Biology subjects

Kim, S.

Publications and source records attributed to Kim, S..

At least 199 records · Page 11Linked to original sources

bioRxiv2025

In vivo self-renewal and expansion of quiescent stem cells from a non-human primate

The development of non-human primate models is essential for the fields of developmental and regenerative biology because those models will more closely approximate human biology than do murine models. Based on single cell RNAseq and fluorescence-activated cell sorting, we report the identification and functional characterization of two quiescent stem cell populations (skeletal muscle stem cells (MuSCs) and mesenchymal stem cells termed fibro-adipogenic progenitors (FAPs)) in the non-human primate Microcebus murinus (the gray mouse lemur). We demonstrate in vivo proliferation, differentiation, and self-renewal of both MuSCs and FAPs. By combining cell phenotyping with cross-species molecular profiling and pharmacological interventions, we show that mouse lemur MuSCs and FAPs are more similar to human than to mouse counterparts. We identify unexpected gene targets involved in regulating primate MuSC proliferation and primate FAP adipogenic differentiation. Moreover, we find that the cellular composition of mouse lemur muscle better models human muscle than does macaque (Macaca fascicularis) muscle. Finally, we note that our approach presents as a generalizable pipeline for the identification, isolation, and characterization of stem cell populations in new animal models.

cell biology↗

bioRxiv2025

Structural basis for Rad54- and Hed1-mediated regulation of Rad51 during the transition from mitotic to meiotic recombination

Rad51 catalyzes the DNA pairing reactions that take place during homologous recombination (HR), and HR must be tightly regulated to ensure physiologically appropriate outcomes. Rad54 is an ATP-dependent DNA motor protein that stimulates Rad51 activity during mitosis. In meiosis Rad51 is downregulated by the protein Hed1, which blocks Rad54 binding to Rad51, and allows Dmc1 to function as the active recombinase. We currently have a poor understanding of the regulatory interplay between Rad54, Hed1, Rad51 and Dmc1. Here, we identify a conserved Rad51 interaction motif within Rad54, and we solve a CryoEM structure of this motif bound to Rad51. We also identify a distinct Rad51 interaction motif within Hed1 and solve its structure bound to Rad51. These structures explain how Rad54 engages Rad51 to promote recombination between sister chromatids during mitosis and how Rad51 is downregulated by Hed1 upon entry into meiosis such that its meiosis-specific homolog Dmc1 can promote recombination between homologous chromosomes.

biochemistry↗

bioRxiv2025

American ginseng (Panax quinquefolius L.) extracts (G1899) reverse stress-induced behavioral abnormalities in mice

Stress affects brain functions, which leads to the development of mental disorders like anxiety, depression, cognitive decline, and social dysfunction. There is increasing focus on the role of nutritional, herbal and nutraceutical compounds on mental and cognitive functioning. Interestingly, studies suggest that American ginseng (Panax quinquefolius L.) extracts (G1899) improve cognition. We thus examined whether G1899 showed protective effects on stress-induced behavioral changes in animals. 200 mg/kg G1899 was orally administered daily for 4 weeks to 2-3-month-old female and male mice before inducing stress. To induce acute stress in animals, we intraperitoneally injected a low dose of lipopolysaccharides (LPS) (10 g/kg), and saline was used as a control. We also used chronic restraint stress (CRS) as a chronic stress model in mice. After LPS injection or CRS, multiple behavioral assays were carried out - a sucrose preference test, an open filed test, reciprocal social interaction, contextual fear conditioning, and a tail suspension test - to determine whether acute or chronic stress affected animals behaviors and whether G1899 had protective effects against stress-induced behavioral dysfunction. We found that both LPS injection and CRS induced stress-related behavioral dysfunction, including depression-like behavior, anhedonia, social dysfunction, and fear memory impairments in both females and males. However, G1899 treatment was sufficient to reverse stress-induced behavioral abnormalities in animals. Our data further suggested that G1899 reduced the activity of hippocampal neurons by suppressing glutamatergic activity. Our study suggests that G1899 supplements can be protective against both acute and chronic stress in mice by suppressing neuronal and synaptic activity. HighlightsO_LIAmerican ginseng (Panax quinquefolius L.) extract (G1899) treatment reverses acute stress-induced behavioral dysfunction in mice. C_LIO_LIG1899 treatment reverses chronic stress-induced behavioral dysfunction in mice. C_LIO_LIG1899 treatment reduces serum corticosterone levels in chronically stressed mice. C_LIO_LIG1899 treatment suppresses glutamatergic activity in hippocampal neurons. C_LI

