Biology subjects

Zhu, Z.

Publications and source records attributed to Zhu, Z..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Machine-Learning-Assisted Exploration of High Entropy-Atom Nanozyme for Anti-Tumor Immunotherapy by Enhancing Enzyme Activity and Disrupting Dual Energy Metabolism

Despite its potential in cancer therapy, single-atom nanozyme (SAzyme) faces challenges like low atomic loading and rapid cancer metabolism. Here, a high-entropy atom nanozyme (HEAzyme), PtNiBiSnSb-anti-CD36, is designed for efficient anti-tumor immunotherapy. The PtNiBiSnSb HEAzyme, incorporating five SAzyme, demonstrates enhanced peroxidase (POD)-like activity due to its abundant active sites, showing a 7.2-fold increase in catalytic efficiency compared to the structurally analogous PtBi nanozyme. Further integrating of density functional theory calculations and machine learning analysis reveals that the main reason is due to the addition of Ni, Sn, and Sb, which reduced the reaction energy barrier and changed the adsorption energy of surface hydroxyl groups. Moreover, PtNiBiSnSb-anti-CD36 not only inhibits normal metabolic processes by depleting nicotinamide adenine dinucleotide (NADH) through its enhanced NADH-POD-like activity, but also suppresses lipid metabolism by blocking CD36-mediated uptake. The dual metabolic inhibition facilitates the mild photothermal therapy induced by PtNiBiSnSb. In this process, the anti-tumor immune response is amplified by inducing immunogenic cell death and inhibiting the growth of immunosuppressive cells through blocking fatty acid uptake. The proposal of HEAzyme for cancer therapy provides a novel approach to enhance the catalytic activity of SAzymes and deepens the theoretical understanding of HEAzyme in the POD-like reaction process.

cancer biology↗

bioRxiv2025

A Paracrine-to-Autocrine Shunt of GREM1 Fuels Colorectal Cancer Metastasis via ACVR1C

Tumor cells typically rely on paracrine stromal signals to guide malignant behaviors, but whether they acquire signaling autonomy to support metastasis remains unclear. We elucidate this in colorectal cancer (CRC) by uncovering a paracrine-to-autocrine shunt of Gremlin1 (GREM1), a canonical stromal-secreted antagonist of bone morphogenetic proteins (BMPs). We demonstrate that while GREM1 remains restricted to stromal cells in earlier-stage (I-III) CRC, its ectopic expression in tumor epithelium increases markedly in stage IV. Mechanistically, we identify ACVR1C as a novel, high-affinity epithelial receptor for GREM1. Their interaction activates SMAD2/3 signaling, which upregulates SNAI1 and GREM1, establishing a feedback loop that amplifies epithelial-mesenchymal transition (EMT). Disrupting this loop impairs CRC metastasis in vivo. Clinically, epithelial GREM1 or ACVR1C expression predicts metastasis and poor survival. These findings define a paradigm in which tumor cells hijack stromal GREM1 to establish a GREM1-ACVR1C autocrine loop that sustains EMT and metastasis, marking a shift toward signaling autonomy and revealing a targetable vulnerability in advanced CRC.

cancer biology↗

bioRxiv2025

Granulin+ macrophages promote lineage plasticity in prostate cancer through paracrine signaling loops

The role of tumor-infiltrating immune cells in driving phenotype switching remains unclear, despite the well-established association between lineage transition and drug resistance in prostate cancer. This study employed an integrated analysis of single-cell multiomics to investigate the dynamics of immune infiltration, transcriptional programs, and cell-cell communication in prostate cancer. Our results demonstrated that granulin (GRN) positive macrophages facilitated the transition from adenocarcinoma to a multilineage state with mesenchymal and stem-like traits by activating intra-tumoral NF-{kappa}B signaling. Subsequently, the multilineage clones induced macrophages to highly express granulin through the secretion of CSF1, forming a positive feedback cell communication loop. Next, we validated the biological function of granulin in mediating epithelial-mesenchymal transition in vitro. Additionally, organoids drug resistance assay demonstrated that granulin drove resistance to androgen receptor (AR)-targeted drug (enzalutamide). Moreover, pharmacologic blockade of the CSF-1/CSF-1R axis in TRAMP mouse models reduced the expression of GRN in macrophages and suppressed the formation of multilineage subclones in prostate malignant cells. Furthermore, multiplex immunofluorescence staining of tumor samples from TRAMP mouse models revealed the VIM lineages were spatially in close contact with macrophages. Meanwhile, Cytometry by Time-Of-Flight (CyTOF) analysis validated our findings at single-cell protein level in patients with castration-resistant prostate cancer. Besides, three distinct tumor-infiltrating subsets associated with disease relapse were identified, including DCN+ endothelial cells, CCL7+ fibroblasts, and IFIT1+ neutrophils. These results offer potential therapeutic targets to address lineage plasticity-driven resistance to AR-targeted therapy.

