Search bioRxiv⌕ Search

Biology subjects

Jiang, Y.

Publications and source records attributed to Jiang, Y..

At least 109 records · Page 6Linked to original sources

Elucidating Odorant Masking Effects in Food Matrices Through Olfactory Receptor-Based Profiling

Dynamic interactions among aroma compounds, especially odorant masking, constitute a key determinant of the intricate flavor profiles of thermally processed foods. However, the molecular and receptor-level mechanisms governing mutual odor suppression remain largely unclear. This study investigated the reciprocal sensory masking between 2,3,5-trimethylpyrazine and L-menthol via systematic sensory evaluation. Olfactory receptor screening identified OR5K1 as the responsive receptor for 2,3,5-trimethylpyrazine (EC50 = 27.67 {+/-} 2.02 mol/L) and OR2W1 as the functional receptor for L-menthol (EC50 = 22.69 {+/-} 3.85 mol/L). Consistently, quantitative cellular response assays further validated that 2,3,5-trimethylpyrazine and L-menthol exert mutual inhibitory effects on their respective receptors, as evidenced by the significant inhibition of receptor signaling. Moreover, molecular modeling predicted that 2,3,5-trimethylpyrazine and L-menthol competitively occupy the same orthosteric pocket via analogous binding conformations. These results provide novel receptor-level insights into odorant inhibitory effects, connecting sensory perception to molecular recognition, and deepen mechanistic understanding of flavor perception.

cell biology↗

Plasma proteomics reveal heterogeneous subtypes of depression linked to inflammation and aging

The clinical heterogeneity of depression has defied biological classification, limiting personalized treatment. Previous neuroimaging- or symptom-based subtyping of depression failed to clarify the underlying pathoetiology, while plasma proteins which integrates signals from multiple organ systems, offers a promising way to define biologically grounded subtypes. Using plasma proteomics from 2,127 incident depression cases in a cohort of 53000 individuals, we identified three biologically distinct subtypes differing in inflammation, aging, and metabolic profiles. The most prevalent subtype ( inflammation/ageing) was characterized by aging-related inflammation, poorest prognosis with hippocampal atrophy and highest suicide risk, mediated by age-related amygdala atrophy; this subtype had highest anhedonia burden. A distinct inflammation/energy dysregulation group had metabolic pathway enrichment with high inflammation and lifestyle risk factors (smoking) but no ageing trend, predominantly physical/psychomotor symptoms and decreased thalamic volume. In contrast, the inflammation-resilient group had the lowest inflammatory proteomic loading, lowest depression severity, more resilient lifestyle and increased hippocampal volume. These proteomic signatures, detectable years before symptom onset, enable risk stratification and suggest subtype-specific targeted physical and lifestyle interventions.

neuroscience↗

Healthcare Infrastructure Shapes Evolutionary Trade-offs and Geographic Dissemination of Multidrug-Resistant Acinetobacter baumannii

Antimicrobial-resistant pathogens pose an existential threat to modern medicine, yet the evolutionary forces driving their adaptation in healthcare systems remain largely unexplored. We revealed that hospital network architecture functions as a primary selective pressure, driving pathogen evolution through infrastructure-dependent virulence-transmission trade-offs. Phylogenomic analysis of 5,023 Acinetobacter baumannii isolates across Chinas centralized healthcare system identifies two co-existing evolutionary strategies: a virulence-optimized clade (ESL2.4) that spread slowly (20.4 km per year) in low-connectivity hospitals, and a transmission-optimized clade (ESL2.5) that disseminate rapidly (65.2 km per year) through mega-city healthcare hubs, likely attributed to its capsule conversion and increased upper respiratory colonization. Comparative analysis with European A. baumannii populations demonstrates that healthcare connectivity, not geography, governs pathogen distribution through convergent genomic adaptations. Our simulation suggests competitive asymmetries of the two clades, following the ecotype principle and enabling stable coexistence. The COVID-19 pandemic provided a natural experiment validating these mechanisms: outpatient restrictions reduced transmission-optimized lineage spread by 89%, while virulence-optimized lineage persisted through inpatient networks. These findings establish healthcare infrastructure as a critical evolutionary driver with immediate implications for predicting and controlling antimicrobial resistance emergence across diverse healthcare systems.

