Biology subjects

Shah, S. J.

Publications and source records attributed to Shah, S. J..

6 recordsLinked to original sources

bioRxiv2025

Multiomics Integration Reveals a Metabolic Myopathy in Cardiometabolic HFpEF

BackgroundSkeletal muscle dysfunction is a major peripheral determinant of exercise intolerance and physical disability in heart failure with preserved ejection fraction (HFpEF). Metabolic and mitochondrial dysfunction are considered to be key components of skeletal muscle dysfunction, but comprehensive profiling of metabolic pathways has not been conducted. Elucidation of dysregulated metabolic pathways is essential to determine viable targets for the treatment of exercise intolerance in HFpEF. MethodsMale ZSF1 Obese rats (HFpEF) and Wistar Kyoto (WKY) lean normotensive controls were studied at 26 weeks of age. Gastrocnemius was subjected to bulk RNA-seq, proteomics, metabolomics, and lipidomics analysis. The R package limma was used to determine differential expression in all omics layers (absolute fold-change>1.5, FDR0.05, unless otherwise indicated). Additional targeted plasma and skeletal muscle (soleus and EDL) metabolomics and lipidomics were performed on HFpEF and control rats. ResultsPathway level analysis for RNA seq and proteomics revealed significant downregulation of oxidative phosphorylation (NES -2.1, p<0.005), electron transport chain (NES -2.0, p<0.005), and TCA cycle (-1.8, p<0.05). The most upregulated pathways were PPAR signaling (NES 2.2, p<0.0001), tryptophan metabolism (NES 1.8, P<0.005), and amino acid oxidation (NES 1.8, p<0.005) pathways. Metabolomics revealed an accumulation of TCA cycle intermediate, isocitrate, and phosphate reduction. Branched-chain amino acids were significantly increased, whereas amino acids related to tryptophan metabolism were reduced and shifted towards increased serotonin accumulation. Phospholipid species were differentially regulated with increased palmitoylated phosphatidylcholines but reduced arachidonoyl-PC species. Phosphatidylethanolamines (PE) species (16:0/16:1-18:0/18:2) were increased. ConclusionOur multiomics analysis of skeletal muscle in HFpEF revealed severe mitochondrial dysfunction that was characterized by reduced complex I and II activity. Mitochondrial and peroxisomal lipid overload results in a shift in membrane phospholipid accumulation and composition. Reduced BCAA oxidation and dysregulation of tryptophan metabolism are key features of amino acid metabolism that reduce anaplerosis and promote the accumulation of toxic metabolites. Comparative analysis of other skeletal muscle disorders suggests that an acquired metabolic myopathy exists in cardiometabolic HFpEF.

physiology↗

bioRxiv2024

Dysregulation of Nitrosylation Dynamics Promotes Nitrosative Stress and Contributes to Cardiometabolic Heart Failure with Preserved Ejection Fraction

