Biology subjects

Zhao, H.

Publications and source records attributed to Zhao, H..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

GmEBS7a-E2 complex dissociation hyperactivates ERAD to impair plant immunity against Phytophthora pathogens

Endoplasmic reticulum-associated degradation (ERAD) pathways are crucial for maintaining plant development and stress responses. While ERAD has been extensively studied for its role in regulating responses to abiotic stress, its specific manipulation by eukaryotic pathogens stress remains unclear. Here, we reported that soybean GmEBS7a, a plant-specific ERAD component, is targeted and stabilized by a transmembrane domain-containing effector Avh131 from Phytophthora sojae. GmEBS7a enhances plant disease susceptibility by increasing ERAD efficiency and ER stress sensitivity. Mechanistically, Avh131 competitively disrupts the interaction with GmEBS7a and the ubiquitin-conjugating enzyme GmUBC32, reducing ubiquitination of GmEBS7a and subsequent inhibition of its degradation. These findings demonstrate that excessive ERAD triggered by stabilized GmEBS7a and its partnering E3 ligase impairs the plants response to biotic stress. Our study uncovers a fine-tuning of the ER protein-folding capacity to promote infection, thereby expanding our understanding of ER-centered immunity during plant-pathogen interactions.

immunology↗

bioRxiv2026

Proteomic composition and mutual assembly of the C2a projection in vertebrate motile cilia

The central apparatus of motile cilia, consisting of central microtubules and various protein projections, is essential for dictating the ciliary movement. Although three proteins (FAP65, FAP147, and FAP70) have been localized to the C2a projection in Chlamydomonas reinhardtii, the full protein composition and functional roles of the vertebrate C2a remain inadequately defined. Here, we use three knockout mouse models corresponding to their respective homologs (Ccdc108, Mycbpap, and Cfap70) to systematically investigate their functions in vertebrates. Notably, all three knockout strains exhibit distinct phenotypes related to primary ciliary dyskinesia (PCD), including hydrocephalus and sinusitis. The ciliary incorporation of CCDC108, MYCBPAP, and CFAP70 is essential for one anothers stability, with the loss of any single component triggering C2a collapse, which destabilizes the central pair microtubules and ultimately alters the ciliary movement pattern. Furthermore, we significantly expand the vertebrate C2a proteome by identifying ARMC3 and MYCBP as additional C2a components. Collectively, our findings illuminate the proteomic composition and strict physiological requirements of the vertebrate C2a projection, providing new insights into the molecular pathogenesis of PCD. Impact StatementDeficiency in any of the interdependent C2a proteins (CCDC108, MYCBPAP, and CFAP70) collapses this central pair microtubule-associated projection, disrupting vertebrate ciliary movement and causing primary ciliary dyskinesia phenotypes in mice.

cell biology↗

bioRxiv2026

Intramolecular loops control SARS-CoV-2 nucleocapsid protein self-association and nucleic acid binding dependent on phosphorylation

The nucleocapsid protein of SARS-CoV-2 scaffolds genomic RNA into ribonucleoprotein complexes (RNP) for assembly in the virion, but also fulfills critical intracellular functions in replication and the suppression of host defense. It is comprised of a folded nucleic acid binding domain (NTD) and a dimerization domain, connected by a disordered linker containing a serine/arginine-rich (SR) region and a leucine-rich sequence (LRS). The switch between intracellular and assembly functions of N-protein is controlled by phosphorylation of the SR region, but the molecular details are unclear. Here we describe a model in which two mutually exclusive intramolecular loops bind the NTD and dynamically control self-association and nucleic acid binding properties dependent on the SR linker phosphorylation state. The model is supported by biophysical properties and interactions of full-length protein, point mutants, and peptide fragments. We find SR linker phosphorylation compacts the protein and inhibits nucleic acid binding and RNP formation, while enhancing self-association through promotion of transient coiled-coils in the LRS of the linker. These changes shift the nucleocapsid protein to a configuration poised for multi-valent interactions that support intracellular functions.

