heterogeneity in both phenotypic evolution and diversification rates. Notably, a male "trait package" enhancing grasping ability likely drives rapid diversification in the recently radiated "South China" lineage. In contrast, grasping traits involving abdominal segment VIII are associated with lower conflict intensity, facilitating greater evolutionary flexibility in female resistance and resulting in lineage-specific counter-adaptations. These findings highlight the heterogeneous dynamics of asymmetrical sexual conflict in shaping diversification and speciation.

evolutionary biology↗

bioRxiv2026

Zinc coordination by the wheat rust effector AvrSr33 provides a structural scaffold required for immune recognition

Abstract/SummaryInteractions between plants and pathogens drive long-term co-evolution through cycles of effector diversification and immune recognition. Effectors play central roles in this molecular interplay, and zinc-binding folds have been identified in a subset of pathogen effectors, yet the contribution of zinc coordination to effector stability and immune recognition remains unclear. Here, we investigated the structure and recognition of the AvrSr33 effector from the wheat stem rust fungus (Puccinia graminis f. sp. tritici, Pgt). Structural and biochemical analyses show that AvrSr33 adopts a fold containing two zinc-binding sites. Transient expression assays in Nicotiana benthamiana show that AvrSr33 directly interacts with Sr33, and comparison of recognised and non-recognised AvrSr33 variants identifies a polymorphic loop associated with recognition. This loop is positioned adjacent to one of the zinc-binding sites with its orientation constrained by zinc coordination. Reciprocal mutations of key surface residues within this region alter recognition, whereas mutation of the zinc-binding site abolishes recognition. Our data suggest that zinc coordination in AvrSr33 provides a structurally constrained scaffold that supports the surface features associated with Sr33 recognition. These findings provide a mechanistic framework for understanding how zinc coordination contributes to effector recognition and may influence the evolutionary trajectories of pathogen effectors.

Plant Biology↗

bioRxiv2026

CD8-mediated organization of the TCR-pMHC interface shapes its force response and dissociation pathways

The mechanical response of the interaction between the T cell receptor (TCR) and the peptide major histocompatibility complex (pMHC) is fundamental to antigen recognition, but the atomic-scale mechanisms by which the CD8 coreceptor modulates the complexs conformational states and force-bearing behavior remain poorly understood. We employed all-atom molecular dynamics and steered molecular dynamics simulations of membrane-embedded TCR-pMHC and TCR-pMHC-CD8 complexes to characterize their dynamics and force-induced dissociation. Microsecond-long molecular dynamics (MD) simulations show that binding of CD8 to the MHC 3 domain applies restraints to the latter one, which leads the MHC 1 helix to stably bind against the TCR complementarity-determining regions (CDRs) and suppresses the fluctuations of the antigenic peptide. Furthermore, under mechanical loading, the TCR-pMHC-CD8 system exhibits a distinct dissociation pathway compared to that of TCR-pMHC complex, which may strengthen the mechanical stability of the binding of TCR-pMHC. Collectively, these findings unravel the molecular mechanisms of CD8-mediated synergistic stabilization and mechanical regulation of TCR-pMHC, providing new mechanistic insights into coreceptor-dependent T cell antigen recognition. SIGNIFICANCEThe TCR-pMHC handshake is the definitive spark that ignites the immune response. It has been shown that the force applied to the TCR-pMHC complex is critical for triggering the downstream signaling. In addition, TCR recognition of pMHC is regulated by force and strongly influenced by coreceptors, such as CD8. Therefore, understanding how coreceptors mediate TCR-pMHC interactions upon the application of force is crucial for revealing the biophysical basis of immune signaling. This study unravels how coreceptors shape the dynamics and mechanical response of the TCR-pMHC complex at the atomic level.

biophysics↗

bioRxiv2026

Identifying cytokine-release signatures of flow-driven endothelial remodelling in an intracranial aneurysm cell culture model

