Biology subjects

Kim, J. Y.

Publications and source records attributed to Kim, J. Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Imbalance between RNA-binding proteins and the WAVE regulatory complex underlies the toxic gain-of-function effects of the CYFIP2 Arg87Cys variant in neurodevelopmental disorders

Pathogenic variants in cytoplasmic FMR1-interacting protein 2 (CYFIP2) cause neurodevelopmental disorders, with hotspot substitutions at arginine 87 (Arg87) associated with particularly severe symptoms. CYFIP2 functions both as a component of the WAVE (Wiskott-Aldrich syndrome protein family verprolin-homologous protein) regulatory complex (WRC), regulating the actin cytoskeleton, and as an interactor of RNA-binding proteins (RBPs) involved in mRNA processing/translation. Although Arg87 variants reduce CYFIP2 protein stability, heterozygous knock-in mice carrying Arg87Cys (Cyfip2+/R87C) show markedly more severe phenotypes than heterozygous knockout (Cyfip2+/-) mice, supporting a toxic gain-of-function mechanism. However, how the dual roles of CYFIP2 contribute to this mechanism remains unclear. To address this, we examined Cyfip2+/R87C mice at postnatal week 7, before overt neuronal loss and gliosis, focusing on the progressive dispersion of hippocampal cornu ammonis 1 (CA1) pyramidal neurons, a phenotype absent in Cyfip2+/- mice. Single-nucleus RNA sequencing suggested candidate alterations related to translation and cell adhesion/migration in CA1 pyramidal neurons. Complementarily, human embryonic kidney 293T cells expressing CYFIP2 Arg87Cys showed defects in proliferation and morphology, accompanied by altered expression of cell adhesion-related genes. Quantitative proteomic analysis of the CA1 region uncovered an imbalance between CYFIP2-associated protein networks, characterized by increased RBPs and reduced WRC components. Phosphoproteomic analysis further revealed altered phosphorylation of synaptic and translational regulators. Consistently, whole-cell recordings and biocytin-based morphological analyses showed increased frequency of miniature excitatory postsynaptic currents and altered dendritic morphology in Cyfip2+/R87C CA1 pyramidal neurons, most prominently in the more severely dispersed deep-layer neurons. Moreover, the cell adhesion molecule Eph receptor A3 was reduced, possibly as a result of RBP dysregulation. Together, these findings suggest that an imbalance between RBP- and WRC-associated pathways underlies the gain-of-function effects of CYFIP2 Arg87Cys and contributes to early neuronal phenotypes, most notably CA1 layer dispersion. This mechanism, distinct from CYFIP2 haploinsufficiency, supports allele-specific therapeutic strategies for Arg87 variants.

neuroscience↗

bioRxiv2026

Requirement of hypoxia-inducible factor 1 alpha for interleukin 1 beta induced glycolysis in colorectal cancer cells

Colorectal cancer cells increase glycolysis to help meet the metabolic demands required for cell growth. Many factors, both endogenous and exogenous, likely drive cellular metabolism and enhance glycolytic flux in colorectal cells. Interleukin-1 beta (IL-1{beta}) is a pro-inflammatory cytokine that is elevated in colorectal cancer. In this study, we investigated the effect of IL-1{beta} toward driving the cancer cell to increase glycolysis, while also suppressing the oxidation of the fiber-derived nutrient butyrate. The results presented here demonstrate that IL-1{beta} stimulated glycolysis and inhibited maximal mitochondrial respiration. IL-1{beta} also increased the phosphorylation of AKT and hypoxia-inducible factor 1 alpha (HIF1) levels. Utilizing colorectal cancer cells with AKT1/2 or HIF1 knocked out showed the requirement of these proteins in mediating the increase in glycolysis following IL-1{beta} treatment. Importantly, AKT1/2 was identified as upstream of HIF1, as IL-1{beta} still increased phosphorylation of AKT even in the absence of HIF1. However, loss of AKT1/2 completely abolished the ability of IL-1{beta} to increase HIF1 protein levels. Tumor necrosis factor alpha (TNF), another cytokine found to be elevated in colorectal cancer, also increased glycolysis in an AKT and HIF1-dependent manner. Our data point to a common pathway through AKT activation and HIF1 upregulation, by which pro-inflammatory cytokines increase glycolysis in colorectal cancer cells to help promote cancer progression.