neuroscience↗

bioRxiv2025

RNF13 mediates pH- and Ca2+-dependent regulation of lysosomal positioning

Environmental factors such as extracellular pH (pHe) and nutritional status influence lysosomal localization and autophagy. However, the mechanisms by which pHe, intracellular pH (pHi), and Ca2+ levels coordinate the bidirectional transport of lysosomes remain poorly understood. In this study, we identify RNF13 as a critical regulator of lysosomal positioning through its ubiquitin- dependent degradation of ARL8B. RNF13 activity is modulated by both pHi and Ca2+ levels. Specifically, we demonstrate that Ca2+-activated apoptosis-linked gene 2 (ALG-2) promotes retrograde lysosomal transport while simultaneously increasing pHi and decreasing lysosomal pH (pHlys). Elevated pHi deprotonates RNF13 at His332, enabling its interaction with Ca2+-bound ALG-2. This interaction activates RNF13, which inhibits ARL8B-mediated anterograde lysosomal transport. Furthermore, we show that alkaline pHe elevates pHlys, activating the lysosomal Ca2+ channel TRPML3. This activation enhances RNF13 activity, driving lysosomes to adopt a perinuclear localization. Thus, conditions such as starvation or alkaline pHe, which induce ALG-2 activation and pHi elevation, facilitate RNF13- mediated ARL8B degradation. In contrast, under acidic pHi conditions, RNF13 activity remains suppressed regardless of ALG-2 activation, leading to increased ARL8B levels. Additionally, we provide evidence linking the loss of RNF13 activity to developmental and epileptic encephalopathy-73, a neurological disorder characterized by severe developmental symptoms. These findings deepen our understanding of lysosomal positioning mechanisms, highlighting the interplay between lysosomal Ca2+ release and dynamic changes in cytoplasmic and lysosomal pH.

cell biology↗

bioRxiv2025

ATP hydrolysis-driven structural transitions within the S. cerevisiae Rad51 and Dmc1 nucleoprotein filaments

Homologous recombination (HR) is essential for the maintenance of genome stability and for generating genetic diversity during meiosis. The eukaryotic protein Rad51 is member of the Rad51/RecA family of DNA recombinases and is responsible for guiding the DNA pairing reactions that take place in HR during mitosis. Dmc1 is a meiosis-specific paralog of Rad51 and is responsible for the DNA pairing reactions that take place in HR during meiosis. Rad51 and Dmc1 are both ATP-dependent DNA-binding proteins and both form extended helical filaments on ssDNA which are key intermediates in HR. The stability of these nucleoprotein filaments is highly regulated and is also tightly coupled to nucleotide binding and hydrolysis. ATP binding promotes filament assembly whereas the hydrolysis of ATP to ADP reduces filament stability to promote filament disassembly. Here, we present CryoEM structures of the Saccharomyces cerevisiae recombinases Rad51 and Dmc1 in the ADP-bound states and provide a detailed structural comparison to the ATP-bound filaments. Our findings yield insights into the structural transitions that take place during the hydrolysis of ATP to ADP and suggest a new model for how these structural changes may be linked to nucleoprotein filament disassembly.

biochemistry↗

bioRxiv2025

Relationship between melanoma vemurafenib tolerance thresholds and metabolic pathway choice and Wnt signaling involvement

