Divergent transcriptomic profiles in skeletal muscle of diabetics with and without heart failure

2021 ◽  
Vol 28 (Supplement_1) ◽  
Author(s):  
N Wood ◽  
CW Cheng ◽  
S Straw ◽  
M Scalabrin ◽  
E Espino-Gonzalez ◽  
...  
Keyword(s):  
Heart Failure ◽  
Skeletal Muscle ◽  
Pathway Analysis ◽  
Enrichment Analysis ◽  
Left Ventricular Ejection ◽  
Rt Pcr ◽  
Lipid Signalling ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Skeletal Muscle Transcriptome

Abstract Funding Acknowledgements Type of funding sources: None. Background Patients with type 2 diabetes mellitus (DM) that have coexistent heart failure (HF) have exacerbated symptoms and prognosis, however beside cardiac dysfunction the mechanisms governing these features are incompletely understood. Evidence indicates abnormalities in the periphery could contribute to this worse clinical phenotype, including a role for skeletal muscle whereby disturbances in the transcriptome could disrupt muscle homeostasis/repair to offer a novel therapeutic approach. Purpose Is the skeletal muscle transcriptome distinguishable between DM patients with and without HF? Methods DM patients without (n = 11) or with HF with reduced left ventricular ejection fraction (LVEF) (n = 16) were included. Muscle biopsies were collected from the pectoralis major during pacemaker implantation. Following RNA extraction and cDNA synthesis, non-bias RNA sequencing (RNAseq) was performed (Cambridge Genomic Services, UK) followed by targeted RT-PCR gene expression of relevant targets. DESeq2 identified differentially expressed genes (DEGs) with a false discovery rate (p < 0.05). Gene enrichment analysis was performed with clusterProfiler v3.16.0 to interrogate the gene ontology database, while pathway analysis was conducted using ReactomePA v1.32.0 to interrogate the Reactome database, using an adjusted p value. Values of p < 0.05 were accepted as significant. Results Groups were not different (p > 0.05) for age (74 ± 11 vs. 66 ± 10 years), BMI (31 ± 7 vs 29 ± 6), sex (n = 2 females per group), or HbA1c (56 ± 10 vs. 57 ± 8 mmol/mol), although LVEF was lower in the group with HF (27 ± 8 vs. 54 ± 2%; p < 0.05).  Of the 19,544 genes analysed, RNAseq identified 53 DEGs between DM patients with and without HF, with several relevant targets related to myofiber homeostasis such as autophagy (RUBCN), protein synthesis (DGKζ), and inflammation/apoptosis (TLE1). Follow-up RT-PCR analysis confirmed a trend towards upregulation of the autophagy-related machinery p62 (p = 0.043) and BNIP3 (p = 0.085) in the HF group, but not ubiquitin-proteasome (MuRF1, MAFbx; p > 0.05). Gene-enrichment analysis of DEGs identified 7 overrepresented terms (P < 0.05), including lipid metabolism/signalling alongside epigenetic modifications related to histone deacetylases (HDAC6/10). Furthermore, pathway analysis identified 4 terms (p < 0.05) related to NOTCH signalling and phosphatidyl inositol-bisphosphate (PIP2) hydrolysis thus indicating alterations to muscle repair and lipid signalling respectively. Conclusion(s): This study confirms that DM patients with and without HF demonstrate distinct skeletal muscle transcriptome profiles. Key differences related to skeletal muscle myogenesis, autophagy, epigenetic regulation, and lipid signalling were identified that could form part of important therapeutic targets. Whether these underlying muscle transcriptome differences contribute to poorer clinical outcomes in DM patients with HF remains to be determined.

scholarly journals Differentially Expressed Circular Non-coding RNAs in Atherosclerotic Aortic Vessels and Their Potential Functions in Endothelial Injury

2021 ◽  
Vol 8 ◽  
Author(s):  
Houwei Li ◽  
Xue Liu ◽  
Na Sun ◽  
Tianshuo Wang ◽  
Jia Zhu ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Enrichment Analysis ◽  
Potential Functions ◽  
Endothelial Injury ◽  
Differentially Expressed ◽  
Vascular Endothelial ◽  
Rt Pcr ◽  
Potential Target ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment

Background: Circular non-coding RNA (circRNA) has a variety of biological functions. However, the expression profile and potential effects of circRNA on atherosclerosis (AS) and vascular endothelial injury have not been fully elucidated. This study aims to identify the differentially expressed circRNAs in atherosclerotic aortic vessels and predict their potential functions in endothelial injury.Method: ApoE-/- mice were fed with high-fat diet for 12 weeks to induce AS. Atherosclerotic plaques were evaluated by H&E and Masson staining and immunohistochemistry; differentially expressed circRNAs were detected by Arraystar Circular RNA Microarray and verified by RT-PCR; the potential target mircoRNAs of circRNAs were predicted by miRanda, Tarbase, Targetscan and their expression changes were verified by RT-PCR; the potential target genes of mircoRNAs were predicted by Targetscan and verified by Western blot; the signaling pathways that they might annotate or regulate and their potential functions in vascular endothelial injury were predicted by gene enrichment analysis.Results: Fifty two circRNAs were up-regulated more than twice and 47 circRNAs were down-regulated more than 1.5 times in AS aortic vessels. Mmmu_circRNA_36781 and 37699 were up-regulated both in AS aortic vessels and H2O2-treated mouse aortic endothelial cells (MAECs). The expression of miR-30d-3p and miR-140-3p, the target microRNA of circRNA_37699 and circRNA_36781, were downregulated both in AS vessels and H2O2-treated MAECs. On the contrary, MKK6 and TP53RK, the potential target gene of miR-140-3p and miR-30d-3p, were upregulated both in AS aortic roots and H2O2-treated MAECs. Besides, gene enrichment analysis showed that MAPK and PI3K-AKT signaling pathway were the most potential signaling pathways regulated by the differentially expressed circRNAs in atherosclerosis.Conclusions: Mmu_circRNA_36781 (circRNA ABCA1) and 37699 (circRNA KHDRBS1) were significantly up-regulated in AS aortic vessels and H2O2-treated MAECs. They have potential regulatory effects on atherosclerosis and vascular endothelial injury by targeting miR-30d-3p-TP53RK and miR-140-3p-MKK6 axis and their downstream signaling pathways.

scholarly journals Effect of flapless osteoperforation-assisted tooth movement on atrophic alveolar ridge: Histomorphometric and gene-enrichment analysis

2017 ◽  
Vol 88 (1) ◽  
pp. 82-90 ◽  
Author(s):  
Ji-Won Lee ◽  
Jung-Yul Cha ◽  
Ki-Ho Park ◽  
Yoon-Goo Kang ◽  
Su-Jung Kim
Keyword(s):  
Signaling Pathway ◽  
Tooth Movement ◽  
Osteoclast Differentiation ◽  
Wnt Signaling Pathway ◽  
Enrichment Analysis ◽  
Tissue Response ◽  
Alveolar Ridge ◽  
Mineral Density ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment

ABSTRACT Objective: To investigate the effect of flapless osteoperforation on the tissue response of the atrophic alveolar ridge affected by orthodontic tooth movement (OTM). Materials and Methods: An atrophic alveolar ridge model was established in the mandibular quadrants of eight beagle dogs. As a split-mouth design, the quadrants were randomly divided into group C (OTM only) and group OP (OTM with flapless osteoperforation). The rate of OTM for 10 weeks was compared between groups, and micro-CT-based histomorphometric analysis and RNA-sequencing-based gene-enrichment analysis were performed targeting the atrophic ridge. Results: Group OP displayed more rapid tooth movement with lower bone mineral density and higher trabecular fraction in the atrophic ridge than did group C, showing no intergroup difference of total ridge volume. As contributing biological functional pathways in group OP, the genes related to osteoclast differentiation and TNF signaling pathway were up-regulated and those associated with Wnt signaling pathway and AMPK signaling pathway were down-regulated. Conclusions: Flapless osteoperforation facilitated the rate of OTM toward the atrophic ridge, maintaining low bone density, whereas it did not increase the volume of the atrophic ridge.

