Biology subjects

Lee, Y.

Publications and source records attributed to Lee, Y..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Hybridity of mainly asexually propagating duckweeds in genus Lemna - dead end or breakthrough?

O_LIThe cosmopolitan, mainly vegetatively propagating, organ-reduced monocotyledonous aquatic duckweeds are the smallest and fastest growing angiosperms, distributed world-wide and flower rarely in nature. Recently, we reported intra- and interspecific hybrids and ploidy variants in the genus Lemna. Thus, contrary to the expectation, sexual propagation may occasionally occur within and between Lemna species. Our main goal was to uncover whether the ecologically successful hybrids are evolutionary dead ends, or initiate further speciation and novel sexual recombination. C_LIO_LIWe investigated flower development, pollen viability, seed set and seed germination in hybrids and their parental species and characterized genome size and genetic markers in the progenies. C_LIO_LIIntraspecific crosses yielded fertile progeny, but all dihaploid and triploid interspecific hybrids were male sterile. Only an established allotetraploid hybrid reproduced sexually, while colchicine-induced allotetraploids from dihaploids did not re-gain sexual competence so far. C_LIO_LIWe concluded that only established allotetraploid hybrids represent an evolutionary break-through in duckweeds. Our results regarding sexual traits within the duckweed genus Lemna, and the sexual competence of diverse hybrids i) pave the way for further investigation in this understudied field, ii) provide fundamental data regarding the evolutionary potential of duckweed hybrids and iii) are important for future breeding efforts on this emerging crop. C_LI

evolutionary biology↗

bioRxiv2025

Deciphering the oxidative modifications via disulfide mapping

Oxidative stress triggers redox-sensitive post-translational modifications, notably disulfide bond formation involving cysteine residues. However, these bonds are often overlooked in proteomics due to the routine use of reducing agents. Here, we employed LC-MS-based metabolomics and non-reducing tandem mass tag (TMT) proteomics to investigate the effects of H2O2 on MDA-MB-231 cells. Metabolomic analysis revealed pathway-specific inhibition of major metabolic pathways including glycolysis, the TCA cycle, and nucleotide biosynthesis. Proteomic analysis using the DBond algorithm revealed extensive and isoform-specific disulfide crosslinks across more than 1,000 proteins. These linkages were enriched at redox-sensitive cysteines near basic residues and displayed high isoform specificity. Our findings demonstrate that disulfide bond formation serves as a selective mechanism of redox regulation. This study highlights the utility of non-reducing proteomics in elucidating redox-controlled protein networks and structural dynamics under oxidative stress. TeaserNon-reducing proteomics uncovers hidden disulfide-linked networks that rewire protein responses to oxidative stress.

cell biology↗

bioRxiv2025

Optimizing twin prime editing components for scalable genome editing and therapy in spinocerebellar ataxia type 3

Recent advances in prime editing technologies using CRISPR modules fused with reverse transcriptase (RT) have enabled efficient and precise reprogramming of target genomic sequences. Twin prime editing using two coordinated prime editor complexes is a promising strategy for inducing extensive genomic modifications via reverse transcribed complementary templates. However, current twin prime editing systems still require improvements in editing efficiency, accuracy, and intended edit predictability. Here, efficiency and precision of twin prime editing were enhanced via engineering and optimizing conventional SpCas9(H840A)-RT-based prime editor components. A La domain-fused prime editor (La-SpCas9(H840A)-RT) and optimized pegRNAs were developed, achieving a 1.75 {+/-} 0.21-fold increase in gene editing efficiency at multiple genomic loci in human-derived cell lines without increasing off-target activity. La-SpCas9(H840A)-RT facilitated efficient [~]2.8 kb GFP transgene knock-in at target loci and eliminated the expanded polyQ tract in ATXN3 in patient-derived mutant cell lines modeling spinocerebellar ataxia type 3. The advanced twin prime editing platform expands genome engineering capabilities beyond existing CRISPR-based systems and holds great promise for diverse biotechnological and therapeutic applications.

bioengineering↗

bioRxiv2025

The Ralstonia solanacearum E3 ligase effector RipV1 targets subfamily IXb receptor-like cytoplasmic kinases that negatively regulate immunity in Nicotiana benthamiana.

