Biology subjects

Kim, A.

Publications and source records attributed to Kim, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Integrated phenotypic screening and chemical proteomics identifies ETF1 ligands that modulate viral translation and replication

Emerging and re-emerging viruses pose a significant threat to global health. Although direct-acting antivirals have shown success, their efficacy is limited by the rapid emergence of drug-resistant viral variants. Hence, there is an urgent need for additional broad spectrum antiviral therapeutic strategies. Here, we identify by phenotypic screening a set of stereochemically defined photoreactive small molecules (photo-stereoprobes) that stereoselectively suppress SARS-CoV-2 replication in human lung epithelial cells. Structure-activity relationship-guided chemical proteomics identified the eukaryotic translation termination factor 1 (ETF1) as a target of the photo-stereoprobes, and this interaction was recapitulated with recombinant purified ETF1. We found that the photo-stereoprobes modulate programmed ribosomal frameshifting mechanisms essential for SARS-CoV-2 infection without causing ETF1 degradation, thus distinguishing the photo-stereoprobes from other known ETF1-directed small molecules. We finally show that the photo-stereoprobes also inhibit the replication of additional viruses with non-canonical ribosomal frameshifting mechanisms. Our findings thus identify a mechanistically distinct class of ETF1 ligands that implicate host translation termination processes as a potential target for antiviral development. SIGNIFICANCE STATEMENTThe identification of broad-spectrum antivirals that target host proteins is a desirable strategy to combat emerging viral infections given the rapid escape potential of viruses and the need to develop new countermeasures for clinically significant pathogens. Here, we integrate phenotypic screening and chemical proteomics to identify photo-stereoprobe small molecules that inhibit the replication of multiple viruses. We show that these compounds bind the protein eukaryotic peptide chain release factor subunit 1 (ETF1) and modulate programmed ribosomal frameshifting. Unlike previously described ligands for ETF1, which lead to proteasomal destruction of the protein, we did not find that the photo-stereoprobes altered ETF1 content in cells. Our findings thus point to an opportunity to pharmacologically modulate a host protein implicated in programmed ribosomal frameshifting as a strategy to combat infection of viruses from different families.

microbiology↗

bioRxiv2025

NAPRT expression and epigenetic regulation in pediatric rhabdomyosarcoma as a potential biomarker for NAMPT inhibition

PurposeNew treatments are needed to improve survival in children with rhabdomyosarcoma (RMS). NAD biosynthesis, regulated by the enzymes NAPRT and NAMPT, represents a metabolic vulnerability due to high NAD turnover in cancers. Although NAMPT inhibitors (NAMPTi) show preclinical promise, clinical translation has been limited by toxicity and the lack of predictive biomarkers. Here, we evaluated NAPRT expression in RMS and its potential as an actionable biomarker to guide NAMPTi therapy. Experimental DesignNAPRT promoter methylation, transcript levels, and protein expression were assessed in RMS cells, PDXs, and primary tumors (n=109) from the Childrens Oncology Group. In vitro sensitivity to NAMPTi was tested in molecularly diverse and isogenic RMS cell lines, examining the role of NAPRT expression in mediating cytotoxicity and the ability of nicotinic acid (NA) to rescue viability. In vivo efficacy was assessed using NAPRT-isogenic orthotopic xenograft models. ResultsNAPRT promoter hypermethylation was found in a subset of RMS models and patient samples. Immunohistochemistry showed loss of NAPRT protein in 30-40% of tumors, defined as <1% tumor cell staining. Methylation modestly correlated with protein expression. NAPRT-silenced cells were highly sensitive to NAMPTi, driven by NAD depletion and not reversible with NA. In vivo, NAMPTi induced significant tumor regression, which was not abrogated with NA administration in NAPRT-silenced models. ConclusionsNAPRT loss occurs in a subset of RMS, offering a potential strategy to expand the therapeutic window of NAMPTi. Further research is needed to understand NAPRT regulation and optimize biomarker assay strategies for use in future clinical trials.

