Biology subjects

Nguyen, Q.

Publications and source records attributed to Nguyen, Q..

At least 19 recordsLinked to original sources

bioRxiv2026

A Practical Framework for Constructing Population-Specific and Alternate-Contig-Aware Genome References: A case study of Vietnam

Current studies in human genomics typically rely on the standard genome reference GRCh38 which is known to be biased toward populations of European ancestry and therefore has limitations when applied to other populations. Although various graph-based pangenome references were constructed for several populations to deal with this bias, their usage in practice is currently still limited compared to linear genome references. Here we present a framework for constructing a population-specific genome reference using GRCh38 as backbone with alternate-contig awareness to enhance genomic data analysis in the target population. We demonstrated the advantages of our framework using both public and in-house Vietnamese whole-genome sequencing (WGS) datasets. Genomic variants derived from high-coverage WGS data of the 1000 Vietnamese Genomes Project (VN1K) were imported into our framework to build a Vietnamese-specific Genome Reference (VGR). VGR was then compared to GRCh38 in read alignment and variant calling using high-coverage WGS data of 99 Vietnamese individuals (KHV) from the 1000 Genomes Project (1kGP). Using Omni array genotyping data from 99 KHV samples as an independent benchmark, we found that VGR improved variant-calling precision and reduced false-positive calls compared to GRCh38. Our framework could be easily used for other populations as long as they have a variant database similar to VN1K. Our code is publicly available at github.com/VinGenome/VGR

genomics↗

bioRxiv2026

Gp130 Orchestrates a Bidirectional Neuron-Microglia Circuit for neuroprotection

Acquired central nervous system (CNS) injury is one of the most common neurological conditions globally, yet effective treatment options are lacking. As the main tissue-resident macrophages of the CNS, microglia have emerged as key functional regulators of CNS repair. However, means to induce neuroprotective microglia and harness their intrinsic repair capabilities have remained elusive. Here we identify gp130 as a key receptor molecule for facilitating bidirectional microglia-neuron communication that improves outcomes from CNS injury. We show that activation of gp130 in CNS-resident microglia triggers the secretion of leukemia inhibitory factor (LIF), a neurotrophic cytokine. LIF induces neuronal IL-6 secretion that then acts back onto the microglial gp130 receptor, thus creating a neuroprotective loop. We demonstrate the broad therapeutic potential of acute gp130 activation across multiple models, including traumatic brain injury, stroke, and spinal cord injury, and that this pathway can be leveraged therapeutically with designer cytokines.

neuroscience↗

bioRxiv2026

A high-throughput, 3D microtissue platform for multiparametric analysis of tissue remodeling.

Extracellular matrix (ECM) remodeling and force generation are fundamental drivers of tissue morphogenesis and repair, yet scalable methods to quantitatively interrogate these dynamic mechanical processes remain limited. Here, we present a high-throughput screening platform that integrates engineered three-dimensional (3D) microtissues within a standardized 96-well format. We introduce a robust mold-casting fabrication process and a layer-by-layer surface modification strategy, that ensures long-term tissue stability and prevents detachment (95% tissue formation success; stable in culture for more than 10 days). This system enables simultaneous, longitudinal quantification of tissue closure, tissue contractility, and tissue compaction from a phase-contrast imaging modality. The computational data analysis tools that accompany this framework ensure reproducibility through deterministic computation and accelerate data extraction 80-fold relative to manual annotation. Using pharmacological compounds, we show that tissue closure dynamics, force generation, and compaction represent independent variables of ECM-driven tissue remodeling, challenging assumptions embedded in commonly used contraction-based assays. Furthermore, benchmarking against reported clinical drug responses demonstrates that the 3D platform better aligns with clinical outcomes (Kendall{tau} -b = 0.72, p=0.045, n =8/10) than a conventional two-dimensional scratch wound assay (Kendall{tau} -b = 0.52, p=0.25, n =4/10). Together, this work establishes a scalable assay for functional screening and quantitative assessment of tissue remodeling dynamics in three-dimensional systems.

bioengineering↗

bioRxiv2026

ApolipoproteinE drives inflammation resolution pathways essential for recovery from Japanese encephalitis

