Biology subjects

Manning, J. R.

Publications and source records attributed to Manning, J. R..

At least 19 recordsLinked to original sources

bioRxiv2025

Essential Role for Trf2 in Cardiac Development and Function

Telomere Repeat-binding Factor 2 (Trf2) is essential for protecting our telomeres. While Trf2 global deletion is lethal, its role in organ-specific development, particularly in the heart, remains less understood. In this study, we investigated the role of Trf2 in cardiac development and function. Our studies reveal that cardiomyocyte (CM)-specific loss of Trf2 leads to profound defects in heart morphology, including impaired ventricular wall formation and compromised CM proliferation, concurrent with no CM telomere length attrition. Further, in vivo functional assessment and molecular analyses of CM-Trf2 deficient ventricles revealed severe cardiac dysfunction and, interestingly, altered nuclear envelope gene expression, respectively. Our work provides new insights into the essential role of Trf2 in heart development and function, and potential avenues for therapeutic intervention targeting telomere biology.

developmental biology↗

bioRxiv2025

Adropin protects against cardiac metabolic remodeling and dysfunction in HFpEF

Cardiometabolic heart failure with preserved ejection fraction (HFpEF) is a heterogenous metabolic disease, which in the heart presents as left ventricle diastolic dysfunction, ventricular stiffness, and myocardial structural remodeling. Deleterious changes in cardiac metabolism are central to HFpEF pathophysiology, and proposed treatments for the disease have focused on repairing these defects. In this study, we used a preclinical mouse model that recapitulates cardiometabolic HFpEF to elucidate the molecular mechanisms driving cardiac dysfunction, and tested whether recombinant Adropin (a liver- and brain-derived endogenous peptide hormone) could reverse observed defects. We show that long-term treatment with Adropin reversed multiple markers of HFpEF-related cardiac dysfunction (including fibrosis, diastolic dysfunction, and cardiomyocyte hypertrophy). Using untargeted metabolomics, we found that Adropin treatment reduced hexosamine biosynthesis pathway activity, leading to a reduction in the O-GlcNAcylation of the cardiac fatty acid oxidation enzyme long chain acyl-CoA dehydrogenase (LCAD). Reducing LCAD O-GlcNAcylation increased LCAD activity in vitro, and reduced the accumulation of long-chain acylcarnitines in HFpEF mouse hearts in vivo. Our results suggest that Adropin may restore cardiac metabolic function in HFpEF, and that targeting this pathway may be a novel therapeutic avenue for this disease. CLINICAL PERSPECTIVE- Adropin is a circulating liver- and brain-derived peptide that regulates energy metabolism in the heart and other high metabolic-demand tissues. The plasma abundance of Adropin is decreased in diabetic, hypertensive, and aged individuals; all comorbid risk factors for the development of heart failure with preserved ejection (HFpEF). We therefore examined the potential role of Adropin in HFpEF pathophysiology. - Patients with HFpEF display significant reductions in circulating Adropin levels, matching those seen in comorbid diseases. In a mouse model of HFpEF, treatment with recombinant Adropin reduced diastolic dysfunction, cardiac fibrosis, and cardiomyocyte hypertrophy. - These data suggest that targeting the Adropin pathway may represent a new therapeutic approach in HFpEF.

physiology↗

bioRxiv2025

Cardiac-specific deletion of GCN5L1 promotes fatty liver disease in HFpEF

The prevalence of cardiometabolic heart failure with preserved ejection fraction (HFpEF) continues to grow, representing over half of heart failure cases in the United States. As no specific medication for HFpEF exists, treatment guidelines focus on the management of comorbidities related to metabolic syndrome (e.g. obesity, diabetes, hypertension) that promote the disease1. These same comorbidities also drive pathology in non-cardiac tissues, and the links between cardiometabolic disease presentations in different organs are increasingly being recognized. Preclinical studies on the potential crosstalk between HFpEF and metabolic disease in the liver (e.g. metabolic dysfunction-associated liver disease; MASLD) have focused on how liver dysfunction may affect the heart, particularly through the release of secreted liver proteins. This may reflect the situation in the clinic, where incident MASLD is a risk factor for future HFpEF development. Here, in contrast to this developing paradigm of liver-initiated cardiac disease, we report for the first time a defect in cardiac metabolism related to the mitochondrial metabolic protein GCN5L1 that drives hepatic steatosis and MASLD in HFpEF.

physiology↗

bioRxiv2023

GCN5L1-mediated acetylation prevents Rictor degradation in cardiac cells after hypoxic stress