cancer biology↗

bioRxiv2025

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

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

bioengineering↗

bioRxiv2025

Identification of Pesticides Associated with an Increased Risk of Parkinson's Disease using a Multi-Screen Approach

Parkinsons Disease (PD) is a progressive neurodegenerative disease characterized by aggregation and transmission of alpha-synuclein (-syn) protein and loss of dopaminergic neurons. The etiology of PD is multifactorial involving both genetic and environmental factors. Pesticide exposure has been associated with PD, but it is still unclear which of the hundreds of chemically and structurally diverse pesticides confer this association. While there are numerous pesticides currently registered for use in the United States, in this study, we focused on 62 pesticides used in the California Central Valley. We used 2 cell-based screens and a recently developed pesticide-wide association study (PWAS) analysis to identify candidates that increase the risk of PD. One cell-based screen tested for pesticides that alter autophagy and the other tested for their effect on -syn transmission. To establish biological plausibility, pesticides that were positive in all 3 screens were tested for dopaminergic neurotoxicity in an in vivo zebrafish (ZF) model. The autophagy screen resulted in a total of 22 hits for alterations to either autophagosomes (16 hits) and lysosomes (14 hits) out of the 62 pesticides tested. The -syn transmission screen resulted in 29 hits, and the PWAS resulted in 34 hits. Six pesticides were positive in all 3 screens and four of these pesticides induced aminergic neuron loss in ZF larvae. The majority of the pesticides identified in our screens have not previously been implicated as risk factors for PD but should be considered in future studies.

pharmacology and toxicology↗

bioRxiv2025

Luminal Vascular Dysfunction Drives Rapid Blood Brain Barrier Injury in Hyperglycemic Stroke: Key Roles for Luminal Glycocalyx and Complement

BackgroundAcute hyperglycemia affects approximately 40% of stroke patients and is associated with worse outcomes. The underlying mechanisms linking this metabolic stress to stroke-induced brain injury remains unclear, and effective therapies are lacking. MethodsIn a mouse model of acute hyperglycemic stroke, luminal disruption, blood-brain barrier (BBB) leakage, neurological deficit, motor function, and mortality were evaluated. Vascular luminal glycocalyx and complement activation were assessed by immunostaining, with glycocalyx loss confirmed by electron microscopy. Complement C3s causal role was tested using C3 knockout mice and site-targeted inhibition with CR2-Crry. To enhance translational relevance, post-mortem human stroke and control brains were immunostained to assess the association between endothelial glycocalyx loss and vascular complement activation. In a separate stroke patient cohort, soluble complement activation products were measured in pre-thrombectomy plasma, and their predictive value for modified Rankin Scale (mRS) outcomes evaluated using elastic net regression. ResultsHyperglycemic stroke mice exhibited accelerated and more severe BBB breakdown, greater functional deficits, and higher mortality than normoglycemic controls, mirroring clinical observations. Acute hyperglycemia triggered rapid vascular luminal injury characterized by loss of endothelial luminal glycocalyx, luminal IgM/IgG deposition, and vascular complement C3 activation, leading to BBB disruption. This vascular luminal injury was corroborated in human stroke brain tissue. These luminal changes persisted despite glucose normalization and were exacerbated by reperfusion, driving injury into the brain parenchyma. Genetic and pharmacological approaches confirmed vascular complement activation as a causal driver of severe BBB disruption and poor outcomes. Importantly, site-targeted pharmacological inhibition of complement after reperfusion preserved BBB integrity and improved outcomes, defining a time-specific, luminal-directed strategy as a promising adjunct to thrombectomy. Notably, soluble complement activation markers in pre-thrombectomy stroke plasma predicted clinical outcomes, highlighting their potential as pre-intervention markers for patient stratification and tailored therapy. ConclusionThis study reframes acute hyperglycemic stroke as a vascular luminal disorder, establishing a novel Metabolic-Complement-Vascular (MCV) axis linking metabolic stress to endothelial luminal glycocalyx loss, vascular complement activation, and BBB breakdown in both mice and humans. This new mechanistic understanding transforms the therapeutic landscape of hyperglycemic stroke, offering a potential time-defined, luminal-focused adjunct therapy alongside thrombectomy. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABS- This study reframes hyperglycemic stroke as an acute vascular luminal problem, marked by rapid loss of endothelial luminal glycocalyx and complement C3 activation at the vascular luminal surface. - The rapid luminal changes, identified in both rodent and human stroke brain tissues, establish a novel Metabolic-Complement-Vascular (MCV) axis linking metabolic stress to luminal damage, blood-brain barrier (BBB) breakdown, and injury progression into the brain parenchyma. - The first clinical evidence that pre-thrombectomy plasma complement activation markers independently predict stroke outcomes -- laying the foundation for risk stratification before reperfusion and precision adjunct therapies. What Are the Clinical Implications?- The rapidity and persistence of the MCV axis activation--even after glucose normalization--help explain the limited efficacy of insulin therapy, shifting the therapeutic focus from glycemic control to luminal-targeted interventions. - Identification of a narrow but actionable window following reperfusion where complement C3 inhibition preserves the BBB and limits injury progression to the parenchyma, offers a promising adjunct to thrombectomy in metabolically vulnerable stroke patients. - Targeting the vascular luminal surface reshapes the therapeutic landscape for hyperglycemic stroke by enabling systemic interventions--bypassing the challenge of BBB penetration, supporting rapid clinical translation using existing FDA-approved C3 inhibitors, and framing the endothelial glycocalyx as a promising area for therapeutic and diagnostic exploration in hyperglycemic stroke and broader cerebrovascular disease.

