Biology subjects

Zhang, L.

Publications and source records attributed to Zhang, L..

At least 289 records · Page 16Linked to original sources

bioRxiv2025

Heterogeneous immune recovery after viral response through a dynamical model of feedback-driven persistence and clearance

Viral infections trigger complex immune responses with heterogeneous outcomes shaped by nonlinear feedbacks. An ordinary differential equation model is developed to investigate immune response dynamics during viral infection, incorporating six modules: viral load, innate immunity, cellular immunity, humoral immunity, immune suppression, and IL-6 levels. Bifurcation analysis reveals that under continuous viral exposure, when viral clearance rate and intrinsic viral death rate satisfy specific conditions, the system exhibits up to five stable equilibria. This indicates that different health and disease states may coexist depending on initial conditions, while severe inflammation mainly arises from strong activation of cellular immunity, highlighting the complexity of immune responses. Simulations of finite-time viral exposure demonstrate multi-timescale recovery characteristics: viral load and IL-6 levels decline rapidly, whereas humoral immune activation and immunosuppression show delayed and sustained patterns. Furthermore, analysis of infectious period and disease duration also indicates that during transition from early acute response to chronic disease, viral replication rate plays a critical role, while immune response intensity is sensitive to both viral clearance and immune self-activation. Subsystem analysis identifies the three-component subsystem of viral load, innate immunity, and cellular immunity as core drivers of bistability and oscillations, while humoral immunity, immune suppression, and IL-6 primarily modulate response amplitude and timing. This work establishes a theoretical framework for analyzing immune response and chronic risks through feedback dynamical modelling, providing insights for intervention strategies.

systems biology↗

bioRxiv2025

Single-cell spatial mapping reveals dynamic bone marrow microarchitectural alterations and enhances clinical diagnostics in MDS

Myelodysplastic neoplasms (MDS) disrupt bone marrow hematopoiesis, yet clinical assessment relies largely on blast enumeration and qualitative morphology, which incompletely capture marrow architecture and disease state. We applied whole-slide multiplex immunofluorescence imaging with single-cell phenotyping to map bone marrow microarchitecture in MDS. Diagnostic biopsies (n=36), longitudinal treatment samples (n=29), precursor states (n=13), and normal controls (n=21) were analyzed, comprising >5 million spatially resolved cells. MDS marrow exhibited coordinated, genotype-imprinted architectural remodeling, including altered progenitor composition and spatial patterning, disrupted erythroid island organization, and displacement of hematopoietic stem and progenitor cells from perivascular niches. Interrogation of 82 cellular and spatial features yielded a composite Microarchitectural Perturbation Score (MDS-MAPS), derived from diagnostic samples and fixed prior to longitudinal analyses. In leave-one-patient-out cross-validation, MDS-MAPS discriminated remission from active disease more accurately than blast percentage (AUC 0.883 vs 0.660) and distinguished low-blast MDS from clonal cytopenia of undetermined significance (CCUS) (AUC 0.815). Mixed-effects modeling showed MAPS decreased in remission statistically independent of blast burden, with architectural normalization during remission and re-emergence at relapse. These findings define quantitative bone marrow architecture as a dynamic tissue-state biomarker that complements molecular and blast-based assessment in MDS.

pathology↗

bioRxiv2025

Hippo/YAP1 Signaling Regulates the Oligodendrocyte-Astrocyte Fate Switch and Ependymal Gene Expression in Adult Spinal Cord Stem Cells

