Biology subjects

Kim, S.

Publications and source records attributed to Kim, S..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

The SAMM50 rs3761472 causes mitochondrial dysfunction and metabolic dysfunction-associated steatotic liver disease

Genome-wide association studies (GWAS) have identified the SAMM50 rs3761472 single nucleotide polymorphism (SNP) as a risk factor for metabolic dysfunction-associated steatotic liver disease (MASLD), although its in vivo functions remain unclear. SAMM50 encodes a mitochondrial outer membrane protein critical for maintaining mitochondrial structure. To investigate the biological effects of rs3761472, we generated Samm50-knock-in (KI) mice harboring a D110G substitution using CRISPR/Cas9. This variant impaired mitochondrial integrity by downregulating key regulators of mitochondrial architecture, dynamics, and quality control. This contributed to reduced ATP production and elevated oxidative stress, inflammation, and hepatocyte death. The mutation also induced insulin resistance and glucose intolerance. Samm50-KI mice fed a high-fat diet exhibited pronounced hepatic lipid accumulation and liver injury, highlighting its pathogenic role in MASLD progression. Our findings demonstrate that SAMM50 rs3761472 is a critical driver of mitochondrial dysfunction and MASLD susceptibility, supporting its potential as a therapeutic target and its relevance to precision medicine.

genetics↗

bioRxiv2025

Tuning viscoelasticity and fine structure of living materials via synthetic adhesion logic and rheological perturbations

Engineered living materials (ELMs) at the multicelluar level represent an innovation that promises programmable properties for biomedical, environmental, and consumer applications. However, the rational tuning of the mechanical properties of such ELMs from first principles remains a challenge. Here we use synthetic cell-cell adhesins to systematically characterize how rheological and viscoelastic properties of multicellular materials made from living bacteria can be tuned via adhesin strength, cell size and shape, and adhesion logic. We confirmed that the previous results obtained for non-living materials also apply to bacterial ELMs. Additionally, the incorporation of synthetic adhesins, combined with the adaptability of bacterial cells in modifying various cellular parameters, now enables novel and precise control over material properties. Furthermore, we demonstrate that rheology is a powerful tool for actively shaping the microscopic structure of ELMs, enabling control over cell aggregation and particle rearrangement, a key feature for complex material design. These results deepen our understanding of tuning the viscoelastic properties and fine structure of ELMs for applications like bioprinting and microbial consortia design including natural systems.

synthetic biology↗

bioRxiv2025

Novel mouse model reveals neurodevelopmental origin of PMM2-CDG brain pathology

Congenital disorders of glycosylation (CDG) are a group of neurogenetic conditions resulting from disruptions in the cellular glycosylation machinery. The majority of CDG patients have compound heterozygous pathogenic variants in the phosphomannomutase 2 (PMM2) gene. Individuals with PMM2-CDG exhibit multi-systemic symptoms, prominently featuring neurological deficits with nearly all patients exhibiting cerebellar hypoplasia and ataxia. To overcome embryonic lethality caused by whole body knock-out of Pmm2 and mimic patient-related compound heterozygous pathogenic variants, we paired a Pmm2 flox allele (Pmm2fl) with a catalytically inactive knock-in allele (Pmm2R137H), commonly present in PMM2-CDG patients. Mice with post-mitotic loss of PMM2 from neurons or astrocytes are indistinguishable from unaffected littermates, including in a broad battery of neurological assessments. In contrast, removal of PMM2 from embryonic neural precursor cells leads to cerebellar hypoplasia, ataxia, seizures, and early lethality. Comprehensive multi-omics profiling, including metabolomics, glycomics, single-cell transcriptomics, proteomics, and glycoproteomics, reveal widespread molecular disturbances throughout the brain, with the cerebellum showing the most pronounced disruption. These findings highlight the heightened dependency of the developing cerebellum on intact N-glycosylation, aligning with clinical observations in PMM2-CDG patients. Importantly, glycoproteomic alterations identified in our mouse model are corroborated in PMM2-CDG patient post-mortem cerebellar tissue, underscoring the translational relevance of our findings and implicating impaired synaptic transmission as a key pathogenic mechanism.