Effective control of viral encephalitis requires immune responses that clear infection without causing damaging neuroinflammation, yet the mechanisms governing resolution and recovery remain unclear. Using a Japanese encephalitis virus mouse model spanning asymptomatic, symptomatic, and lethal trajectories, together with single-cell spatial transcriptomics and RNA-seq, we identify apolipoprotein E (ApoE) as a driver of neuroinflammation resolution. Apoe was upregulated in microglia and infiltrating myeloid cells of symptomatic survivors, where Apoe-Trem2-Tyrobp signalling promoted a phagocytic, anti-inflammatory program. In contrast, immune cells in lethal disease failed to induce Apoe and remained pro-inflammatory. ApoE-deficient mice were unable to recover following encephalitis onset, demonstrating that ApoE signalling is essential for resolution and recovery. Analysis of cerebrospinal fluid from acute encephalitis patients linked APOE isoforms to neuroinflammation resolution, with APOE{varepsilon}2 carriers exhibiting reduced neutrophils and shorter hospitalisation. These findings identify ApoE as a critical driver of neuroinflammation resolution and a promising therapeutic target for viral encephalitis.

microbiology↗

bioRxiv2026

Mapping fibrotic microenvironments: single-cell and spatial profiling of Schistosoma mansoni-induced tissue fibrosis

Schistosoma-induced tissue fibrosis, driven by immune response to trapped schistosome eggs, is the principal cause of pathology and schistosomiasis-related morbidity. While praziquantel effectively clears adult parasites, no therapies exist to target eggs or egg-induced tissue fibrosis. Here, we utilise single-cell spatial transcriptomics to define the high-resolution molecular architecture of the fibrotic niche in Schistosoma mansoni-infected mice at 8 weeks post-infection. Our data reveal that the host executes divergent, organ-specific biological programs: constructing a rigid, concentric fibrotic granuloma for permanent egg sequestration in the liver while building a flexible, discontinuous collagen architecture in the intestine to facilitate egg transit. Spatially resolved cell-cell interaction analysis, unprecedented in schistosome-induced fibrosis, identifies the strongest cellular interactions between macrophages and collagen-producing cells, with TGF-{beta}-dominant ligand-receptor pairs in the hepatic niche and integrin-centered pairs in the intestine. Despite this architectural divergence, we detected a core signature of five ligand-receptor pairs shared across both tissues, suggesting shared signalling interactions that could be leveraged for pan-tissue therapeutics for treating schistosome-induced fibrosis. Together, these findings provide the first high-resolution spatial atlas of schistosomiasis-associated fibrosis and provide a foundational framework for discovering novel drug targets capable of reversing established tissue damage, addressing a critical clinical gap where current therapies fail.

molecular biology↗

bioRxiv2026

Explainable Prototype Booster: Enhancing Latent Representations of Foundation Models for Gene Expression Prediction

Spatial transcriptomics (ST) is a cutting-edge technology that measures gene expression while preserving spatial context and generating pathology-grade tissue images. Although ST has enabled numerous discoveries and demonstrated a huge application potential in pathological diagnosis and prognosis, the technology remains time-consuming and costly. The ability to predict gene markers of cancer from histological H&E-stained tissue images can overcome these technological barriers to open new horizons for precision and personalised pathology. Recently, foundation models have demonstrated improvements in generating general-purpose embeddings of H&E-images. However, these improved representations are not optimized for gene expression prediction and lack task-specific adaptability. To address this limitation, we propose the Explainable Prototype Booster (EP-Booster), which incorporates biological prior knowledge to guide the construction and training of learnable prototypes for embedding refinement, thereby improving gene expression prediction. Importantly, model predictions are inherently interpretable through pathway-level attributions associated with the prototypes. Extensive experiments across multiple datasets, cancer types, and spatial transcriptomics platforms demonstrate that EP-Booster consistently outperforms existing methods. Moreover, EP-Booster can be integrated with diverse foundation models to enhance task-specific representations, thereby improving predictive performance and biological interpretability in clinically relevant applications, including cancer biomarker prediction, survival analysis, and drug response prediction.

bioinformatics↗

bioRxiv2026

Adaptive Integration of Heterogeneous Foundation Models to Find Histologically Predictable Genes in Breast Cancer