cell biology↗

bioRxiv2026

Cell identities along the proximal-distal and micropylar-chalazal axes in the Arabidopsis heart-stage seed

* Seeds are complex reproductive organs consisting of diverse maternal and filial tissues. During development, the embryo and specialized tissues for nutrient storage required for seed germination and early seedling establishment emerge. * To explore the cellular diversity and differentiation of seeds, we performed single cell RNA-sequencing on heart stage Arabidopsis seeds and identified 20,097 cells that were grouped into [≥]21 distinct cell clusters. 20 of the 21 clusters were spatially assigned by combining bioinformatic analysis, imaging reporter fusion marker lines, and spatial transcriptomics. * Our analysis revealed a high degree of differentiation of epidermal cell and inner cell layers along the rotational and axial seed axes, highlighting the importance of cell position and ontogenesis. We identified unexpected spatial domains, including a cluster marked by abscission zone-specific transcripts, and a nucellar cluster shaped by developmentally programmed cell death. Surprisingly, embryo and endosperm showed similarities in transcript profiles despite distinct and complementary functions. * In summary, our findings establish seeds as a transcriptionally complex organ with high cell type heterogeneity and provide a basis for investigating the differentiation of diverse cell layers and spatial transcript profiles.

cell biology↗

bioRxiv2026

Midgut damage triggers thromboxane A2-dependent hemocyte recruitment in Culex pipiens molestus

Mosquitoes transmit diverse pathogens through repeated blood feeding, a process that subjects the midgut to significant mechanical stress and cellular damage. While hemocyte association with the midgut is known to occur following injury, the mechanisms promoting their recruitment remain poorly defined. Given the conserved roles of eicosanoid signaling in injury responses, we hypothesized that thromboxane A2 (TXA2) mediates hemocyte recruitment to the damaged midgut. Here, we demonstrate that chemically induced midgut damage significantly increases both the number of hemocytes attached to the midgut and those in circulation. Pharmacological inhibition of cyclooxygenase suppresses hemocyte recruitment whereas supplementation with a stable TXA2 analog restores the response, indicating that TXA2 signaling is required for this process. To identify candidate enzymes involved in TXA2 biosynthesis, we performed in silico docking analyses and identified two cytochrome P450 (CYP) candidates. Among these, CYP6D3 was shown to be strongly upregulated in hemocyte populations following midgut damage. RNA interference-mediated knockdown of CYP6D3 significantly reduced both hemocyte recruitment to the midgut and systemic TXB2 levels, supporting its role in the eicosanoid-mediated immune response. Together, our findings demonstrate that TXA2 signaling drives hemocyte recruitment to the damaged mosquito midgut and suggest a conserved lipid-mediated mechanism underlying insect tissue-associated immune responses that may influence vector competence.

biochemistry↗

bioRxiv2026

Time-structured communication through cross-frequency bursts

Adaptive brain function requires communication that is selective in both space and time, yet the circuit mechanisms that transiently favor specific routes of information transfer remain unclear. Here we show that, when coupled, spiking populations with distinct inhibitory timescales can reprogram one anothers intrinsic burst preferences, generating irregular multi-frequency bursts that self-organize into Multi-Frequency Oscillatory Patterns (MFOPs). State-resolved transfer entropy revealed that different MFOPs were associated with distinct Information Routing Patterns (IRPs), defining transient windows of enhanced directed transfer with specific delays and directions. At the microscopic level, the same oscillatory states selectively increased or decreased delayed spike transmission across monosynaptic pathways, yielding transmission barcodes that significantly resembled the corresponding IRPs. This repertoire was markedly reduced when inhibitory diversity was removed. These results identify coordinated multi-frequency bursting as a mechanism by which recurrent circuits can dynamically filter inputs according to source and latency.