neuroscience↗

bioRxiv2025

CTCF-binding sites demarcate chromatin domains enriched with H3K9me2 or H3K9me3 and restrict the spreading of these histone modifications in human cells

CTCF-binding sites are frequently found at the boundaries of chromatin domains enriched with specific histone modifications in vertebrate genomes, where they function as barriers that limit the spreading of these modifications. However, their role in domains marked by H3K9me2 or H3K9me3 remains poorly understood. In this study, we analyzed CTCF-binding sites and the distribution of H3K9me2 and H3K9me3 around them in human K562 cells, and investigated the spreading of these modifications following CTCF depletion. Genome-wide analysis revealed that certain CTCF-binding sites are located at the boundaries of chromatin domains enriched with H3K9me2 or H3K9me3. Upon loss of CTCF binding, both modifications spread to neighboring chromatin at over half of the boundaries delimiting highly and distinctly enriched domains. Boundaries where such spreading did not occur were flanked by chromatin in a more active state compared to those where spreading occurred. Gene transcription was significantly reduced in neighboring regions where H3K9me2 or H3K9me3 had spread. Further comprehensive analysis revealed that this transcriptional reduction was specifically associated with the spread of H3K9me2. These findings suggest that CTCF-binding sites demarcate chromatin domains enriched with H3K9me2 or H3K9me3 and act as barriers to restrict the spread of these modifications in mammalian cells. Notably, the spread of H3K9me2 appears to play a specific role in transcriptional repression.

molecular biology↗

bioRxiv2025

Mitochondrial Dysfunction Induces Hepatic Lipid Accumulation and Inflammatory Responses in mtDNA Mutator Mice