Foundation models for computational pathology have rapidly emerged as powerful tools for extracting rich biological and morphological representations from histopathology images. However, variations in model architecture, pre-training data, and optimization objectives often lead to task-dependent performance, rather than universal generalization. As a result, effective strategies for integrating their complementary strengths are essential to fully realize the potential of foundation models for robust histopathology analysis. Meanwhile, recent breakthroughs such as spatial transcriptomics provide an unprecedented opportunity to integrate genetic and histopathology information from the same patient sample, thereby maximizing both molecular and anatomical pathology insights. Specifically, each models embedding is first mapped to gene-level predictions via a dedicated prediction head, enabling model-specific feature utilization. A lightweight weighting network then adaptively aggregates these predictions to produce a unified and robust output at gene and spatial location levels. Across multiple spatial transcriptomics datasets, our approach consistently outperforms both individual foundation models and classical ensembling methods. Focusing on breast cancer, we observe substantial gains in prediction accuracy for clinically relevant PAM50 subtype markers and drug-target genes. Moreover, the proposed framework improves interpretability by revealing model-specific contributions and specialization at the gene level. Overall, our work presents an effective solution to integrating multiple foundation models for enhancing the genetic analyses of histopathology images.

bioinformatics↗

bioRxiv2026

E-Selectin Orchestrates IL-1B-Dependent Neuroinflammation via NLRP3 in Vincristine-Induced Neuropathy

Vincristine-induced peripheral neuropathy (VIPN) is a frequent and dose-limiting complication of cancer therapy, yet the upstream mechanisms coupling vascular activation to neuroinflammation remain poorly defined. Here we identify E-selectin as a critical orchestrator of vincristine-induced neuropathy. Systematic interrogation of endothelial adhesion molecules in a murine model of VIPN revealed that blockade of E-selectin, but not ICAM-1, PECAM-1 or P-selectin, completely prevented mechanical hypersensitivity and markedly reduced F4/80 immune cell accumulation in dorsal root ganglia and peripheral nerves. Genetic deletion of E-selectin conferred equivalent protection, despite the absence of structural loss of intraepidermal or myelinated fibres, indicating a predominantly functional neuroimmune pathology. Spatial transcriptomics demonstrated that vincristine induces a conserved stress and neuroinflammation-associated transcriptional programme in dorsal root ganglia, with immune and stromal populations acting as dominant signalling hubs. Genetic or pharmacological perturbation of E-selectin did not abolish injury-associated pathways but redistributed cell-cell communication networks, reducing immune-cell dominance and reshaping interferon and metabolic signalling states without inducing Sele expression. Mechanistically, E-selectin exerted non-canonical effects beyond endothelial adhesion. Local E-selectin administration was sufficient to induce macrophage-dependent mechanical hypersensitivity that was abolished in Fut4/7-deficient mice and following phagocyte depletion. In macrophages, E-selectin enhanced vincristine-driven NF-{kappa}B activation, NLRP3 inflammasome assembly and IL-1{beta} release. Together, these findings position E-selectin as an upstream regulator of IL-1{beta}-dependent neuroinflammation in VIPN and identify selective targeting of E-selectin-mediated immune-neuron interactions as a therapeutic strategy for chemotherapy-induced neuropathy.

neuroscience↗

bioRxiv2026

Two anchoring proteins control daughter apical complex assembly in Toxoplasma gondii

During Toxoplasma gondii division, the apical complex--comprising the conoid, apical polar ring (APR), and preconoidal rings--assembles with precise spatiotemporal coordination to form functional daughter buds. Despite their essential roles in invasion, motility, and division, the scaffolding proteins orchestrating this ordered assembly have remained largely unidentified. Here, we identify and characterize RCC1-2 and APR8 as essential factors directing distinct, sequential phases of daughter cell apical complex construction. Both proteins are recruited with precise spatial and temporal dynamics to the daughter buds, where they function as scaffolds rather than static structural components. APR8 transiently occupies the basal region of the APR specifically in early daughter cells. It is dispensable for conoid and PCR initiation, yet its loss causes APR collapse, abolishes SPMT anchoring, and eventually arrests conoid maturation. In contrast, RCC1-2 localizes beneath the APR basal layer and persists throughout daughter cell development, where it contributes to stabilizing the attachment of SPMTs to the APR. Notably, in situ cryo-electron tomography further reveals that the interspersed pillars bridging SPMTs ends to the APR fail to form properly in RCC1-2-depleted parasites. These findings map a hierarchical RCC1-2/APR8-dependent scaffolding process that advances our understanding of parasite replication.