Cardiomyocyte apoptosis and cardiac fibrosis are the leading causes of mortality in patients with ischemic heart disease. As such, these processes represent potential therapeutic targets to treat heart failure resulting from ischemic insult. We previously demonstrated that the mitochondrial acetyltransferase protein GCN5L1 regulates cardiomyocyte cytoprotective signaling in ischemia- reperfusion injury in vivo and hypoxia-reoxygenation injury in vitro. The current study investigated the mechanism underlying GCN5L1-mediated regulation of the Akt/mTORC2 cardioprotective signaling pathway. Rictor protein levels in cardiac tissues from human ischemic heart disease patients were significantly decreased relative to non-ischemic controls. Rictor protein levels were similarly decreased in cardiac AC16 cells following hypoxic stress, while mRNA levels remained unchanged. The reduction in Rictor protein levels after hypoxia was enhanced by the knockdown of GCN5L1, and was blocked by GCN5L1 overexpression. These findings correlated with changes in Rictor lysine acetylation, which were mediated by GCN5L1 acetyltransferase activity. Rictor degradation was regulated by proteasomal activity, which was antagonized by increased Rictor acetylation. Finally, we found that GCN5L1 knockdown restricted cytoprotective Akt signaling, in conjunction with decreased mTOR abundance and activity. In summary, these studies suggest that GCN5L1 promotes cardioprotective Akt/mTORC2 signaling by maintaining Rictor protein levels through enhanced lysine acetylation.

cell biology↗

bioRxiv2023

High-level cognition is supported by information-rich but compressible brain activity patterns

Brain activity patterns are highly flexible and often complex, but also highly structured. Here we examined how fundamental properties of brain activity patterns relate to ongoing cognitive processes. To this end, we applied dimensionality reduction algorithms and pattern classifiers to functional neuroimaging data collected as participants listened to a story, temporally scrambled versions of the story, or underwent a resting state scanning session. These experimental conditions were intended to require different depths of processing and inspire different levels of cognitive engagement. We considered two primary aspects of the data. First, we treated the maximum achievable decoding accuracy across participants as an indicator of the "informativeness" of the recorded patterns. Second, we treated the number of features (components) required to achieve a threshold decoding accuracy as a proxy for the "compressibility" of the neural patterns (where fewer components indicate greater compression). Overall, we found that the peak decoding accuracy (achievable without restricting the numbers of features) was highest in the intact (unscrambled) story listening condition. However, the number of features required to achieve comparable classification accuracy was also lowest in the intact story listening condition. Taken together, our work suggests that our brain networks flexibly reconfigure according to ongoing task demands, and that the activity patterns associated with higher-order cognition and high engagement are both more informative and more compressible than the activity patterns associated with lower-order tasks and lower levels of engagement. Significance StatementHow our brains respond to ongoing experiences depends on what we are doing and thinking about, among other factors. To study how brain activity reflects ongoing cognition, we examined two fundamental aspects of brain activity under different cognitive circumstances: informativeness and compressibility. Informativeness refers to the extent to which brain patterns are both temporally specific and consistent across different people. Compressibility refers to how robust the informativeness of brain patterns is to dimensionality reduction. Brain activity evoked by higher-level cognitive tasks are both more informative and more compressible than activity evoked by lower-level tasks. Our findings suggest that our brains flexibly reconfigure themselves to optimize different aspects of how they function according to ongoing cognitive demands.

neuroscience↗

bioRxiv2022

Reduced acetylation of TFAM promotes bioenergetic dysfunction in the failing heart

General Control of Amino-Acid Synthesis 5-like 1 (GCN5L1) was previously identified as a key regulator of protein lysine acetylation in mitochondria. Subsequent studies demonstrated that GCN5L1 regulates the acetylation status and activity of mitochondrial fuel substrate metabolism enzymes. However, the role of GCN5L1 in response to chronic hemodynamic stress is largely unknown. Here, we show that cardiomyocyte-specific GCN5L1 knockout mice (cGCN5L1 KO) display exacerbated pressure overload-induced heart failure progression following transaortic constriction (TAC). Mitochondrial DNA and mitochondrial electron transport chain protein levels were decreased in cGCN5L1 KO hearts after TAC, and isolated neonatal cardiomyocytes with reduced GCN5L1 expression had lower bioenergetic output in response to hypertrophic stress. Loss of GCN5L1 expression led to a decrease in the acetylation status of mitochondrial transcription factor A (TFAM) after TAC in vivo, which was linked to a reduction in mtDNA levels in vitro. Together, these data suggest that GCN5L1 may protect from hemodynamic stress by maintaining mitochondrial bioenergetic output. HighlightsO_LIReduced GCN5L1 expression in the failing heart promotes contractile dysfunction C_LIO_LIMitochondrial DNA (mtDNA) levels are reduced in cardiomyocyte-specific GCN5L1 knockout mice following hemodynamic stress C_LIO_LIGCN5L1 knockdown reduces, and GCN5L1 overexpression increases, bioenergetic output in hypertrophic cardiomyocytes C_LIO_LIGCN5L1-mediated acetylation of TFAM promotes increased mtDNA levels C_LI

