Biology subjects

Day, S. M.

Publications and source records attributed to Day, S. M..

12 recordsLinked to original sources

bioRxiv2026

Pathogenic MYBPC3 missense variants alter protein-protein interactions within the sarcomere

BackgroundHypertrophic cardiomyopathy (HCM) is a genetic heart disease that leads to left ventricular hypertrophy, heart failure, and arrhythmias. Pathogenic missense variants in the gene myosin binding protein C (MYBPC3) cluster within its internal subdomains C3 and C6. The protein (MyBP-C), carrying these missense variants, localizes normally to the myofilaments, leaving uncertainty regarding the mechanism(s) by which they cause HCM. MethodsWe probed the molecular pathogenesis of these variants by analyzing (1) their prevalence in an international registry of patients with HCM, (2) total MyBP-C levels and the allelic fraction of mutant MyBP-C in human left ventricular heart tissue, and (3) performing flag-immunoprecipitation and proximity labeling mass spectrometry of wild-type MyBP-C and four pathogenic missense variants (Arg495Gln, Arg502Trp- C3, Trp792Arg, Arg810His- C6) to determine the change in MyBP-C interacting and proximity proteins induced by these variants. ResultsWe found that among patients with HCM who had any MYBPC3 pathogenic variant, 17.9% had a missense variant within the C3 or C6 subdomain. Unlike truncating variants, these C3 or C6 missense variants did not reduce MyBP-C content relative to myosin. The mutant allelic fraction of MyBP-C varied from 10.0-67.0% across samples. Flag-immunoprecipitation mass spectrometry identified 252 MyBP-C interacting proteins. Pathogenic missense variants disrupted 23 MyBP-C protein interactions, including lysosomal Ragulator-Rag complex proteins (RRAGA, RRAGC, LAMTOR4). Proximity labeling mass spectrometry was more sensitive, identifying 3,240 MyBP-C proximity proteins. Pathogenic missense variant(s) altered the proximity to MyBP-C of 789 proteins (69.4% increased and 30.5% decreased). Proteins that were increased in proximity to the missense MyBP-C were enriched for thin-filament proteins. ConclusionPathogenic MYBPC3 missense variants within the C3 and C6 subdomains are present in a substantial subset of patients with HCM. Our findings imply unique mechanisms of these variants distinct from haploinsufficiency, potentially driven by enhanced proximity to the thin filament within myofilaments.

cell biology↗

bioRxiv2025

Effects of Sodium Glucose Co-Transporter Inhibitors on Work in Human Hypertrophic Cardiomyopathy Living Myocardial Slices

BackgroundDisease modifying therapies for hypertrophic cardiomyopathy (HCM) remain a prevailing unmet need. Human-based experimental platforms capable of controlled manipulation of preload and afterload can distinguish direct myocardial and systemic effects and facilitate development of targeted cardiac therapeutics. Sodium glucose cotransporter inhibitors (SGLTi) may directly affect cardiac contractility, potentially related to increased ketone availability. These effects have not been adequately studied in human HCM myocardium under defined loading conditions. AimsWe sought to establish human living myocardial slices (LMS) as a platform to interrogate load-dependent myocardial mechanics in HCM and to quantify the acute effects of metabolic and pharmacologic interventions--including SGLTi--on myocardial work under physiologic loading conditions. MethodsHuman myocardial tissue was procured from non-failing donor hearts or individuals with HCM undergoing septal myectomy. Freshly prepared human LMS were mechanically tested to generate biomimetic work loops across a range of physiologic preloads and afterloads in either glucose-only fuel or glucose supplemented with ketone. Following baseline measurements, slices were loaded with drug (isoproterenol, mavacamten, sotagliflozin, or empagliflozin) or vehicle (DMSO) and work loop analysis was repeated, allowing each slice to serve as its own control. Mixed effects linear regression models incorporating random effects for heart and slice and fixed effects for clinical characteristics evaluated determinants of myocardial work and drug response across loading conditions. ResultsA total of 120 LMS from 32 individuals (16 non-failing and 16 HCM) were analyzed. At baseline, myocardial work was positively associated with younger age, hypertension, and ejection fraction. Ketone supplementation augmented work and work-strain slope particularly in HCM LMS at high afterloads. We validated our drug testing methodology by demonstrating increased work with known positive inotrope isoproterenol, decreased work with negative inotrope mavacamtem most pronounced in HCM LMS, and a null effect of DMSO. Acute exposure to SGLTi sotagliflozin and empagliflozin directly reduced myocardial work, with increased potency of sotagliflozin at high afterloads. ConclusionsOur LMS platform enables assessment of myocardial mechanics across controlled loading conditions and is an ideal platform to rigorously phenotype human myocardial tissue and interrogate direct effects of pharmacologic intervention. We demonstrate that SGLTi and ketones have distinct and discordant effects on human myocardial contractility.