Plants detect microbe-associated molecular patterns from pathogens via plasma membrane- localized receptors which activate multiple signaling cascades that lead to pattern-triggered immunity (PTI). Receptor-like cytoplasmic kinases (RLCKs) are essential hubs of plant immune signaling, associating with receptors and intracellular proteins through phosphorylation events. As a consequence, RLCKs have emerged as common targets of pathogen effectors. To improve our knowledge on Solanaceae responses to the bacterial wilt pathogen Ralstonia solanacearum, we conducted a yeast two-hybrid screen between tomato RLCKs and effectors conserved in R. solanacearum Korean isolates. Several members of RLCK subfamily IXb, which contain a ubiquitin-ligase plant U-box domain in addition to the kinase domain, interacted with RipV1, an effector containing a novel E3 ligase domain (NEL). In vitro assays revealed that RLCK-IXb-1 displayed ubiquitin-ligase activity but no detectable kinase activity. RipV1 could trans- ubiquitinate RLCK-IXb-1 in vitro and promote its stability in planta. Using virus-induced gene silencing of RLCK-IXb homologs in Nicotiana benthamiana, we could further show that several RLCK-IXb proteins act as negative regulators of early PTI signaling. RipV1 was previously reported to contribute to R. solanacearum virulence in potato and to elicit cell death in an E3 ligase activity-dependent manner in N. benthamiana. Here we show that RipV1-induced cell death occurred in plants impaired for effector recognition but could be suppressed by over-expression of RLCK-IXb-1, suggesting that this response is related to the virulence function of RipV1. Altogether, our work identifies possible substrates of an NEL effector and underlines the complex roles of RLCKs in plant immune signaling.

plant biology↗

bioRxiv2025

Disulfide Crosslinking Induces Rapid Degradation of Arc/Arg3.1 via Hsp70-Mediated Ubiquitin Ligase Pathway

Activity-regulated cytoskeleton-associated protein (Arc/Arg3.1) is an immediate-early gene (IEG) induced by stress and synaptic activity, characterized by transient expression and rapid degradation. However, the mechanisms governing its degradation remain unclear. In this study, we identify a novel degradation pathway for Arc/Arg3.1, driven by its structural features. We demonstrate that the proteasomal degradation of Arc/Arg3.1 is modulated by the Hsp70-CHIP complex, with ubiquitination being impaired in HSF1 knockout cells. The formation of a Cys34-Cys159 disulfide bond crosslinks Arc/Arg3.1 into high-molecular-weight oligomers, altering its ubiquitination pattern and degradation kinetics compared to the C159A mutant. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) revealed that wild-type (WT) Arc/Arg3.1 adopts a more compact structure than the C159A mutant. Notably, the C159A mutant fails to interact with HSF1, resulting in Hsp70 induction upon heat shock. Our findings propose a feedback loop in which disulfide crosslinking of Arc/Arg3.1 induces rapid degradation through Hsp70-mediated ubiquitination, which in turn modulates the heat shock response by inhibiting HSF1 function.

biochemistry↗

bioRxiv2025

Engineered ADARs enable single-nucleotide resolution DNA A-to-G editing without bystander effects

The adenine base editor (ABE), which enables A*T-to-G*C base conversion, has emerged as a powerful tool for therapeutic applications. However, conventional ABEs suffer from bystander nucleotide conversions, limiting their utility for precise editing. Here, we present a single-nucleotide resolution ABE (snuABE) created by fusing a nickase Cas9, nCas9(H840A), with the deaminase domain of ADAR, which acts on DNA:RNA hybrids, instead of TadA, which acts on single-stranded DNA in conventional ABEs. snuABE requires a specially designed target-adenine guide RNA (tagRNA) that introduces a mismatch at the target adenine, enabling highly specific A-to-G editing by ADAR. Engineering ADAR from Pediculus humanus using the in silico protein evolution algorithm EvolvePro, along with 3-end protection of the tagRNA, further enhances the editing activity of snuABE in human cells. Moreover, snuABE exhibits significantly reduced DNA off-target activity, highlighting its potential as a safer and more precise base editing technology for therapeutic applications.

bioengineering↗

bioRxiv2025

Huntington's disease LIG1 modifier variant increases ligase fidelity and suppresses somatic CAG repeat expansion