neuroscience↗

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

AURKA inhibition amplifies DNA replication stress to foster WEE1 kinase dependency and synergistic antitumor effects with WEE1 inhibition in cancers

Highly elevated expression of the oncogene Aurora kinase A (AURKA) occurs in numerous human cancers harboring defective p53, nominating AURKA as a potential vulnerability in TP53-mutated cancer. However, clinical trials have indicated modest monotherapy activity of AURKA inhibitors. Here, we demonstrate that AURKA inhibition promotes phosphorylation of Replication Protein A (RPA), resulting in stalled DNA replication fork progression and eliciting a replication stress response in multiple TP53-mutated models, creating a druggable dependence on the mitotic checkpoint kinase WEE1. Combined inhibition of AURKA and WEE1 synergistically enhanced replication stress, tumor-specific apoptotic cell death, and mitotic catastrophe, and lead to marked tumor regression in cell line- and patient-derived xenograft models of TP53-mutated cancer. Our findings define enhanced DNA replication stress as underlying the strong synergy between AURKA and WEE1 inhibitors and offer preclinical confirmation of efficacy, indicating high potential for clinical translation of this synthetic lethal strategy for TP53-mutated carcinomas. Statement of significanceWe demonstrate that a small molecule AURKA inhibitor amplifies DNA replication stress in TP53-mutated carcinomas. This amplification of DNA replication stress can be leveraged this for synthetic lethal therapy in a combination with WEE1 inhibition that enhances antitumor effects in in vitro, in xenografts and in patient-derived xenograft models, advancing a promising novel combination therapy.

cancer biology↗

bioRxiv2025

Extracellular Ca2+-Sensing Receptor (CaSR) Regulates Hypothalamic Function to Control Energy and Skeletal Metabolism in Mice

Introductory paragraphThe extracellular Calcium-sensing receptor (CaSR) regulates cellular responsiveness to physiological changes in ionized calcium (Ca2+) concentrations. The CaSR is expressed in the brain, including in hypothalamic growth hormone stimulating GHRH and anorectic POMC neurons that control growth and energy homeostasis. We embryonically deleted the Casr gene in neurons to create NeuronCaSR-/- mice to delineate the role of this receptor in regulating growth, skeletal development, and energy metabolism. NeuronCaSR-/- mice had reduced size, weight and bone mass compared to littermate controls, with a dysregulated growth hormone axis. They also showed increased adiposity and circulating leptin levels, leptin resistance, and decreased glucose tolerance, along with reduced expression of the anorectic precursor peptide POMC and secondary increases in the expression of the anorectic peptide AgRP in the hypothalamus of NeuronCaSR-/- mice. Knockdown of CaSR in adult mice specifically in the hypothalamic arcuate nucleus, where GHRH, POMC and AgRP neurons reside, also resulted in increased body weight, adiposity, leptin resistance, and glucose intolerance, and reduced bone mass. Together these data suggest that neuronal CaSR critically regulates energy and skeletal metabolism and body growth by modulating hypothalamic function, representing a new paradigm for central integration of calcaemic activities with body function.

physiology↗

bioRxiv2025

A Salmonella type I toxin promotes systemic infection by inhibiting FoF1 ATP synthase

Intracellular pathogens including Salmonella Typhimurium survive within macrophage phagosomes by forming non-replicating persisters. Toxins from toxin-antitoxin systems have been implicated in persister formation as key contributors, although the biological targets of toxins remain largely unknown. Here, we report that Salmonella IbsA, a 19-amino-acid-long type I toxin, induces growth arrest and decreases intracellular ATP levels. An unbiased large-scale bacterial two-hybrid screen identified 54 IbsA-interacting targets, including proteins involved in oxidative phosphorylation and cell division. Among these, IbsA toxin specifically targets two subunits of the bacterial FoF1 ATP synthase. IbsA interacts with the a and b subunits in the membrane-bound Fo sector and inhibits proton translocation, thereby decreasing ATP levels. In turn, this IbsA-mediated decrease facilitates Salmonella spread between macrophages, promoting systemic infection. Accordingly, ibsA deletion decreases bacterial burden in organs and attenuates mouse virulence. Therefore, unlike other bacterial toxins, the IbsA toxin enhances Salmonella pathogenicity by decreasing the bacteriums ATP levels.