cancer biology↗

bioRxiv2025

Improving Joint Estimation of Vital Rates in IPMs via Gaussian Processes and ABC

O_LIDeveloping population dynamic models that can flexibly adapt to different species remains a challenge due to the context-dependent nature of demographic studies. This work introduces ABC GP IPM, a novel Integral Projection Model (IPM) framework, aimed at mitigating key limitations associated with traditional IPMs, including (i) reliance on predefined vital rate models with restrictive assumptions, (ii) omission of potential vital rate interactions, and (iii) limited flexibility in incorporating domain- or user-specific knowledge. The purpose of this work is to enhance the adaptability and accuracy of IPMs across various ecological and evolutionary studies. C_LIO_LIOur methodology integrates Gaussian Process (GP) models with Approximate Bayesian Computation (ABC). GP models introduce a non-parametric structure that accommodates a broader range of demographic patterns, reducing sensitivity to specific model choices. The incorporation of ABC methods allows IPMs to integrate additional population-level information, enabling potential interactions among vital rates to be reflected in model outcomes without requiring additional datasets. The information can be user-modified, facilitating the tailoring of IPMs to specific requirements or domain-specific knowledge. Recognising the inherent challenge of selecting appropriate summary statistics in ABC applications, we further propose a systematic procedure tailored to navigate this complexity effectively when applying ABC GP to IPMs. C_LIO_LIThe method demonstrated strong flexibility and adaptability across different modeling scenarios. In simulation studies, ABC GP IPM showed notable improvements over traditional GLM-based IPMs across multiple population metrics commonly used in biological research. When applied to real-world datasets, the method captured complex demographic patterns more effectively, supporting its potential as a practical and adaptable alternative to existing IPM frameworks. C_LIO_LIThe ABC GP IPM framework provides greater flexibility in model specification, accommodating potential non-linearities with fewer assumptions. It also facilitates the incorporation of user expertise and domain-specific knowledge, enhancing its applicability to context-dependent demographic studies. While offering a more adaptable modeling approach, the method remains accessible to users without specialized expertise in statistical modeling. Importantly, ABC GP IPM delivers these improved outcomes using identical datasets as standard IPMs, facilitating easier adoption for studies that have applied traditional IPMs. C_LI

evolutionary biology↗

bioRxiv2025

ABC for high-dimensional modular models via MCMC samples

Many complex systems are modelled using modular models, where individual sub-models are estimated separately and then combined. While this simplifies inference, it fails to account for interactions between components. A natural solution is to estimate all components jointly, but this is often impractical due to intractable likelihoods. Approximate Bayesian Computation (ABC) provides a likelihood-free alternative, but its standard implementations are computationally inefficient, particularly when applied to high-dimensional modular models, or when sub-models involve costly machine learning methods, like Gaussian Process (GP) models. The ABC-Population Monte Carlo (ABC-PMC) framework improves on vanilla ABC by using sequential Monte Carlo sampling with adaptive tolerances and proposal kernels, yielding much higher acceptance rates and more efficient exploration of parameter space. Existing ABC-PMC algorithms are not, however, especially efficient in the high-dimensional parameter setting typical of modular models. We introduce a novel modification of the ABC-PMC method that leverages model modularity. Our approach refines the prior distribution and perturbation kernel by using precomputed Markov Chain Monte Carlo (MCMC) samples from individual sub-models, making parameter updates more efficient. Additionally, we employ an adaptive summary statistic weighting strategy that dynamically adjusts the contribution of different statistics, reducing the influence of less informative statistics. These modifications greatly reduce overall computational cost. In our case studies, the runtime for 10,000 simulation attempts drops from over 20 days to under 1 minute, following a one-off preprocessing step that consists of standard MCMC sampling for each sub-model (typically 3-10 hours, depending on model complexity). We apply our method to an ecological case study using an Integral Projection Model (IPM) for Cryptantha flava, where survival, growth, and reproduction processes are modelled using GP models. The results of the simulated and the real case studies demonstrate greatly improved computational efficiency while preserving inference quality. While the case study focuses on ecology, the method is applicable to a broad range of modular models where capturing interactions among sub-models is essential.