microbiology↗

Cross-species insights into placental evolution and diseases at the single-cell resolution

The placenta is a highly specialized organ in mammals, mediating the exchange of nutrients, gases, and waste between the mother and the fetus while orchestrating intricate immunological interactions to sustain a successful pregnancy. Despite its essential roles, the molecular evolution underlying the diversity of placentas across mammalian species remains largely elusive. Here, we constructed a comprehensive mammalian placental single-cell transcriptomic atlas from approximately 300,000 cells spanning ten species that could well represent the four primary placental types: (discoid, cotyledonary, diffuse, and zonary. Our cross-species analysis highlights trophoblast lineages as key drivers for placental evolution. By reconstructing differentiation trajectories, we elucidate the gene expression dynamics and regulatory networks shaping trophoblast development across diverse placental architectures. Besides, we propose that the association of human trophoblasts with conditions such as pre-eclampsia and miscarriage arises from their unique gene expression profile, which distinguishes them from trophoblasts of other species. The functional experiments further demonstrate that TGIF1 acts as an upstream regulator of key functional genes in extravillous trophoblast cells, modulating their growth, invasion, and migration. Additionally, TGIF1, along with its target genes, such as ADAM12, WNT3A, and ZNF831, is associated with preeclampsia and pregnancy loss. Collectively, these findings provide a high-resolution framework to understand the molecular evolution of the placenta and its role in reproductive success and diseases.

evolutionary biology↗

A Foundational Generative Model for Cross-platform Unified Enhancement of Spatial Transcriptomics

Spatial transcriptomics (ST) platforms are limited by spatial resolution, sensitivity to low expression levels, alignment with tissue structures, and the balance across tissue complexity. Computational enhancement typically targets a single challenge, e.g., super-resolution using hematoxylin and eosin (H&E) images or sensitivity enhancement with single-cell RNA sequencing (scRNA-seq). However, most ignore the interdependence across challenges, yielding biologically inconsistent enhancement. Here we introduce FOCUS, a foundational generative model for unified ST enhancement, conditioned on H&E images, scRNA-seq references, and spatial co-expression priors. With large-scale pretrained encoders, FOCUS uses a modular design for multimodal integration and a cross-challenge coordination strategy to target co-occurring challenges, enabling joint optimization. FOCUS was trained and comprehensively benchmarked on >1.7 million H&E-ST pairs and >5.8 million single-cell profiles, demonstrating state-of-the-art performance across ten ST platforms, on both individual and coupled challenges. The real-world utility and generalizability were validated on a rare suprasellar tumor, papillary craniopharyngioma, and an unseen ST platform (Open-ST) for primary and metastatic head and neck squamous cell carcinoma.

bioengineering↗

Helix: a structure-aware deep learning model for accurate prediction of A-to-I RNA editing by endogenous ADARs

Adenosine deaminase acting on RNA (ADAR) converts adenosine to inosine within double-stranded RNA (dsRNA) and can be co-opted for therapeutic RNA editing by introducing dsRNA substrates in trans using programmable guide RNAs (gRNAs). However, ADARs natural promiscuity necessitates sophisticated gRNA designs to achieve efficient and specific editing. Here we present Helix, a predictive model that achieves highly accurate, zero-shot per-adenosine editing predictions for any target sequence. Helixs performance arises from two architectural choices: a transformer framework that scales effectively with increasing and imbalanced training data; and a structure-aware attention mechanism that incorporates predicted RNA secondary structure, a key determinant of ADAR activity. Helixs predictive accuracy enables seamless integration with DeepREAD, our previously reported generative model, in a noisy-student distillation framework termed DeepHelix. This workflow supports both zero-shot gRNA design and the generation of complex, constraint-based designs. We demonstrate DeepHelixs utility by designing gRNAs that efficiently edit a therapeutically relevant adenosine and by leveraging its flexible design space to engineer species cross-reactive gRNAs to accelerate pre-clinical development.