physiology↗

bioRxiv2022

G-PROTEIN COUPLED RECEPTOR 19 (GPR19) KNOCKOUT MICE DISPLAY SEX-DEPENDENT METABOLIC DYSFUNCTION

G-protein coupled receptors (GPCRs) mediate signal transduction from the cellular surface to intracellular metabolic pathways. While the function of many GPCRs has been delineated previously, a significant number require further characterization to elucidate their cellular function. G-protein coupled receptor 19 (GPR19) is a poorly characterized class A GPCR which has been implicated in the regulation of circadian rhythm, tumor metastasis, and mitochondrial homeostasis. In this report, we use a novel knockout (KO) mouse model to examine the role of GPR19 in whole-body metabolic regulation. We show that loss of GPR19 promotes increased energy expenditure and decreased activity in both male and female mice. However, only male GPR19 KO mice display glucose intolerance in response to a high fat diet (HFD). Loss of GPR19 expression in male mice, but not female mice, resulted in diet-induced hepatomegaly, which was associated with decreased expression of key fatty acid oxidation genes in male GPR19 KO livers. Overall, our data suggest that loss of GPR19 impacts whole-body energy metabolism in diet-induced obese mice in a sex-dependent manner.

physiology↗

bioRxiv2021

Fitness tracking reveals task-specific associations between memory, mental health, and exercise

Physical activity can benefit both physical and mental well-being. Different forms of exercise (e.g., aerobic versus anaerobic; running versus walking, swimming, or yoga; high-intensity interval training versus endurance workouts; etc.) impact physical fitness in different ways. For example, running may substantially impact leg and heart strength but only moderately impact arm strength. We hypothesized that the mental benefits of physical activity might be similarly differentiated. We focused specifically on how different intensities of physical activity might relate to different aspects of memory and mental health. To test our hypothesis, we collected (in aggregate) roughly a centurys worth of fitness data. We then asked participants to fill out surveys asking them to self-report on different aspects of their mental health. We also asked participants to engage in a battery of memory tasks that tested their short and long term episodic, semantic, and spatial memory performance. We found that participants with similar physical activity habits and fitness profiles tended to also exhibit similar mental health and task performance profiles. These effects were task-specific in that different physical activity patterns or fitness characteristics varied with different aspects of memory, on different tasks. Taken together, these findings provide foundational work for designing physical activity interventions that target specific components of cognitive performance and mental health by leveraging low-cost fitness tracking devices.

neuroscience↗

bioRxiv2021

Diet-induced obese mice are resistant to improvements in cardiac function resulting from short-term adropin treatment

Previous studies have shown that treatment with recombinant adropin, a circulating peptide secreted by the liver and brain, restores glucose utilization in the hearts of diet-induced obese mice. This restoration of fuel substrate flexibility, which is lost in obese and diabetic animals, has the potential to improve contractile function in the diabetic heart. Using an ex vivo approach, we examined whether short-term adropin treatment could enhance cardiac function in a mouse model of diet-induced obesity. Our study showed that acute adropin treatment reduces inhibitory phosphorylation of pyruvate dehydrogenase in primary neonatal cardiomyocytes, and leads to moderate improvements in ex vivo cardiac function in mice fed a low fat diet. Conversely, short-term exposure to adropin led to a small decrease in cardiac function in mice fed a long-term high fat diet. Insulin treatment did not significantly alter cardiac function in adropin treated hearts from either low or high fat diet mice, however acute adropin treatment did moderately restore downstream insulin signaling in high fat diet fed mice. Overall, these data suggest that in an ex vivo setting, acute adropin treatment alone is not sufficient to promote improved cardiac function in obese animals.

physiology↗

bioRxiv2021

GPER-dependent estrogen signaling increases cardiac GCN5L1 expression and MCAD activity