physiology↗

bioRxiv2025

Adolescent intermittent ethanol exacerbates Aβ with age in the dorsal hippocampus of female TgF344-AD rats.

BackgroundAlcohol misuse increases Alzheimers disease (AD) risk, however the mechanisms linking these conditions are unknown. In rodents, chronic and acute ethanol increases amyloid-{beta} (A{beta}), however those studies have been limited to a single sex or brain region. ObjectiveThis study explored how adolescent intermittent ethanol (AIE), alters A{beta} in multiple regions of the brain in female and male TgF344-AD rats as they age. MethodsFrom P28-P58, female and male TgF344-AD rats were administered either water (CON) or 5.0 g/kg ethanol (AIE; 20% ethanol w/v) via intragastric gavage on a 2-day on/off cycle. In Experiment 1, A{beta} was measured in the medial prefrontal cortex (mPFC), orbitofrontal cortex (OFC), piriform cortex (PC), entorhinal cortex (EC), ventral hippocampus (vHPC), and dorsal hippocampus (dHPC) in 6- and 10-month-old rats. In Experiment 2, in vivo microdialysis was used in 3-month-old female rats to measure how ethanol directly modulates A{beta} levels in the dHPC. ResultsIn the OFC, PC, EC, vHPC, and dHPC, A{beta}40 and A{beta}42 was higher in 6-month-old female TgF344-AD rats compared to males. However, at 10 months A{beta}40 and A{beta}42 levels were only elevated in the dHPC of AIE-treated females, compared to all other groups. An acute ethanol challenge at 3 months selectively evoked a sustained increase in ISF A{beta}40 levels in AIE-treated females. ConclusionsIn aged females, the dHPC is a region sensitive to ethanol-associated A{beta} pathology. This may be due to disruptions in A{beta} clearance in early life, which may have an additive effect on A{beta} aggregation over the lifespan.

neuroscience↗

bioRxiv2025

Investigating the role of long non-coding RNA in hypertrophic cardiomyopathy

Long non-coding RNA (lncRNA) are transcripts that do not typically code for protein but have essential roles in the regulation of transcription and translation in health and disease. The objective of this study was to identify potential lncRNAs that could play a role in the pathophysiology of hypertrophic cardiomyopathy (HCM). We analyzed RNA-Seq data for lncRNA expression from a mouse model of HCM and cross-referenced transcripts to a published human HCM tissue dataset. We identified a total of 9,140 lncRNA transcripts in the mouse dataset, of which 35 were differentially expressed between transgenic TNNT2 {Delta}160 mice (TG) and non-transgenic mice (nTG, p-adj < 0.05). Of these, 13 had a human ortholog as predicted by ortho2align. We used the computational tools MiPepid, AlphaFold, and PhyloCSF to predict potential micropeptides that could be coded for by these 13 mouse lncRNAs. We found that predicted micropeptides from 3 of these lncRNAs-G730003C15Rik, 9830004L10Rik, and Gm45012-have higher AlphaFold folding confidence metrics than random peptides or truly non-coding lncRNA negative controls (p < 0.05). Another 2 of these lncRNAs, 6330403L08Rik and 2900072N19Rik, have positive PhyloCSF scores, also indicating micropeptide coding potential. In summary, we developed a computational workflow to identify differentially expressed lncRNAs in a mouse model of HCM that can be prioritized for future experimental studies based on their cross-species conservation and micropeptide coding potential. NEW & NOTEWORTHYThis is the first analysis of RNA-Seq data for lncRNA expression in an HCM mouse model and the first cross-species analysis of HCM lncRNA RNA-Seq data. Additionally, this study demonstrated a novel computational pipeline that combines several tools-RNA-Seq, MiPepid, AlphaFold, and PhyloCSF-to identify potential lncRNAs of interest from RNA-Seq data.

bioinformatics↗

bioRxiv2022

An unbiased screen identified the Hsp70-BAG3 complex as a regulator of myosin binding protein C3 stability.