The adult mammalian spinal cord harbors ependymal cells that retain neural stem-cell properties. Although they possess a latent capacity to generate oligodendrocytes, these cells predominantly differentiate into astrocytes after injury. The molecular cues that govern their lineage commitment toward astrocytic versus oligodendroglial fates remain poorly defined. In this study, we addressed this gap in vitro by investigating the emergence of PDGFRA oligodendrocyte precursor cells (OPCs) in neurosphere cultures derived from adult spinal cord stem cells. We first observed that neurosphere cells exhibited a hybrid identity, co-expressing transcription factors of both astrocytic (NFIA, SOX9) and oligodendrocytic (OLIG1/2, SOX4, NKX2.2, TCF4) lineages. Upon differentiation, oligodendrocytic transcription factors were selectively maintained in OPCs but reduced in other cells. Using PdgfraH2B-GFP mice, we then isolated newly formed PDGFRA OPCs from neurospheres and performed multi-omic profiling. OPC formation was associated with the upregulation of chromatin remodelers and the downregulation of stem-cell markers such as EGFR, HES1, and TNC. Strikingly, OPC specification coincided with reduced expression of YAP1 and its partner TEAD1, key effectors of the Hippo pathway. Functional analyses revealed that YAP1 loss enhanced oligodendrocytic differentiation while reducing astrocytic and ependymal/cilia-associated gene expression. Conversely, constitutive YAP1 activation blocked differentiation into both lineages and promoted an ependymal-like transcriptional program, including upregulation of the ependymal marker CD24a and cilia-related proteins such as CROCC (Rootletin). Collectively, these findings uncover previously unrecognized roles for YAP1 in adult spinal cord stem-cell fate decisions and provide a molecular framework for leveraging these cells in regenerative strategies targeting spinal cord repair.

cell biology↗

bioRxiv2025

Collagen-Based Tumor Spheroid Model for Investigating Tumor-Macrophage Interactions through Extracellular Matrix Remodeling

Macrophages in the tumor microenvironment (TME) can constitute up to 50% of tumor mass and play a critical role in cancer cell proliferation, invasion, and metastasis. While their contribution to extracellular matrix (ECM) degradation through matrix metalloproteinases (MMPs) has been explored, the role of other macrophage-derived factors in ECM remodeling and their impacts beyond degradation remain poorly understood. Here, we describe the development of a 3D collagen-based tumor spheroid model to investigate the impact of peripheral blood mononuclear cell (PBMC)-derived macrophages on cancer cell-ECM and cancer cell-macrophage interactions within the TME. We observed that cancer cells stimulated PBMC-derived macrophages into an M2-like phenotype and that tumor spheroid conditioned macrophages (TSCMs) shifted cancer cell populations toward phenotypes with greater invasion distances and reduced circularity, indicative of increased malignancy. Such observations can be explained by macrophage-mediated ECM remodeling. Specifically, we demonstrate that TSCMs secreted a variety of soluble factors that are known to contribute to ECM remodeling, including ECM degradation and fiber realignment. These processes collectively create a tumor-favoring environment by loosening the collagen matrix and aligning fibers that serve as invasion tracks for migrating tumor cells that facilitate cancer cell migration and invasion. This model provides a robust platform to study the interactions between cellular and non-cellular components in the TME and to identify the molecular mechanisms underlying cancer progression. These insights may aid in the development of novel therapeutic strategies targeting macrophage-mediated processes in cancer. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/679587v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@17d1f9forg.highwire.dtl.DTLVardef@1a71500org.highwire.dtl.DTLVardef@53deeeorg.highwire.dtl.DTLVardef@510268_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Leveraging AI for facioscapulohumeral muscular dystrophy prediction and omics biomarker identification

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant muscle disorder characterized by a complex genetic etiology, variable prognosis, and a lack of effective therapies. Previous studies have identified candidate protein and miRNA biomarkers using various profiling techniques, underscoring their potential for monitoring FSHD, assessing prognosis, and evaluating pharmacodynamic responses. However, the feasibility of applying machine learning (ML) models to predict FSHD using these molecular signatures has not been explored. In this study, we developed ML models to predict FSHD using a multi-omics dataset comprising protein abundance and miRNA expression profiles. Key predictive features were identified using Random Forest and the Support Vector Machine-Recursive Feature Elimination (SVM-RFE) methods. Performance evaluations demonstrated the robustness of the ML classifiers, with logistic regression consistently achieving the robust predictive accuracy in distinguishing FSHD from healthy conditions. Additionally, we assessed the predictive power of the identified features by comparing them with biomarker sets reported in previous studies. Our findings highlight the potential of AI to improve prediction accuracy and facilitate the cost- and time-efficient strategy for identifying FSHD biomarker candidates, even with limited sample sizes in the context of rare diseases.