Vemurafenib constitutes an important therapeutic for BRAFV600 mutant melanomas, but despite high initial response rates, resistance to BRAF and MEK inhibitors quickly develops. Here, we performed an integrative analysis of metabolomic consequences and transcriptome alterations to uncover mechanisms involved in adaptive vemurafenib resistance (VemR) development and their relationship with vemurafenib tolerance thresholds. We developed BRAFV600E isogenic models of VemR utilizing M14 and A2058 lines, and patient-derived melanomas with V600E or normal BRAF to verify vemurafenib selectivity. MEK or PI3K inhibitors only partially inhibited VemR cell proliferation, indicating cross-resistance to these inhibitors. MITF and {beta}-catenin levels were induced and treatment with Wnt/{beta}-catenin inhibitor ICG-001 restored vemurafenib sensitivity with concomitant reductions in {beta}-catenin-regulated gene expressions, phospho-ERK1/2, and VemR-induced mitochondrial mass and respiration. Targeted metabolite, MitoPlate-S1, Mito-stress and transcriptome/metabolomic analysis showed that melanoma cells with elevated vemurafenib tolerance thresholds such as A2058 VemR cells utilize Wnt/{beta}-catenin signaling for mitochondrial metabolism while VemR cells with low tolerance such as M14 VemR cells rely on Wnt/{beta}-catenin signaling for pentose phosphate pathway. Pathways associated with cytokine-cytokine receptor, ECM receptor, and neuroactive ligand receptor interactions were similarly enriched in BRAFV600E patient-derived melanoma as M14 and A2058 cells whereas distinct pathways involving cell cycle, DNA replication, Fanconi anemia and DNA repair pathways are upregulated in wild type BRAF expressing patient derived melanoma. These data show for the first time that the metabolic pathway choices made by VemR BRAF mutant melanomas are controlled by vemurafenib tolerance and endurance thresholds and Wnt/{beta}-catenin signaling plays a central role in coordinating expression of genes controlling VemR and metabolic pathway shifts.

cancer biology↗

bioRxiv2025

TMEM145 is a key component in stereociliary link structures of outer hair cells

Outer hair cells (OHCs) in the cochlea contain specialized stereociliary structures essential for auditory function. These include horizontal top connectors (HTCs), linking adjacent stereocilia and tectorial membrane-attachment crowns (TM-ACs), anchoring the tallest stereocilia to the tectorial membrane. The known molecular components of these structures, such as stereocilin, otogelin, otogelin-like, and tubby, lack transmembrane domains, suggesting the existence of anchoring proteins. This study identified TMEM145, a transmembrane protein with a Golgi dynamics (GOLD) domain, as a crucial OHC stereocilia component. TMEM145 was expressed in both OHCs and spiral ganglion neurons, with specific localization to TM-ACs and HTCs in OHCs. Tmem145 knockout (KO) mice exhibited profound hearing impairment at three weeks of age, with complete loss of distortion product otoacoustic emissions, indicating OHC dysfunction. Immunostaining and scanning electron microscopy revealed the absence of TM-ACs and HTCs in Tmem145 KO mice. In heterologous cell systems, TMEM145 interacted with stereocilin and tubby, facilitating their extracellular secretion. TMEM145 was undetectable in stereocilin KO and tubby mutant mice, indicating interdependence among these proteins. These findings establish TMEM145 as an essential membrane protein for the structural integrity of OHC stereocilia, providing insights into the molecular architecture of cochlear hair cells and their role in auditory function.

neuroscience↗

bioRxiv2025

Basin-scale dynamics and enrichment-enabled genomics of marine nitrifiers: seasonality, niches, interactions, and genomic uniqueness

Nitrification occurs widely from the deep sea to animal holobionts, but the eco-evolutionary forces shaping the niches and dynamics of the lineages of the chemoautotrophic bacteria and archaea responsible remain largely unknown. To make strides towards this goal in a rapidly changing, exemplar marine ecosystem, the Baltic Sea, we studied basin-scale nitrifier spatio-temporal dynamics, coupled with enrichment-enabled comparative genomics. Based on metagenomes and rRNA gene sequencing, we found nitrifiers to be persistently relatively abundant throughout deep depths (>25 m), and from late-fall to spring in surface waters, as revealed by twice-weekly sampling across two years in the southwest Baltic Sea surface waters. In these surface waters, we observed time-lagged dynamics between ammonia- and nitrite-oxidizers, which were positively correlated with nitrite, nitrate, and diverse other prokaryotes, and negatively correlated with day length, light, and chlorophyll. For the dominant nitrifiers, ammonia-oxidizing archaea (AOA), we enriched five novel species including the dominant deep Baltic Sea species, and obtained genomes from all dominant AOA phylotypes. Among these genomes, which enabled fine-scale niche-differentiation, we observed a high degree of gene conservation, with most differences related to genes associated with interactions with the external environment, including genes involved in signal transduction, cell wall/membrane biogenesis, and inorganic ion transport, indicating these may be the primary drivers of strain-variability. We also observed differences in nitrogen and phosphorus metabolism between two dominant surface types. Together our study provides key insights into the niche of nitrifiers, and begins the process of understanding the mechanisms and functional implications of these patterns.