BackgroundNon-Alcoholic Fatty Liver Disease (NAFLD), now referred to as Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD), is a widespread and complex health issue characterized by the accumulation of lipids in liver cells, not linked to alcohol consumption or other known liver problems. Despite its strong association with insulin resistance and obesity, a notable proportion of lean individuals develop NAFLD, suggesting the involvement of additional factors. Mitochondrial dysfunction has emerged as a potential contributor, given its role in lipid homeostasis and the generation of reactive oxidative species (ROS). MethodsIn this study, we took advantage of the mtDNA mutator mouse model, characterized by oxidative phosphorylation deficiency due to accelerated accumulation of mitochondrial DNA (mtDNA) mutations, to investigate how mitochondrial dysfunction affects liver homeostasis triggering fat accumulation. ResultsWe found that mitochondrial dysfunction induces liver steatosis and inflammation in this mouse model at a young age, independent of obesity. Using quantitative mass spectrometry, we reveal that mitochondrial dysfunction alters the levels of multiple proteins involved in lipid metabolism, cholesterol homeostasis, and inflammation. In vitro data show a shift in cellular metabolism toward the glycolytic pathway and confirm the upregulation of inflammatory genes. These changes are associated with oxidative stress and occur independently of mtDNA molecule release into the cytoplasm. ConclusionOur findings demonstrate that liver steatosis might develop as result of mitochondrial dysfunction without obesity and insulin resistance, underscoring the importance of mitochondrial dysfunction in NAFLD development in lean individuals and providing valuable insights into the molecular mechanisms underlying this complex metabolic disorder. This mouse model offers a unique platform for further investigations aimed at unraveling the intricacies of NAFLD pathogenesis and potential therapeutic targets beyond conventional risk factors.

cell biology↗

bioRxiv2025

TARP γ-8 is a target of ethanol that regulates self-administration and relapse in mice

BackgroundBehavioral pathologies that characterize alcohol use disorder (AUD) are driven by the powerful reinforcing, or rewarding, properties of the drug. We have shown that glutamate AMPA receptor (AMPAR) activity is both necessary and sufficient for alcohol (ethanol) reinforcement. Transmembrane AMPAR regulatory protein (TARP) {gamma}-8 is an essential auxiliary protein that regulates AMPAR expression and activity; however, the role of TARP {gamma}-8 in AUD or other forms of addiction remains largely unexplored. ObjectivesThis study investigated the mechanistic role of TARP {gamma}-8 in operant ethanol self-administration (model of primary reinforcement) and cue-induced reinstatement of ethanol-seeking behavior (model of conditioned reinforcement) using TARP {gamma}-8 heterozygous null (+/-) mice. To determine if TARP {gamma}-8 signaling is targeted by ethanol use, we evaluated protein expression of TARP {gamma}-8, GluA1, CaMKII, and PSD-95 following ethanol self-administration. ResultsA battery of tests evaluating food and water intake, taste reactivity, anxiety-like behavior, and object recognition memory showed no fundamental behavioral deficits in TARP {gamma}-8 (+/-) mice, and no differences in response to acute ethanol or home-cage drinking as compared to wild-types. However, TARP {gamma}-8 (+/-) mice exhibited significantly reduced acquisition and escalation of operant ethanol self-administration and reduced cue-induced reinstatement of ethanol-seeking behavior, with no differences in parallel sucrose-only controls. In wild-type mice, ethanol self-administration increased TARP {gamma}-8 expression in the amygdala, nucleus accumbens, and hippocampus, and increased GluA1 expression in the amygdala and prefrontal cortex, compared to sucrose controls. ConclusionThese findings highlight the specificity of TARP {gamma}-8 regulation of ethanol reinforcement mechanisms and identify this crucial AMPAR auxiliary protein as a target of ethanol in reward-related brain regions, highlighting its potential for development of novel pharmacotherapies for AUD.