Huntingtons disease (HD) is a fatal neurodegenerative disorder caused by inheriting an expanded CAG repeat tract in the huntingtin gene (HTT) that further expands in somatic cells over an individuals lifetime. Genome-wide association studies have provided critical insight into factors that modify the course of disease. These include DNA repair genes that alter the rate of somatic expansion and other genes that do not appear to directly influence this process. One modifier gene is DNA ligase 1 (LIG1), in which a variant specifying a lysine to asparagine substitution (K845N) is associated with a profound (7-8 year) delay in the onset of motor signs. Here, we have taken a multifaceted approach to gain insight into the protective nature of this variant in HD. We demonstrate using in vitro ligase assays and enzyme kinetics that K845N enhances discrimination towards mismatched substrates and increases repair fidelity. Consistent with increased ligation fidelity, K845N confers protection against oxidative stress in cell-based assays. Finally, we demonstrate that the mouse LIG1 K843N orthologue suppresses somatic CAG expansion in HD knock-in mice. Overall, our data provide evidence that altered LIG1 function due to the K845N substitution may contribute to HD clinical delay by slowing somatic expansion in the brain and protecting the genome globally against damage. Significantly, our results provide a mechanistic foundation for considering DNA ligase fidelity as a therapeutic target in HD and potentially in other trinucleotide repeat disorders. Significance StatementWe analyzed a missense variant in DNA Ligase 1 (K845N) that is associated with a profound delay in the onset of Huntingtons disease (HD). We find that K845N enhances substrate discrimination towards mismatched substrates, thus increasing repair fidelity, conferring protection against oxidative stress and slows somatic expansion of the HD CAG repeat. Our observations provide insight into underlying mechanisms of disease modification and suggest avenues that can be harnessed for disease-modifying therapeutic intervention. Classification: Biological Sciences, Genetics

genetics↗

bioRxiv2025

Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders

Loss-of-function mutations in DNMT3A, a DNA methyltransferase, or NSD1, a histone methyltransferase, cause overgrowth syndromes. Conversely, disruption of the DNMT3A domain that binds NSD1-deposited H3K36 dimethylation (H3K36me2) results in growth restriction. To investigate the molecular basis of these opposing growth outcomes, we generated isogenic human embryonic stem cells carrying growth syndrome-associated mutations in DNMT3A and NSD1. Unexpectedly, both overgrowth- and growth restriction- associated DNMT3A mutations led to DNA hypomethylation in a shared subset of active enhancers, implicating H3K36me2 in directing enhancer methylation maintenance. In contrast, bivalent chromatin--marked by both active and repressive chromatin modifications--showed divergent DNA methylation changes: hypermethylation in growth restriction-associated DNMT3A mutants and hypomethylation in overgrowth-associated DNMT3A or NSD1 loss-of-function mutants. These findings identify locus-specific DNA methylation defects as a common molecular feature and nominate dysregulated DNA methylation at bivalent chromatin as a potential driver of abnormal growth phenotypes.

genomics↗

bioRxiv2025

A hierarchical abscission program regulates reproductive allocation in Prunus yedoensis and Prunus sargentii

O_LIorgan abscission is essential for optimal reproduction, yet its regulation in perennial woody plant species is poorly understood. To investigate how abscission is spatially and temporally regulated during reproduction, we analyzed five sequential abscission events in the cherry species Prunus yedoensis and Prunus sargentii: abscission of the petals, calyces, flower pedicels, fruit pedicels, and peduncles. C_LIO_LIThe abscission zone (AZ) of the calyx formed de novo upon activation, whereas other AZs were pre-formed but developmentally arrested. Localized ethylene responsiveness reactivated these zones, promoting cell division, differentiation of residuum and secession cells on either side of the AZ, and lignin deposition in some cases. This progression was accompanied by reactive oxygen species accumulation and pH shifts. C_LIO_LIWe observed species-specific differences during early floral abscission: P. yedoensis shed petals rapidly in a pollination-independent manner, whereas P. sargentii retained petals on unpollinated flowers, which later abscised with the pedicel, potentially extending the fertilization window. C_LIO_LIBoth species employed a post-fertilization checkpoint via fruit pedicel abscission to selectively eliminate small, slow-growing fruits. These findings reveal that Prunus species coordinate a hierarchical abscission program functioning as a multilayered reproductive filter, progressively refining investment decisions to determine the final fruit set. C_LI