biophysics↗

bioRxiv2026

Chromatin context-dependent deacetylation by the asymmetric Rpd3L

The regulation of gene expression requires precise control of chromatin-associated complexes that respond to diverse structural and epigenetic cues. The Rpd3 Large (Rpd3L) complex is a Sin3 histone deacetylase (HDAC) complex that dynamically adapt to chromatin states to reinforce transcriptional silencing, yet the mechanisms governing the catalytic activation in chromatin context-dependent manner remain unclear. Here we present the cryo-EM structure of Rpd3L bound to both mono- and di-nucleosome substrate at near-atomic resolution, uncovering a substrate-guided allosteric activation mechanism. Rpd3L adopts an asymmetric architecture, in which the proximal catalytic module anchors the first nucleosome, while the Sin3 PAH domains engage linker DNA to reposition a second nucleosome. This spatial configuration brings the distal catalytic module into proximity with chromatin and unlocks its latent deacetylase activity. Biochemical and mass spectrometry analyses confirm that dual nucleosome engagement selectively enhances Rpd3L activity and broadens substrate specificity. Together, these findings establish a hierarchical mechanism by which Rpd3L interprets histone modifications and nucleosome organization to modulate its enzymatic output at promoter regions. Our study provides a framework for understanding higher-order chromatin repression mechanisms by chromatin-regulation complexes and co-repressors.

molecular biology↗

bioRxiv2026

A single-cell transcriptomic atlas of the periventricular proliferative zone in the late gestation fetal brain in the pigtail macaque

BackgroundThe fetal brain undergoes rapid changes in late gestation, when waves of neurogenesis and gliogenesis shape cortical circuitry. The periventricular proliferative region and adjacent white matter are enriched in neuroprogenitor cells, newborn neurons, and interneurons, which is challenging to study in the late gestation human fetal brain. The nonhuman primate (NHP) provides a powerful translational model to overcome this limitation, given its close similarity to human neurodevelopmental trajectories. The study objective was to construct a single-cell RNA-Seq (scRNA-Seq) atlas of the late-gestation fetal brain of the pigtail macaque (Macaca nemestrina), focused on the periventricular proliferative zone. MethodsA sample of the lateral ventricular wall, subventricular zone, and overlying white/gray matter was dissociated into single cells and processed through the 10X Genomics pipeline, followed by SoupX removal of ambient RNA, and Seurats pipeline to aggregate, cluster and annotate single-cell populations. Monocle3 was used to determine pseudotime and map lineage progression. ResultsThis analysis captured diverse populations of neuroprogenitors, newborn neurons, developing lineages of excitatory and inhibitory neurons, oligodendrocyte and astrocyte lineages, and resident immune and endothelial cells. ConclusionsSingle-cell populations from the third-trimester nonhuman primate fetal brain are highly similar to those in the human fetus. This late-gestation single-cell atlas of the periventricular proliferative zone provides a unique reference for progenitor, neuronal, glial, vascular, and immune cell states during a critical window of primate neurodevelopment, enabling mechanistic interrogation of how inflammatory, infectious, or hypoxic insults disrupt vulnerable neurogenic niches.

genomics↗

bioRxiv2026

TRPV4 Inhibition by a Natural Product Mediates Analgesia

The transient receptor potential vanilloid 4 (TRPV4) channel, a polymodal calcium-permeable cation channel, is activated by diverse stimuli, including hyposmolarity, moderate heat, mechanical stress, and acidic pH. TRPV4 plays a critical role in the onset and progression of pain and is implicated in multiple pathological conditions, positioning it as an attractive therapeutic target. However, the development of TRPV4-targeted therapeutics has been hindered by limited mechanistic understanding of its inhibition. Here, the natural product (R)-1-(3-ethylphenyl)ethane-1,2-diol (AH001) is identified as a potent, subtype-selective TRPV4 inhibitor. A potential gating mechanism of TRPV4 inhibition is proposed through a combination of structural analyses and site-directed mutagenesis. Electrophysiological studies and cryo-electron microscopy (cryo-EM) further reveal that AH001s glucuronide metabolite, AHP, retains robust TRPV4 inhibitory activity, providing a critical structural basis for rational optimization of AH001 as a lead compound. Notably, AH001 demonstrated significant efficacy in reducing neuronal hyperexcitability in dorsal root ganglia (DRGs) and produced pronounced analgesic effects across multiple pain models, highlighting its therapeutic potential in pain relief. This study offers critical structural and mechanistic insights into TRPV4 inhibition and lays the groundwork for the structure-based design of TRPV4-targeted therapeutics.