Structured AbstractO_ST_ABSObjectiveC_ST_ABSWe aim to identify regulators of myosin binding protein C3 (MyBP-C) protein homeostasis. BackgroundVariants in myosin binding protein C3 (MYBPC3) account for approximately 50% of familial hypertrophic cardiomyopathy (HCM). Most pathogenic variants in MYBPC3 are truncating variants that lead to reduced total levels of MyBP-C protein. Elucidation of the pathways that regulate MyBP-C protein homeostasis could uncover new therapeutic strategies that restore normal protein levels. MethodWe developed a high-throughput screen to identify compounds that can increase or decrease steady-state levels of MyBP-C in an induced pluripotent stem cell cardiomyocyte (iPSC-CM) model derived from a patient with HCM. To normalize results, we also monitored effects on myosin heavy chain (MYH) and focused on those molecules that selectively modulated MyBP-C levels. ResultsScreening a library of 2,426 known biologically active compounds, we identified compounds which either decreased (241/2426, 9.9%) or increased (29/2426, 1.2%) MyBP-C/MYH levels. After a rigorous validation process, including a counter screen for cellular toxicity, two compounds (JG98 and parthenolide) were confirmed as decreasing MyBP-C levels and no compounds were confirmed to increase MyBP-C levels. For further studies, we focused on JG98, which is an allosteric modulator of heat shock protein 70 (Hsp70), inhibiting its interaction with BAG domain co-chaperones. We found that genetic reduction of BAG3 phenocopies treatment with JG98 by reducing MyBP-C protein levels. ConclusionAn unbiased compound screen identified the Hsp70-BAG3 complex as a regulator of MyBP-C stability. Thus, approaches that stimulate this complexs function may be beneficial in the treatment of HCM. Highlights- Hypertrophic cardiomyopathy (HCM) is commonly caused by pathogenic MYBPC3 variants that reduce total wild-type MyBP-C (the protein encoded by MYBPC3). - It is critical to understand the regulators of MyBP-C protein homeostasis to uncover novel therapeutic strategies. - We developed and executed a high-throughput chemical screen in iPSC-CMs to identify compounds which alter steady-state levels of MyBP-C protein, revealing two compounds, JG98 and parthenolide, that significantly reduced MyBP-C levels. - Validation studies suggest that the complex between heat shock protein 70 (Hsp70) and its co-chaperone BAG3 is a dynamic regulator of MyBP-C stability, suggesting that this axis could be a new therapeutic target for HCM.