neuroscience↗

bioRxiv2025

An In Vivo Model of Alpha-Synuclein Spread from Gut to Brain

BackgroundParkinsons disease is a progressive neurodegenerative disorder characterized by the presence of pathological aggregation of the protein alpha-synuclein and the loss of dopaminergic neurons in the substantia nigra. There is evidence that misfolding and propagation of alpha-synuclein aggregates through networks of interconnected neurons is responsible for the pathological spread and progressive neuron loss. However, in vivo models demonstrating such pathological progression remain elusive. ResultsThis study utilizes a zebrafish model in order to interrogate the mechanisms of alpha-synuclein toxicity and spread. We describe the development of a zebrafish model of endogenous neuronal human alpha-synuclein expression that causes, in young fish, behavioral and neuronal changes as well as microglia activation. In aged fish, alpha-synuclein expression induces a slow but progressive pathological phenotype manifesting in neuron loss within the gut and the CNS. This model is further utilized to seed gut pathology by incorporating a novel method of feeding human alpha-synuclein preformed fibrils in order to initiate protein misfolding at an early age. The combination of endogenous neuronal expression of alpha-synuclein and the exogenous addition of misfolded protein facilitates the development of brain pathology and subsequent neuron loss in the CNS. In addition to the pathological alterations induced with the fibril feeding model, genetic changes were identified by single cell RNA sequencing. These gene changes resulted in pathway alteration that implicate neurodegenerative disease processes. ConclusionThis model of alpha-synuclein pathology is useful for understanding mechanisms underlying disease initiation and can replicate the progressive development of pathological synuclein accumulation. It has the potential to induce neuron to neuron spread and also offers a way to explore what interventions may prevent such pathological progression.

neuroscience↗

bioRxiv2025

HKU5 bat merbecoviruses use divergent mechanisms to engage bat and mink ACE2 as entry receptors

Identifying receptors for bat coronaviruses is critical for spillover risk assessment, countermeasure development, and pandemic preparedness. While Middle East respiratory syndrome coronavirus (MERS-CoV) uses DPP4 for entry, the receptors of many MERS-related betacoronaviruses remain unknown. The bat merbecovirus HKU5 was previously shown to have an entry restriction in human cells. Using both pseudotyped and full-length virus, we show that HKU5 uses Pipistrellus abramus bat ACE2 but not human ACE2 or DPP4 as a receptor. Cryo-electron microscopy (cryo-EM) analysis of the virus-receptor complex and structure-guided mutagenesis reveal a spike and ACE2 interaction that is distinct from other ACE2-using coronaviruses. MERS-CoV vaccine sera poorly neutralize HKU5 informing pan-merbecovirus vaccine design. Notably, HKU5 can also engage American mink and stoat ACE2, revealing mustelids as potential intermediate hosts. These findings highlight the versatility of merbecovirus receptor use and underscore the need for continued surveillance of bat and mustelid species.

microbiology↗

bioRxiv2025

USP7 inhibition perturbs proteostasis and tumorigenesis in triple negative breast cancer

The deubiquitinase USP7 is a critical regulator of tumorigenesis, known for stabilizing the MDM2-p53 pathway. Emerging evidence highlights USP7s p53-independent roles in proliferation and tumorigenesis. Triple negative breast cancers frequently inactivate p53 and this disease subtype remains difficult to treat and in need of new therapeutic options. Our study reveals that USP7 is upregulated in TNBC patient tumors. Importantly, genetic and pharmacologic USP7 inactivation impaired tumor progression in TNBC models. To explore USP7s role in p53-mutant TNBCs, we performed deep quantitative proteomics across TNBC cell lines, identifying shared USP7 targets involved in cell proliferation, genome stability, and proteostasis. Acute USP7 inactivation allowed us to infer proximally controlled proteins which are likely direct targets. Surprisingly, many of the proteins downregulated by USP7 inhibition are E3 ubiquitin ligases. Thus, a key USP7 function in TNBC is to antagonize the degradation of ubiquitinating enzymes, since these enzymes are often susceptible to auto-ubiquitination and degradation. Notably, we identified TOPORS, a dual ubiquitin- and SUMO-ligase, among novel USP7 substrates. TOPORS interacts with the BRCA1-A DNA damage repair complex suggesting a USP7-TOPORS-BRAC1-A axis that might further explain the continued proliferation of genomically unstable TNBCs. Collectively, these data nominate USP7 as a potential therapeutic in TNBC.