ecology↗

bioRxiv2025

The glomerulus as a selective gate for tumor-derived extracellular vesicles in urine

Urinary small extracellular vesicles (sEVs), which can reflect systemic conditions, hold great promise for non-invasive cancer diagnostics, yet the mechanism by which tumor-derived sEVs reach urine remains unclear. Here, we demonstrate that the glomerulus actively transcytoses circulating tumor-derived sEVs into urine. Using CRISPR gRNA-tagged glioma sEVs and bioluminescent/fluorescent GeNL-tagged lung and pancreatic cancer sEVs, we tracked their journey from tumors to urine in multiple mouse models. In vivo and in vitro analyses revealed endocytic uptake and transcytotic release by glomerular cells, accompanied by changes in sEV size and surface composition. GeNL-tagged sEVs consistently showed higher signals in urine than plasma, indicating selective excretion. These findings redefine the glomerulus as a dynamic regulator of EV processing and establish a mechanistic foundation for urinary liquid biopsy.

cancer biology↗

bioRxiv2025

Cytoprotective roles of "E3 ubiquitin ligases-NF-κB-autophagy" axis in Pacific oysters Crassostrea gigas exposed to phenanthrene

Phenanthrene (PHE), as one of the most frequently found polycyclic aromatic hydrocarbons can induce immunotoxicity, oxidative stress, and endocrine disruption in marine organisms. However, whether autophagy can be induced by PHE and the regulatory mechanism and cytoprotective roles of autophagy under PHE stress condition have not been unveiled. Our data first unveil a "E3 ubiquitin ligases-NF-{kappa}B-autophagy" axis, which play cytoprotective roles in Pacific oysters Crassostrea gigas exposed to PHE. The results of confocal laser scanning microscope, flow cytometry and transmission electron microscope confirmed that PHE could induce autophagy in the haemocytes of Pacific oysters, and the presence of autophagosomes was also confirmed. The proteomics results showed that the expression of the E3 ubiquitin ligase HUWE1, TRIM36, and autophagy-related protein 7 (ATG7) were significantly upregulated. The expression of genes of the "axis" were significantly upregulated, and the expression of genes of autophagy was downregulated after the inhibition of the NF-{kappa}B, indicating that the expression of the "axis"-related genes can be stimulated by PHE, and thus autophagy is activated. The upregulation of the expression of "axis"-related genes in mouse macrophages, further demonstrating the existence of the "axis" proposed by this study and the "axis" can be activated by PHE. Incorporating with changes of cell number, apoptosis rate, phagocytic capacity, and ROS levels of lymphocytes, we demonstrated that autophagy plays a cytoprotective role in cellular defence against PHE. This study proposed a novel pathway and supplied a comprehensive understanding of the protective role of autophagy in Pacific oysters to cope with pollutants.

cell biology↗

bioRxiv2025

Single-cell spatial map of cis-regulatory elements for disease-related genes in the macaque cortex

Single-cell spatial transcriptomes have demonstrated molecular and cellular diversity in the brain1, 2, 3, 4, 5, 6, 7, 8, but gene regulatory mechanisms underlying transcriptomic profiles and disease pathogenesis remain largely unknown in primates. Here we performed single-nucleus Assay for Transposase-Accessible Chromatin followed by sequencing (snATAC-seq) for [~]1.6 million cells from 142 cortical regions of two male cynomolgus monkeys (Macaca fascicularis), and identified distinct chromatin accessibility profiles of cis-regulatory elements (CREs) for various cell types. By integrative analysis with large-scale spatial transcriptome data, we found that these CREs showed laminar and regional preferences, with their regional accessibility exhibiting striking dependence on the regions hierarchical level. Cross-species comparison of snATAC-seq data revealed human/macaque-enriched layer-4 glutamatergic neurons and LAMP5/LHX6-expressing GABAergic neurons as well as human/macaque-biased CREs for genes related to neurodevelopment and psychiatric diseases. Importantly, risk single-nucleotide polymorphisms for many brain disorders strongly associated with human/macaque-biased CREs in glutamatergic neuronal types and those for Alzhemers disease strongly associated with CREs exclusively in microglia. Our results provided the basis for understanding the spatial gene regulatory mechanisms underlying cellular diversity and disease pathogenesis in the primate cortex.