biochemistry↗

bioRxiv2025

Extracellular matrix regulates lineage plasticity in prostate cancer through YAP/TEAD

Treatment-related neuroendocrine prostate cancer (NEPC) is an increasingly frequent mechanism of resistance to androgen receptor pathway inhibitor (ARPI) therapy in prostate adenocarcinoma (PRAD). This lineage transition is dependent on upregulation of the NE-specifying transcription factor ASCL1, typically in a genetic background of RB1 and TP53 loss. Here we identify extracellular matrix-integrin-YAP1/TEAD signaling as a critical brake on NEPC lineage transition. Deletion of Itgb1, the shared B1 subunit required for collagen and laminin-mediated integrin activation, is sufficient to induce ASCL1 and NE lineage gene expression, by activating LATS1/2 kinases with subsequent inactivation of YAP1/TEAD signaling. Conversely, restoration of YAP1/TEAD signaling by pharmacological LATS1/2 inhibition, or by expression of constitutively active YAP1/TAZ mutants, prevents or reverts NEPC lineage transition. NOTCH and AR cooperate with YAP/TEAD to repress ASCL1, such that combined inhibition leads to complete reprograming of PRAD into NEPC in vitro, providing a dynamic platform to dissect the molecular events responsible for lineage transition over time. We find that lineage transition is accompanied by a redistribution of FOXA1 and TEAD cistromes from PRAD to NEPC-specific enhancers and requires the pioneering activity of FOXA1. Thus, extracellular matrix/integrin signaling in the PRAD tumor microenvironment restrains NE lineage plasticity, highlighting a potential path for pharmacological inhibitors in modulating treatment-induced lineage change.

cancer biology↗

bioRxiv2025

Comprehensive perturbation of transcription factors in human cardiomyocytes reveals the regulatory architecture of congenital heart disease

Transcription factors (TFs), including DNA binding proteins and epigenetic co-regulators, control the timing of gene programs during lineage commitment1. However, systematically defining the dynamic activities of the human genomes nearly 2000 TFs during development remains challenging2,3. Here, we use Perturb-Seq to map the transcriptional impact of nearly all human TFs and a subset of enhancers during cardiomyocyte differentiation. Our results suggest that developmental regulatory networks are distributed across highly connected hub TFs4-6 that are dynamic across lineage and time, rather than organizing into top-down hierarchies directed by "master regulators". We also identify distinct TF ensembles that regulate sequential decision points during cardiac cell-fate specification by coordinating lineage-specific activation with alternate lineage repression. Separately, analysis of TF-TF cooperativity uncovers a dynamic interaction between MEF2 family TFs7 and members of the Polycomb Repressive complex 18-10 to execute alternative fate repression. Building on these regulatory interactions, we construct a deep learning transformer model to accurately predict perturbed TFs driving altered regulatory networks in patient-derived transcriptomes. Together, our results define the regulatory network architecture of human lineage specification and provide a platform for predicting TF function and interpreting disease mechanisms.

genomics↗

bioRxiv2025

Super-CUT&Tag: A Sensitive, Spatially Resolved Approach for Epigenomic Profiling in Tissue Sections