plant biology↗

bioRxiv2025

Conformational analysis of liganded human hemoglobin by cryo electron microscopy

The long-standing debate on the preferred conformation of liganded hemoglobin (Hb) in solution has yet to be completely resolved. While some studies have used lyophilized human hemoglobin for structural studies by cryo-EM, we recently presented the first cryo-EM analysis of freshly prepared human and crocodilian Hbs. Further three-dimensional (3D) classification analysis of these datasets reveals distinct structural characteristics. CO-bound adult human Hb (CO-HbA) shows a mixture of conformations, with the R2 conformation most populated, R strongly represented, and other intermediate states present in sufficient quantity to produce maps. CO-bound crocodile Hb showed the R conformation and, unexpectedly, a smaller population of molecules in a T-like conformation. The amino acid substitution Glu {beta}39 [->] Arg, unique to crocodilian Hbs, appears to favour the R conformation over R2.

molecular biology↗

bioRxiv2025

A global genetic interaction map of a human cell reveals conserved principles of genetic networks

We generated a genome-scale, genetic interaction network from the analysis of more than 4 million double mutants in the haploid human cell line, HAP1. The network maps [~]90,000 genetic interactions, including thousands of extreme synthetic lethal and genetic suppression interactions. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes, pathways, biological processes, and cellular compartments. Comparative analyses showed that general principles of genetic networks are conserved from yeast to human cells. A genetic interaction network mapped in a single genetic background complements the DepMap gene co-essentiality network, recapitulating many of the same biological connections and also capturing unique functional information to reveal roles of uncharacterized genes and molecular determinants of specific cancer cell line genetic dependencies.

systems biology↗

bioRxiv2025

Human ribomes reveal DNA-embedded ribonucleotides as a new type of epigenetic mark

Ribonucleoside monophosphates (rNMPs) are abundant in DNA, but their distribution and function in human nuclear genomes remain unknown. Here, we mapped nearly one million rNMPs per genome across diverse human cell types, defining a nuclear "ribome" with non-random distribution patterns. rNMPs are enriched in C/G-rich sequences, epigenetically marked regions, and telomeres. Conserved ribonucleotide-enriched zones (REZs) overlap with CpG islands and R-loops. rNMP concentration near transcription start sites (TSSs) correlates positively with gene expression. Wild-type cells display a broader gene-expression range than ribonuclease H2A (RNH2A) knockouts, in which loss of rNMP cleavage causes pronounced retention of embedded rG and strand-biased rC near TSSs, both increasing with gene expression. These findings establish DNA-embedded rNMPs as a novel epigenetic mark that modulates human gene expression.

molecular biology↗

bioRxiv2025

CPT1B-Mediated Fatty Acid Oxidation Induces Pigmentation in Solar Lentigo

IntroductionCellular senescence is associated with altered lipid metabolism, including increased cellular lipid uptake, upregulated lipid biosynthesis, and deregulated lipid breakdown. Previous studies have reported that carnitine palmitoyltransferase (CPT), the rate-limiting enzyme in fatty acid oxidation that catalyzes the conversion of acyl-CoA to acylcarnitine, is involved in various senescence-related diseases. Although solar lentigo (SL) is an age-related pigmentary disorder characterized by the accumulation of senescent cells, its role in metabolic dysregulation has rarely been investigated. Methods and ResultsIntegrated transcriptomic profiling of SL skin samples, combining mRNA sequencing, differential gene expression, pathway enrichment analyses, metabolic flux simulations, and protein-protein interaction analysis, was conducted to demonstrate the molecular alterations in SL compared to perilesional normal skin. We found transcriptomic alterations in mitochondrial energy metabolism-associated genes. Metabolic flux simulations revealed that carnitine-associated reactions involved in fatty acid oxidation were upregulated. Using a multi-omics approach, CPT1B was selected as a potential marker for SL, which was confirmed via its overexpression in immunohistochemical studies. Using a zebrafish model, CPT1B was implicated in melanogenesis. DiscussionCPT1B-mediated metabolic alteration is a key driver of SL pathogenesis. Targeting CPT1B and the associated lipid metabolism pathways is a novel therapeutic approach for managing SL and age-related pigmentation disorders. Research HighlightsSolar lentigo (SL) exhibits altered mitochondrial metabolism and fatty acid oxidation. CPT1B activation regulates pigmentation, suggesting that targeting CPT1B may offer a novel therapy for SL and other age-related pigmentary disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=176 HEIGHT=200 SRC="FIGDIR/small/659823v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@81fce3org.highwire.dtl.DTLVardef@1bf3forg.highwire.dtl.DTLVardef@b2c119org.highwire.dtl.DTLVardef@1a38b23_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2025