neuroscience↗

bioRxiv2025

Th1 effector CD4 T cells rely on IFN-γ production to induce alopecia areata

Alopecia areata (AA) is an autoimmune disease that is clinically characterized by hair loss and histologically by a peribulbar infiltrate of CD8 and CD4 T cells. Prior studies have focused on the role of CD8 T cells in the development of AA; however, the role of CD4 T cells remains unclear. Here, we demonstrate that CD4 T cells from the skin draining lymph nodes (SDLN) of AA mice transferred disease into recipient mice. Further, these cells exhibited a T-helper type 1 (Th1) effector transcriptional and phenotypic profile. The pathogenic activity of these CD4 T cells was dependent upon the presence of endogenous CD8 T cells and host IFN-{gamma} responsiveness. Targeted deletion of CD4 T cell-mediated production of IFN-{gamma} abrogated the ability of this cell population to transfer disease. Together, these data provide mechanistic insights into pathways that lead to AA development, strengthening our understanding of the disease and inviting studies into exploring novel therapeutic strategies for human patients.

immunology↗

bioRxiv2025

Kinetochore mutations and histone phosphorylation pattern changes preceded holo- and macro-monocentromere evolution

Centromeres are essential for kinetochore assembly and spindle attachment. While chromosomes of most species are monocentric with a single centromere, a minority exhibit holocentricity, with a centromere along the chromatid length. Sporadic emergence of holocentricity suggests multiple independent transitions. To explore this, we compared the centromere and (epi)genome organization of two sister genera with contrasting centromere types: Chamaelirium luteum with large "macro-monocentromeres" and Chionographis japonica with holocentromeres. Both exhibit chromosome-wide histone phosphorylation patterns distinct from typical monocentric species. Kinetochore analysis revealed similar chimeric Borealin in both species, with additional KNL2 loss and NSL1 chimerism in Cha. luteum. The broad-scale synteny between both genomes supports de novo holocentromere formation in Chi. japonica. Despite sharing features with both centromere types, macro-monocentromeres do not represent a direct link between mono- and holocentromeres. We propose a model for the divergent evolution involving kinetochore gene mutations, altered histone phosphorylation patterns, and centromeric satellite DNA amplification.

evolutionary biology↗

bioRxiv2025

Systematic evaluation of blood contamination in nanoparticle-based plasma proteomics

Circulating blood proteomics enables minimally invasive biomarker discovery. Nanoparticle (NP)-based circulating plasma proteomics studies have reported varying number of proteins, ranging from ca 2000 to 7000 but its not clear whether higher protein number is more informative. Here, we first develop OmniProt - a silica-NP workflow for plasma proteomics which is optimized through systematic evaluation of NP types and protein corona formation parameters. Next, we present an Astral spectral library for 10,109 protein groups expressed in human plasma. Using Astral with a throughput of 60 sample-per-day, OmniProt identifies ca 3000 to 6000 protein groups from human plasma. Notably, we found that platelet/erythrocyte/coagulation-related contamination artificially elevates protein identifications and compromises quantification accuracy for circulating plasma proteins in NP-enriched samples. Through controlled contamination experiments, we identified and validated protein biomarkers for contaminations of platelet, erythrocyte, and coagulation, respectively, in NP-based plasma proteomics experiments. We further developed an open-access software Baize for accessing plasma proteomics contamination. Finally, we validated our OmniProt workflow and Baize software in a clinical cohort of 193 patients with CT-indistinct benign nodules or early lung cancers. On average, we identified ca 4400 protein groups for each plasma sample without significant contamination. Five samples were flagged out as contaminated. In conclusion, this study reveals that contamination of plasma samples significantly alters the protein identification and quantification in NP-based plasma proteomics experiments, and presents an open-access software Baize to evaluate plasma proteome contamination.