microbiology↗

bioRxiv2025

Single Cell Spatial Transcriptomics Reveals Immunotherapy-Driven Bone Marrow Niche Remodeling in AML

Given the successful graft-versus-leukemia cell treatment effect observed with allogeneic hematopoietic stem cell transplant for patients with refractory or relapsed acute myeloid leukemia, immunotherapies have also been investigated in the nontransplant setting. Here, we use a multi-omic approach to investigate spatiotemporal interactions in the bone marrow niche between leukemia cells and immune cells in patients with refractory or relapsed acute myeloid leukemia treated with a combination of the immune checkpoint inhibitor pembrolizumab and hypomethylating agent decitabine. We derived precise segmentation data by extensively training nuclear and membrane cell segmentation models, which enabled accurate transcript assignment and deep learning-feature-based image analysis. To overcome read-depth limitations, we integrated the single-cell RNA sequencing data with single-cell-resolution spatial transcriptomic data from the same sample. Quantifying cell-cell distances between cell edges rather than cell centroids allowed us to conduct a more accurate downstream analysis of the tumor microenvironment, revealing that multiple cell types of interest had global enrichment or local enrichment proximal to leukemia cells after pembrolizumab treatment, which could be associated with their clinical responses. Furthermore, ligand-receptor analysis indicated a potential increase in TWEAK signaling between leukemia cells and immune cells after pembrolizumab treatment. HighlightsO_LISpatial transcriptomic analysis of R-AML bone marrow niches provides detailed information about intercellular interactions in the tumor microenvironment. C_LIO_LIImmunotherapy shifts the cell composition of the leukemia neighborhood. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/634753v1_ufig1.gif" ALT="Figure 1"> View larger version (93K): org.highwire.dtl.DTLVardef@955273org.highwire.dtl.DTLVardef@158234corg.highwire.dtl.DTLVardef@175837borg.highwire.dtl.DTLVardef@b0a38_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Single-molecule tweezers decoding hidden dimerization patterns of membrane proteins within lipid bilayers

Dimerization of transmembrane (TM) proteins is an essential biological process within cellular membranes, playing a key role in diverse pathophysiological pathways and serving as a promising therapeutic target. Although often simplified as a two-state transition from freely diffusing monomers to fully formed dimers, the dimerization process after monomer diffusion--the post-diffusion dimerization--is likely more complex due to intricate inter-residue interactions. Here, we introduce a single-molecule tweezer platform to map detailed profiles of the post-diffusion transitions in TM protein dimerization. This approach captures reversible dimerization events of a single TM dimer, revealing hidden intermediate states that emerge following the quiescent phase of monomer diffusion. Profiling the post-diffusion intermediates, kinetics, and energy landscapes--integrated with molecular dynamics simulations--uncovers the dimerization pathway, the effects of residue interactions and lipid bilayers, and the kinetic and energetic contributions of distinct dimerization domains. Furthermore, this platform characterizes selective and localized modulations via peptide binding, underscoring its potential to elucidate the mechanisms of action of TM dimer-targeting drugs at single-molecule resolution.

biophysics↗

bioRxiv2025

Inhibition of cytosolic translation mitigates mitochondrial dysfunction in C. elegans

The mitochondrial unfolded protein response (UPRmt), which promotes mitochondrial proteostasis and biogenesis is regulated by the transcription factor ATFS-1. In C. elegans, impaired atfs-1 expression perturbs mitochondrial function and slows development. Here, via an RNAi suppressor screen, we found that inhibition of the nuclear hormone receptor NHR-180 increases mitochondrial function and the rate of development in atfs-1(null) worms. NHR-180 is activated during mitochondrial dysfunction and induces transcription of genes required for protein synthesis on cytosolic and mitochondrial ribosomes. Importantly, the NHR-180 ligand binding domain interacts with AMP, which results in increased protein synthesis potentially to promote mitochondrial biogenesis and recovery from transient mitochondrial perturbations. However, NHR-180 exacerbates the mitochondrial dysfunction caused by mutations in genes required for oxidative phosphorylation. Consistent with these findings, we found that inhibition of the S6 kinase homolog RSKS-1 also increased mitochondrial function in atfs-1(null) worms. Importantly, treatment with an S6 kinase inhibitor also increased respiration and mtDNA content in mammalian ATF5-knockout cells and OXPHOS-deficient models, suggesting that translation regulation is a conserved, targetable approach for restoring mitochondrial function in disease.