Spatial profiling of protein-DNA interactions is essential for understanding gene regulatory processes, but current methods suffer from low sensitivity, limited resolution, and complex workflows. Here we introduce Super-CUT&Tag (Solid-phase interface embedded with an Ultra-dense DNA barcode array to Profile Epigenomic landscapes for spatially Resolved CUT&Tag), a robust spatial epigenomic method that directly transfers in situ protein-DNA interactions from tissue sections onto a pre-fabricated spatially barcoded array. Incorporating 3D polyamidoamine (PAMAM) dendrimers markedly improves chromatin capture efficiency, achieving several-fold higher sensitivity compared to current spatial CUT&Tag approaches. Using Super-CUT&Tag, we profile H3K27ac spatial landscape and uncover previously hidden active-chromatin heterogeneity across mouse embryonic tissues and stages. Integration with spatial transcriptomics further reveals spatiotemporal enhancer regulation dynamics of Neurod2 during corticogenesis. By overcoming key bottlenecks in sensitivity, resolution and usability, Super-CUT&Tag establishes a powerful platform for spatial epigenomic profiling in complex tissues.

genetics↗

bioRxiv2025

Elucidation and engineering of arabinofuranosyltransferase to enable total de novo biosynthesis of paris saponins in yeast

Paris saponins (PSs) are structurally complex steroidal saponins that, due to their diverse glycosylation patterns, exhibit a range of significant pharmacological activities, including anti-tumor and antibacterial effects. However, incomplete characterization of the key enzymes responsible for glycosylation modifications has hindered their efficient heterologous biosynthesis. In this study, we reprogrammed the sugar donor specificity of a steroidal rhamnosyltransferase (UGT93M3) to enable the transfer of arabinofuranose (Araf). Through structural analysis, we identified key amino acid residues (368H/Q) that play an important role in determining Araf donor specificity. Guided by this insight, we successfully reconstructed the paris saponin I (PSI) biosynthetic pathway in Saccharomyces cerevisiae using engineered enzymes. To address challenges related to donor availability, we introduced UDP-sugar biosynthetic modules (UDP-Rha and UDP-Araf) into yeast. With this integrated platform, we were able to de novo produce a range of paris saponins, including diosgenin-3-O-glucosyl-(1[->]6)-glucoside (DGG), diosgenin-3-O-rhamnosyl(1[->]2) [glucosyl(1[->]6)]glucoside (DRGG) and paris saponin II. This work establishes a novel microbial platform for the sustainable production of paris saponins, particularly PSI, advancing the biosynthesis of steroidal glycosides and providing a potential strategy for the industrial-scale production of bioactive saponins. TeaserIn this study, we report the first complete de novo biosynthesis of four bioactive PSs, PSI, PSII, DGG and DRGG, in Saccharomyces cerevisiae from simple carbon source. Key advances include: (i) A single amino-acid switch (N368H) in the rhamnosyltransferase UGT93M3 endowed high-efficiency transfer of the rare five-membered arabinofuranose, solving a bottleneck in PS I biosynthesis; (ii) Elucidation of the molecular basis for sugar-donor specificity through AlphaFold3 docking and 300-ns molecular-dynamics simulations, revealing a histidine "latch" that stabilizes UDP-Araf in the catalytic pose; (iii) Construction of a 16-gene yeast chassis that integrates plant P450s, optimized glycosyltransferases, and de novo modules for UDP-rhamnose and UDP-arabinofuranose supply, achieving de novo microbial production of PS II, DGG, DRGG and PS I from glucose alone.

synthetic biology↗

bioRxiv2025

BrainBridge Characterizes Key Factors affecting Alzheimer's Disease and Associated Phenotypes

Single-cell RNA sequencing (scRNA-seq) has significantly advanced our understanding of Alzheimers disease and aging by revealing cellular heterogeneity and shifts in cell-type composition between diseased/old and healthy/young individuals. However, few existing studies utilize the rich information in single-cell transcriptomic atlases for robust patient-level modeling and biological feature selection. To address this gap, we present BrainBridge, a deep learning-based framework designed to integrate atlas-scale single-cell transcriptomic data with phenotypic information to model the biomolecular complexity of the human brain. BrainBridge functions both as a powerful predictor and an embedding model for representing sample-level expression profiles and covariates through comprehensive benchmarking. We also demonstrate its effectiveness in prioritizing key genes and cell types associated with disease progression, aging, and sex differences. We further validate our findings using external resources, including genome-wide and epigenome-wide association studies (GWAS and EWAS), spatial transcriptomics, and perturb-seq experiments. Finally, we deploy BrainBridge within an interactive, agent-powered interface that enables intuitive and user-friendly model interactions, promoting broader accessibility and application in biomedical research.