microbiology↗

bioRxiv2026

Spatial pharmaco-multiomics reveals drug distribution, metabolic niches, and spatially constrained resistance in medulloblastoma

Single-cell and spatial transcriptomic studies have provided insights into the developmental origins and intratumoural heterogeneity of SHH medulloblastoma (SHH-MB) and suggested how targeted drugs such as CDK4/6 inhibitors remodel tumour ecosystems, yet the interplay between local drug exposure, metabolism, cell state, and drug resistance remains poorly understood. Here we developed a same-section spatial pharmaco-multiomics framework that integrates MALDI-MSI-based spatial metabolomics with Visium whole-transcriptome profiling and high-resolution Xenium imaging to map palbociclib distribution, metabolite landscapes, and transcriptional programs within the same histological contexts of an SHH-MB PDOX model and primary human tumours. Palbociclib-rich tumour bulk exhibited broad suppression of E2F-driven proliferation and a shift toward neuronal differentiation, corroborating and extending prior findings. In contrast, drug-poor tumour-brain interfaces and perivascular regions retained E2F-high proliferative states and were enriched for mesenchymal-like stromal cells and ECM-remodelling genes, indicating anatomically constrained reservoirs of tolerance. Spatial metabolomics linked these interface niches to ganglioside (GM2) and sphingomyelin enrichment, while differentiated, drug-exposed regions displayed phosphatidylcholine, phosphatidic-acid signatures consistent with neuronal maturation. Integrated pathway analysis further revealed a "mitochondrial tuning" program, with upregulation of histidine, folate/one-carbon, CoA, and lipoate metabolism with redox and oxidative-phosphorylation support. These signatures were specific to therapy-exposed border cells. Rare palbociclib-positive, E2F-high resistant spots additionally exhibited mitotic checkpoint and DNA-repair signatures, implying a drug-induced resistance axis independent of scarcity. Together, our study provides a generalisable same-section spatial pharmaco-multiomics pipeline and a spatially resolved model of CDK4/6 response, nominating interface-focused metabolic and cell-intrinsic vulnerabilities for combination therapy.

cancer biology↗

bioRxiv2025

Dynamic O-GlcNAcylation of Sec23-interacting protein regulates COPII function

About one-third of the eukaryotic proteome transits the secretory pathway to reach its correct cellular or extracellular destination. At the earliest stage, transport from the endoplasmic reticulum (ER) to the ER-Golgi intermediate compartment (ERGIC) or Golgi apparatus is mediated by coat protein complex II (COPII). COPII coats consist of inner and outer layers formed by Sec23-Sec24 heterodimers and Sec13-Sec31 heterotetramers, respectively, which initially assemble at ER exit sites (ERES) to form transport carriers. Sec23-interacting protein (Sec23IP) links the inner and outer coats through its interactions with both Sec23A and Sec31A, positioning it as a key potential regulator of COPII function. However, the mechanisms controlling Sec23IP activity remain poorly understood. Here, we investigate how physiological stimuli regulate COPII function through the dynamic modification of Sec23IP by O-linked {beta}-N-acetylglucosamine (O-GlcNAc), a reversible, intracellular form of glycosylation. We first validated Sec23IP as a bona fide O-GlcNAcylated protein. Rescue experiments in Sec23IP knockout cells with a nearly unglycosylatable mutant protein demonstrated the essential role of O-GlcNAcylation in the intrinsically disordered domain in protein transport and in recruiting Sec31A to ERES. Moreover, O-GlcNAcylation of Sec23IP increased during protein transport, coinciding with a reduction in its interaction with Sec31A. These results indicate that distinct site-specific O-GlcNAcylation of Sec23IP spatiotemporally modulates its association with Sec31A to fine-tune ERES recruitment and COPII assembly/disassembly. Our work provides new insight into Sec23IP regulation and suggests that O-GlcNAc on other COPII proteins may govern carrier formation, uncoating, and transport.

cell biology↗

bioRxiv2025

Myeloid HDAC7 drives liver inflammation and systemic glucose dysregulation during diet-induced obesity