bioengineering↗

Correlated Motion-Based Residue Network Analysis Reveals the Distal Thermal Activation in Soybean Lipoxygenase

Enzyme catalysis has been shown to depend on distal pathways that channel thermal energy from solvent to the active site. In soybean lipoxygenase (SLO), experiments identified a cone-shaped network connecting loop residue Gln322 to Leu546 but not Leu754 in the active site. Here, microsecond molecular dynamics and a correlated motion-based protocol provide an atomistic analysis of such long-range communication. The developed approach enables systematic screening of communication between active site-specific residues that directly contact bound substrate and surface-exposed residues on the protein-solvent interface. In doing so, it provides a deeper molecular insight into experimentally mapped networks by resolving communication trends across diverse conformational ensembles. The simulations recover the experimentally demonstrated thermal initiation loop and the Leu546-directed cone in SLO, exclude the negative-control Ser596, and explain the preference for Leu546 over Leu754 through shorter, more correlated helical pathways. Mutational analysis further reveals the impact of single-site mutations on the network preference between Leu546 and Leu754. These results unify experiments and computation, corroborating an anisotropic channeling of thermal energy in SLO and establishing a general framework for computing distal intra-protein pathways that may enable the thermal activation of enzyme function.

biophysics↗

Lemborexant Reduces Infarct Volume and Improves Long-Term Functional Recovery in a Murine Model of Ischemic Stroke

IntroductionRecovery following ischemic stroke is highly variable and often incomplete, underscoring the urgent need to develop novel targeted poststroke treatments. While the mechanisms underlying poststroke recovery remain incompletely understood, sleep fragmentation, a common consequence of stroke, has been linked to worse patient outcomes. Lemborexant is a dual orexin receptor antagonist that promotes sleep by suppressing wakefulness and enhancing sleep continuity. We hypothesized that lemborexant would reduce poststroke sleep disturbances and promote recovery in a rodent model of stroke. MethodsWe examined the effects of lemborexant (10 mg/kg and 30 mg/kg) and zolpidem (30 mg/kg) on sleep macrostructure, fragmentation, and EEG spectra in both healthy mice and in stroke model mice, which underwent photothrombotic ischemia of the forelimb somatosensory cortex. We also evaluated whether 12 days of drug administration altered infarct volume and functional recovery following the experimental induction of stroke in model mice. ResultsLemborexant treatment (30 mg/kg) increased the percentage of NREM sleep, while preserving sleep continuity, in both healthy and stroke model mice. In contrast, zolpidem increased NREM sleep after stroke, but also increased sleep fragmentation in both groups. Lemborexant treatment at 10 mg/kg and 30 mg/kg significantly reduced infarct volume eight weeks after the induction of stroke. In addition, lemborexant-treated mice showed greater use of the impaired limb four weeks after stroke. InterpretationThese preclinical findings suggest that lemborexant stabilizes sleep and promotes structural and functional recovery following the experimental induction of stroke in model mice, supporting its potential as a novel therapeutic intervention following ischemic stroke. Summary for Social Media if PublishedO_LIIf you and/or a co-author has a X handle that you would like to be tagged, please enter it here. (format: @AUTHORSHANDLE). @EricLandsness C_LIO_LIWhat is the current knowledge on the topic? Sleep plays a critical role in structural and functional recovery after stroke, but most pharmacologic sleep aids, such as benzodiazepines and zolpidem, can fragment sleep and impair neuroplasticity. Dual orexin receptor antagonists like lemborexant may offer a newer, mechanistically distinct approach with potential neuroprotective benefits. C_LIO_LIWhat question did this study address? This study investigated whether the dual orexin receptor antagonist lemborexant could improve sleep quality, reduce ischemic injury, and enhance functional recovery following stroke in adult mice, compared with the sleep-promoting agent zolpidem. C_LIO_LIWhat does this study add to our knowledge? Lemborexant increased NREM sleep without causing fragmentation, reduced infarct volume, and improved motor recovery when administered. These findings suggest that modulating sleep architecture through orexin antagonism during the subacute phase after stroke can promote neural repair and functional recovery. C_LIO_LIHow might this potentially impact on the practice of neurology? Since lemborexant is already FDA-approved for insomnia, these results could be rapidly translated into a therapeutic opportunity to improve stroke recovery through targeted sleep modulation. This approach may shift poststroke care toward integrating neurorestorative, sleep-based interventions during the subacute phase. C_LI

neuroscience↗

Benchmarking Cell-Type-Specific Spatially Variable Gene Detection Methods Using a Realistic and Decomposable Simulation Framework