microbiology↗

bioRxiv2025

Spatial Biology and Organoid Technologies Reveal a Potential Therapy-Resistant Cancer Stem Cell Population in Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies with a 5-year survival rate of less than 10%. Chemotherapy is the current standard-of-care (SOC) for advanced PDAC; however, treatment resistance driven by a complex and immunosuppressive tumor microenvironment (TME) limits its effectiveness. To address mechanisms of resistance, we studied cabozantinib (cabo), a multi-kinase inhibitor approved for several solid tumors. Cabo has shown promise in preclinical PDAC models and clinical trials, particularly when combined with immunotherapy, but its mechanisms of action within the human PDAC TME and its potential to overcome therapy resistance remain unclear. Using CosMx Spatial Molecular Imaging (CosMx SMI) and Orion Multiplex Immunofluorescence (MxIF), we analyzed PDAC tissues collected after first line systemic chemotherapy and the Whipple surgical procedure, as well as from liver or lung metastatic sites from patients with PDAC. To functionally model the TME, we established matched patient-derived organoid (PDO) co-cultures harboring cancer associated fibroblasts (CAFs), and autologous immune cells (IMM) (PDO/CAF/IMM). These models were used to evaluate the effects of cabo and pembrolizumab, an anti-PD1 immune checkpoint inhibitor, with benchmarking of findings to the patients TME. Spatial analysis of post-chemotherapy and metastatic PDAC tissues revealed heterogeneous cellular neighborhoods within the TME, including enrichment of Schwann cells, CAFs, T regulatory cells, and cancer stem cells (CSCs). Distinct niches were observed in metastatic liver tissues, characterized by mesenchymal stem cells, fibroblasts, including myCAFs and iCAFs, and CSCs expressing CD44 and TROP2. In PDO/CAF/IMM co-cultures, treatment with cabo in combination with pembrolizumab enhanced cancer cell death by depleting myeloid-derived suppressor cells (MDSCs) and promoted cytotoxic T lymphocyte proliferation. Across both patient tissues and treated co-cultures, a persistent SOC-resistant cancer stem cell population emerged that expressed CD44 variant 9 (CD44v9). Taken together, these integrative spatial and organoid-based studies demonstrate that cabo can remodel the PDAC TME and potentiate PD-1 immunotherapy in preclinical models, while resistance associates with a CD44v9+ CSC population, revealing a potential therapeutic target.

cancer biology↗

bioRxiv2025

CoVET: Cryo-Electron Tomography guided by optical electrophysiology

Neurons exhibit varying electrophysiological properties due to dynamic changes in spatiotemporal molecular networks. In situ cryo-electron tomography (cryo-ET) provides unique advantages for high-resolution visualization of macromolecular complexes within their cellular context. Although correlation with fluorescent labeling allows cryo-ET to target specific cellular regions, it does not adequately reflect the electrophysiological properties of heterogeneous neurons. To bridge high-resolution molecular imaging with electrophysiological properties of individual neurons, we developed a Correlative-Voltage Imaging and cryo-ET (CoVET) technique. The nondestructive nature of voltage imaging is compatible with cryo-ET, enabling a direct correlation between neuronal electrophysiology and molecular structures. Neurons were clustered based on their electrophysiological properties, allowing for single-cell-guided structural analysis using cryo-ET. We analyzed the translational landscapes of individual neurons and found distinct translational profiles and contextual information among ribosomes from different electrophysiological clusters. Our results highlight the importance of the correlation between the electrophysiological properties and molecular structures.

biophysics↗

bioRxiv2025

Alcohol Use Disorder Associated Gene FNDC4 Alters Glutamatergic and GABAergic Neurogenesis