cell biology↗

bioRxiv2022

Ethanol exposure alters Alzheimer's-related pathology, behavior, and metabolism

Chronic ethanol exposure can increase amyloid-{beta} (A{beta}) and tau in rodent models of Alzheimers-disease (AD)-like pathology, yet the underlying mechanisms are poorly understood. In this study, a moderate two-bottle choice drinking paradigm was used to identify how chronic ethanol exposure alters A{beta}-related pathology, metabolism, and behavior. Complementary in vivo microdialysis experiments were used to measure how acute ethanol directly modulates A{beta} in the hippocampal interstitial fluid (ISF). Ethanol-exposed APPswe/PSEN1dE9 (APP/PS1) mice showed increased brain atrophy and an increased number of amyloid plaques. Further analysis revealed that ethanol exposure led to a shift in the distribution of plaque size in the cortex and hippocampus. Ethanol-exposed mice developed a greater number of smaller plaques, potentially setting the stage for increased plaque proliferation in later life. Ethanol also induced changes in N-methyl-D-aspartate and {gamma}-aminobutyric acid type-A receptor (NMDAR and GABAAR, respectively) expression, possibly reflecting changes in the excitatory and inhibitory (E/I) balance in the brain. Ethanol exposure also led to a diurnal shift in feeding behavior which was associated with changes in glucose homeostasis and glucose intolerance. Ethanol exposure also exacerbated alterations in the open-field test and deficits in nest-building behaviors in APP/PS1mice. Lastly, an acute dose of ethanol bidirectionally altered hippocampal ISF A{beta} levels - decreasing during the initial exposure and increasing during withdrawal. Acute ethanol exposure increased hippocampal ISF glucose levels, suggesting changes in cerebral glucose metabolism occur in response to ethanol. These experiments indicate that ethanol exacerbates an AD-like phenotype by altering A{beta} deposition, behavior, and metabolism. Here, even a moderate drinking paradigm culminates in an interaction between alcohol use and AD-related phenotypes with a potentiation of AD-related pathology, behavioral dysfunction, and metabolic impairment. HighlightsO_LIChronic ethanol exposure increases brain atrophy in APP/PS1 mice. C_LIO_LIChronic ethanol exposure increased the number of plaques in the brains of APP/PS1 mice. C_LIO_LIChronic ethanol exposure led to dysregulated metabolism in APP/PS1 mice. C_LIO_LIChronic ethanol exposure altered anxiety- and dementia-related behaviors in APP/PS1 mice. C_LIO_LIAcute ethanol exposure bidirectionally alters interstitial fluid (ISF) levels of amyloid-{beta} in APP/PS1 mice during exposure and withdrawal. C_LI

neuroscience↗

bioRxiv2021

Sulfonylureas target the neurovascular response to decrease Alzheimer's pathology

Hyperexcitability is a defining feature of Alzheimers disease (AD), where aberrant neuronal activity is both a cause and consequence of AD. Therefore, identifying novel targets that modulate cellular excitability is an important strategy for treating AD. ATP-sensitive potassium (KATP) channels are metabolic sensors that modulate cellular excitability. Sulfonylureas are KATP channel antagonists traditionally used to combat hyperglycemia in diabetic patients by inhibiting pancreatic KATP channels, thereby stimulating insulin release. However, KATP channels are not limited to the pancreas and systemic modulation of KATP channels has pleotropic physiological effects, including profound effects on vascular function. Here, we demonstrate that human AD patients have higher cortical expression of vascular KATP channels, important modulators of vasoreactivity. We demonstrate that peripheral treatment with the sulfonylurea and KATP channel inhibitor, glyburide, reduced the aggregation and activity-dependent production of amyloid-beta (A{beta}), a hallmark of AD, in mice. Since glyburide does not readily cross the blood brain barrier, our data suggests that glyburide targets vascular KATP channel activity to reduce arterial stiffness, improve vasoreactivity, and normalize pericyte-endothelial cell morphology, offering a novel therapeutic target for AD. Graphical abstractTargeting vascular KATP channel activity for the treatment of Alzheimers disease pathology. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

neuroscience↗

bioRxiv2020

Computational prediction of protein subdomain stability in MYBPC3 enables clinical risk stratification in hypertrophic cardiomyopathy and enhances variant interpretation.

PurposeVariants in MYBPC3 causing loss-of-function are the most common cause of HCM. However, a substantial number of patients carry missense variants of uncertain significance (VUS) in MYBPC3. We hypothesize that a structural-based algorithm, STRUM, which estimates the effect of missense variants on protein folding, will improve clinical risk stratification of patients with HCM and a MYBPC3 VUS. MethodsAmong 7,963 patients in the multi-center Sarcomeric Human Cardiomyopathy Registry, 120 unique missense VUSs in MYBPC3 were identified. Variants were evaluated for their effect on subdomain folding and a stratified time-to-event analysis for an overall composite endpoint (first occurrence of ventricular arrhythmia, heart failure, all-cause mortality, atrial fibrillation, and stroke) was performed for patients with HCM and a MYBPC3 missense VUS. ResultsWe demonstrated that patients carrying a MYBPC3 VUS predicted to cause subdomain misfolding (STRUM +, {Delta}{Delta}G [≤]-1.2 kcal/mol) exhibited a higher rate of adverse events compared to those with a STRUM-VUS (Hazard Ratio=2.29, P=0.0282). In silico saturation mutagenesis of MYBPC3 identified 4,943/23,427 (21%) missense variants that were predicted to cause subdomain misfolding. ConclusionsSTRUM enables clinical risk stratification of patients with HCM and a MYBPC3 VUS and has the capacity to improve prognostic predictions and clinical decision making.