neuroscience↗

bioRxiv2026

Fibroblast-specific Deletion of Yap/Taz Impairs Mouse Postnatal Dermal Development by Suppressing Collagen Production and Deposition

The Hippo pathway effectors YAP and TAZ are key regulators of cell proliferation, apoptosis, and differentiation, thereby maintaining tissue homeostasis and controlling organ size. While their roles in epithelial tissues and cancer are well established, their role in dermal fibroblast extracellular matrix (ECM) regulation is less understood. Here, we investigated the role of Yap/Taz during postnatal skin dermis development. During postnatal growth, mouse skin steadily grows and undergoes significant surface expansion. Postnatal deletion of Yap/Taz in dermal fibroblasts, the primary cells responsible for dermal ECM homeostasis, significantly impaired dermal maturation, as evidenced by marked deficiencies in collagen synthesis and deposition. Isolated fibroblasts from Yap/Taz knockout mice showed reduced proliferation and diminished expression of Yap/Taz target genes (Ccn2, Col1a1), which were rescued by reintroduction of active Yap/Taz. RNA-seq, and spatial transcriptomics and proteomics of Yap/Taz knockout skin revealed substantial downregulation of matrisome genes, including type I (Col1a1, Col1a2) and type III (Col1a3) collagens, which together constitute more than 90% of the skins collagen content. These findings demonstrate that Yap/Taz are essential for dermal ECM homeostasis, highlighting their therapeutic potential in skin regeneration, fibrosis, and aging-related ECM decline.

cell biology↗

bioRxiv2026

Inflammation is the Driver of Butyrate-Producing Bacteria Change in Interleukin10 Knockout Mice

BackgroundAlterations of gut microbiota have been implicated in the development of inflammatory bowel disease. Specifically, patients with IBD show the reduced levels of gut bacteria to produce butyrate, a crucial metabolite for maintaining gut homeostasis, along with decreased levels of fecal butyrate. However, there is limited research on changes in butyrate-producing bacteria at various taxonomic levels during the development of inflammatory bowel disease. ResultsWe investigated the changes of butyrate-producing bacteria in interleukin10 knockout mice, a suitable IBD model, as these mice require gut microbiota to develop spontaneous chronic colitis. Our findings indicate increased inflammation and a metabolic shift from butyrate oxidation toward glycolysis in 9-week-old interleukin10 knockout mice. Furthermore, we observed significant changes in two terminal enzymes involved in butyrate production: a significant increase of butyrate kinase and a significant decrease of butyryl-CoA:acetate-CoA-transferase. These observations align with an increased abundance of Coprococcus comes, which utilizes butyrate kinase, and a decreased abundance of Faecalibacterium prausnitzii that utilizes butyryl-CoA:acetate-CoA-transferase. Moreover, reduced levels of acetate, a necessary co-substrate for butyryl-CoA:acetate-CoA-transferase activity, were observed in interleukin10 knockout mice. ConclusionsThese findings enhance our understanding of changes in butyrate-producing bacteria populations at various taxonomic levels, ranging from phylum to gene level in 9-week-old interleukin10 knockout mice. Furthermore, these data suggest a potential for diagnosing IBD at an early stage by analyzing the composition of butyrate-producing bacteria.

microbiology↗

bioRxiv2025

TMPO promotes cellular dissemination and metastasis in circulating tumor cells

Metastasis--the process by which cancer cells spread beyond the primary tumor to distant organs--accounts for the vast majority of cancer-related deaths. To elucidate mechanisms underlying dissemination and metastasis in prostate cancer, we have investigated circulating tumor cells (CTCs) obtained from genetically engineered mouse models (GEMMs). The phenotypic and molecular properties of the CTCs, and organoids derived from these CTCs, closely model the tumor and metastatic phenotypes of their parental GEMMs. Moreover, organoids derived from individual CTCs exhibit molecular and morphological heterogeneity that is associated with distinct metabolic states as well as differences in human prostate cancer outcome. Using computational systems analyses, we have identified TMPO, encoding the nuclear membrane protein lamina-associated polypeptide 2 (Lap2), as a key driver of this heterogeneity. TMPO activity is upregulated in advanced human prostate tumors, metastases, and CTCs, and is associated with adverse clinical outcome. Our findings indicate that TMPO promotes dissemination and metastasis in vivo by enhancing survival in conditions of metabolic stress, and reveal a novel mechanistic link between CTC heterogeneity, stress adaptation, and metastatic potential.