biochemistry↗

bioRxiv2025

A Novel No-Wash (Homogenous) High-Throughput Toxicity Assay on Primary Cells

Mitochondrial membrane potential (MMP) is a critical marker of mitochondrial and, therefore, cellular function. However, current dyes used for MMP measurement possess significant limitations: nonspecific targeting, long incubation times, potential mitochondrial toxicity, poor water solubility, and numerous wash steps. Using a novel fluorescent dye--mitochondrial membrane potential indicator (m-MPI)--in combination with a masking dye, we overcame said limitations and successfully measured MMP changes on different cell lines, as well as four different human primary cells. This no-wash assay has been miniaturized into a 384-well format. It is robust with Z value > 0.5 on both HepG2 and HeLa cells and can be used for high throughput screening. The reagents in the m-MPI homogeneous assay kit are not toxic to cells, as was demonstrated on HepG2 and HeLa cell lines using Dexorgens EnerCount ATP assay. Using this assay, we conducted a mini screening on human hepatocytes against the Library of Pharmacologically Active Compounds (LOPAC) (Sigma). The resulting hits were then confirmed with follow-up studies.

cell biology↗

bioRxiv2025

Hepatic isomiR landscaping reveals new biological insights into metabolic dysfunction in steatotic liver disease

Post-transcriptionally modified microRNA (miRNA), called isomiRs, expand the repertoire of transcripts that can leveraged for therapeutic targets and biological insights. However, the expression of isomiRs has not been characterized in metabolic dysfunction-associated steatotic liver disease (MASLD). Therefore, we assessed the isomiR expression profile in liver biopsies from 79 patients with MASLD and modeled their potential role in disease biology. MiRNAs represented 75% of the sequencing reads and over 65% of them were attributed to isomiRs, demonstrating their higher expression and diversity compared to canonically annotated miRNAs. Differential expression and machine-learning analyses were used to identify 173 isomiRs associated to MASLD severity and 58 isomiRs associated to fibrosis score. Candidate target mRNAs were identified for each isomiR based on sequence complementarity. Using matched mRNA sequencing data, and supported by data from an independent study, we proposed key dysregulated mRNA targets involved in a selection of 33 disease-associated pathways. Importantly, isomiRs offered novel and unique mRNA targets compared to the canonical miRNA, e.g. isomiR-122 targeting INSIG1 (insulin and cholesterol metabolism), and isomiR-21 targeting HMGCS2 and PPARA (PARR and TGF-beta signaling). Our work advances knowledge regarding the role of isomiRs in MASLD and lays a foundation for therapeutic targets identification. HighlightsOur results provide a comprehensive analysis of microRNA (isomiRs) in liver tissue. Machine learning identified isomiRs whose expression is associated with MASLD. Multi-omic analysis uncovered novel isomiR regulatory mechanisms involved in MASLD.

bioinformatics↗

bioRxiv2025

Gene traffic mediated by transposable elements shaped the dynamic evolution of ancient sex chromosomes of varanid lizard

Lizards exhibit rapid turnovers and a much greater diversity of sex determination mechanisms compared to birds and eutherians. This makes the conserved ZW sex chromosomes of anguimorph lizards originated over 115 million years ago a seeming exception. We recently discovered in an anguimorph lizard Varanus acanthurus (Vac) that its entire W chromosome (chrW), but not chrZ is homologous to part of the chr2 by cytogenetic mapping, suggesting a complex history of its sex chromosome evolution yet to be elucidated. To address this, we assembled a chromosome-level genome, and provided evidence that the Vac sex chromosome pair had undergone at least three times of recombination suppression, forming a similar pattern of evolutionary strata to that of birds or mammals. We identified the putative sex-determining genes in the oldest evolutionary stratum that had first lost recombination. Comparison to other lizard genomes dated the stepwise propagation of specific retrotransposon subfamilies shared by chrW and chr2 to the varanid ancestor. These retrotransposons are also enriched near the duplicated genes shared by the two chromosomes and probably mediated the recruitment of many autosomal genes that rejuvenated the degenerating chrW, including members of a large vomeronasal chemosensory receptor gene family V2R. Our results challenge the canonical model of sex chromosome evolution, and suggest that the W or Y chromosome as a refugium of repetitive elements, may recurrently recruit short-lived functional genes responsible for sexual dimorphisms during its long-term course of degeneration.

evolutionary biology↗

bioRxiv2025

ELF3 controls trait heterogeneity by tuning the rate of maturation in Arabidopsis and barley