bioinformatics↗

bioRxiv2025

Acidic transcription factors position the genome at nuclear speckles through transcription dependent and independent mechanisms

A small fraction of the genome positions reproducibly near nuclear speckles (NS), increasing expression and/or splicing efficiency of NS-associated genes. How specific genomic regions target to NS remains unclear. Here, we demonstrate that establishment of genome-wide NS-association occurs independent of active transcription. We show that DNA sequences derived from NS-associated regions integrated as transgenes autonomously target to NS. By systematically dissecting one such genomic locus, the COL1A1-SGCA locus, we identified redundant NS-targeting cis regulatory elements, including a [~]600 bp fragment with 17 binding motifs for 8 transcription factors (TFs). Four NS-targeting TFs within this fragment contain acidic activation domains (AADs) that provide both chromatin-context and transcription-dependent NS-targeting, a property that appears common among several other tested AADs. A subset of acidic activator TFs contain an additional, transcription-independent NS-targeting activity. Our findings establish diverse and partially redundant NS-targeting activities, which may facilitate dynamic gene positioning at NS periphery for context-specific transcriptional responses.

cell biology↗

bioRxiv2025

Disrupted Regional Dynamics of Structure-Function Connectivity Coupling in Euthymic Bipolar Disorder

BackgroundBipolar disorder (BD) is characterized by persistent disturbances in emotional regulation and cognitive function, even during euthymia, yet its neural mechanisms remain unclear. Given evidence of structural and dynamic functional connectivity (dFC) abnormalities in BD, investigating dynamic structure-function connectivity coupling (SC-FC coupling) may provide insights into the pathophysiology of the disorder. MethodsDiffusion tensor imaging and resting-state fMRI data were collected from 61 euthymic BD-I patients and 54 healthy controls (HC). Structural connectivity was derived using probabilistic tractography, and dFC was estimated with a sliding-window approach. SC-FC coupling was quantified as the extent to which structural features predicted dFC using multivariate linear regression. Abnormal SC-FC coupling in BD was assessed at both the network and regional levels, relative to HC. Over time, SC-FC coupling was categorized into high- and low-coupling states, and dynamic state analyses of dwell time, occurrence rate, and transition probabilities were performed in the affected brain regions. ResultsNetwork-level analyses indicated that BD exhibits lower SC-FC coupling in subcortical regions compared with HC. Regional analyses revealed significantly reduced dynamic SC-FC coupling in two thalamic subregions (medial posterior and rostral temporal) and in the right primary somatosensory cortex in BD compared to HC. Dynamic analyses further demonstrated thalamic instability: BD showed shorter dwell times in high-coupling states, increased occurrence of low-coupling states, and more frequent high-to-low coupling transitions than HC. These abnormalities suggest that BD is characterized by disrupted structure-function integration and unstable thalamocortical dynamics. ConclusionOur findings reveal regional abnormalities in SC-FC coupling dynamics in BD, indicating persistent dysfunction of structure-function integration during euthymia. Dynamic coupling measures may provide preliminary insights into potential biomarkers for disease monitoring.

neuroscience↗

bioRxiv2025

scRGP: Prediction of Single-cell Genetic Perturbation Transcriptional Responses based on Rank in Multiple Scenarios

Single-cell perturbation sequencing technologies (e.g., Perturb-seq, CROP-seq), which integrate CRISPR-based gene editing with single-cell transcriptome profiling, have revolutionized the analysis of transcriptomic changes induced by genetic perturbations at single-cell resolution. These technologies serve as a powerful tool for identifying key genes that inhibit tumor growth or reverse cancer cell phenotypes. However, they face two major challenges: data explosion with high experimental costs, and data complexity characterized by high dimensionality, noise, sparsity, and heterogeneity. To address these challenges, we developed the single-cell Rank-based Genetic Perturbation predictor (scRGP), the first deep learning framework leveraging gene expression rank-order information for this task. scRGP demonstrates superior performance in terms of robustness, cross-cell-line perturbation prediction, and high-throughput screening. Specifically, scRGP achieves an approximately 10-16 percentage points improvement in Pearson correlation coefficient (PCC) over state-of-the-art methods (e.g., GEARS and scFoundation) for single- and double-gene perturbation predictions, while also extending prediction capability to triple-gene perturbations. Furthermore, it outperforms these methods by approximately 5-9 percentage points in cross-cell-line predictions. These advancements promise to shift the paradigm of single-cell perturbation studies from experiment-driven to computation-driven approaches, providing new support for functional genomics and precision medicine.