cell biology↗

bioRxiv2025

Reprogramming the Rossmann Fold Signature Motif Creates Orthogonal Redox Biocatalysts

Biological reducing power is carried by nicotinamide adenine dinucleotide (phosphate) (NAD(P)/H), which supports cellular functions and cannot be specifically directed to engineered metabolic pathways. Nicotinamide mononucleotide (NMN(H)) has emerged as an orthogonal redox cofactor to address this challenge, yet strategies remain elusive for creating NMN(H)-specific enzymes that no longer interact with the cellular NAD(P)/H pools. Previous designs avoided perturbing the most ancient and conserved GxGxxG motif in Rossmann fold enzymes, the root cause of persistent NAD(P)/H recognition. Herein, we demonstrated that this motif, though long considered essential, is in fact mutable to yield active NMN+-specific enzymes. This is implemented on two unrelated model enzymes chosen to garner orthogonal reducing power from either the cheap electron source phosphite or glycolysis. On phosphite dehydrogenase (PTDH), variants NRC-01 and NRC-02 eliminated electron leaking to numerous NAD(P)H-dependent side reactions in whole cells and crude cell lysates while driving NMNH-dependent biotransformation with [~]240-fold higher productivity than existing catalysts. On glyceraldehyde-3-phosphate dehydrogenase (GapA), variant RSQ featured a [~]2.9x104-fold cofactor specificity switch to NMN+ from NAD+. Combined Rosetta modeling, systematic structural alignment, and experimental results revealed that Rossmann fold reprogramming, paired with engineered structural reinforcement, may offer a general route to orthogonal redox biocatalysts.

molecular biology↗

bioRxiv2025

A simple method of mechanical scarification to break seed dormancy in Viola odorata

AbstractsViola odorata, also known as sweet violet, is a valuable plant for its fragrance and medicinal properties, but the cultivation is hindered by poor seed germination due to dormancy. The dormancy of V. odorata mainly resulted from a hard seed coat, and various methods has been reported in breaking the seed dormancy. However, most engaged in corrosive chemicals and highly dependent on the variety, or a lack of uniformity when using sandpapers. This study presents a simple, effective mechanical scarification method using rat-tooth tweezers to gently nick the seed coat tip. This mechanical scarification significantly increased germination, reaching a 70% rate after eight weeks, while non-scarified seeds failed to germinate. Combining mechanical scarification with cold stratification further enhanced germination compared to room-temperature (RT) storage. Additionally, growth at 18 {degrees}C produced higher rates than at RT and the addition of gibberellic acid (GA3) in the media promoted both germination and seedling growth, accompanied by increased water uptake. These findings propose a combination of mechanical scarification, cold stratification, and optimal GA3 treatment as a reliable, broadly applicable strategy for breaking dormancy and facilitating large-scale propagation and breeding of V. odorata.