Abstract 12549: Circulating Irisin is a Novel Biomarker Providing Prognostic Information in Patients With Heart Failure With Reduced Ejection Fraction

Circulation ◽  
2014 ◽  
Vol 130 (suppl_2) ◽  
Author(s):  
Shinsuke Hanatani ◽  
Yasuhiro Izumiya ◽  
Yuichi Kimura ◽  
Yoshiro Onoue ◽  
Satoshi Araki ◽  
...  
Keyword(s):  
Heart Failure ◽  
Skeletal Muscle ◽  
Ejection Fraction ◽  
Disease Severity ◽  
Cardiovascular Events ◽  
Roc Analysis ◽  
Left Ventricular Ejection ◽  
Prognostic Information ◽  
Reduced Ejection Fraction ◽  
One Year

Introduction: Reduced skeletal muscle function link to poor prognosis in patients with chronic heart failure (HF). Irisin is a newly identified muscle-derived protein found in human serum. The gene expression of irisin precursor fibronectin domain containing protein 5 in skeletal muscle is associated with exercise tolerance in HF patients. Hypothesis: Irisin could be a useful biomarker for disease severity and future adverse cardiovascular events in patients with HF with reduced ejection fraction (HFrEF). Methods and results: We measured serum irisin levels in 84 patients with HFrEF. HFrEF was defined as left ventricular ejection fraction≦50% and meet the Framingham criteria of HF. Serum irisin concentrations were measured by ELISA. The endpoint of this study was a composite of total mortality, cardiovascular hospitalization and coronary revascularization. Serum irisin levels were negatively correlated with serum high sensitive troponin T levels (r=-0.24, p=0.048). Right heart catheterization revealed that serum irisin levels had significant negative correlation with pulmonary capillary wedge pressure (r=-0.23, p=0.044). In receiver operating characteristic (ROC) analysis, cut-off values of irisin and BNP for prediction of one-year events were 55.548 ng/mL and 324.8 pg/mL, respectively. Kaplan Meier curve demonstrated that the event-free rate was decreased in the low irisin (≦cut-off value) group (log-rank test p=0.024). The combination of low irisin and high BNP (≧cut-off value) identified patients with a significantly higher probability of adverse events (p=0.008). Multivariate Cox hazard analysis identified low levels of irisin (≦cut-off value) (hazard ratio [HR]: 3.08; 95% confidence interval [CI]: 1.31-7.21, p=0.01) and ischemic etiology (HR: 3.32; 95% CI: 1.50-7.35, p=0.003) as independent predictors of mortality and cardiovascular events. ROC analysis revealed that irisin achieved an area under the curve (AUC) of 0.67 for one-year events (p=0.031), and that the AUC increased when irisin was added to BNP level (alone: 0.64, BNP+irisin: 0.74). Conclusions: Irisin could be a useful biomarker for evaluating disease severity and providing incremental prognostic information in patients with HFrEF.

scholarly journals Clinical Response to Personalized Exercise Therapy in Heart Failure Patients with Reduced Ejection Fraction Is Accompanied by Skeletal Muscle Histological Alterations

2019 ◽  
Vol 20 (21) ◽  
pp. 5514 ◽  
Author(s):  
Tatiana Lelyavina ◽  
Victoria Galenko ◽  
Oksana Ivanova ◽  
Margarita Komarova ◽  
Elena Ignatieva ◽  
...  
Keyword(s):  
Heart Failure ◽  
Skeletal Muscle ◽  
Ejection Fraction ◽  
Clinical Response ◽  
Exercise Therapy ◽  
Left Ventricular ◽  
Exercise Intolerance ◽  
Left Ventricular Ejection ◽  
Histological Alterations ◽  
Before And After