BackgroundRecent reports suggest increased myocardial iNOS expression leads to excessive protein s-nitrosylation, contributing to the pathophysiology of HFpEF. However, the relationship between NO bioavailability, dynamic regulation of protein s-nitrosylation by trans- and de-nitrosylases, and HFpEF pathophysiology has not been elucidated. Here, we provide novel insights into the delicate interplay between NO bioavailability and protein s-nitrosylation in HFpEF. MethodsPlasma nitrite, nitrosothiols (RsNO), and 3-nitrotyrosine (3-NT) were measured in HFpEF patients and in controls. Studies in WKY or ZSF1 obese rats were performed to evaluate HFpEF severity, NO signaling, and total nitroso-species (Rx(s)NO) levels. snRNA sequencing was performed to identify key genes involved in NO signaling and s-nitrosylation regulation. ResultsIn HFpEF patients, circulating RsNO and 3-NT were significantly elevated while nitrite, a biomarker for NO bioavailability, remained unchanged. In ZSF1 obese rats, NO bioavailability was significantly reduced while Rx(s)NO levels exhibited an age-dependent increase as HFpEF progressed. snRNA seq highlighted significant upregulation of a trans-nitrosylase, hemoglobin-beta subunit (HBb), which was corroborated in human HFpEF hearts1. Subsequent experiments confirmed HBb upregulation and revealed significant reductions in enzyme activity of two major de-nitrosylases, Trx2 and GSNOR in ZSF1 obese hearts. Further, elevated RxNO levels, increased HBb expression, and reduced activity of Trx2 and GSNOR were identified in the kidney and liver of the ZSF1 obese rats. ConclusionsOur data reveal circulating markers of nitrosative stress (RsNO and 3-NT) are significantly elevated in HFpEF patients. Data from the ZSF1 obese rat model mirror the results from HFpEF patients and reveal that pathological accumulation of RxNO/nitrosative stress in HFpEF may be in part, due to the upregulation of the trans-nitrosylase, HBb, and impaired activity of the de-nitrosylases, Trx2 and GSNOR. Our data suggest that dysregulated protein nitrosylation dynamics in the heart, liver, and kidney contribute to the pathogenesis of cardiometabolic HFpEF. Translational PerspectiveOur findings describe for the first time that circulating RsNO and 3-NT are significantly upregulated in HFpEF patients suggesting systemic nitrosative stress in HFpEF, and demonstrate a profound disconnect between insufficient physiological NO signaling and pathological nitrosative stress in HFpEF, which is in stark contrast to HFrEF in which both NO bioavailability and protein s-nitrosylation are attenuated. Further, this study provides novel mechanistic insights into a critical molecular feature of HFpEF in humans and animal models: nitrosative stress arises predominantly from imbalance of trans-nitrosylases and de-nitrosylases, thereby leading to impaired NO bioavailability concomitant with increased protein s-nitrosylation. Importantly, these perturbations extend beyond the heart to the kidney and liver, suggesting HFpEF is characterized by a systemic derangement in trans- and de-nitrosylase activity and providing a unifying molecular lesion for the systemic presentation of HFpEF pathophysiology. These findings have direct clinical implications for the modulation of NO levels in the HFpEF patient, and indicate that restoring the balance between trans- and denitrosylases may be novel therapeutic targets to ameliorate disease symptoms in HFpEF patients.

physiology↗

bioRxiv2020

Hyperactive end joining repair mediates resistance to DNA damaging therapy in p53-deficient cells

TP53 mutations in cancer are associated with poor patient outcomes and resistance to DNA damaging therapies1-3. However, the mechanisms underlying treatment resistance in p53-deficient cells remain poorly characterized. Here, we show that p53-deficient cells exhibit hyperactive repair of therapy-induced DNA double strand breaks (DSBs), which is suppressed by inhibition of DNA-dependent protein kinase (DNA-PK). Single-cell analyses of DSB repair kinetics and cell cycle state transitions reveal an essential role for DNA-PK in suppressing S phase DNA damage and mitotic catastrophe in p53-deficient cells. Yet, a subset of p53-deficient cells exhibit intrinsic resistance to therapeutic DSBs due to a repair pathway that is not sensitive to DNA-PK inhibition. We show that p53 deficiency induces overexpression of DNA Polymerase Theta (Pol {theta}), which mediates an alternative end-joining repair pathway that becomes hyperactivated by DNA-PK inhibition4. Combined inhibition of DNA-PK and Pol {theta} restores therapeutic DNA damage sensitivity in p53-deficient cells. Thus, our study identifies two targetable DSB end joining pathways that can be suppressed as a strategy to overcome resistance to DNA-damaging therapies in p53-deficient cancers.

cell biology↗

bioRxiv2018

Host factors influence the sex of nematodes parasitizing roots of Arabidopsis thaliana