developmental biology↗

bioRxiv2025

Anxiety-associated behaviors following ablation of Miro1 from cortical excitatory neurons

Autism spectrum disorder, schizophrenia, and bipolar disorder are neuropsychiatric disorders that manifest early in life with a wide range of phenotypes, including repetitive behavior, agitation, and anxiety (American Psychological Association, 2013). While the etiology of these disorders is not completely understood, recent data implicate a role for mitochondrial dysfunction. To function optimally mitochondria must translocate to metabolically active intracellular compartments to support energetics and free-radical buffering; failure to achieve this localization results in cellular dysfunction (Picard et al., 2016). Mitochondrial Rho-GTPase 1 (Miro1) resides on the outer mitochondrial membrane and participates in neuronal microtubule-mediated mitochondrial motility and homeostasis (Fransson et al., 2003). Previous research implicates the loss of MIRO1 as a contributor to the onset/progression of neurodegenerative diseases including amyotrophic lateral sclerosis, Alzheimers disease, and Parkinsons disease (Kay et al., 2018). We have hypothesized that MIRO1 also has a role in nervous system development and function (Lin-Hendel et al., 2016). To test this, we ablated Miro1 from cortical excitatory progenitors by crossing floxed Miro1 mice with Emx1-cre mice. We found that mitochondrial mis-localization in migrating excitatory neurons was associated with reduced brain weight, decreased cortical volume, and subtle disruptions in cortical organization. Adult Miro1 conditional mutants exhibit agitative-like behaviors, including decreased nesting behavior and abnormal home cage activity. Open field testing revealed anxiety-like behavior and elevated plus maze and wide/narrow box testing found the mice avoided confined spaces. Our data link MIRO1 function with mitochondrial dynamics in the pathogenesis of several neuropsychiatric disorders and implicate mitochondrial localization in anxiety-like behaviors. SignificanceNeuropsychological disorders such as autism spectrum disorder, schizophrenia, and bipolar disorder have overlapping symptoms and behaviors. While the mechanisms underlying these disorders are not completely understood, recent evidence suggests mitochondrial dysfunction and mis-localization within a cell could play a role. Mitochondria are organelles that provide energy and other self-regulating processes to the cell. Previous research from our lab has shown distinct dynamic localization patterns within migrating excitatory and inhibitory neurons may be important during development. To further examine the importance of mitochondrial localization, we ablated MIRO1, a protein important for coupling mitochondria to motor proteins, in excitatory neurons. Mitochondria mis-localize in migrating excitatory neurons, and this is associated with a loss of motor skills and anxiety-like behavior in post-natal mice.

neuroscience↗

bioRxiv2025

CARDBiomedBench: A Benchmark for Evaluating Large Language Model Performance in Biomedical Research

BackgroundsBiomedical research requires sophisticated understanding and reasoning across multiple specializations. While large language models (LLMs) show promise in scientific applications, their capability to safely and accurately support complex biomedical research remains uncertain. MethodsWe present CARDBiomedBench, a novel question-and-answer benchmark for evaluating LLMs in biomedical research. For our pilot implementation, we focus on neurodegenerative diseases (NDDs), a domain requiring integration of genetic, molecular, and clinical knowledge. The benchmark combines expert-annotated question-answer (Q/A) pairs with semi-automated data augmentation, drawing from authoritative public resources including drug development data, genome-wide association studies (GWAS), and Summary-data based Mendelian Randomization (SMR) analyses. We evaluated seven private and open-source LLMs across ten biological categories and nine reasoning skills, using novel metrics to assess both response quality and safety. ResultsOur benchmark comprises over 68,000 Q/A pairs, enabling robust evaluation of LLM performance. Current state-of-the-art models show significant limitations: models like Claude-3.5-Sonnet demonstrates excessive caution (Response Quality Rate: 25% [95% CI: 25% {+/-} 1], Safety Rate: 76% {+/-} 1), while others like ChatGPT-4o exhibits both poor accuracy and unsafe behavior (Response Quality Rate: 37% {+/-} 1, Safety Rate: 31% {+/-} 1). These findings reveal fundamental gaps in LLMs ability to handle complex biomedical information. ConclusionCARDBiomedBench establishes a rigorous standard for assessing LLM capabilities in biomedical research. Our pilot evaluation in the NDD domain reveals critical limitations in current models ability to safely and accurately process complex scientific information. Future iterations will expand to other biomedical domains, supporting the development of more reliable AI systems for accelerating scientific discovery.