Heart failure (HF) is associated with skeletal muscle wasting and exercise intolerance. This study aimed to evaluate the exercise-induced clinical response and histological alterations. One hundred and forty-four HF patients were enrolled. The individual training program was determined as a workload at or close to the lactate threshold (LT1); clinical data were collected before and after 12 weeks/6 months of training. The muscle biopsies from eight patients were taken before and after 12 weeks of training: histology analysis was used to evaluate muscle morphology. Most of the patients demonstrated a positive response after 12 weeks of the physical rehabilitation program in one or several parameters tested, and 30% of those showed improvement in all four of the following parameters: oxygen uptake (VO2) peak, left ventricular ejection fraction (LVEF), exercise tolerance (ET), and quality of life (QOL); the walking speed at LT1 after six months of training showed a significant rise. Along with clinical response, the histological analysis detected a small but significant decrease in both fiber and endomysium thickness after the exercise training course indicating the stabilization of muscle mechanotransduction system. Together, our data show that the beneficial effect of personalized exercise therapy in HF patients depends, at least in part, on the improvement in skeletal muscle physiological and biochemical performance.

scholarly journals Decomposing the Mechanism of Qishen Granules in the Treatment of Heart Failure by a Quantitative Pathway Analysis Method

Molecules ◽  
2018 ◽  
Vol 23 (7) ◽  
pp. 1829 ◽  
Author(s):  
Weiquan Ren ◽  
Sheng Gao ◽  
Huimin Zhang ◽  
Yinglu Ren ◽  
Xue Yu ◽  
...  
Keyword(s):  
Heart Failure ◽  
Energy Metabolism ◽  
Pathway Analysis ◽  
Ventricular Remodeling ◽  
Left Ventricular ◽  
Left Ventricular Ejection ◽  
Therapeutic Effects ◽  
Analysis Tool ◽  
Ventricular Ejection Fraction ◽  
Pathway Analysis Tool

Qishen granules (QSG) have beneficial therapeutic effects for heart failure, but the effects of decomposed recipes, including Wenyang Yiqi Huoxue (WYH) and Qingre Jiedu (QJ), are not clear. In this study, the efficacy of WYH and QJ on heart failure is evaluated by using transverse aortic constriction (TAC) induced mice and the significantly changed genes in heart tissues were screened with a DNA array. Furthermore, a new quantitative pathway analysis tool is developed to evaluate the differences of pathways in different groups and to identify the pharmacological contributions of the decomposed recipes. Finally, the related genes in the significantly changed pathways are verified by a real-time polymerase chain reaction and a Western blot. Our data show that both QJ and WYH improve the left ventricular ejection fraction, which explain their contributions to protect against heart failure. In the energy metabolism, QJ achieves the therapeutic effects of QSG through nicotinamide nucleotide transhydrogenase (Nnt)-mediated mechanisms. In ventricular remodeling and inflammation reactions, QJ and WYH undertake the therapeutic effects through 5′-nucleotidase ecto (Nt5e)-mediated mechanisms. Together, QJ and WYH constitute the therapeutic effects of QSG and play important roles in myocardial energy metabolism and inflammation, which can exert therapeutic effects for heart failure.

scholarly journals Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions

2008 ◽  
Vol 36 (7) ◽  
pp. e43-e43 ◽  
Author(s):  
K. De Preter ◽  
R. Barriot ◽  
F. Speleman ◽  
J. Vandesompele ◽  
Y. Moreau
Keyword(s):  
High Resolution ◽  
Enrichment Analysis ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Gene Sets

scholarly journals A Network Pharmacology Approach to Uncover the Multiple Mechanisms of Hedyotis diffusa Willd. on Colorectal Cancer

2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Xinkui Liu ◽  
Jiarui Wu ◽  
Dan Zhang ◽  
Kaihuan Wang ◽  
Xiaojiao Duan ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Network Analysis ◽  
Chinese Herb ◽  
Endocrine System ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Hedyotis Diffusa