Identifying spatially variable genes within individual cell types is essential for characterizing spatially organized cell states and microenvironments from spatial transcriptomics data. Several computational methods have been developed for identifying cell-type-specific spatially variable genes (ctSVGs), but their relative performance and practical utility under realistic biological complexity remain largely unknown. To address this gap, we present the first systematic bench-mark study of all five existing ctSVG detection methods--CELINA, STANCE, C-SIDE, CTSV and spVC--using an integrated evaluation framework that combines idealized simulations, Xenium-based realistic simulations, and a decomposition-based diagnostic analysis. We compared the methods in terms of detection accuracy, scalability, and usability. Across realistic datasets generated on various tissue types, all methods experienced sharp declines in detection accuracy and substantial inflation of false discoveries compared to idealized simulations. To explain this failure, we developed a new simulation framework that decomposes the "realness" of the realistic simulation into interpretable biological and technical components, enabling us to attribute method-specific performance losses to specific components, including realistic diversity of cell types, heterogeneous cell layouts, null gene distributions, capture efficiency and realistic intra-cell-type spatial patterns. Together, our results show that no single method dominates across detection accuracy, scalability and usability, and we further clarify why current ctSVG methods fall short in realistic settings. We summarize these tradeoffs into a practical user guide to support method selection and highlight key challenges in developing robust, scalable ctSVG detection tools for real spatial transcriptomics data.

bioinformatics↗

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↗

ATHENA: A deep learning-based AI for functional prediction of genomic mutations and synergistic vulnerabilities in prostate cancer

Identifying functional mutations that drive therapy resistance remains a major challenge in prostate cancer. Large-scale sequencing often produces extensive lists of mutations but provides limited insight into which alterations are functionally relevant. To overcome this gap, we developed ATHENA (Attention-based Therapeutic Network Analyzer), a deep learning-based AI framework that predicts the functional impact of genomic mutations and reveals their synergistic vulnerabilities. Integrated with our RNA/DNA-informed variant discovery pipeline OncoVar, ATHENA models nonlinear dependencies among mutations to distinguish driver events from passenger variants. Trained on large multi-cohort datasets and interpreted using SHAP analysis, ATHENA not only stratifies patients by clinical outcomes but also predicts which specific mutations alter tumor behavior and therapy response, enabling direct validation through base editing experiments. Applied to prostate cancer progression models, the OncoVar-ATHENA framework identified stage-specific driver signatures across castration-resistant, AR-variant-driven, and metastatic disease, and uncovered cooperative interactions such as SYVN1-STC2 that promote tumor proliferation. By moving beyond simple mutation identification, ATHENA enables functional prediction of genomic interactions. This approach accelerates the discovery of actionable targets and provides a foundation for rational design of next-generation combination therapies in advanced prostate cancer.

cancer biology↗

ATRX Loss Predicts Poor Outcomes and Reveals a Therapeutic Vulnerability to TEAD Inhibition in Soft Tissue Sarcomas