bioinformatics↗

bioRxiv2025

Deep learning molecular interaction motifs from Receptor structure alone

Interactions of proteins with other molecules are often mediated by a set of critical binding motifs on their surfaces. The majority of traditional binder design relied on motifs borrowed from known binder molecules, which highly restricted its applicability to novel targets or to new binding sites. In this work, we present a deep learning network MotifGen that predicts potential binder motifs directly from receptor structures without any further supporting information. MotifGen generates motif profiles at the receptor surface for 14 types of functional groups or 6 chemical interaction classes. These profiles are not only highly human interpretable, but also provide pre-trained embedding inputs for versatile few-shot binder design applications. We demonstrate MotifGens effectiveness through its application to peptide binder design and small-molecule binding site prediction, where it either surpassed existing methods or added significant value when integrated together. We expect our motif-centric binder design strategy can facilitate discovering novel binders for challenging receptor targets.

biochemistry↗

bioRxiv2024

Identification of neuron-glia signaling feedback in human schizophrenia using patient-derived, mix-and-match forebrain assembloids

Although abnormal activities across multiple cell types are believed to contribute to the development of various neurodevelopmental disorders, current brain organoid technologies fall short in accurately modeling the dynamic cellular interactions in the human brain. Recently, we developed a cellular reconstitution technology to create human forebrain assembloids with enhanced cellular diversity, representing dynamic interactions between neurons and glial cells. Here, we created patient-derived, mix-and-match forebrain assembloids, in which neurons, astrocytes, and microglia from both healthy individuals and schizophrenia patients were reconstituted in a combinatorial manner, and identified aberrant cellular interactions between neurons and glial cells in human schizophrenia. At the early stage, schizophrenia forebrain assembloids showed premature neurogenesis induced by the abnormal proliferation and differentiation of neural progenitor cells. Integrated modular analysis of gene expression in post-mortem schizophrenia brain tissue and brain assembloids found increased expression of tumor protein p53 (TP53) and nuclear factor of activated T-cells 4 (NFATC4), which functioned as master transcriptional regulators to epigenetically reprogram the transcriptome involved in the cellular dynamics of neuronal progenitor cells, leading to premature neurogenesis. At the later stage, we observed weakened structures of laminar organization of the cortical layers in forebrain assembloids and identified the neuron-dependent transcriptional plasticity of glial cells and their altered signaling feedback with neurons, in which neuronal urocortin (UCN) and protein tyrosine phosphatase receptor type F (PTPRF) elicited the expression of Wnt family member 11 (WNT11) and thrombospondin 4 (THBS4) in astrocytes and microglia, respectively. These aberrant signaling axes altered the neuronal transcriptome associated with neuronal response to various stimuli and synthetic processes of biomolecules, resulting in reduced synapse connectivity. Thus, we elucidated developmental stage-specific, multifactorial mechanisms by which dynamic cellular interplay among neural progenitor cells, neurons, and glial cells contribute to the development of the human schizophrenia brain. Our study further demonstrated the potential and applicability of patient-derived forebrain assembloid technology to advance our understanding of the pathogenesis of various neurodevelopmental disorders.

neuroscience↗

bioRxiv2024

Integrative multiomics analysis of metabolic dysregulation induced by occupational benzene exposure in mice