ObjectivesHistone deacetylase 7 (HDAC7), a classical HDAC family member, promotes LPS-inducible glycolysis and inflammatory mediator production in macrophages, innate immune cells that contribute to pathology in metabolic diseases. Here, we investigated myeloid HDAC7 functions in obesity-driven metabolic disease. MethodsWe used gain- and loss-of-function genetic approaches in mice to investigate myeloid HDAC7 functions in hepatic inflammation and metabolic disease, as well as associations with hepatic gene signatures characteristic of advanced chronic liver disease (CLD). ResultsTransgenic expression of Hdac7 in myeloid cells increased liver inflammation and liver mRNA levels of Ccl2 and Il1b, key inflammatory mediators linked to CLD. Liver glycogen levels were also decreased, another feature of CLD. Transgenic expression of Hdac7 in myeloid cells mimicked the hepatic inflammatory phenotype that was observed in mice fed a high fat, high cholesterol, and high sucrose (HFHCHS) diet, an obesity model that mimics some features of metabolic dysfunction-associated steatotic liver disease. In myeloid Hdac7 transgenic mice fed a HFHCHS diet, relative weight gain was increased, fasted glucose levels were elevated and glucose tolerance was dysregulated by comparison to control mice. Conversely, fasted blood glucose levels were reduced and glucose tolerance was improved in myeloid Hdac7-deleted mice on a HFHCHS diet. HDAC7 mRNA levels were also elevated in the livers of people with advanced CLD and spatial transcriptomics revealed that myeloid HDAC7 directs hepatic gene signatures characteristic of advanced CLD. ConclusionsMyeloid HDAC7 contributes to hepatic inflammation and systemic glucose dysregulation in a mouse model of obesity and liver inflammation.

immunology↗

bioRxiv2025

Modelling mental disorders in zebrafish. Neurexins severely modulate anxiety, social behaviours and aggression.

Can we reproduce mental disorders in zebrafish? To explore this question, we manipulated the neurexin gene family. Neurexin (nrxn) genes encode synaptic cell-adhesion molecules that have been repetitively associated with neurodevelopmental and mental disorders. While the zebrafish animal model offers tremendous advantages for dissecting neural development/function, no robust nrxn zebrafish models are currently available. In this study, we generated the first collection of zebrafish knockout lines for each nrxn gene, with mutations ranging from transmembrane domain- to full genomic locus-deletions. Surprisingly, all homozygous lines developed normally, presenting no gross neurodevelopmental or obvious early behavioural abnormalities. However, this absence of early phenotypes translated into profound, paralog-specific behavioural alterations emerging during juvenile-to-adult stages. All neurexin knockouts affected mating behaviour, complicating the generation and maintenance of homozygous lines. Except for this shared behavioural alteration, nrxn1, but not nrxn2 or nrxn3, led to marked changes in social behaviour and aggression. In contrast, nrxn2 mutants exhibited severe anxiety-like behaviours, including bottom-dwelling and repetitive freezing/seizure events. Strikingly, nrxn1 full-locus deletion mutants showed opposing behaviour, spending most of their time near the surface. The two also displayed opposite responses to open/closed field transitions; confinement alleviated nrxn2 anxiety but enhanced nrxn1 surface-dwelling. Meanwhile, nrxn3 mutants behaved normally in all our initial tests. In summary, our study introduces a complete set of zebrafish mutants covering the whole nrxn gene family, presenting striking juvenile/adult behavioural alterations despite the absence of noticeable early defects; echoing the delayed onset of human psychiatric disorders such as schizophrenia. This work demonstrates the value of zebrafish to study mental disorders and unlock a novel platform to unravel the pathogenic contribution of neurexin and associated subtle neurodevelopmental changes/timing that drive the emergence of mental illnesses.

neuroscience↗

bioRxiv2025

Genetic Ablation and Multi-Omics Profiling Reveal CEP55 as a Key Driver of Tumorigenesis in Diverse Cancer Models