Large-cohort genome-wide association studies (GWAS) for alcohol use disorder (AUD) and AUD-related phenotypes have identified more than one hundred genetic loci. Functional study of those GWAS-identified loci might represent an important step toward understanding AUD pathophysiology. We found that genetic loci which are splicing quantitative trait loci (sQTLs) for the fibronectin III domain containing 4 (FNDC4) gene in the brain were identified by GWAS for both AUD drug treatment outcomes and AUD risk. However, FNDC4 function in the brain and how it might contribute to AUD pathophysiology remain unknown. In the present study, we characterized GWAS locus-associated FNDC4 splice isoforms, studies which suggested that FNDC4 alternative splicing results in loss-of-function for FNDC4. We also investigated FNDC4 function using CRISPR/cas9 gene editing, and the creation of human induced pluripotent stem cell (iPSC)-derived neural organoids joined with single-nucleus RNA sequencing. We observed that knock-out (KO) of FNDC4 resulted in a striking shift in the relative proportions of glutamatergic and GABAergic neurons in iPSC-derived neural organoids, suggesting a possible important role for FNDC4 in neurogenesis. We also explored potential mechanism(s) of FNDC4-dependent neurogenesis with results that suggested a role for FNDC4 in mediating neural cell-cell interaction. In summary, this series of experiments indicates that FNDC4 plays a role in regulating cerebral cortical neurogenesis in the brain. This regulation may contribute to the response to AUD pharmacotherapy as well as the effects of alcohol on the brain.

genomics↗

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

EZH1 Q571R-mediated chromatin compaction and its oncogenic potential in thyroid cancer

Dysregulation of Polycomb Repressive Complex 2 (PRC2) is established to contribute to cancer. Of its catalytic subunits, EZH1 and EZH2, EZH2 mutations in cancer have been extensively identified and studied, but the role of EZH1 in cancer remains largely unexplored. The recurrent presence of the EZH1Q571R mutation in follicular thyroid cancer suggests its involvement in tumor progression. Using EZH1 ChIP-seq, ATAC-seq, and H3K27me3 CUT&Tag, we demonstrated that EZH1Q571R enhances chromatin binding and compaction and stimulates PRC2-EZH1 catalytic activity, leading to increased H3K27me3 levels and repression of tumor suppressor genes. Purified PRC2-EZH1Q571R demonstrated a significant increase in histone methyltransferase activity compared to PRC2-EZH1WT via enhanced nucleosome binding and DNA compaction. Notably, this effect is particularly observed with EZH1Q571R but only to a lesser extent with the corresponding EZH2Q570R mutation, highlighting it as an EZH1-specific mechanism. We additionally demonstrated PRC2-EZH1Q571R to efficiently methylate H3K27 in pre-existing H3K36me2/3 nucleosomes, disrupting chromatin homeostasis. Our findings provide key insights into the molecular pathogenesis of EZH1Q571R-driven follicular thyroid cancer.

molecular biology↗

bioRxiv2025

All-Atom Modeling and Simulation of Biopolymer Interface: Dual Role of Antifouling Polymer Brushes

Antifouling polymers are highly valuable in a variety of applications, including antiviral coatings, targeted drug delivery, and marine coatings, where preventing unwanted protein adsorption is critical. Although extensive experimental studies have characterized polymer-protein interactions, computational studies remain limited due to the inherent difficulty of modeling and integrating these distinct components within a unified system. This study presents molecular modeling and simulation of polyelectrolyte and polyzwitterionic brushes--poly(dimethylaminoethyl methacrylate) (PDMAEMA), poly(2-(N-oxide-N,N-dimethylamino)ethyl methacrylate) (PNOMA), and poly(2-(N-3-sulfopropyl-N,N-dimethylammonium)ethyl methacrylate) (PSBMA)--grafted onto -quartz substrates in the presence of lysozyme protein. The brush models were developed to closely replicate experimentally synthesized brush samples and to provide detailed insights into structural and dynamical changes at the molecular level during protein adsorption. Using steered molecular dynamics simulations, we show that the PSBMA brush, due to its high local density, exhibits the greatest resistance to protein insertion. C root-mean-square deviation and interaction patterns analyses further reveal that PSBMA also induces the most significant destabilization of lysozyme, while PDMAEMA brush enhances protein stability through ion-mediated interactions. The PNOMA brush, while requiring the lowest force for protein adsorption, induces greater protein destabilization than the PDMAEMA brush primarily due to electrostatic repulsion caused by a short carbon spacer length. To the best of our knowledge, this study presents the first comprehensive and realistic model system--comprising nanomaterials, polymers, and proteins, specifically antifouling polyzwitterions and polyelectrolytes grafted onto -quartz substrates via linkers. These findings highlight the dual role of antifouling polymer brushes: resisting protein adsorption and modulating protein structural dynamics, offering valuable insights for the rational design of next-generation antifouling materials. TOC GRAPHICS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/651893v1_ufig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@9620b8org.highwire.dtl.DTLVardef@3e395dorg.highwire.dtl.DTLVardef@1282169org.highwire.dtl.DTLVardef@1a997f7_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Microengineered transplantation of human solid tumors for in vitro studies of CAR T immunotherapy