Altered kinematics and muscle activities during half squats in people with ankle sprain history

Regardless of the high recurrence rate, copers manage the damage after a sprain. Copers do not experience ankle instability and continue their daily activities. However, it is unclear whether copers can use movement strategies similar to people without an ankle sprain. Identifying movement strategies can improve efficacy and prevent unwanted effects during training. Therefore, we aimed to compare the kinematics and muscular activities of the lower limbs during half squats and gait between copers and healthy controls. Ten copers (7 men, 3 women; age = 21.6 {+/-} 1.1 years) and 10 controls (6 men, 4 women; age = 22.5 {+/-} 2.8 years) were included in the cross-sectional study. We compared angles of the thigh, shank, and foot calculated from inertial measurement units and muscle activities of the biceps femoris long head, rectus femoris, gastrocnemius, and tibialis anterior between copers and controls during half squats and gait. For half squats, copers demonstrated thigh restriction with an effect size of 0.67-1.35, whereas we observed no significant differences in the shank and foot angles in the descending phase. Copers demonstrated less activity with an effect size of 0.61-1.58 in all four muscles. Copers showed lower activities of the rectus femoris and tibialis anterior during the same period of thigh restriction. For gait, there were no significant differences in lower limb angles and muscle activities between copers and controls. Copers may restrict thigh rotation unintentionally, leading to less muscle activity during half squats. Removing unconscious restrictions using sensor-based quantitative feedback can enable copers to obtain more efficient training. Our results suggest that assessing the limb movements of copers is important for efficient training, even if they do not experience instability to continue with their daily activities.

physiology↗

bioRxiv2025

Gene-embedding-based prediction and functional evaluation of perturbation expression responses with PRESAGE

Understanding the impact of genetic perturbations on cellular behavior is crucial for biological research, but comprehensive experimental mapping remains infeasible. We introduce PRESAGE (Perturbation Response EStimation with Aggregated Gene Embeddings), a simple, modular, and interpretable framework that predicts perturbation-induced expression changes by integrating diverse knowledge sources via gene embeddings. PRESAGE transforms gene embeddings through an attention-based model to predict perturbation expression outcomes. To assess model performance, we introduce a comprehensive evaluation suite with novel functional metrics that move beyond traditional regression tasks, including measures of accuracy in effect size prediction, in identifying perturbations with similar expression profiles (phenocopy), and in prediction of perturbations with the strongest impact on specific gene set scores. PRESAGE outperforms existing methods in both classical regression metrics and our novel functional evaluations. Through ablation studies, we demonstrate that knowledge source selection is more critical for predictive performance than architectural complexity, with cross-system Perturb-seq data providing particularly strong predictive power. We also find that performance saturates quickly with training set size, suggesting that experimental design strategies might benefit from collecting sparse perturbation data across multiple biological systems rather than exhaustive profiling of individual systems. Overall, PRESAGE establishes a robust framework for advancing perturbation response prediction and facilitating the design of targeted biological experiments, significantly improving our ability to predict cellular responses across diverse biological systems.

bioinformatics↗

bioRxiv2025

PerTurboAgent: A Self-Planning Agent for Boosting Sequential Perturb-seq Experiments