Reversible lysine acetylation regulates the activity of cardiac metabolic enzymes, including those controlling fuel substrate metabolism. Mitochondrial-targeted GCN5L1 and SIRT3 have been shown to regulate the acetylation status of mitochondrial enzymes, which results in alterations to the relative oxidation rates of fatty acids, glucose, and other fuels for contractile activity. However, the role that lysine acetylation plays in driving metabolic differences between male and female hearts is not currently known. In this study, we report that estrogens induce the expression of GCN5L1 via GPER agonism in cardiac cells, which increases the enzymatic activity and acetylation status of the fatty acid oxidation enzyme medium chain acyl-CoA dehydrogenase (MCAD).

physiology↗

bioRxiv2021

Inhibitory Acetylation of Pyruvate Dehydrogenase Promotes Diastolic Dysfunction in Mice

Left ventricular diastolic dysfunction is a structural and functional condition that precedes the development of heart failure with preserved ejection fraction (HFpEF). The etiology of diastolic dysfunction includes alterations in fuel substrate metabolism that negatively impact cardiac bioenergetics, and may precipitate the eventual transition to heart failure. To date, the molecular mechanisms that regulate early changes in fuel metabolism leading to diastolic dysfunction remain unclear. In this report, we use a diet-induced obesity model and quantitative acetylproteomics in aged mice to show that inhibitory lysine acetylation of the pyruvate dehydrogenase (PDH) complex promotes energetic deficits and diastolic dysfunction in mouse hearts. Cardiomyocyte-specific deletion of the mitochondrial lysine acetylation regulatory protein GCN5L1 prevented hyperacetylation of the PDH complex subunit PDHA1, allowing aged obese mice to continue using pyruvate as a bioenergetic substrate in the heart. Our findings suggest that changes in mitochondrial protein lysine acetylation represent a key metabolic component of diastolic dysfunction that precedes the development of heart failure.

physiology↗

bioRxiv2021

Minimal functional alignment of ventromedial prefrontal cortex intracranial EEG signals during naturalistic viewing

The ventromedial prefrontal cortex (vmPFC) has been thought to play an important role in processing endogenous information such as generating subjective affective meaning. Unlike sensory cortex, which processes exogenous information about the external world similarly across individuals, prior work has posited that vmPFC activity may be idiosyncratic to each individual, even when exposed to the same external stimulus. In this study, we recorded local field potentials (LFPs) from intracranial stereotactic electrodes implanted in patients with intractable epilepsy while they watched an emotionally engaging television show episode and evaluated temporal synchronization of these signals across participants in auditory cortex and vmPFC. Overall, we observed markedly lower intersubject synchronization of signals recorded from electrodes implanted in vmPFC compared to auditory cortex. A subset of patients, however, appeared to share similar vmPFC states during the more emotionally salient scenes. This work suggests that the vmPFC is involved in processing affective responses to ongoing experience in a state-like manner, but the specific states and temporal sequences are idiosyncratic to each individual, even when viewing the same television episode.

neuroscience↗

bioRxiv2021

Unexpected false feelings of familiarity about faces are associated with increased pupil dilations

Our subjective sense that something we encounter is familiar to us is reflected by changes in pupil size. Although pupil dilation effects of familiarity have been well documented, familiarity is not the only, or even the strongest, contributing factor to pupil dilation. Changes in pupil dilation also reflect changes in brightness, affective or emotional responses, hormonal release, expected value or utility, and surprise, among others. Because many factors can affect pupil dilation, important questions remain about how pupil dilation changes reflect high-order cognitive processes, like attention and memory. For example, because surprise and familiarity are often difficult to fully distinguish (since new experiences can be surprising or unexpected), it can be difficult to tease apart pupil dilation effects of surprise versus familiarity. To better understand the effects of surprise and familiarity on pupil dilation, we examined pupil responses during a recognition memory task involving photographs of faces and outdoor scenes. When participants rated novel face images as "familiar," we observed a robust pupil dilation response.