Treatment of solid malignancies using chimeric antigen receptor (CAR) T cells remains a significant challenge, but current efforts to advance this therapy are challenged by our limited capacity to probe and understand cancer-immune interactions in human solid tumors. Here, we present a microengineered platform for in vitro modeling of malignant solid tumors during CAR T therapy. This system makes it possible to vascularize human tumor explants and perfuse them with blood-borne immune cells in a controlled manner. We first present a microphysiological model of human lung adenocarcinomas infused with CAR-T cells and show how this system can be used to simulate, visualize, and interrogate tumor-directed trafficking and effector function of CAR T cells. We then demonstrate the proof-of-principle of testing a chemokine-directed CAR T cell engineering strategy in a model of malignant pleural mesothelioma and validating our in vitro assessment using a matching in vivo mouse model. Finally, we describe a potential therapeutic target discovered by single-cell RNA sequencing that can be pharmacologically modulated to increase the efficacy of CAR T cells for lung adenocarcinoma, for which we also present specific biomarkers identified by global metabolomics analysis. We believe that the bioengineering principle demonstrated here will make important contributions to developing new capabilities for preclinical studies of adoptive cell therapies for cancer and other complex diseases.

bioengineering↗

bioRxiv2025

Modulating populational variance of methyl-guanine methyl transferase expression through miR-181d degradation: a novel mechanism of temozolomide resistance

Intratumoral heterogeneity plays a pivotal role in cancer evolution, providing the substrate for adaptation to selective pressures, including treatment with chemotherapy. Here, we show that micro-RNA regulation of variance in the expression of the DNA repair protein methyl-guanine methyl transferase (MGMT) contributes to this heterogeneity and acquired therapeutic resistance. In cell lines derived from glioblastomas, the most common form of primary brain tumor, treatment with standard-of-care temozolomide chemotherapy triggers a feed-forward loop between polyribonucleotide nucleotidyltransferase 1 (PNPT1) and miR-181d, an MGMT regulating miRNA, expediting miR-181d degradation. This degradation requires the activation of Ataxia Telangiectasia and Rad3-related (ATR) kinase. The degradation of miR-181d in glioblastoma cells increased both the mean and the variance of MGMT expression in the cell population. Subclone reconstituted cell populations with similar populational mean MGMT levels but with differences in the variance of MGMT expression exhibited differential temozolomide sensitivity, with the higher MGMT variance population showing increased resistance. This resistance is suppressed by exogenously transfected miR-181d. These findings suggest a key role for miRNA in regulating intra-tumoral heterogeneity through modulation of key DNA repair enzymes and provide a compelling rationale for miRNA delivery as a platform for glioblastoma therapy. Significance StatementThis study demonstrates a mechanistic link between a feed-forward loop mediating microRNA degradation and cell-to-cell variance in gene expression, and the contribution of this mechanism to intratumoral heterogeneity and therapeutic resistance. We show that when glioblastoma, the most common form of adult primary brain tumor, is treated with standard-of-care chemotherapy, temozolomide, a feed-forward loop between miR-181d and PNPT1 is initiated, causing rapid degradation of miR-181d. This degradation increases the cell-to-cell variability in methyl-guanine methyl transferase (MGMT) expression, expanding intra-tumoral heterogeneity and contributing to acquired temozolomide resistance. This process can be suppressed by therapeutic delivery of microRNA, providing compelling considerations for clinical translation.