BackgroundCEP55 is a centrosomal protein with emerging oncogenic roles. It is overexpressed in many cancers, where it drives genomic instability, phenocopies PTEN loss and hyperactivates the PI3K/AKT pathway, thereby promoting aggressive and therapy-resistant tumors. MethodsWe developed an inducible Cep55 knockout (KO) mouse model as well as generated primary, immortalized (SV40), and transformed (E1A/Ras) mouse embryonic fibroblasts (MEFs) for functional and proteomic assays. Tumorigenesis was studied using E1A/Ras MEF transplantation and a Pten-deficient genetically engineered mouse model (GEMM). Multi-omics apparatus including proteomics, and spatial transcriptomics, histopathology, immunobloting and functional assays were employed to elucidate underlying mechanisms. Findings were cross-validated using human cancer datasets. ResultsCep55 ablation remodeled the extracellular matrix (ECM), disrupted integrin and oncogenic signaling, reduced AKT/ERK activation, and induced stress pathways. Cep55 knockouts (KO) cells showed impaired proliferation, migration, invasion, and adhesion. In vivo, unlike the embryonic lethality observed in constitutive KOs, the inducible Cep55 deletion was well-tolerated in adult mice. Strikingly, tumors derived from Cep55-null EIA/RAS-transformed MEFs exhibited delayed onset and progression. In the genetically engineered cancer-prone mouse model, Cep55 deletion on a Pten-deficient background led to a greater than seven-fold increase in median survival. Spatial transcriptomics on cancerous tissues revealed that CEP55 regulates ECM remodeling, integrin expression, trafficking, and cell adhesion, supporting its critical role in tumor progression to metastasis. ConclusionCEP55 is dispensable for adult homeostasis but essential for tumorigenesis, especially with PTEN loss. Its deletion suppresses transformation, delays tumor growth, and prolongs survival, supporting CEP55 as a therapeutic target in PTEN-deficient cancers. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/685219v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@3d81e8org.highwire.dtl.DTLVardef@1bd5a7org.highwire.dtl.DTLVardef@167ecf3org.highwire.dtl.DTLVardef@1f57b95_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Analyzing and Visualizing Distance Measures for Clonal Trees

Cancer is an evolutionary process, in that a tumor results from a series of genomic mutations that are acquired over time. The history of how a tumor evolved is often represented using a clonal tree: a particular type of rooted tree where vertices represent tumor cell clones and edges represent ancestral relationships between them. In recent years, numerous algorithms have been developed that infer clonal trees from sequencing data. Correspondingly, researchers have also developed distance measures to compare clonal trees. While such distance measures have proven valuable, they are limited in a variety of ways. First off, they usually only utilize one or a few types of specific information when being computed - making it challenging to assess how well they capture other common types of differences between clonal trees. Secondly, their final output is just a single numerical value - meaning that information on what parts of the trees contributed to the distance is not being readily conveyed. In this work, we address both of these issues. We define a set of four classes of tree differences that describe common ways that clonal trees might differ from each other and analyze these classes using three different clonal tree distance measures. We then introduce a visualization tool called VECTr (Visual Encodings for Clonal Trees) that provides an enhanced pairwise comparison of clonal trees using the same three distance measures. In particular, VECTr contains three types of visualizations that allow a user to easily identify what parts of a tree contribute to its distance, including information relevant to when the trees differ in a manner that corresponds to one of our four classes of tree differences. We demonstrate the utility of our visualization tool using a variety of different use cases, including application to both simulated and real clonal trees. Code associated with the project is freely available at: https://github.com/quocodile/visualize-clonal-trees CCS ConceptsApplied computing Molecular evolution; Computational genomics; Computational biology.

bioinformatics↗

bioRxiv2025

A systemic clock brake: Period1 stabilizes the circadian network under environmental stress

Precise alignment between internal circadian clocks and environmental light cycles is essential for physiological homeostasis and survival. However, the molecular mechanisms that preserve this synchrony across central and peripheral tissues remain poorly defined. Here, we uncover an unexpected role for the core clock gene Period1 (Per1) as a systemic modulator of circadian stability, regulating light-induced re-entrainment across the brain and body. In Per1-deficient mice, we show that loss of Per1 accelerates clock realignment, influencing transcriptomic, metabolic, hormonal, and behavioral indicators of circadian realignment across multiple organ systems, including the suprachiasmatic nucleus (SCN) and peripheral tissues such as the liver, adipose tissue, and adrenal glands. Notably, this accelerated adaptation confers protection against jetlag-induced sleep disturbances, weight gain, and metabolic imbalance, underscoring a systemic role for Per1 in maintaining circadian network stability. Mechanistically, unbiased spatial transcriptomics identified reduced expression of the arginine vasopressin (AVP), a key neuropeptide mediating SCN intercellular coupling, as the driver of circadian network instability. Weakened SCN synchrony permits enhanced flexibility of peripheral oscillator responses, expediting whole-body adaptation to shifted light-dark schedules. These findings position Per1 as a critical regulator of circadian robustness, a buffer against light over-responsiveness, identifying a potential molecular target for mitigating circadian misalignment in contexts such as jetlag, shift work, and metabolic disease. TeaserWhat if beating jetlag was as simple as switching off a gene? Researchers show that disabling Per1, a core circadian regulator, accelerates body clock realignment and protects against sleep and metabolic disruption--highlighting new therapeutic possibilities for jetlag and shift work.