plant biology↗

bioRxiv2025

Androgens Drive SOX9 Upregulation in Injured Proximal Tubular Cells

IntroductionSex influences susceptibility, recovery, and long-term outcomes after acute kidney injury (AKI) in humans. Rodent models have been invaluable for elucidating AKI mechanisms; however, most studies have focused on males, assuming direct applicability to females, an assumption that remains largely untested. In males, the transcription factor SOX9 regulates injury-associated proximal tubule cell states, supporting survival during injury but also contributing to maladaptive repair. Given the well-described role of SOX9 in sex determination during development and its emerging importance in AKI, we investigated whether it mediates sex-specific tubular responses in the adult kidney. MethodsWe first optimized differential ischemic and cisplatin conditions in males and females to generate injury-matched models. We then used these models to ask whether proximal tubular cell responses, particularly Sox9 upregulation, are sex dependent. Tubule-specific knockout models of Sox9, Sox4, Sox11, Vgf, Zfp24, and the androgen receptor (Ar), along with gonadectomy and hormone replacement studies, combined with gene and protein analyses, were used to define regulatory networks. ResultsIn both ischemic and nephrotoxic AKI, SOX9 expression was markedly blunted in females, with levels more than fivefold lower than in males. While injury biomarkers such as NGAL and KIM1 were equally induced in both sexes, Sox9 and its downstream target Vgf showed markedly reduced induction in females, whereas the upstream regulator Zfp24 was functionally relevant only in males. Deletion of Sox9, Zfp24, or Vgf worsened injury in males but not in females. In contrast, Sox4 and Sox11 were equally upregulated and protective in both sexes. Castration or proximal tubule-specific deletion of Ar in males abolished Sox9 induction, establishing a testosterone-dependent regulatory axis. ConclusionsThese findings define a hormone-driven, male-specific tubular repair program and demonstrate that injury and recovery pathways differ fundamentally between sexes, underscoring the need for sex-inclusive therapeutic strategies for AKI. Translational StatementSex influences susceptibility and outcomes after AKI, but the molecular basis remains unclear. SOX9, a transcription factor recently identified as one of the most highly upregulated genes in proximal tubular cells during AKI in both mice and humans, has been presumed to mediate a universal protective program. Using injury-matched murine models of AKI, we now demonstrate that this response is restricted to males, driven by testosterone and androgen receptor signaling, while SOX9 induction is markedly blunted and functionally dispensable in females. These findings reveal that tubular protective pathways differ fundamentally between sexes despite equivalent injury severity. Because SOX9 activation confers epithelial protection in males, therapeutic targeting of this pathway may have clinical relevance primarily in male patients. These data underscore the importance of incorporating biological sex into mechanistic, translational, and clinical studies of kidney injury and recovery.

cell biology↗

bioRxiv2025

Optimal inhibitory-to-excitatory ratio governs slow and fast oscillations for enhanced neural communication

Neural oscillations at distinct frequency bands facilitate communication within and between neural populations. While single-frequency oscillations are well-characterized, the simultaneous emergence of slow (beta) and fast (gamma) oscillations within the same network remains unclear. Here, we demon-strate that multi-frequency oscillations naturally arise when the ratio of inhibitory-to-excitatory synaptic strength falls within a specific regime using a biologically plausible Izhikevich model. We show that this regime maximizes both information capacity and transmission efficiency, suggesting an optimal balance for neural communication. Deviations from this range lead to single-frequency oscillations and reduced communication efficiency, mirroring disruptions observed in neurological disorders. These findings provide mechanistic insight into how the brain leverages multiple oscillatory frequencies for efficient information processing and suggest a potential biomarker for impaired neural communication. 1. SIGNIFICANCE STATEMENTBeta (slow) and gamma (fast) oscillations often coexist in the brain, yet their origin and functional role remain unclear. Our study reveals that the inhibitory-to-excitatory synaptic strength ratio governs the emergence of this multifrequency state. Furthermore, we demonstrate that information capacity and transmission efficiency are maximized in this regime, leading to significantly enhanced neural communication. These findings provide mechanistic insight into how multiple oscillatory frequencies support efficient brain function and offer a potential framework for understanding disruptions in neural communication associated with neurological disorders.

neuroscience↗

bioRxiv2025

High-throughput microbiome profiling and co-occurrence with antibiotic resistance genes in Lucilia sericata