ATRX is one of the most frequently altered genes in sarcoma and encodes an ATP-dependent chromatin remodeler implicated in maintaining heterochromatin. However, ATRX alterations have not been leveraged for sarcoma treatment. We observed loss of ATRX protein in 14% of soft tissue leiomyosarcoma (STLMS, n =127), 53% of uterine leiomyosarcoma (ULMS, n = 95), 37% of undifferentiated pleomorphic sarcoma (UPS, n = 82), and 8% of dedifferentiated liposarcoma (DDLPS, n = 84). ATRX loss was associated with significantly worse outcomes in ULMS, UPS, and DDLPS. ATRX knockout in sarcoma cells increased proliferation in cooperation with TP53 deletion. ATRX knockout led to chromatin de-repression and enrichment of PRDM4 and NFIX transcription factor (TF) motifs. PRDM4 and NFIX knockdown in ATRX-mutant sarcoma lines resulted in reduced proliferation and invasion suggesting epistatic relationship. Consistent with the known functional relationship between PRMD4 and YAP1, we observed that ATRX/TP53 KO cells were more sensitive to the TEAD inhibitor VT103 compared to TP53 KO and ATRX WT controls. Overall, our results identify ATRX loss as a prognostic factor of worse outcomes, implicate the ATRX-PRDM4-YAP1 axis as a novel underlying mechanism, and suggest use of TEAD inhibition as a potential therapeutic strategy for ATRX-deficient sarcomas. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=45 SRC="FIGDIR/small/689992v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@a759ecorg.highwire.dtl.DTLVardef@100c580org.highwire.dtl.DTLVardef@1a675c9org.highwire.dtl.DTLVardef@17f1f91_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Graded Notch Signaling Functions as a Rheostat of Lineage Plasticity and Therapy Resistance in Prostate Cancer

Resistance to androgen receptor (AR)-targeted therapies such as enzalutamide in castration-resistant prostate cancer (CRPC) often arises through lineage plasticity, yet the molecular mechanisms that define this process remain incompletely understood. While previous studies reported that Notch1 and Notch2 exert distinct and sometimes opposing effects in prostate cancer differentiation, the integrated role of Notch pathway activity has not been systematically explored. Here, we identify Notch signaling as a graded Rheostat that governs prostate cancer cell fate transitions. Integrative transcriptomic and functional analyses revealed that intermediate Notch activity maintains a stem-like progenitor state, whereas reduced or elevated signaling drives divergent differentiation trajectories toward luminal or neuroendocrine lineages, respectively. During CRPC progression and enzalutamide resistance, Notch signaling becomes dynamically rewired, peaking in progenitor-like populations that sustain plasticity and survival. Both CRISPR-mediated knockout and pharmacologic inhibition of Notch signaling depleted these progenitor cells and restored enzalutamide sensitivity. These findings demonstrate that the level, rather than the binary presence, of Notch signaling dictates lineage directionality and therapeutic response in CRPC, establishing it as a tunable and actionable driver of resistance.

cancer biology↗

Clusters, Fingers, and Singles: A Mechanical Landscape of Tumor Invasion

Collective invasion is a key mechanism by which tumors disseminate and metastasize, involving coordinated migration of heterogeneous cell populations. Experimental studies have identified specialized leader and follower cells that work together during this process, but the biophysical rules governing their interaction remain unclear. We present a mechanistic, cell-based computational model using the Cellular Potts framework to investigate how heterotypic adhesion, leader motility, and follower proliferation jointly shape invasion. Leader-follower tumors were simulated across 13,310 parameter sets, and invasion was quantified by invasive and infiltrative areas, finger-like protrusions, solitary defectors, and detached clusters. From these simulations, we identified four distinct invasion phenotypes: non-invasive, bulk collective, single-cell, and multimodal. Multimodal invasion--the coexistence of cohesive strands, solitary cells, and small clusters--emerged as the most prevalent phenotype, particularly under moderate adhesion, high motility, and intermediate proliferation. Proliferation exhibited nonlinear effects: moderate division reinforced cohesive invasion, whereas excessive growth destabilized tumor architecture. Mapping outcomes across the parameter space revealed sharp transitions between invasion modes, underscoring trade-offs between adhesion and motility in shaping invasion complexity. Our results show that hybrid invasion behaviors, previously considered rare, arise robustly from simple mechanical rules and are favored in a broad region of the parameter space. This framework reconciles binary models of invasion with experimental observations of heterogeneity, providing predictive insights into how modulating adhesion, motility, or proliferation can restrict metastatic spread. Author summaryWhen cancer cells leave a primary tumor, they do not just invade as lone cells but also as cohesive fingers and small cell clusters, depending on how strongly cells stick together, how hard some cells pull, and how fast the population grows. We built a simple, physics-based computational model in which a small number of leader cells pull on the more proliferative followers. By systematically varying three key properties, cell-cell adhesion, leader motility, and follower proliferation, we generated a large simulation of invasion patterns and grouped them into four invasion modes. The resulting phase diagram shows where tumors grow as compact masses (no invasion), or invade as protruding "fingers," as single cells, or in a mixed multimodal fashion with fingers, clusters, and single cells. Surprisingly, this mixed state was the most common outcome, arising when adhesion is moderate and leader motility is strong. This map provides intuition and practical rules for thinking about how changes in adhesion or motility might reorganize invasion, such as shifting cluster-forming fronts toward more compact, less dissemination-prone configurations.