bioinformatics↗

bioRxiv2025

Glycan recognition by a plant sentinel immune receptor

Pathogens target and degrade the extracellular matrix surrounding plant cells. A central question is how cell wall-derived damage-associated molecular patterns (DAMPs) are recognized and integrated to trigger immune responses. We address this question by determining the structure of the multidomain receptor IGP1 in both apo form and bound to the cellulose-derived DAMP cellotriose. Structural analyses reveal that constitutive Leucine Rich Repeat-malectin interactions preconfigure IGP1 for ligand recognition and that the receptor features a highly specific sugar-binding pocket in the LRR domain capable of distinguishing fine variations in glycan structures. By directly sensing cello-oligomers, IGP1 acts as a cell wall sentinel that links pathogen-induced wall degradation to immune alerting, equipping plants to mount rapid and robust defense responses.

plant biology↗

bioRxiv2025

Interaction of Carbamoyl-Phosphate Synthase 1 with Agmatinase in the Liver of Torpid Bats

Mammalian torpor imposes unique metabolic constraints, yet the mechanisms of nitrogen metabolism during this state remain unclear. In this study, we show that the urea cycle is selectively regulated rather than broadly suppressed in torpid bats. A significantly increased abundance of carbamoyl-phosphate synthase 1 (CPS1) maintained its functional capacity during torpor and arousal in Myotis ricketti. Proteomic analyses and confocal microscopy identified a specific association and co-localization between CPS1 and agmatinase (AGMAT), an ATP-independent enzyme involved in nitrogen metabolism. Co-localization of CPS1 and AGMAT was also observed in torpid Rhinolophus ferrumequinum, a phylogenetically distant species. Fluorescence resonance energy transfer (FRET) further supported an indirect CPS1-AGMAT interaction. Most urea cycle enzymes exhibited stable or only moderately reduced expression during bat torpor, and metabolic profiling demonstrated sustained nitrogen flux. Together, these findings reveal a conserved adaptive mechanism that maintains urea cycle function, potentially enhancing osmotic stability and energy efficiency during prolonged fasting and water scarcity.

zoology↗

bioRxiv2025

Programmable Aptamer-Embedded Circular RNAs for Targeted Antigen-Presenting Cells Immunotherapy

The targeted delivery of mRNA to specific cell types in vivo remains a major unmet need in mRNA-based therapeutics. Conventional strategies rely on nanocarriers engineered with various modifications. However, these exogenous materials could cause adverse reactions, and their complex manufacturing processes often hinder clinical application. By leveraging the innate programmability of RNA sequences, we herein report a carrier-free, scalable, and programmable aptamer-embedded circular RNAs (Apt-circRNAs) design that confers targeting capability through the strategic incorporation of different aptamers at varying densities, while retaining circular RNA stability and protein production capability. Experimental results show that antigen-loaded Apt-circRNAs enable targeted delivery to antigen-presenting cells (APCs), drive endogenous antigen expression, activate antigen-specific T cells, and elicit potent immune responses that mediate clearance of both early-and late-stage tumors in mouse models. In humanized models of colorectal cancer, the combination of Apt-circRNA and PD-1 blockade produced synergistic antitumor effects and significantly reshaped the tumor microenvironment. In a first-in-human (FIH) clinical trial, Apt-circRNA vaccine encoding KRAS G12D/G12V neoantigens exhibited a favorable safety profile and induced robust immune activation, T cell mobilization, and neoantigen-specific immune responses. With this study, we have established a new paradigm in carrier-free, APC-targeted RNA vaccine design, offering a safe and effective platform for next-generation cancer immunotherapy.