cancer biology↗

bioRxiv2025

Neural dynamics of emergent social roles in collective foraging by mice

We investigated how neural dynamics support role differentiation in group foraging by mice cohabiting with a predator-like spider robot serving as a mobile food platform. While solitary foraging behaviors were consistent among mice, group foraging revealed distinct roles-working, participating, and freeriding-that solidified over time, leading to an imbalance (Gini = 0.5) across five groups. Recordings from the medial prefrontal cortex (mPFC), nucleus accumbens (NAc), and basolateral amygdala (BLA) revealed enhanced beta power in active foragers. Workers exhibited a stronger fast beta drive from mPFC to BLA compared to participants, and role prediction accuracy based on spectral features improved over trials. Our findings highlight how neural dynamics underlie the emergence of distinct roles in collective action by mice. One-Sentence SummaryDistinct foraging roles emerge in group-housed mice, driven by fast beta (24-32 Hz) activity in the mPFC-NAc-BLA circuit.

animal behavior and cognition↗

bioRxiv2025

Rif-seq reveals Caulobacter crescentus mRNA decay is globally coordinated with transcription and translation

While transcription and translation have been shown to be coordinated with mRNA decay across various single-gene studies, their global coordination remains poorly defined. Therefore, we performed Rif-seq experiments in C. crescentus to measure genome-wide mRNA lifetimes and analyzed the impact of transcription and translation. Based upon the RNAP elongation speed, we identified that approximately 20% of mRNAs were cotranscriptionally degraded. We generated absolute quantitative estimates of mRNA copy numbers in C. crescentus, a useful systems biology resource, revealing that some gene categories have coordinated mRNA turnover. To investigate translations impact on mRNA decay, we found that translation efficiency measured by ribosome profiling correlates with mRNA lifetime. We compared the 5 P cleavage sites to ribosome occupancy and found that cleavage sites occur preferentially in regions of low ribosome occupancy. Using the translation initiation inhibitor retapamulin, which traps ribosomes at the start codon, and chloramphenicol, which arrests elongating ribosomes, shows that chloramphenicol leads to global mRNA stabilization. Surprisingly, we find that the codon adaptation index is inversely correlated with mRNA lifetime, suggesting slow translation elongation may be stabilizing mRNAs from decay. We confirmed the roles of translation initiation and elongation on mRNA lifetimes by generating synthetic YFP and mCherry reporter mRNAs. Taken together, mRNA decay is globally interconnected with transcription and translation. Highlights[bullet] Quantitative analysis yields absolute mRNA abundance and half-lives for C. crescentus [bullet]Identification of 47 new stable ncRNAs [bullet]Both transcription and translation are globally coordinated with mRNA decay [bullet]Translation initiation and elongation impact mRNA decay through ribosome occupancy

systems biology↗

bioRxiv2025

Linoleic acid metabolite, 13-S-hydroxyoctadecadienoic acid, suppresses cancer cell growth by inhibiting mTOR

Mechanistic target of rapamycin (mTOR) is a key protein kinase that integrates various internal and external signals to control biological events including cell growth. Whereas substantial efforts were made to elucidate protein subunits interacting with mTOR, endogenous metabolite-mTOR interactions remain largely unknown. Using affinity protein purification and mass spectrometry, we identified direct binding of mTOR to 13-S-hydroxyoctadecadienoic acid (13-S-HODE) which is an oxygenated metabolite of linoleic acid, a polyunsaturated essential fatty acid. Interaction of 13-S-HODE with the catalytic ATP-binding domain of mTOR prevented its kinase activity in an ATP-competitive manner. Furthermore, either 13-S-HODE treatment or expression of arachidonate 15-lipoxygenase (ALOX15), an enzyme responsible for 13-S-HODE production, reduced mTOR signaling, thereby suppressing the growth of cancer cells as well as tumor xenografts. Our results highlight the importance of 13-S-HODE serving as a tumor suppressive, mTOR-inhibiting metabolite that links polyunsaturated fatty acid metabolism and the mTOR signaling in controlling cancer cell growth.

biochemistry↗