genetics↗

bioRxiv2020

Mediterranean Diet, Stress Resilience, and Aging in Nonhuman Primates

Persistent psychological stress increases the risk of many chronic diseases of aging. Little progress has been made to effectively reduce stress responses or mitigate stress effects suggesting a need for better understanding of factors that influence stress responses. Limited evidence suggests that diet may be a factor in modifying the effects of stress. However, long-term studies of diet effects on stress reactive systems are not available, and controlled randomized clinical trials are difficult and costly. Here we report the outcomes of a controlled, randomized preclinical trial of the effects of long-term consumption (31 months, [~] equivalent to 9 human years) of Western versus Mediterranean - like diets on behavioral and physiological responses to acute (brief social separation) and chronic (social subordination) psychosocial stress in 38 adult, socially-housed, female cynomolgus macaques. Compared to animals fed a Western diet, those fed the Mediterranean diet exhibited enhanced stress resilience as indicated by lower sympathetic activity, brisker and more overt heart rate responses to acute stress, more rapid recovery, and lower cortisol responses to acute psychological stress and adrenocorticotropin (ACTH) challenge. Furthermore, age-related increases in sympathetic activity and cortisol responses to stress were delayed by the Mediterranean diet. Population level diet modification in humans has been shown to be feasible. Our findings suggest that population-wide adoption of a Mediterranean-like diet pattern may provide a cost-effective intervention on psychological stress and promote healthy aging with the potential for widespread efficacy. HighlightsO_LIThere is no population level treatment to reduce stress and associated disease. C_LIO_LIMediterranean diet reduced sympathetic activity. C_LIO_LIMediterranean diet reduced cortisol response to acute stress and to ACTH challenge. C_LIO_LIMediterranean diet delayed age-related increases in sympathetic activity and cortisol responses to stress. C_LIO_LIThese results suggest a dietary strategy to increase stress resilience. C_LI

physiology↗

bioRxiv2020

Disease-specific variant pathogenicity prediction significantly improves variant interpretation in inherited cardiac conditions

BackgroundAccurate discrimination of benign and pathogenic rare variation remains a priority for clinical genome interpretation. State-of-the-art machine learning tools are useful for genome-wide variant prioritisation but remain imprecise. Since the relationship between molecular consequence and likelihood of pathogenicity varies between genes with distinct molecular mechanisms, we hypothesised that a disease-specific classifier may outperform existing genome-wide tools. MethodsWe present a novel disease-specific variant classification tool, CardioBoost, that estimates the probability of pathogenicity for rare missense variants in inherited cardiomyopathies and arrhythmias, trained with variants of known clinical effect. To benchmark against state-of-the-art genome-wide pathogenicity classification tools, we assessed classification of hold-out test variants using both overall performance metrics, and metrics of high-confidence (>90%) classifications relevant to variant interpretation. We further evaluated the prioritisation of variants associated with disease and patient clinical outcomes, providing validations that are robust to potential mis-classification in gold-standard reference datasets. ResultsCardioBoost has higher discriminating power than published genome-wide variant classification tools in distinguishing between pathogenic and benign variants based on overall classification performance measures with the highest area under the Precision-Recall Curve as 91% for cardiomyopathies and as 96% for inherited arrhythmias. When assessed at high-confidence (>90%) classification thresholds, prediction accuracy is improved by at least 120% over existing tools for both cardiomyopathies and arrhythmias, with significantly improved sensitivity and specificity. Finally, CardioBoost improves prioritisation of variants significantly associated with disease, and stratifies survival of patients with cardiomyopathies, confirming biologically relevant variant classification. ConclusionsWe demonstrate that a disease-specific variant pathogenicity prediction tool outperforms state-of-the-art genome-wide tools for the classification of rare missense variants of uncertain significance for inherited cardiac conditions. To facilitate evaluation of CardioBoost, we provide pre-computed pathogenicity scores for all possible rare missense variants in genes associated with cardiomyopathies and arrhythmias (https://www.cardiodb.org/cardioboost/). Our results also highlight the need to develop and evaluate variant classification tools focused on specific diseases and clinical application contexts. Our proposed model for assessing variants in known disease genes, and the use of application-specific evaluations, is broadly applicable to improve variant interpretation across a wide range of Mendelian diseases.