Blow flies such as Lucilia sericata (Diptera: Calliphoridae) serve important ecological functions as decomposers. However, due to their close association with decaying organic matter they also play potential roles as reservoirs for pathogenic bacteria and antimicrobial resistance genes (ARGs). In this study, we characterized the bacterial communities and resistome profiles of L. sericata specimens collected from six provinces across South Korea using 16S rRNA gene metabarcoding and targeted PCR screening. The microbiome was dominated by Dysgonomonas, Vagococcus, Pseudomonas, Ignatzschineria, and Providencia with geographic variation in community structure. Flies from Chungnam exhibited the lowest microbial diversity, while samples from Jeonnam and Gyeonggi showed greater richness and evenness. Beta diversity analyses confirmed geographic structuring of bacterial communities, with semi-urban, rural locations harboring more diverse taxa. Notably, opportunistic pathogens such as Proteus mirabilis and Providencia were detected, alongside a range of ARGs (blaTEM, ermB, sul1, aac(6')-Ib-cr, cat and mecA) and integron elements (intI and intII), suggesting that L. sericata may act as a reservoir of clinically important microbes and resistance genes. ImportanceThe environment plays a significant role in shaping the microbiome of flies. Due to their motile nature and close association with decomposing matter blow flies of the species Lucilia sericata can harbor diverse bacterial communities, including potential pathogens that threaten human and animal health. Furthermore, due to their synanthropic lifestyle, this species is also exposed to bacteria that host antibiotic resistance genes (ARGs). Here we investigate the role of blowflies as reservoirs of potential pathogens and ARGs using metabarcoding. Our study revealed a diverse microbiome and resistome shaped by location and possible biotic or abiotic factors. These findings provide baseline information for wildlife surveillance and emphasize the importance of including synanthropic flies in strategies aimed at controlling the dissemination of antibiotic resistance.

ecology↗

bioRxiv2025

Bazedoxifene rescues sexually dimorphic autistic-like abnormalities in mice carrying a biallelic MDGA1 mutation

In the accompanying study, we describe two pairs of MDGA1 missense mutations (Val116Met/Ala688Val and Tyr635Cys/Glu756Gln) from two patients with autism spectrum disorders (ASDs) and how these mutations exert distinct abnormalities in biological processes during central nervous system development. Here, we generated knockin (KI) mice harboring the murine version of Tyr635Cys/Glu756Gln MDGA1 (Mdga1Y636C/E751Q) and performed extensive behavioral analyses. Male KI mouse pups and adults exhibited impaired ultrasonic vocalizations and sensorimotor gating (ASD-relevant behavioral deficits), and thus exhibited phenotypes different from those of male Mdga1 conditional knockout (cKO) mice. In contrast, adult female KI mice did not exhibit a range of ASD-like behavioral abnormalities. Electrophysiological analyses performed using both juvenile and adult Mdga1Y636C/E751Q mice revealed sexually dimorphic and developmental stage-dependent compromises of GABAergic synaptic inhibition. In addition, proteomics analyses showed that the phospho-proteomic phenotypes differed between Mdga1Y636C/E751Q and Mdga1-cKO mice. Treatment of male Mdga1Y636C/E751Q KI mice with the FDA-approved estrogen receptor modulator, bazedoxifene, restores the KI-related molecular, GABAergic synapse, and behavioral changes. Collectively, our results suggest a novel treatment strategy for ASDs that present developmentally regulated and/or sexually dimorphic features.

neuroscience↗

bioRxiv2025

Engineering the key central metabolic enzyme to utilize a non-canonical redox cofactor

Redesigning central metabolism enzymes to utilize non-canonical cofactors that are orthogonal to NAD+ and NADP+ may allow partitioning of reducing power into a distinct redox cofactor pool that is preserved for user-desired biosynthetic tasks, without being dissipated by the complex natural metabolism in the cells. Here, we engineer Escherichia coli glyceraldehyde-3-phosphate dehydrogenase (GapA), the key enzyme in glycolysis, to utilize nicotinamide mononucleotide (NMN+) while greatly reducing its original activity with its native cofactor, NAD+. Through rational design, we identify the variant A180S with a [~]3-fold increase in NMN+ specific activity compared to that of the wildtype (WT). Next, we design a double mutant, G10R-A180S (RS), where G10R mutation hampers the catalytic efficiency for NAD+ but also decreased the activity toward NMN+. Importantly, based on the hypothesis that the role of NAD+ in coordinating oligomer interface must be recapitulated in NMN+-utilizing enzymes, we develop a triple mutant G10R-A180S-G187Q (RSQ). Rosetta modeling predicts that the new mutation G187Q bridges separate subunits across the cofactor binding pocket, which possibly affords stronger association of the GapA tetramer, the active form of this enzyme. This final GapA variant features a [~]2.8 x 104 switch of cofactor specificity from GapAs natural cofactor NAD+ to the non-canonical cofactor NMN+. Overall, this work demonstrates the engineering of a highly conserved, central metabolic enzyme for the utilization of a non-canonical redox cofactor NMN+. The design principle discovered here may be broadly applicable to many enzymes that bind cofactors using an intersubunit pocket.