cancer biology↗

bioRxiv2025

Microbiota assembly of specific pathogen-free neonatal mice

BackgroundNeonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We address this gap by characterizing the assembly of the bacterial microbiota of C57BL/6 and BALB/c litters from birth to adulthood across multiple independent litters. ResultsThe fecal microbiome of young pups is simple, dominated by only a few pioneering bacterial taxa. These taxa are present at low levels in the microbiota of multiple maternal body sites, precluding a clear identification of maternal source. The pup microbiota begins diversifying after fourteen days, coinciding with the beginning of coprophagy and the consumption of solid foods. Pup stool bacterial community composition and diversity are not significantly different from dams from day 21 onwards. Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species. ConclusionsAssembly of the murine microbiome occurs over the first weeks of postnatal life and is largely complete by day 21. This detailed view of bacterial community development across multiple commonly employed mouse strains informs experimental design, allowing researchers to better target interventions before, during, or after the maturation of the bacterial microbiota. The source of pioneer bacterial strains appears heterogeneous, as the most abundant taxa identified in young pup stool were found at low levels across multiple maternal body sites, suggesting diverse routes for seeding of the murine microbiome.

microbiology↗

bioRxiv2024

Donor HLA DQ reactive B cells clonally expand under chronic immunosuppression and include atypical CD21lowCD27- B cells with high avidity germline B cell receptors.

Long-term allograft survival is limited by humoral-associated chronic allograft rejection, suggesting inadequate constraint of humoral alloimmunity by contemporary immunosuppression. Heterogeneity in alloreactive B cells and the incomplete definition of which B cells participate in chronic rejection in immunosuppressed transplant recipients limits our ability to develop effective therapies. Using a double-fluorochrome single-HLA tetramer approach combined with single-cell in vitro culture, we investigated the B-cell receptor (BCR) repertoire characteristics, avidity, and phenotype of donor HLA-DQ reactive B cells in a transplant recipient with end-stage donor specific antibody (DSA)-associated cardiac allograft vasculopathy while receiving maintenance immunosuppression (tacrolimus, mycophenolate mofetil, prednisone). Donor DQB1*03:02/DQA1*03:01 (DQ8)-reactive IgG+ B cells were enriched for minimally mutated and germline encoded high avidity BCRs (median KD 4.26x10-09) with an atypical, antigen-experienced and proliferative phenotype (CD27-CD21lowCD71+CD11c+/-). These B cells coexisted with a smaller subset of more highly mutated, affinity matured IgG+CD27+ B cells. Circulating donor-reactive B cells and DSA remained detectable after rituximab, contrasting with the marked reduction in DSA after allograft explant and retransplant. Together, these findings define the persistence of germline high-avidity HLA-DQ alloreactive B cells and their co-existence with affinity matured clones that were both driven by the allograft despite conventional immunosuppression.

immunology↗

bioRxiv2024

Exploring Organ-Specific Extracellular Vesicles in Metabolic Improvements Following Bariatric Surgery in Adolescents with Obesity