bioengineering↗

bioRxiv2025

An SR45-dependent exonic splicing enhancer is essential for regulating alternative splicing in Arabidopsis

Alternative splicing (AS) is a critical gene regulatory mechanism that underpins developmental plasticity and environmental adaptation in eukaryotes. Although numerous cis-elements and trans-factors governing AS have been characterized in animals, their functional roles in plants remain largely unexplored. We previously identified the Arabidopsis sot5 mutant, which exhibits leaf virescence due to a mutation in the conserved 5 splice site (5ss) of intron 7. Here, through characterization of a suppressor of sot5 (E61), we found that E61 harbors a G to A mutation in exon 8 of the SOT5 gene. Interestingly, this mutation creates a synonymous codon but disrupts the exonic splicing enhancer (ESE) motif (AAGAAGA), thereby reducing the splicing efficiency of the adjacent intron 7. Retention of this intron produces a functional protein that rescues the sot5 virescent phenotype. We confirmed the causal role of this ESE by using a cytidine base editor (CBE) to convert the ESE sequence to AAGAAAA or AAAAAAA in sot5. The edited plants phenocopied the suppressor E61. Genetic analyses revealed that mutations of SR45 encoding an RNA-binding protein but not its paralog SR45a similarly rescues the sot5 phenotype by impairing intron 7 splicing. Furthermore, we demonstrated that SR45 directly binds to the ESE motif in vitro, and that mutating the proximal ESEs in intron 2 of another SR45 target, GPDHC1 (Glycerol-3-Phosphate Dehydrogenase C1), recapitulates the splicing defect observed in the sr45 mutant. These findings establish that SR45 specifically recognizes AAG-repeat ESEs to enhance the splicing of adjacent weak introns, revealing a potent strategy for fine-tuning gene expression through targeted editing of splicing regulatory elements for crop improvement.

molecular biology↗

bioRxiv2025

Directed evolution of a compact TranC11a system for efficient genome editing

The recently discovered TranC systems represent programmable RNA-guided DNA endonucleases of transposon origin with compact protein sizes ideal for therapeutic delivery. However, their editing efficiency in human and plant cells is limited. Here, we evolved TranC11a and engineered its sgRNA to enhance overall editing efficiencies. TranC11a systems exhibit up to 9.2-fold higher editing activity than its parent and achieves efficiency comparable to SpCas9 across multiple human genome endogenous sites, significantly outperforming compact editors NovaIscB and enTnpB1c. TranC11a enables efficient editing of disease-relevant genes in human cells and breeding traits in maize. With its high editing activity and compact size (574 aa), TranC11a demonstrates strong potential for future in vivo genome editing and crop engineering.

synthetic biology↗

bioRxiv2025

A Multi-Layered Atlas of Spatial Regulatory Programs and Therapeutic Vulnerabilities in Glioblastoma

Glioblastoma (GBM) is marked by profound spatial heterogeneity. This complexity fuels tumor progression and therapy resistance. Although recent spatial transcriptomics (ST) studies have defined transcriptional niches, or metaprograms, the systems level regulatory logic linking upstream signaling, transcriptional programs, and therapeutic vulnerabilities remains unresolved. Here, we introduce an integrated, multi layered framework that unifies transcription factor and pathway activity inference (STAN and SPAN) with ligand/receptor and drug target mapping, thereby constructing a systems-level regulatory atlas of GBM across 26 tumors. This atlas uncovers spatial niches organized around transcriptional hubs and signaling programs, including hypoxic mesenchymal regions coordinated by HIF1A and SOX2 with mTORC1 signaling, macrophage rich areas driven by STAT3 mediated immune modulation, and astrocyte-like states shaped by lipid metabolic regulators such as SREBF2. By coupling this regulatory atlas to drug target predictions, we identify niche specific therapeutic vulnerabilities, such as VEGF blockade in HIF1A high regions and MAO-B inhibition in mesenchymal states. Finally, we provide an open, interactive web resource to make these data broadly accessible. This work provides a generalizable blueprint for linking spatial regulation to therapeutic hypotheses across diverse human diseases.