Plant-parasitic cyst nematodes induce hypermetabolic syncytial nurse cells in the roots of their host plants. Syncytia are their only food source. Cyst nematodes are sexually dimorphic, with their differentiation into male or female strongly influenced by host environmental conditions. Under favorable conditions with plenty of nutrients, more females develop, whereas mainly male nematodes develop under adverse conditions such as in resistant plants. Here, we developed and validated a method to predict the sex of beet cyst nematode (Heterodera schachtii) during the early stages of its parasitism in the host plant Arabidopsis thaliana. We collected root segments containing male-associated syncytia (MAS) or female-associated syncytia (FAS), isolated syncytial cells by laser microdissection, and performed a comparative transcriptome analysis. Genes belonging to categories of defense, nutrient deficiency, and nutrient starvation were overrepresented in MAS as compared to FAS. Conversely, gene categories related to metabolism, modification, and biosynthesis of cell walls were overrepresented in FAS. We used {beta}-glucuronidase (GUS) analysis, qRT-PCR, and loss-of-function mutants to characterize FAS- and MAS-specific candidate genes. Our results demonstrated that various plant-based factors, including immune response, nutrient availability, and structural modifications, influence the sexual fate sex determination of cyst the nematodes.

plant biology↗

bioRxiv2017

Machine Learning of the Cardiac Phenome and Skin Transcriptome to Categorize Heart Disease in Systemic Sclerosis

BackgroundCardiac involvement is a leading cause of death in systemic sclerosis (SSc/scleroderma). The complexity of SSc cardiac manifestations is not fully captured by the current clinical SSc classification, which is based on extent of skin involvement and specific autoantibodies. Therefore, we sought to develop a clinically relevant SSc cardiac disease classification to improve clinical care and increase understanding of SSc cardiac disease pathobiology. We hypothesized that machine learning could identify novel SSc cardiac disease subgroups, and that gene expression assessment of skin could provide insights into molecular pathogenesis of these SSc pheno-groups.\n\nMethodsWe used unsupervised model-based clustering (phenomapping) of SSc patient echocardiographic and clinical data to identify clinically relevant SSc pheno-groups in a discovery cohort (n=316), and validated these findings in an external SSc validation cohort (n=67). Cox regression was used to evaluate survival differences among groups. Gene expression profiles from skin biopsies from a subset of SSc patients (n=68) and controls (n=18) were analyzed with weighted gene co-expression network analyses to identify gene modules that were associated with cardiac pheno-groups and echocardiographic parameters.\n\nResultsFour SSc cardiac pheno-groups were identified with distinct profiles. Pheno-group #1 displayed a predominant cutaneous phenotype without cardiac involvement; pheno-group #2 had long-standing SSc with limited skin and cardiac involvement; pheno-group #3 had diffuse skin involvement, a high frequency of interstitial lung disease (88%), and significant right heart remodeling/dysfunction; and pheno-group #4 had prolonged SSc disease duration, limited skin involvement, and marked biventricular cardiac involvement. After multivariable adjustment, pheno-group #3 (hazard ratio [HR] 7.8, 95% confidence interval [CI] 1.5-33.0) and pheno-group #4 (HR 10.5, 95% CI 2.1-52.7) remained associated with mortality (P<0.05). The addition of pheno-group classification was additive to conventional survival models (P<0.05 by likelihood ratio test for all models), a finding that was replicated in the validation cohort. Skin gene expression analysis identified 2 gene modules (representing fibrosis and skin integrity, respectively) that differed among the cardiac pheno-groups and were associated with specific echocardiographic parameters.\n\nConclusionsMachine learning of echocardiographic and skin gene expression data in SSc identifies clinically relevant subgroups with distinct cardiac phenotypes, survival, and associated molecular pathways in skin.

genomics↗

bioRxiv2017

Parent of Origin Effects on Quantitative Phenotypes in a Founder Population

The impact of the parental origin of associated alleles in GWAS has been largely ignored. Yet sequence variants could affect traits differently depending on whether they are inherited from the mother or the father. To explore this possibility, we studied 21 quantitative phenotypes in a large Hutterite pedigree. We first identified variants with significant single parent (maternal-only or paternal-only) effects, and then used a novel statistical model to identify variants with opposite parental effects. Overall, we identified parent of origin effects (POEs) on 11 phenotypes, most of which are risk factors for cardiovascular disease. Many of the loci with POEs have features of imprinted regions and many of the variants with POE are associated with the expression of nearby genes. Overall, our results indicate that POEs, which are often opposite in direction, are relatively common in humans, have potentially important clinical effects, and will be missed in traditional GWAS.

genetics↗