genetics↗

bioRxiv2019

Type-2-diabetes alters CSF but not plasma metabolomic and AD risk profiles in vervet monkeys

Epidemiological studies suggest that individuals with type 2 diabetes (T2D) have a 2-4 fold increased risk for developing Alzheimers disease (AD), however the exact mechanisms linking the two disease is unknown. In both conditions, the majority of pathophysiological changes (including glucose and insulin dysregulation, insulin resistance, and AD-related changes in A{beta} and tau) occur decades before the onset of clinical symptoms and diagnosis. In this study, we investigated the relationship between metabolic biomarkers associated with T2D and AD-related pathology, including A{beta} levels, from cerebrospinal fluid (CSF) and fasting plasma of healthy, prediabetic (PreD), and T2D vervet monkeys (Chlorocebus aethiops sabeus). Consistent with the human disease, T2D monkeys have increased plasma and CSF glucose levels as they transition from normoglycemia to pre-diabetic and diabetic states. Although plasma levels of acylcarnitines and amino acids remained largely unchanged, peripheral hyperglycemia correlated with decreased CSF acylcarnitines and CSF amino acids, including branched chain amino acid (BCAA) concentrations, suggesting profound changes in cerebral metabolism coincident with systemic glucose dysregulation. Moreover, CSF A{beta}40 and CSF A{beta}42 levels decreased in T2D monkeys, a phenomenon observed in the human course of AD which coincides with increased amyloid deposition within the brain. In agreement with our previous studies in mice, CSF A{beta}40 and CSF A{beta}42 were highly correlated with CSF glucose levels, suggesting that glucose levels in the brain are associated with changes in A{beta} metabolism. Interestingly, CSF A{beta}40 and CSF A{beta}42 levels were also highly correlated with plasma but not CSF lactate levels, suggesting that plasma lactate might serve as a potential biomarker of disease progression in AD. Moreover, CSF glucose and plasma lactate levels were correlated with CSF amino acid and acylcarnitine levels, demonstrating alterations in cerebral metabolism occurring with the onset of T2D. Together, these data suggest that peripheral metabolic changes associated with the development of T2D produce alterations in brain metabolism that lead to early changes in the amyloid cascade, similar to those observed in pre-symptomatic AD.

neuroscience↗

bioRxiv2018

Quantitative approaches to variant classification increase the yield and precision of genetic testing in Mendelian diseases: The case of hypertrophic cardiomyopathy

BackgroundInternational guidelines for variant interpretation in Mendelian disease set stringent criteria to report a variant as (likely) pathogenic, prioritising control of false positive rate over test sensitivity and diagnostic yield. Genetic testing is also more likely informative in individuals with well-characterised variants from extensively studied European-ancestry populations. Inherited cardiomyopathies are relatively common Mendelian diseases that allow empirical calibration and assessment of this framework.\n\nResultsWe compared rare variants in large hypertrophic cardiomyopathy (HCM) cohorts to reference populations to identify variant classes with high prior likelihoods of pathogenicity, as defined by etiological fraction (EF). Analysis of variant distribution identified regions in which variants are significantly enriched in cases and variant location was a better discriminator of pathogenicity than generic computational functional prediction algorithms. Non-truncating variant classes with an EF[≥]0.95, and therefore clinically actionable, were identified in 5 established HCM genes. Applying this approach leads to an estimated 14-20% increase in cases with actionable HCM variants.\n\nConclusionsWhen found in a patient confirmed to have disease, novel variants in some genes and regions are empirically shown to have a sufficiently high probability of pathogenicity to support a \"likely pathogenic\" classification, even without additional segregation or functional data. This could increase the yield of high confidence actionable variants, consistent with the framework and recommendations of current guidelines. The techniques outlined offer a consistent, unbiased and equitable approach to variant interpretation for Mendelian disease genetic testing. We propose adaptations to ACMG/AMP guidelines to incorporate such evidence in a quantitative and transparent manner.

genetics↗