bioinformatics↗

bioRxiv2025

GLIS3 Marks a Neural-like Progenitor Cell State that Drives Metastasis in Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) has a high rate of recurrence and metastasis despite intensive therapy. The neural-like progenitor (NRP) transcriptional program is enriched in residual disease after neoadjuvant chemotherapy and radiotherapy; however, the mechanisms for increased NRP expression in the post-treatment setting remain unclear. Here, we find that NRP signatures are strongly enriched in tissue injury and regeneration, and NRP cancer cells co-express transcription factors involved in pancreatic development. We identify both cell autonomous and ligand mediated mechanisms for inducing NRP expression in vitro. We establish and characterize isogenic mouse organoid overexpression models for transcription factors associated with the NRP, classical, and basal-like states. We discovered that Glis3 is a key NRP-associated transcription factor that drives malignant properties including greater clonogenicity, tumor growth, and metastasis compared to isogenic models for the classical and basal-like states. Our work highlights the emergence of clinically relevant developmental regeneration programs in the post-treatment context.

cancer biology↗

bioRxiv2025

Local translation of circular RNAs is required for synaptic activity and memory

Circular RNAs (circRNAs) are enriched in synapses and implicated in cognitive processes, and recent studies have shown that circRNAs can encode micropeptides, which suggests that there may be novel synaptic proteoforms in the brain that await discovery. Here we report widespread learning-induced local circRNA translation in the prefrontal cortex of male C57BL/6 mice. More than 1500 synapse-enriched circRNAs contain active IRES elements, with 842 interacting with the ribosome and 241 exhibiting direct evidence of activity-induced translation. We discovered a synapse-enriched micropeptide (P1) that is derived from a single exon circRNA, the mRNA host of which encodes an enzyme associated with protein repair. Although P1 is only a third of the size of the full-length protein, it is locally expressed, enzymatically active, and interacts with plasticity-related proteins, including CaMKII. In addition to direct effects on synaptic activity, targeted P1 knockdown impairs whereas its overexpression enhances fear extinction memory. These findings shed new light on the dark proteome in the brain and reveal local circRNA translation as a novel mechanism of plasticity and memory.

neuroscience↗

bioRxiv2025

SomaMutDB 2.0: A comprehensive database for exploring somatic mutations and their functional impact in normal human tissues

Recent advances in ultra-accurate sequencing technologies have revealed that somatic mutations accumulate across the human lifespan and may contribute to both normal aging and disease. These mutations are highly diverse, often non-recurrent, and functionally heterogeneous, which makes their biological impact difficult to evaluate systematically. Although many studies have profiled somatic mutations in individual tissues or limited cohorts, a centralized and scalable platform that integrates discoveries and supports functional interpretation has been lacking. To address this gap, we present SomaMutDB 2.0 (https://somamutdb.org/SomaMutDB/), a substantially expanded database that catalogs 8.9 million mutations (8.57 million SNVs and 0.29 million INDELs) from 10,852 samples of 607 human subjects across 47 studies. Beyond expanded data coverage, SomaMutDB 2.0 introduces a comprehensive functional annotation framework that applies 22 predictive models, encompassing coding, regulatory, expression-based, and ensemble predictors, to systematically assess mutational impact. Users can browse pre-annotated variants through an interactive interface or upload their own variants for real-time analysis, with results contextualized against all mutations from normal, non-diseased tissues in the database. Together, these advances establish SomaMutDB 2.0 as the most comprehensive resource currently available for characterizing somatic mosaicism and functional interpretation in human health and aging. Graphical AbstractSomaMutDB 2.0 provides an expanded catalog of 8.9 million somatic mutations across 30 tissues, along with pipelines for mutational signature analysis and 22-tool functional annotation that enable user-submitted variant interpretation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/676124v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1c76484org.highwire.dtl.DTLVardef@1984f71org.highwire.dtl.DTLVardef@8789a9org.highwire.dtl.DTLVardef@5ed54a_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

A Human Neuronal Co-Culture System Reveals Early Tumor-Neuron Communication and Targetable Pathways in Glioblastoma