Aims/hypothesisVertical sleeve gastrectomy (VSG) leads to significant metabolic improvements, though the underlying molecular mechanisms are not yet fully understood. Emerging evidence suggests that small extracellular vesicles (sEVs) contribute to metabolic improvements post-VSG; however, it is still unclear which organ-specific sEV correlate with various metabolic parameters and how they exert these effects. The study aimed to establish the role of organ-specific sEVs in the metabolic improvements associated with VSG. MethodsDemographic, anthropometric, and blood samples were collected pre-VSG and 3- and 6-month post-VSG in adolescents with obesity. Blood samples were utilized to measure metabolic parameters and to isolate sEVs. sEV RNAs were analyzed via small RNA sequencing then bioinformatics analyses. ResultsA significant reduction in mRNA cargo from liver-specific genes was observed post- VSG, whereas adipose tissue- or skeletal muscle-specific genes showed no such reduction. Liver-derived RNA correlated with BMI, leptin, and resistin, while adipose-derived RNA correlated with leptin. Analysis of delta values (post-minus pre-surgery) revealed that adipose-derived RNA cargo correlated with markers of liver damage and HOMA-IR, whereas liver-derived RNA cargo correlated with BCAAs. ConclusionsVSG modulates the EV system in the liver and adipose tissue. Liver-derived sEVs appear to regulate adipose metabolism, while adipose-derived sEVs are associated with liver function, suggesting a dynamic crosstalk between these tissues through sEVs that shapes systemic metabolic outcomes. Research in ContextO_ST_ABSWhat is already known about this subject?C_ST_ABS- Vertical sleeve gastrectomy (VSG) is the most performed bariatric surgery, leading to significant metabolic improvements. - Small extracellular vesicles (sEVs) and their RNA cargo play a crucial role in metabolic regulation. - Levels of branched-chain amino acids (BCAAs), which are known metabolic regulators, decrease following bariatric surgery. What is the key question?- How do sEVs, BCAA and other metabolic molecules interact to drive the significant metabolic improvements observed after VSG? What are the new findings?- The levels of liver-specific RNA cargo in sEVs decrease after VSG and are correlated with BMI and leptin levels at 6 months post-surgery, suggesting a potential role for liver-specific RNA cargo in the metabolic benefits associated with VSG. - Changes in BCAA levels from baseline to 6 months post-surgery correlate with changes in liver-specific RNA cargo in sEVs, indicating liver-specific RNA cargo in sEVs may influence metabolic parameters through BCAA modulation. - Changes in the level of adipose-specific RNA cargo in sEVs from baseline to 6 month post-surgery correlate with changes HOMA-IR and ALT levels. How might this impact on clinical practice in the foreseeable future?The study identifies liver- and adipose-derived sEV RNA cargo as potential targets for non-invasive therapies that could replicate the metabolic benefits of VSG. While further investigation is needed, these findings suggest a tentative alternative for adolescents facing obesity who may be ineligible or reluctant to undergo bariatric surgery.

cell biology↗

bioRxiv2024

Effects of Aging on the Immune and Periosteal Response to Fracture in Mice

Aging predisposes individuals to reduced bone mass and fragility fractures, which are costly and linked to high mortality. Understanding how aging affects fracture healing is essential for developing therapies to enhance bone regeneration in older adults. During the inflammatory phase of fracture healing, immune cells are recruited to the injury site as periosteal skeletal stem/progenitor cells (pSSPCs) rapidly proliferate and differentiate into osteochondral lineages, allowing for fibrocartilaginous callus formation and complete bone healing. Irrespective of age, how periosteal mesenchymal and immune cells interact during early fracture healing is incompletely understood, limiting our ability to potentially modulate these processes. To address this, we directly analyzed, in parallel, at a single-cell level, isolated murine CD45(+) and CD45(-) periosteal cells dissected from intact and fractured bones, collected three days after injury. Through comprehensive analysis, corroborated by bulk RNA-sequencing, flow cytometry, and histology, we found aging decreases pSSPCs proliferative, marked by a reduced expression of genes required for callus formation and an increased senescence signature. We found that the chemokine Cxcl9 was highly upregulated in aged intact Prrx1+ pSSPCs, predicted to interact with other pSSPCs directly, and associated with increased recruitment of CD8+ T cells at the fracture site three days after injury. Cell-to-cell communication analysis provided insight into the complexity of interactions among the many cell types regulating fracture healing and the impact of aging on these processes. Together, these results provide insight into age-induced alterations in fracture healing, informing the development of improved therapeutic approaches for fragility fractures.

cell biology↗

bioRxiv2024

Statistical relationships across epigenomes using large-scale hierarchical clustering

Environmental toxins and pathogens can influence epigenetic modifications on chromosomes, thereby leaving trace evidence of exposures. However, the avalanche of epigenomic data is difficult to parse for biological interpretation given non-linear complex patterns and relationships. This attractive challenge in epigenomic data lends itself to machine learning for discerning infectivity and susceptibility. In this study, we explore over 3,000 epigenomes of uninfected individuals and provide a comprehensive characterization of the relationships among epigenetic modifiers, their modifiers, and specific immune cell types across all chromosomes using hierarchical clustering.