bioinformatics↗

bioRxiv2025

Improving nanobody structure prediction with self-distillation

Nanobodies are increasingly attractive therapeutic and biotechnological molecules, yet accurate structure prediction of their highly variable H-CDR3 loops remains a central challenge for machine learning models. Here, we investigate whether nanobody-specific structure prediction can be improved through curated synthetic data strategies. We systematically evaluate different data augmentation regimes, including self-distillation from unlabelled VHH sequences. To ensure structural plausibility of synthetic training samples, we develop NanoKink, the first sequence-based classifier of kinked versus extended H-CDR3 conformations, and apply stringent filtering criteria for non-canonical disulfide bond placement and confor-mational accuracy. On a curated benchmark enriched for challenging nanobody features, we show that, for a fixed training compute budget, a nanobody-specific model trained with filtered synthetic data significantly improves over baseline models and NanobodyBuilder2, achieving lower mean H-CDR3 RMSD and fewer structural violations, while remaining competitive with AlphaFold3 at approximately two orders of magnitude lower per-structure inference time. Our results highlight promising directions in synthetic data generation for nanobody structure modelling and provide a practical framework for optimisation of VHH structure prediction models.

bioengineering↗

bioRxiv2025

Longitudinal Proteomic Profiling Defines Robust Molecular Subtypes Underlying the Heterogeneity of Parkinson's Disease

Heterogeneity of Parkinsons disease (PD) pathology is a barrier to developing therapeutics and understanding progression and prognosis. High throughput proteomic measures can be used to better interpret PD pathophysiology and generate clusters to define disease subtypes. Identification of subtypes related to clinical phenotypes will help researchers understand PD progression. We analyzed longitudinal proteomic data from the Tracking Parkinsons Cohort, consisting of recent-onset PD patients across 72 UK sites. 794 patients were measured on the Somalogic platform (7596 proteins) for three time points. Weighted Gene Co-Expression Network Analysis (WGCNA) at each time point revealed consistent protein co-expression modules. Two modules were strongly preserved across all three time points and in validation in the Global Neurodegenerative Proteomics Consortia (GNPC) datasets. The brown module was enriched for metabolite pathways and the blue module with cellular signaling pathways and associated with quality of life scores. Conversely, the smaller red module had distinct cognitive function phenotypes and changed protein expression between visit time points. Using detailed characterization of proteomic clusters we have provided a comprehensive view of PD progression offering deeper insights into the conservation of proteomic expression, suggesting new module subsets and providing candidate target proteins for further study.

neuroscience↗

bioRxiv2025

IgG-Bridging-Seeded Synergistic Aggregation of SARS-CoV-2 Spikes Underlies Potent Neutralization by A Low-Affinity Antibody

Mechanistic studies of viral neutralization typically prioritize high-affinity antibodies, relegating low-affinity binders to the sidelines. We report P5-1C8, a Class 1 SARS-CoV-2 antibody that exemplifies this underexplored "low-affinity yet high-potency" phenotype, retaining strong neutralization of Omicron JN.1 despite markedly weakened trimer binding (KD = 225 nM; IC50 = 0.06 nM). Structural and biophysical analyses reveal that P5-1C8 engages WT and BA.1 spikes through canonical intra-spike bivalency, but with JN.1 it induces aggregation. Using virion-like nanoparticles displaying multiple spikes, we show that IgG remains bound with no detectable dissociation and triggers pronounced aggregation. Coarse-grained molecular dynamics delineate the stepwise pathway in which weak IgG-spike contacts seed aggregation via transient inter-spike bridging. Together, these findings establish the first mechanistic framework demonstrating how weak-binding antibodies can nonetheless achieve potent neutralization through higher-order aggregation, thereby expanding the conceptual landscape of antibody function and opening new directions for antibody evaluation and design. Graphical AbstractLow-affinity antibodies are frequently disregarded in discovery pipelines. This work reports P5-1C8, a Class 1 SARS-CoV-2 antibody with weak trimer binding (KD-to-IC50 > 3,700-fold) yet potent neutralization of Omicron JN.1. Structural, biophysical, functional and coarse-grained simulations collectively demonstrate that transient inter-spike IgG bridging seeds higher-order aggregation, which in turn drives neutralization and provides a mechanistic framework. O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/691454v1_ufig1.gif" ALT="Figure 1000"> View larger version (79K): org.highwire.dtl.DTLVardef@1d4f132org.highwire.dtl.DTLVardef@1274400org.highwire.dtl.DTLVardef@e186a6org.highwire.dtl.DTLVardef@4f1870_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