BackgroundGlioblastoma (GB, IDH wild type) is the most aggressive primary brain tumor in adults, with recurrence driven by residual tumor cells that re-establish interaction with surrounding neurons. While neuronal activity is recognized as a driver of GB progression, the earliest neuronal responses to tumor contact remain poorly understood. Existing models rarely capture these acute events or the heterogeneity of responses generated by tumors of different origins, limiting insight into the earliest neuron-tumor interactions. MethodsWe developed a dual-interface human iPSC-derived neuronal culture system to investigate acute neuronal responses to glioblastoma exposure. Neurons were challenged with either established GB cell lines or patient-derived glioblastoma cells (PDGCs). Using quantitative proteomics, high-resolution imaging, and immunological assays, we characterized compartment-specific neuronal changes and mapped activated signaling pathways. We also screened selective inhibitors for their effects on both tumor proliferation and neuronal integrity. FindingsWithin 24 hours of exposure, neurons displayed synaptic remodeling and activation of GB-related signaling cascades. Proteomic analysis of GB exposed neurons revealed enrichment of pathways associated with GB and abnormalities in neuronal circuits. Notably, the U-87MG cell line, but not PDGCs, induced pronounced synaptic disruption, neurite retraction, and MAPK pathway activation, with distinct molecular signatures across neuronal compartments. ERK1/2 and p38 MAPK signaling were differentially activated depending on the GB cells source, correlating with specific structural and functional synaptic alterations. Targeted inhibition of MAPK components significantly suppressed U-87MG proliferation and preserved neuronal architecture. InterpretationWe present a human neuronal culture model that detects and discriminates the earliest neuron-derived responses to glioblastoma from diverse tumor sources. By linking neuronal remodeling to tumor-specific signaling pathways, the platform uncovers both the heterogeneity of neuron-tumor interactions and early, targetable vulnerabilities. This system offers a translational tool to advance understanding of GB recurrence and to guide development of therapies with dual neuroprotective and anti-tumor efficacy. In BriefEarly interactions between glioblastoma and human neurons drive rapid, source-specific synaptic remodeling mediated by compartmental MAPK pathway activation. This neuronal co-culture model identifies distinct profiles of tumor-neuron communication, highlights synaptic vulnerability as a therapeutic axis, and demonstrates that MAPK pathway inhibition yields both neuroprotective and anti-tumor effects. SummaryGlioblastoma (GB) co-opts neuronal circuits to drive tumor progression, yet the earliest neuronal responses that may shape recurrence remain poorly defined. We developed a human iPSC-derived neuronal co-culture model that captures acute communication between neurons and glioblastoma from diverse sources, including serum-adapted cell lines and patient-derived cells. Within 24 hours, glioma-exposed neurons exhibited synaptic remodeling and activation of tumor-associated signaling pathways. High-resolution imaging and proteomics revealed compartment-specific synaptic alterations, with ERK1/2 and p38 MAPK signaling differentially engaged depending on the tumor source, corresponding to distinct structural and functional outcomes. Pharmacologic inhibition of MAPK components both suppressed tumor cells growth and preserved neuronal integrity. By modeling source-dependent and early neuron-tumor interactions, this platform not only identifies MAPK signaling as a critical mediator of synaptic vulnerability but also provides a clinically relevant tool for investigating the mechanisms of glioblastoma recurrence. It offers a framework for developing therapies that target the dual vulnerabilities of tumor progression and circuit remodeling. Highlights O_LIA dual-interface human iPSC-derived neuronal co-culture system models early neuron-glioblastoma (GB) interaction. C_LIO_LISerum-adapted U-87MG, but not serum-free patient-derived GB cells, induces pronounced synaptic disruption and neurite retraction. C_LIO_LIGlobal proteome of neurons reveals GB-associated signatures and neuronal circuit alterations in response to both U-87MG and patient-derived GB cells. C_LIO_LIERK1/2 and p38 MAPK signaling are differentially activated in neuronal compartments, depending on GB source. C_LIO_LIMAPK pathway inhibition suppresses U-87MG proliferation and preserves neuronal integrity, revealing actionable neuroprotective and anti-tumor targets. C_LI

cancer biology↗