cancer biology↗

Extracting task-relevant preserved dynamics from contrastive aligned neural recordings

Recent work indicates that low-dimensional dynamics of neural and behavioral data are often preserved across days and subjects. However, extracting these preserved dynamics remains challenging: high-dimensional neural population activity and the recorded neuron populations vary across recording sessions. While existing modeling tools can improve alignment between neural and behavioral data, they often operate on a per-subject basis or discretize behavior into categories, disrupting its natural continuity and failing to capture the underlying dynamics. We introduce Contrastive Aligned Neural DYnamics (CANDY), an end-to-end framework that aligns neural and behavioral data using rank-based contrastive learning, adapted for continuous behavioral variables, to project neural activity from different sessions onto a shared low-dimensional embedding space. CANDY fits a shared linear dynamical system to the aligned embeddings, enabling an interpretable model of the conserved temporal structure in the latent space. We validate CANDY on synthetic and real-world datasets spanning multiple species, behaviors, and recording modalities. Our results show that CANDY is able to learn aligned latent embeddings and preserved dynamics across neural recording sessions and subjects, and it achieves improved cross-session behavior decoding performance. We further show that the latent linear dynamical system generalizes to new sessions and subjects, achieving comparable or even superior behavior decoding performance to models trained from scratch. These advances enable robust cross-session behavioral decoding and offer a path towards identifying shared neural dynamics that underlie behavior across individuals and recording conditions. The code and two-photon imaging data of striatal neural activity that we acquired here are available at https://github.com/schnitzer-lab/CANDY-public.git.

neuroscience↗

Targeting C5aR1 Reveals Protective Macrophage Maturation States in Intestinal Injury

Inflammatory intestinal injury, which may occur following cytotoxic cancer treatments such as radiotherapy, compromises homeostasis when intestinal stem cells undergo apoptosis and regeneration programmes are not effectively engaged. Recent evidence indicates the importance of macrophages in regulating stem regeneration following injury, but how to therapeutically promote specific macrophage subtypes which may tip the balance away from apoptosis and towards regeneration is still unclear. Here we show that targeting complement C5a receptor 1 (C5aR1) reduces radiation-induced intestinal injury by promoting macrophage phenotypes which reduce intestinal stem cell apoptosis. Specifically, C5aR1 signalling attenuates a macrophage maturation response characterised by increased IL10 and CX3CR1 expression. Our data indicate that increased IL10 signalling, and macrophage maturation induced following C5aR1 targeting are important for regulating crypt cell loss via radiotherapy-induced apoptosis. Interestingly, IL10-signalling is also critical for the improved tumour radiation response observed following C5aR1 targeting.

immunology↗

Missense Mutation ADNP p.C687R Disrupts Chromatin Regulation and GABAergic Differentiation in HVDAS