genetics↗

bioRxiv2024

Uncovering locomotor learning dynamics in people with Parkinson's disease

Locomotor learning is important for improving gait and balance impairments in people with Parkinsons disease (PD). While PD disrupts neural networks involved in motor learning, there is a limited understanding of how PD influences the time course of locomotor learning and retention. Here, we used a virtual obstacle negotiation task to investigate whether the early stages of PD affect the acquisition and retention of locomotor skills. On Day 1, 15 participants with PD and 20 age-matched controls were instructed to achieve a specified level of foot clearance while repeatedly stepping over two different virtual obstacles on a treadmill. We assessed online performance improvement on Day 1 and overnight retention after at least 24 hours on Day 2. We used a hierarchical Bayesian state-space model to estimate the learning rate and the degree of interference between the two obstacles. There was a 93% probability that people with PD learned the locomotor skill faster than controls, but there was limited evidence of group differences in interference between the two heights of obstacles. Both groups improved their performance to a similar magnitude during skill acquisition and performed similarly during retention on Day 2. Notably, a slower learning rate was associated with greater online performance improvement, while lower interference was linked to better overnight retention, and this effect was strongest for the control group. These results highlight that people with early-stage PD retain the ability to use multisensory information to acquire and retain locomotor skills. In particular, our finding that people with early-stage PD learned faster than age-matched controls may reflect the emergence of compensatory motor learning strategies used to offset early motor impairments in people with PD.

neuroscience↗

bioRxiv2024

2.6-A resolution cryo-EM structure of a class Ia ribonucleotide reductase trapped with mechanism-based inhibitor N3CDP

Ribonucleotide reductases (RNRs) reduce ribonucleotides to deoxyribonucleotides using radical-based chemistry. For class Ia RNRs, the radical species is stored in a separate subunit ({beta}2) from the subunit housing the active site (2), requiring the formation of a short-lived 2{beta}2 complex and long-range radical transfer (RT). RT occurs via proton-coupled electron transfer (PCET) over a long distance (~32-[A]) and involves the formation and decay of multiple amino acid radical species. Here, we use cryogenic-electron microscopy and a mechanism-based inhibitor 2'-azido-2'-deoxycytidine-5'-diphosphate (N3CDP) to trap a wild-type 2{beta}2 complex of E. coli class Ia RNR. We find that one subunit has turned over and that the other is trapped, bound to {beta} in a mid-turnover state. Instead of N3CDP in the active site, forward RT has resulted in N2 loss, migration of the third nitrogen from the ribose C2' to C3' positions, and attachment of this nitrogen to the sulfur of cysteine-225. To the best of our knowledge, this is the first time an inhibitor has been visualized as an adduct to an RNR. Additionally, this structure reveals the positions of PCET residues following forward RT, complementing the previous structure that depicted a pre-turnover PCET pathway and suggesting how PCET is gated at the -{beta} interface. This N3CDP-trapped structure is also of sufficient resolution (2.6 [A]) to visualize water molecules, allowing us to evaluate the proposal that water molecules are proton acceptors and donors as part of the PCET process. Significance StatementSeveral FDA-approved cancer drugs target human ribonucleotide reductase (RNR), a radical enzyme that produces the requisite deoxyribonucleotides for DNA biosynthesis and repair. Human RNR is a class Ia enzyme that requires radical transfer (RT) from a {beta}2 subunit to an 2 subunit on every round of turnover. Long-range RT is both a remarkable feature and an Achilles heel, given that inhibitors can intercept the radical species. Here we present a cryogenic electron microscopy (cryo-EM) structure of the best studied class Ia RNR, the enzyme from E. coli, in which 2 and {beta}2 subunits have been trapped together using a mechanism-based inhibitor. This structure provides insight into both the mechanism of RNR inhibition and the mechanism of long-range RT.

biophysics↗