Background. As one of the most frequently diagnosed cancer diseases globally, colorectal cancer (CRC) remains an important cause of cancer-related death. Although the traditional Chinese herb Hedyotis diffusa Willd. (HDW) has been proven to be effective for treating CRC in clinical practice, its definite mechanisms have not been completely deciphered. Objective. The aim of our research is to systematically explore the multiple mechanisms of HDW on CRC. Methods. This study adopted the network pharmacology approach, which was mainly composed of active component gathering, target prediction, CRC gene collection, network analysis, and gene enrichment analysis. Results. The network analysis showed that 10 targets might be the therapeutic targets of HDW on CRC, namely, HRAS, PIK3CA, KRAS, TP53, APC, BRAF, GSK3B, CDK2, AKT1, and RAF1. The gene enrichment analysis implied that HDW probably benefits patients with CRC by modulating pathways related to cancers, infectious diseases, endocrine system, immune system, nervous system, signal transduction, cellular community, and cell motility. Conclusions. This study partially verified and predicted the pharmacological and molecular mechanism of HDW against CRC from a holistic perspective, which will also lay a foundation for the further experimental research and clinical rational application of HDW.

scholarly journals Network pharmacology-based elucidation of the molecular mechanism underlying the anti-migraine effect of Asari Radix et Rhizoma

2021 ◽  
Vol 18 (10) ◽  
pp. 2067-2074
Author(s):  
Yun-Bin Jiang ◽  
Mei Zhong ◽  
Ting Huang ◽  
Zhong-Hua Dai ◽  
Xing-Bao Tao ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Scientific Basis ◽  
Network Pharmacology ◽  
Overlapping Genes ◽  
Hub Genes ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Tnf Gene

Purpose: To determine the molecular mechanism involved in the anti-migraine effect of Asari Radix et Rhizoma (ARR) using network pharmacology. Methods: The compounds present in ARR were identified through information retrieval from literature and public databases, and were screened based on absorption, distribution, metabolism, excretion and toxicity. Target genes related to the selected compounds and migraine were identified or predicted from public databases. Hub genes in ARR against migraine were identified through analysis of interactions in overlapping genes between compounds and migraine target genes, based on STRING database. Gene enrichment analysis of overlapping genes was performed using Database for Annotation, Visualization and Integrated Discovery. Results: A total of 138 compounds were selected as potential bioactive compounds in ARR. Target genes related to the selected compounds (611 genes) and migraine (278 genes) were obtained, including 71 overlapping genes. The hub genes in the anti-migraine effect of ARR were BDNF, IL6, COMT, APP and TNF. Gene enrichment analysis showed the top 10 biological processes or pathways involved in the mechanism of anti-migraine action of ARR. The tissue source of the overlapping genes was not limited to the brain. The results from gene enrichment analysis revealed that the effect of ARR on migraine was holistic, which is characteristic of traditional Chinese medicines. Conclusion: Network pharmacology has been used to decipher the molecular mechanism involved in the action of ARR against migraine. The results provide a scientific basis for the clinical effect of ARR on migraine.

scholarly journals From Protein Variations to Biological Processes and Pathways with NET-GE

2017 ◽  
Vol 3 (3) ◽  
pp. 45 ◽  
Author(s):  
Samuele Bovo ◽  
Pietro Di Lena ◽  
Pier Luigi Martelli ◽  
Piero Fariselli ◽  
Rita Casadio
Keyword(s):  
Biological Networks ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Biological Processes ◽  
Obsessive Compulsive ◽  
Compulsive Disorder ◽  
Hyperactivity Disorder ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Common Technique

Gene enrichment analysis is a common technique for highlighting molecular pathways and biological processes of a phenotype. Such technique has recently evolved exploiting the information contained in biological networks. We developed NET-GE, a web server for network-based gene enrichment analyses. NET-GE defines functional associations between a list of genes/proteins and biological processes or pathways by identifying function-specific modules in a molecular interaction network. The peculiarity of NET-GE is the possibility to enrich terms not detectable by standard enrichment procedure. Here, we highlight with two specific applications the performances of NET-GE by computing which functional phenotypes can be associated with two different sets of genes related to Attention Deficit Hyperactivity Disorder and to an Obsessive-compulsive disorder, respectively.

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