Intracranial aneurysm (IA) rupture is catastrophic, yet current models of rupture-risk inadequately capture underlying IA remodelling mechanisms. Endothelial-haemodynamic interactions are central to these processes, but in vitro flow platforms often lack vessel-relevant geometry or long-term perfusion. Here, temporal and spatial endothelial responses to haemodynamic stress were investigated across idealised and patient-specific vascular models. Polydimethylsiloxane models were endothelialised with human aortic endothelial cells then perfused at up to 1.6 Pa wall shear stress for five days. IA models were exposed to steady or cardiovascular flow waveforms, with endothelial phenotype assessed by immunofluorescence and cytokine profiling. Flow initiation induced a transient inflammatory response, with elevated MCP-1 and TNF- at day two, followed by a resolution of cytokine levels by day five, including a [~]7.5-fold reduction in MCP-1, despite increased haemodynamic loading. Endothelial cells retained a cobblestone-like morphology with eNOS undetected, resembling a partially activated phenotype. Compared with steady flow, cardiovascular flow reduced TGF-{beta}1 and IL-8 secretion and decreased FGF-b consumption ([~]2.5 fold), suggesting enhanced phenotypic stability. This study presents the first in vitro IA model incorporating a cardiovascular flow waveform and identifies cytokine signatures with potential utility as biomarkers of IA remodelling, highlighting the importance of long-term perfusion for modelling chronic vascular disease. Table of Contents FigureAn in vitro model of an intracranial aneurysm was developed to investigate how fluid flow dynamics impact endothelial remodelling and inflammation. Pulsatile cardiac flow promoted stabilisation of inflammatory signalling, which was sustained under a steady flow regime. Cytokine signatures emerged with potential utility as biomarkers of IA remodelling, highlighting the importance of long-term perfusion for modelling chronic vascular disease. The schematic of the cytokine release dynamics used in the graphical abstract below was generated with the assistance of AI-based tools including ChatGPT (v5.5) and M365 Copilot to align with key results from this manuscript. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/733289v1_ufig1.gif" ALT="Figure 1000"> View larger version (80K): org.highwire.dtl.DTLVardef@709204org.highwire.dtl.DTLVardef@825f81org.highwire.dtl.DTLVardef@14c345eorg.highwire.dtl.DTLVardef@222a8_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Structure of full-length APOBEC3B bound to EBV BORF2 reveals coordinated neutralization of a cancer-associated mutator

The double-domain APOBEC3B (A3B) contains an N-terminal non-catalytic and C-terminal active cytidine deaminase domains (NTD and CTD). A3B restricts viral infection yet is also a major endogenous mutator in human cancer, driving tumor evolution and drug resistance. A previous study showed that the Epstein-Barr virus (EBV) ribonucleotide reductase large subunit BORF2 binds the active site of the A3B CTD and neutralizes the activity of the isolated catalytic domain. However, the three-dimensional organization of full-length A3B (fl-A3B) and the contribution of A3B NTD to BORF2-mediated neutralization have remained unclear. Here, we report a 2.77 [A] cryo-electron microscopy structure of fl-A3B in complex with EBV BORF2. The structure reveals an elongated hetero-octamer comprising two A3B2/BORF22 tetramers linked through alternating canonical and non-canonical BORF2 dimer interfaces. Full-length A3B adopts a defined NTD-CTD arrangement distinct from previously characterized APOBEC3G conformations. The A3B CTD binds BORF2 and occludes access to the catalytic site, while the A3B NTD simultaneously contacts a second BORF2 subunit, stabilizing a previously uncharacterized BORF2 canonical dimer interface required for higher-order assembly. Disruption of either BORF2 dimer interface prevents formation of filamentous A3B-BORF2 assemblies. These findings establish the structural architecture of full-length A3B and reveal how dual-domain engagement by A3B promotes higher-order BORF2 assembly, providing a structural framework for understanding EBV-mediated neutralization of an antiviral and cancer-associated mutator.

Cancer Biology↗