NSUN2-dependent 5-methylcytosine Modification Regulates Influenza A virus Gene Expression and Genomic Packaging

Emerging evidence indicates that methyltransferase NSUN2 catalyzes 5-methylcytosine (m5C) modifications on various viral RNAs and plays important roles in viral biology. However, the regulatory roles of NSUN2 in influenza A virus (IAV) replication have not been elucidated. Here, we revealed that NSUN2 negatively regulated the viral RNA transcription and protein production by knocking out and over-expressing NSUN2. By m5C MeRIP-seq and RNA-BisSeq, NSUN2-dependent m5C sites were identified on both the plus and minus viral RNA strands. In NSUN2-KO cells, the m5C modification on vRNAs was reduced, resulting in the production of a large number of deficient interfering particles (DIPs) which had lower vRNA content, imbalanced genome fragments, abnormal morphology and reduced pathogenicity. Mutation of m5C sites at the 5 and 3 ends of PB2 vRNA interfered with the selective packaging of the 8 vRNA segments into virus particles, resulting in the formation of a variety of abnormally packaged virus particles. PB2-vRNA mutants also had reduced replication ability and pathogenicity in mice. Overall, these data demonstrate that the m5C residues catalyzed by NSUN2 are required on vRNAs for the proper assembly of infectious viral particles, suggesting the depletion of m5C modification as a potential strategy that can be utilized to attenuate IAV strains. Significance StatementInfluenza A virus (IAV) infections pose a significant threat to global public health by causing substantial morbidity and mortality. The segmented nature of the IAV genome requires precise regulation of the genomic assembly to produce infectious progeny virus particles. In this study, we demonstrate that m5C modification is crucial for the proper assembly of infectious viral particles. The lowered level of m5C modifications on vRNAs leads to the generation of defective interfering particles with reduced replication capacity and pathogenicity. Our data shed new light on the selective packaging mechanism of IAV segmented genome and highlight a potential new strategy for attenuating IAV strains by targeting the m5C modification machinery.

microbiology↗

bioRxiv2025

Sexually dimorphic role of estrogen receptor α in preserving right ventricular endothelial integrity

Right ventricular (RV) function and adaptation to afterload increase determine survival in pulmonary hypertension (PH). RV adaptation in PH is sexually dimorphic and more preserved in females, mediated by protective estrogen receptor (ER) signaling in cardiomyocytes. However, the effects of ER on RV endothelial cells (RVECs), a critical mediator of RV homeostasis and adaptation, are unknown. We hypothesized that ER exerts sexually dimorphic pro-angiogenic effects on RVECs in vitro and promotes RV vascularization in vivo. Compared to cells isolated from wild-type animals, RVECs from male and female rats with an ER loss-of-function mutation (ERMut) showed reduced ability to form pseudo-vascular networks and migrate. RVECs from female ERMut rats demonstrated increased apoptosis. In a PH model induced by monocrotaline (MCT), female ERMut rats exhibited increased RV hypertrophy and reduced RV capillary density before (10 days) and at the time of established PH (28 days). Capillary rarefaction was associated with increased RVEC apoptosis, and, as identified by single-nucleus RNA-sequencing, by a net loss of the endocardial RVEC sub-population. Differentially expressed gene analysis and pathway analysis identified that capillary and endocardial RVECs from female MCT-PH ERMut rats demonstrated decreased expression of migration pathways and increased expression of apoptosis pathways. These findings reveal a sex-specific endothelial-intrinsic role of ER that is essential for angiogenesis in the RV under both homeostatic and pathological conditions. This effect appears to stem from the enhanced survival and migration capacity of capillary and endocardial RVEC. Collectively, our results identify ER as a potential target for developing sex-specific RV-directed therapies in PH. Translational perspectiveEffects of ER on vascular function in RV failure induced by PH are poorly understood. We unveiled a novel sexually dimorphic role of ER in regulating RV vascularization and RVEC function. Single nucleus RNA-Sequencing in female wild-type and ER loss-of-function rats with PH identified 5 unique RVEC sub-populations under transcriptional control of ER. Our findings provide insights into previously undescribed pro-angiogenic, pro-migratory and anti-apoptotic roles of ER in female RVs and RVECs. Promoting RVEC migration or inhibiting RVEC apoptosis to enhance RV angiogenesis may be viable pathways to maintain RV function in PH patients of either sex. These findings offer novel opportunities and potential therapeutic avenues for preventing or treating RV failure.