Background: Type 2 Diabetes Mellitus (T2DM) is a significant public health burden. Emerging evidence links volatile organic compounds (VOCs), such as benzene to endocrine disruption and metabolic dysfunction. However, the effects of chronic environmentally relevant VOC exposures on metabolic health are still emerging. Objective: Building on our previous findings that benzene exposure at smoking levels (50 ppm) induces metabolic impairments in male mice, we investigated the effects of occupationally relevant, below OSHA approved, benzene exposure on metabolic health. Methods: Adult male C57BL/6 mice were exposed to 0.9ppm benzene 8 hours a day for 9 weeks. We assessed measures of metabolic homeostasis and conducted RNA and proteome sequencing on insulin-sensitive organs (liver, skeletal muscle, adipose tissue). Results: This low-dose exposure caused significant metabolic disruptions, including hyperglycemia, hyperinsulinemia, and insulin resistance. Transcriptomic analysis of liver, skeletal muscle, and adipose tissue identified key changes in metabolic and immune pathways especially in liver. Proteomic analysis of the liver revealed mitochondrial dysfunction as a shared feature, with disruptions in oxidative phosphorylation, mitophagy, and immune activation. Comparative analysis with high-dose (50 ppm) exposure showed both conserved and dose-specific transcriptomic changes in liver, particularly in metabolic and immune responses. Conclusions: Our study is the first to comprehensively assess the impacts of occupational benzene exposure on metabolic health, highlighting mitochondrial dysfunction as a central mechanism and the dose-dependent molecular pathways in insulin-sensitive organs driving benzene-induced metabolic imbalance. Our data indicate that current OSHA occupational exposure limits for benzene are insufficient, as they could result in adverse metabolic health in exposed workers, particularly men, following chronic exposure.

pharmacology and toxicology↗

bioRxiv2024

Multi-Step Pathway Engineering in Probiotic Saccharomyces boulardii for Abscisic Acid Production in the Gut

The plant hormone abscisic acid (ABA) has gained attention for its role in animals and humans, particularly due to its protective effects in various immune and inflammatory disorders. Given its high concentrations in fruits like figs, bilberries and apricots, ABA shows promise as a nutraceutical. However scalability, short half-life and cost limit the use of ABA-enriched fruit extracts and synthetic supplements. In this study, we propose an alternative ABA administration method to overcome these challenges. We genetically engineered a strain of the probiotic Saccharomyces boulardii to produce and deliver ABA directly to the gut of mice. Using the biosynthesis pathway from Botrytis cinerea, four genes (bcaba1-4) were integrated into S. boulardii, enabling ABA production at 30{degrees}C, as previously described in Saccharomyces cerevisiae. Introducing an additional cytochrome P450 reductase gene resulted in a 7-fold increase in ABA titers, surpassing previous ABA-producing S. cerevisiae strains. Supplementation of the ABA-producing S. boulardii in the diet of mice (at a concentration of 5 x 108 CFU/g) led to effective gut colonization but resulted in low serum ABA levels (approximately 1.8 ng/mL). The absence of detectable serum ABA after administration of the ABA-producing probiotic through oral gavage, prompted further investigation to determine the underlying cause. The physiological body temperature (37{degrees}C) was identified as a major bottleneck for ABA production. Modifications to enhance the mevalonate pathway flux improved ABA levels at 37{degrees}C. However, additional modifications are needed to optimize ABA production before testing this probiotic in disease contexts in mice.

synthetic biology↗

bioRxiv2024

A Co-essentiality Network of Cancer Driver Genes Better Prioritizes Anticancer Drugs

Diverse molecular networks have been extensively studied to discover therapeutic targets and repurpose approved drugs. However, it is necessary to select a suitable network since the performance of network medicine relies heavily on the completeness and characteristics of the selected network. Although a network using gene essentiality from cancer cells could be an effective platform for identifying anticancer targets, efforts to apply these networks in therapeutic applications have been limited. We constructed a phenotype-level network using the co-essentiality relationship between genes in CRISPR screens across 769 cancer cells to discover therapeutic targets for diverse cancer types. Leveraging cancer driver genes and network propagation on the networks, we found that the co-essentiality network better prioritized anticancer targets and biomarkers and predicted more precise drug responses in cancer cells than other molecular networks. The co-essentiality network outperformed conventional molecular networks in drug repurposing, which were validated in silico by clinical trial records. Notably, the co-essentiality network provided 37 repurposed drugs that the other networks have yet to cover, and we showcased three approved drugs repurposed for lung adenocarcinoma (Pioglitazone hydrochloride, Atovaquone, and Eflornithine). Our study provides a novel network for precision oncology to improve the identification of therapeutic targets in specific cancers.

bioinformatics↗