neuroscience↗

bioRxiv2025

A Developmental Mechanism Linking Heart Evolution and Congenital Defects

The evolution of double circulation in vertebrates required precise remodeling of the embryonic outflow tract (OFT), but the mechanisms enabling this transition remain unclear. Here, we show that oxygen acts as a developmental switch regulating apoptosis during OFT septation. In chick embryos, transient hypoxia disrupts apoptosis and produces atavistic phenotypes resembling ancestral vertebrate hearts with a single circulation. Comparative evidence suggests that developmental mode and associated oxygen levels facilitated OFT septation and the evolution of double circulation. This oxygen dependence also explains why CHD risk is elevated in hypoxic conditions, such as high-altitude pregnancy and maternal cardiovascular disease. Our findings establish a mechanistic link between heart development, evolution, and congenital defects, highlighting oxygen as both a driver of innovation and a source of vulnerability. This work challenges traditional views of cardiogenesis and underscores the need for integrative approaches to heart development and disease. SummaryThe evolution of warm-bloodedness in birds and mammals required profound physiological innovations, including a four-chambered heart with separate pulmonary and systemic circulation. This restructuring allowed for more efficient oxygen transport, supporting the high metabolic demands of sustained activity. While the anatomical and functional advantages of this transition are well understood, the developmental mechanisms that enabled it remain unclear. Here, we propose that changes in embryonic oxygen availability directly shaped the evolution of heart structure. We show that oxygen levels regulate programmed cell death during the remodeling of the hearts outflow tract, a critical process in the formation of separate circulatory circuits. Experimentally reducing oxygen in developing chick embryos prevented this programmed cell death, disrupted heart remodeling, and produced ancestral-like cardiac structures resembling those of cold-blooded vertebrates. These findings provide a developmental mechanism linking oxygen availability to heart evolution, explaining how changes in embryonic environment could have facilitated the transition to double circulation. They also suggest that congenital heart defects arise when this oxygen-sensitive developmental process is disrupted, offering new insights into why some heart malformations resemble ancestral states. By identifying oxygen as a key environmental cue in heart development, our study underscores the importance of non-genetic factors in shaping evolutionary transitions.

evolutionary biology↗

bioRxiv2025

Caspase-1 self-terminates protease activity to enforce homeostasis and prevent inflammasome-driven diseases

Signal shutdown mechanisms must exist to silence the potent inflammatory programs initiated by the caspase-1 (CASP1) protease, to allow inflammation to resolve and reinstate tissue homeostasis. It is unknown how CASP1 terminates its activity in vivo. Here, we use a knock-in mouse model in which the CASP1 CARD domain linker (CDL) is mutated to prevent self-cleavage (Casp1.CDL mice) to show that CASP1 CDL autoproteolysis terminates CASP1 activity in vivo. We examined these mice under homeostatic conditions and in response to major physiological challenges. In the brain, CASP1 CDL mutation caused anxiety-like behaviour under homeostatic conditions, and exacerbated hippocampal spatial learning deficits in the APP23 genetic model of amyloid-induced neurodegeneration. In the bone marrow, CASP1 CDL mutation promoted steady-state granulopoiesis. In a model of diet-induced liver disease, CASP1 CDL mutation accelerated liver steatosis and promoted liver immune cell infiltration, inflammation and damage. In a liver healing model, CASP1 CDL mutation delayed disease resolution, indicating that CASP1 autocleavage is required to restore homeostasis after a major challenge to organ function. Our data reveal that CASP1 CDL self-cleavage terminates CASP1 inflammatory programs in vivo to maintain homeostasis in steady-state, restore homeostasis after a major challenge to organ function, and suppress inflammasome-driven diseases. These data identify CASP1 as a prime anti-inflammatory drug target, as CASP1 inhibitors may enforce homeostasis and prevent inflammasome-driven diseases.

immunology↗