Understanding how genetic interventions affect a cells phenotype is key to revealing causal gene regulatory mechanisms and finding novel drug targets. Pooled, high-content perturbation screening methods like Perturb-seq allow us to assess the impact of each of a large number of genetic interventions on a rich cellular profile of RNA or other features, facilitating such discoveries. However, the overall scale of perturbations, especially when considering combinations of genes for perturbation, cannot be tackled exhaustively in the lab. An alternative is to use an iterative design: By leveraging the modularity and sparsity of gene circuits along with prior biological knowledge, we can predict the impact of unseen genetic perturbations on these profiles and group genes with similar effects into co-functional modules, followed by a new round of Perturb-Seq to test these predictions and improve the overall performance of the model. These iterative cycles of experiment and prediction allow prioritizing genes for testing, maximizing the knowledge gleaned from fixed experimental resources, and opening the way to learn general predictive models. Designing these experiments requires a system that can analyze a cellular system, incorporate new and existing knowledge, use statistical tools, predict the effects of unseen perturbations, and prioritize the set of perturbations for the next iteration. These can be time-consuming tasks for scientists and require multiple different skills. Here, we developed PerTurboAgent, an LLM-based agent that excels in predicting candidate gene panels for iterative Perturb-Seq experiments through self-directed data analysis and knowledge retrieval. We evaluated PerTurboAgent based on its ability to identify genes with a phenotypic impact on gene expression upon perturbation in genome-scale perturbation data. PerTurboAgent outperforms existing agent-based and active learning strategies, offering an efficient and understandable approach to designing sequential perturbation experiments.

bioinformatics↗

bioRxiv2025

Rapid ethylene-triggered protein complex remodeling in dark grown hypocotyls

Protein-level cellular dynamics, including multimerization, play a crucial role in rapid adaptation of plants during developmental transitions and environmental stresses. The gaseous hormone ethylene is a key regulator of rapid cellular growth modulation. During soil emergence, etiolated seedlings undergo crucial morphological changes to their apical hooks and hypocotyls, with ethylene inhibiting hypocotyl axial elongation while promoting radial expansion. Ethylene triggers these growth responses within two hours; however, the protein machineries and cellular processes that mediate morphogenesis control are not known. Here, we used quantitative proteomics and co-fractionation mass spectrometry to test for rapid ethylene-dependent changes in protein abundance and protein complex composition. Protein multimerization responses were numerous and diverse. There were instances of protein complex assembly and disassembly, with varying degrees of completeness. Small-scale validation tests indicate that the identified proteins play a role in hypocotyl development and suggest that this novel approach to gene discovery identifies potential targets for ethylene-mediated growth regulation and enhanced seedling adaptability during early development.

plant biology↗

bioRxiv2025

Longitudinal deep phenotyping in a mouse model of West syndrome reveals temporal dynamics of synapse remodeling, gliosis, and proteomic and lipidomic changes during seizure evolution

Neurodevelopmental disorders can have long-lasting effects, causing not only early pediatric symptoms but also a range of neurological issues throughout adulthood. West syndrome is a severe neurodevelopmental disorder marked by infantile spasms, an early symptom that typically subsides with age. However, many patients progress to other seizure forms, known as seizure evolution, which is closely linked to poor long-term outcomes. Despite its clinical significance, the neurobiological mechanisms behind seizure evolution in West syndrome remain poorly understood. Recent genetic studies have consistently identified the CYFIP2 p.Arg87Cys variant in West syndrome patients, and the Cyfip2+/R87C mouse model carrying this mutation has been shown to recapitulate key symptoms of the disorder, including infantile spasms. In this study, we aimed to gain deeper insight into seizure evolution by conducting longitudinal deep phenotyping of the Cyfip2+/R87C mouse model from the neonatal stage to seven months of age. We tracked seizure activity through behavioral and EEG recordings and employed multi-omic analyses, including tissue and single-cell level transcriptomics, ultrastructural analysis, proteomics, and lipidomics, to capture a comprehensive view of molecular and cellular changes. Our results showed that after an initial period of neonatal spasms, Cyfip2+/R87C mice entered a seizure-free phase, followed by spontaneous recurrent seizures in adulthood, ultimately leading to premature death. This progression was associated with synaptic remodeling, sequential activation of different glial cell types, lipid droplet accumulation in astrocytes, and significant proteomic and lipidomic changes in the brain. These findings suggest that seizure evolution in West syndrome involves complex, time-dependent interactions between neurons and glial cells, along with alterations in lipid metabolism. Our study highlights the potential of longitudinal multi-omic approaches to uncover underlying mechanisms of seizure evolution and suggests that targeting these changes could offer novel therapeutic strategies. Additionally, the dataset generated here may provide valuable insights for other epilepsy and neurodevelopmental disorder models.

neuroscience↗