Activity-dependent neuroprotective protein (ADNP) is a key regulator of neurodevelopment and a high-risk gene for autism spectrum disorder (ASD). Most pathogenic variants cause loss-of-function in Helsmoortel-Van der Aa syndrome (HVDAS), yet the impact of missense mutations remains unclear. Here, we characterized a ADNP missense mutation (p.C687R) identified from a HVDAS patient, predicted to disrupt its ninth zinc finger domain. Overexpression of p.C687R altered subnuclear localization and affected wild-type ADNP distribution. In utero electroporation revealed impaired neuronal migration and cortical branching. CUT&Tag profiling showed mutant- specific chromatin binding, preferentially targeting histone modification genes through both direct and distal interactions. Patient-derived iPSCs carrying p.C687R exhibited upregulated bivalent histone marks (H3K4me3 and H3K27me3) on neurodevelopmental genes, including regulators of GABAergic differentiation, which became transcriptionally activated in neural progenitors. These findings reveal a gain-of-function mechanism by which ADNP p.C687R perturbs chromatin regulation and disrupts GABAergic lineage specification, expanding the molecular framework of ADNP pathogenesis. The Paper Explained ProblemMutations in the gene ADNP cause Helsmoortel-Van der Aa syndrome (HVDAS), a severe neurodevelopmental disorder, and also increase the risk for autism spectrum disorder (ASD). While most known ADNP mutations lead to loss of protein function, many missense mutations that alter a single amino acid remain poorly understood regarding their effects on brain development and disease contribution. ResultsWe characterized a specific missense mutation, ADNP p.C687R, from a patient diagnosed with HVDAS, and found that it does not simply inactivate the protein but instead confers a disruptive new function. Across multiple models, from cells to mice, the p.C687R mutant exhibits abnormal chromatin binding, altered subnuclear localization, and impaired neuronal migration and differentiation. Importantly, in patient-derived iPSCs, it marks distinct neurodevelopmental genes with bivalent histone modifications, which become aberrantly activated during differentiation into GABAergic neural progenitor cells. ImpactThese findings confirm the pathogenicity of the missense mutation ADNP p.C687R in HVDAS, reveal a gain-of-function mechanism whereby the mutant disrupts chromatin regulation and GABAergic lineage specification, and advance our understanding of ADNP-related neurodevelopmental disorders.

neuroscience↗

Disruption of ADAMTSL4 Causes Ectopia Pupillae in Zebrafish via COL8A1-Driven Cell Migration

Congenital ectopia lentis (EL) poses a significant threat to visual outcomes in children. Although emerging causative genes have been identified, their biological functions remain poorly understood. In this study, we investigated the contribution of ADAMTSL4 variants to congenital EL in a cohort of 702 pedigrees. Pathogenic variants in ADAMTSL4 were identified in 23 probands (3.28%), comprising 29 distinct variants, with 14 being novel, making ADAMTSL4 the second most frequently mutated gene in the cohort. All affected individuals exhibited EL, and 26.09% also presented with ectopia pupillae (EP), also referred to as ectopia lentis et pupillae. To explore the functional consequences of ADAMTSL4 deficiency, we generated a CRISPR/Cas9-mediated adamtsl4-knockout zebrafish model, that faithfully recapitulated cardinal human disease features with an incidence comparable to that observed in affected patients. Histological and ultrastructural analysis revealed disrupted zonular fiber anchorage at the lens capsule, even in mutated eyes without overt EL or EP. Transgenic overexpression of adamtsl4 successfully reversed the ocular phenotypes, confirming the genes essential role in ocular development. Single-cell RNA-sequencing and fluorescence in situ hybridization demonstrated enriched ADAMTSL4/adamtsl4 expression in the equatorial lens epithelium, retinal pigment epithelium (RPE), iris anterior pigmented epithelium, and choroid fibroblast. Functional assays using zebrafish and human RPEs revealed that ADAMTSL4 deficiency compromised cell adhesion and promoted cell migration. Transcriptomic profiling revealed significant enrichment of extracellular matrix organization and cell adhesion pathways, with cross-species validation identifying consistent upregulation of COL8A1/col8a1b. Notably, COL8A1 knockdown in ADAMTSL4-deficient RPEs partially reversed the aberrant migratory phenotype, suggesting a functional interaction. Together, these findings establish ADAMTSL4 as a major causative gene in ectopia lentis et pupillae, highlight its role in orchestrating ocular integrity via regulation of extracellular matrix and cell behavior.

genetics↗