neuroscience↗

bioRxiv2020

A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework

BackgroundThe vast ecosystem of single-cell RNA-seq tools has until recently been plagued by an excess of diverging analysis strategies, inconsistent file formats, and compatibility issues between different software suites. The uptake of 10x Genomics datasets has begun to calm this diversity, and the bioinformatics community leans once more towards the large computing requirements and the statistically-driven methods needed to process and understand these ever-growing datasets. ResultsHere we outline several Galaxy workflows and learning resources for scRNA-seq, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The Galaxy reproducible bioinformatics framework provides tools, workflows and trainings that not only enable users to perform one-click 10x preprocessing, but also empowers them to demultiplex raw sequencing from custom tagged and full-length sequencing protocols. The downstream analysis supports a wide range of high-quality interoperable suites separated into common stages of analysis: inspection, filtering, normalization, confounder removal and clustering. The teaching resources cover an assortment of different concepts from computer science to cell biology. Access to all resources is provided at the singlecell.usegalaxy.eu portal. ConclusionsThe reproducible and training-oriented Galaxy framework provides a sustainable HPC environment for users to run flexible analyses on both 10x and alternative platforms. The tutorials from the Galaxy Training Network along with the frequent training workshops hosted by the Galaxy Community provide a means for users to learn, publish and teach scRNA-seq analysis. Key PointsO_LISingle-cell RNA-seq has stabilised towards 10x Genomics datasets. C_LIO_LIGalaxy provides rich and reproducible scRNA-seq workflows with a wide range of robust tools. C_LIO_LIThe Galaxy Training Network provides tutorials for the processing of both 10x and non-10x datasets. C_LI

bioinformatics↗

bioRxiv2020

User-friendly, scalable tools and workflows for single-cell analysis

Single-cell RNA-Seq (scRNA-Seq) data analysis requires expertise in command-line tools, programming languages and scaling on compute infrastructure. As scRNA-Seq becomes widespread, computational pipelines need to be more accessible, simpler and scalable. We introduce an interactive analysis environment for scRNA-Seq, based on Galaxy, with ~70 functions from major single-cell analysis tools, which can be run on compute clusters, cloud providers or single machines, to bring compute to the data in scRNA-Seq.

bioinformatics↗

bioRxiv2020

Biomarkers of Depression Symptoms Defined by Direct Intracranial Neurophysiology

Quantitative biological substrates of depression remain elusive. We carried out this study to determine whether application of a novel computational approach to high spatiotemporal resolution direct neural recordings may unlock the functional organization and coordinated activity patterns of depression networks. We identified two subnetworks conserved across the majority of individuals studied. The first was characterized by left temporal lobe hypoconnectivity and pathological beta activity. The second was characterized by a hypoactive, but hyperconnected left frontal cortex. These findings identify distributed circuit activity associated with depression, link neural activity with functional connectivity profiles, and inform strategies for personalized targeted intervention.

neuroscience↗

bioRxiv2020

eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs

An increasing number of gene expression quantitative trait locus (eQTL) studies have made summary statistics publicly available, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and colocalisation. However, differences between these datasets, in their variants tested, allele codings, and in the transcriptional features quantified, are a barrier to their widespread use. Consequently, target genes for most GWAS signals have still not been identified. Here, we present the eQTL Catalogue (https://www.ebi.ac.uk/eqtl/), a resource which contains quality controlled, uniformly recomputed QTLs from 21 eQTL studies. We find that for matching cell types and tissues, the eQTL effect sizes are highly reproducible between studies, enabling the integrative analysis of these data. Although most cis-eQTLs were shared between most bulk tissues, the analysis of purified cell types identified a greater diversity of cell-type-specific eQTLs, a subset of which also manifested as novel disease colocalisations. Our summary statistics can be downloaded by FTP, accessed via a REST API, and visualised on the Ensembl genome browser. New datasets will continuously be added to the eQTL Catalogue, enabling the systematic interpretation of human GWAS associations across many cell types and tissues.

genomics↗

bioRxiv2020

Between-subject prediction reveals a shared representational geometry in the rodent hippocampus

The rodent hippocampus constructs statistically independent representations across environments ("global remapping") and assigns individual neuron firing fields to locations within an environment in an apparently random fashion, processes thought to contribute to the role of the hippocampus in episodic memory. This random mapping implies that it should be challenging to predict hippocampal encoding of a given experience in one subject based on the encoding of that same experience in another subject. Contrary to this prediction, we find that by constructing a common representational space across rats in which neural activity is aligned using geometric operations (rotation, reflection, and translation; "hyperalignment"), we can predict data of "right" trials (R) on a T-maze in a target rat based on 1) the "left" trials (L) of the target rat, and 2) the relationship between L and R trials from a different source rat. These cross-subject predictions relied on ensemble activity patterns including both firing rate and field location, and outperformed a number of control mappings, such as those based on permuted data that broke the relationship between L and R activity for individual neurons, and those based solely on within-subject prediction. This work constitutes proof-of-principle for successful cross-subject prediction of ensemble activity patterns in the hippocampus, and provides new insights in understanding how different experiences are structured, enabling further work identifying what aspects of experience encoding are shared vs. unique to an individual.

neuroscience↗