cell biology↗

bioRxiv2025

The 9p21.3 Coronary Artery Disease Risk Locus Modulates Vascular Cell-State Transitions via Enhancer-Driven Regulation of MTAP

The 9p21.3 locus is the strongest genetic association with coronary artery disease (CAD), yet its causal mechanisms remain unresolved. We map the regulatory architecture of 9p21.3 in disease-relevant vascular cells, identifying 12 enhancers within the CAD risk haplotype that respond dynamically to inflammatory and metabolic stress in fibroblasts and smooth muscle cells. These activated states are enriched for CAD heritability, implicating stress-responsive vascular wall cells in disease pathophysiology. Dense CRISPRi tiling integrated with fine-mapping and genomic constraint across >500,000 individuals nominates MTAP as the effector gene, with rs1537371 as a likely causal variant. Perturbation and multi-modal analyses show that MTAP loss induces pro-fibrotic and angiogenic programs and sensitizes vascular cells to TGF-{beta}-driven pathological transitions. Our findings reveal a vascular-specific enhancer network through which noncoding variation at 9p21.3 modulates CAD risk via MTAP--a previously unrecognized regulator of vascular remodeling located 269 kb from the risk haplotype. HighlightsO_LI9p21.3 CAD risk locus harbors 12 functional enhancers active in vascular wall cell types C_LIO_LICAD heritability is enriched in stressed vascular fibroblasts and smooth muscle cells C_LIO_LIHigh-resolution CRISPRi-MAC-seq maps 9p21.3 enhancer-gene and SNP-gene interactions C_LIO_LIMTAP identified as a causal effector gene regulated by 9p21.3 fine-mapped and constrained variants C_LIO_LIMTAP modulates TGF-{beta}-driven pathological vascular cell transitions C_LI

genomics↗

bioRxiv2025

Dynamic interactions in human amygdala subregions support hierarchical processing of fearful faces

Fearful-expression recognition is critical for adaptive responses to potential threats and relies on both rapid threat detection and fine-grained face encoding. Yet how human amygdala subregions differentially support these distinct cognitive components remains unclear. Here, we recorded intracranial EEG from lateral and medial amygdala in epilepsy patients performing an emotional face-matching task and combined multivariate decoding, time-frequency and directed-connectivity analyses with intracranial stimulation. The lateral amygdala exhibited early fear-specific responses, characterized by higher decoding accuracy and increased theta/alpha-band (4-12 Hz) power, and transmitted this fear-related information to the medial amygdala, which showed delayed and sustained activation. By contrast, the medial amygdala encoded face-specific information at later stages in the 2-16 Hz band with superior decoding accuracy and then relayed this information back to the lateral amygdala. Intracranial stimulation produced a double dissociation in behavior, with lateral amygdala stimulation disrupting fear detection, whereas medial amygdala stimulation selectively accelerated neutral-face recognition. Together, these findings reveal a temporal hierarchy in the human amygdala, whereby dynamic bidirectional interactions between subregions implement distinct components of fearful-expression recognition, providing a circuit-level framework for understanding social threat processing.

neuroscience↗