Trait heterogeneity in a population increases the likelihood that some individuals will survive an unpredictable environmental stress. Individual plants mature at different rates due to genetics, environmental factors, and random chance. All of this contributes to trait heterogeneity. EARLY FLOWERING3 (ELF3), a core circadian clock component, determines developmental timing, and here we tested the hypothesis that it would shape trait heterogeneity. We developed a model predicting that faster-developing populations exhibit greater heterogeneity during development but reduced heterogeneity at maturity, while slower-growing populations show the opposite pattern. Experiments in Arabidopsis elf3 and barley Hvelf3 mutants supported this prediction. In Arabidopsis, ELF3 controlled hypocotyl elongation variability via maturation rate rather than direct regulation. Bolting time heterogeneity also decreased in faster-growing plants. In barley, Hvelf3 altered growth heterogeneity, but this was initially masked by germination timing differences. Finally, smaller barley plants were found to be more resilient to osmotic stress, suggesting that ELF3-driven trait heterogeneity may contribute to bet hedging. These findings highlight how modifying developmental rates influences population-level trait distributions and stress resilience.

plant biology↗

bioRxiv2025

Pangenome insights into structural variation and functional diversification of barley CCT motif genes

CCT motif genes play a key role in barley development and flowering, yet their genetic diversity remains underexplored. Leveraging a barley pangenome (76 genotypes) and pan-transcriptome (subset of 20 genotypes), we examined CCT gene variation and evolutionary dynamics. Motif-based searches, combined with genome assembly validation, revealed annotation limitations and novel frameshift variants (e.g., HvCO10), indicating active diversification. Pangenome-wide phylogenetic analysis identified clade-specific domain expansions, including B-box domain additions in HvCO clades. Tissue-specific expression patterns further supported functional divergence among paralogs. Notably, VRN2, a canonical floral repressor associated with winter growth, was retained in spring genotypes, challenging its presumed exclusive role in vernalization. Discrepancies between VRN1 expression, VRN2 deletion, and growth habits implicated additional regulatory mechanisms. These findings highlight the power of pangenomes in resolving gene family complexity, refining annotations, and advancing the understanding of CCT genes to enhance barley resilience and adaptability.

plant biology↗

bioRxiv2025

cfMethDB: a comprehensive cfDNA methylation data resource for cancer biomarkers

Cancer is a major global health threat, and early detection of cancer is crucial for improving patient outcomes. DNA methylation in circulating cell-free DNA (cfDNA) has emerged as a promising biomarker for non-invasive cancer diagnosis. However, the integration and utilization of existing cfDNA methylation data have been limited, hindering comprehensive research efforts, especially in the discovery of cfDNA methylation biomarkers. To address this challenge, we introduce cfMethDB, a comprehensive database dedicated to cfDNA methylation in cancer that encompasses 4828 publicly available datasets. Through standardized analysis, we identified 1,048,770 differentially methylated cytosines (DMCs) as candidate biomarkers across seven cancer types. With cfMethDB, we not only identified known cfDNA methylation biomarkers, but also discovered several genes, such as ZIC4, that could be novel biomarkers. Moreover, cfMethDB offers a suite of user-friendly tools, including biomarker evaluation, pan-cancer search and end motif analysis. We hope that cfMethDB will serve as a valuable platform for the discovery of novel cancer cfDNA methylation biomarkers and will facilitate cancer research and clinical applications. cfMethDB is publicly available at: https://cfmethdb.hzau.edu.cn/home.

genomics↗

bioRxiv2025

CDKL5 modulates structural plasticity of excitatory synapses via liquid-liquid phase separation

Activity-dependent synaptic remodeling, essential for neural circuit plasticity, is orchestrated by central organizers within the postsynaptic density (PSD), including the scaffolding protein PSD95. However, the molecular mechanisms driving this process remain incompletely understood. Here, we identify CDKL5, a protein associated with a severe neurodevelopmental condition known as CDKL5 deficiency disorder (CDD), as a critical regulator of structural plasticity at excitatory synapses. We show that CDKL5 undergoes liquid-liquid phase separation (LLPS) in vitro and in cultured neurons, forming co-condensates with PSD95. This LLPS-driven process spatially organizes synaptic components, specifically enabling the synaptic recruitment of Kalirin7 to promote dendritic spine enlargement. Pathogenic mutations disrupt condensate formation by impairing the LLPS capacity of CDKL5, directly linking phase separation defects to the pathogenesis of CDD. Our findings reveal a crucial role for CDKL5 in synaptic plasticity and establish LLPS as a fundamental mechanism by which CDKL5 coordinates molecular events to reorganize PSD architecture during synaptic remodeling.

neuroscience↗