molecular 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↗

bioRxiv2025

Docking 14 million virtual isoquinuclidines against the mu and kappa opioid receptors reveals dual antagonists-inverse agonists with reduced withdrawal effects

Large library docking of tangible molecules has revealed potent ligands across many targets. While make-on-demand libraries now exceed 75 billion enumerated molecules, their synthetic routes are dominated by a few reaction types, reducing diversity and inevitably leaving many interesting bioactive-like chemotypes unexplored. Here, we investigate the large-scale enumeration and targeted docking of isoquinuclidines. These "natural-product-like" molecules are rare in the current libraries and are functionally congested, making them interesting as receptor probes. Using a modular, four-component reaction scheme, we built and docked a virtual library of over 14.6 million isoquinuclidines against both the {micro}- and{kappa} -opioid receptors (MOR and KOR, respectively). Synthesis and experimental testing of 18 prioritized compounds found nine ligands with low {micro}M affinities. Structure-based optimization revealed low- and sub- nM antagonists and inverse agonists targeting both receptors. Cryo-electron microscopy (cryoEM) structures illuminate the origins of activity on each target. In mouse behavioral studies, a potent member of the series with joint MOR-antagonist and KOR-inverse-agonist activity reversed morphine-induced analgesia, phenocopying the MOR-selective anti-overdose agent naloxone. Encouragingly, the new molecule induced less severe opioid-induced withdrawal symptoms compared to naloxone during withdrawal precipitation, and did not induce conditioned-place aversion, likely reflecting a reduction of dysphoria due to the compounds KOR-inverse agonism. The strengths and weaknesses of bespoke library docking, and of docking for opioid receptor polypharmacology, will be considered.

biophysics↗

bioRxiv2024

A forward genetic screen identifies Sirtuin1 as a driver of neuroendocrine prostate cancer

Although localized prostate cancer is relatively indolent, advanced prostate cancer manifests with aggressive and often lethal variants, including neuroendocrine prostate cancer (NEPC). To identify drivers of aggressive prostate cancer, we leveraged Sleeping Beauty (SB) transposon mutagenesis in a mouse model based on prostate-specific loss-of-function of Pten and Tp53. Compared with control mice, SB mice developed more aggressive prostate tumors, with increased incidence of metastasis. Notably, a significant percentage of the SB prostate tumors display NEPC phenotypes, and the transcriptomic features of these SB mouse tumors recapitulated those of human NEPC. We identified common SB transposon insertion sites (CIS) and prioritized associated CIS-genes differentially expressed in NEPC versus non-NEPC SB tumors. Integrated analysis of CIS-genes encoding for proteins representing upstream, post-translational modulators of master regulators controlling the transcriptional state of SB-mouse and human NEPC tumors identified sirtuin 1 (Sirt1) as a candidate mechanistic determinant of NEPC. Gain-of-function studies in human prostate cancer cell lines confirmed that SIRT1 promotes NEPC, while its loss-of-function or pharmacological inhibition abrogates NEPC. This integrative analysis is generalizable and can be used to identify novel cancer drivers for other malignancies. SummaryUsing an unbiased forward mutagenesis screen in an autochthonous mouse model, we have investigated mechanistic determinants of aggressive prostate cancer. SIRT1 emerged as a key regulator of neuroendocrine prostate cancer differentiation and a potential target for therapeutic intervention.

cancer biology↗