Metabolic responses of shrimp Palaemonetes sinensis to isopod Tachaea chinensis parasitization

2020 ◽  
Vol 138 ◽  
pp. 227-235 ◽  
Author(s):  
Y Li ◽  
W Xu ◽  
X Li ◽  
Z Han ◽  
R Zhang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Inflammatory Responses ◽  
Grass Shrimp ◽  
Enrichment Analysis ◽  
Tca Cycle ◽  
Metabolic Responses ◽  
Pathway Enrichment Analysis ◽  
Primary Metabolite ◽  
Mineral Absorption ◽  
Host Interaction

Tachaea chinensis, a parasitic isopod, negatively affects the production of several commercially important shrimp species in China. The mechanism of parasite-host interaction cannot be accurately described by transcriptomic and proteomic approaches individually. Here, comparative metabolite profiling was used to achieve a broad coverage of primary metabolite changes in Chinese grass shrimp Palaemonetes sinensis following T. chinensis parasitization. In total, 66 metabolites were significantly differentially accumulated between the control and infected groups; of these, 19 were upregulated and 47 were downregulated after T. chinensis infection. Moreover, the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that 10 pathways were significantly enriched. The protein digestion and absorption pathways were highly enriched, followed by the mineral absorption, aminoacyl-tRNA biosynthesis, biosynthesis of amino acids, and metabolic metabolism pathways. Parasitization by T. chinensis enhanced the glycolytic pathway and tricarboxylic acid (TCA) cycle in P. sinensis, thereby releasing more energy for swimming, foraging, and evading predation. Glucogenic amino acids such as alanine, histidine, glutamine, and proline were consumed to generate glutamate and enhance the TCA cycle. Nucleotide-related metabolic pathways were downregulated, possibly because T. chinensis can secrete molecules to degrade nucleotides and inhibit hemostasis and inflammatory responses. These results suggest that the isopod parasite can increase the host’s metabolic burden by enhancing the host’s TCA cycle and secreting molecules to degrade host proteins, thereby enabling the parasite to feed on the host and inhibit an inflammatory response. The results will be a valuable contribution to understanding the metabolic responses of crustaceans to isopod parasitism.

scholarly journals Metabolic responses to elevated pCO2 in the gills of the Pacific Oyster (Magallana gigas) using a GC-TOF-MS-based metabolomics approach

2018 ◽  
Author(s):  
Zengjie Jiang ◽  
Xiaoqin Wang ◽  
Samuel P.S. Rastrick ◽  
Jinghui Fang ◽  
Meirong Du ◽  
...  
Keyword(s):  
Atmospheric Carbon Dioxide ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Tca Cycle ◽  
Potential Effect ◽  
Metabolic Responses ◽  
Pathway Enrichment Analysis ◽  
Human Fossil ◽  
Flight Mass Spectrometry ◽  
Tof Ms

Rising atmospheric carbon dioxide (CO2), primarily from human fossil fuel combustion and cement production, are resulting in increasing absorption of CO2 by the oceans, which has led to a decline in ocean pH in a process known as ocean acidification (OA). There is a growing body of evidence demonstrating the potential effect of OA on life-history traits of marine organisms. Consequently, gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) based metabolic profiling approach was applied to examine the metabolic responses of Magallana gigas to elevated pCO2 levels, under otherwise natural field conditions. CO2. Oysters were exposed natural environmental pCO2 (~625.40 μatm) and elevated pCO2 (~1432.94 μatm) levels for 30 days. Results indicated that 36 differential metabolites with variable importance in the projection (VIP) value greater than 1 and Student's t-test lower than 0.05 were identified. Differential metabolites were mapped in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to search for the related metabolic pathways. Pathway enrichment analysis indicates that alanine, aspartate and glutamate metabolism and glycine, serine and threonine metabolism were the most statistically enriched pathways. Further analysis suggested that elevated pCO2 disturb the TCA cycle via succinate accumulation and Magallana gigas most likely adjust their energy metabolic via alanine and GABA accumulation accordingly to cope with elevated pCO2. These findings provide an understanding of the molecular mechanisms involved in modulating metabolism under elevated pCO2 levels associated with predicted OA.

scholarly journals Metabolic responses to elevated pCO2 in the gills of the Pacific Oyster (Magallana gigas) using a GC-TOF-MS-based metabolomics approach

2018 ◽  
Author(s):  
Zengjie Jiang ◽  
Xiaoqin Wang ◽  
Samuel P.S. Rastrick ◽  
Jinghui Fang ◽  
Meirong Du ◽  
...  
Keyword(s):  
Atmospheric Carbon Dioxide ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Tca Cycle ◽  
Potential Effect ◽  
Metabolic Responses ◽  
Pathway Enrichment Analysis ◽  
Human Fossil ◽  
Flight Mass Spectrometry ◽  
Tof Ms

Rising atmospheric carbon dioxide (CO2), primarily from human fossil fuel combustion and cement production, are resulting in increasing absorption of CO2 by the oceans, which has led to a decline in ocean pH in a process known as ocean acidification (OA). There is a growing body of evidence demonstrating the potential effect of OA on life-history traits of marine organisms. Consequently, gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) based metabolic profiling approach was applied to examine the metabolic responses of Magallana gigas to elevated pCO2 levels, under otherwise natural field conditions. CO2. Oysters were exposed natural environmental pCO2 (~625.40 μatm) and elevated pCO2 (~1432.94 μatm) levels for 30 days. Results indicated that 36 differential metabolites with variable importance in the projection (VIP) value greater than 1 and Student's t-test lower than 0.05 were identified. Differential metabolites were mapped in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to search for the related metabolic pathways. Pathway enrichment analysis indicates that alanine, aspartate and glutamate metabolism and glycine, serine and threonine metabolism were the most statistically enriched pathways. Further analysis suggested that elevated pCO2 disturb the TCA cycle via succinate accumulation and Magallana gigas most likely adjust their energy metabolic via alanine and GABA accumulation accordingly to cope with elevated pCO2. These findings provide an understanding of the molecular mechanisms involved in modulating metabolism under elevated pCO2 levels associated with predicted OA.

scholarly journals Bioinformatics-Based Study to Investigate Potential Differentially Expressed Genes and miRNAs in Hashimoto’s Thyroiditis

2021 ◽  
Author(s):  
Li Guoquan ◽  
Du Junwei ◽  
He Qi ◽  
Fu Xinghao ◽  
Ji Feihong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Inflammatory Responses ◽  
Expression Profiles ◽  
Treatment Options ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Chronic Lymphocytic Thyroiditis ◽  
Hub Genes

Abstract BackgroundHashimoto's thyroiditis (HT), also known as chronic lymphocytic thyroiditis, is a common autoimmune disease, which mainly occurs in women. The early manifestation was hyperthyroidism, however, hypothyroidism may occur if HT was not controlled for a long time. Numerous studies have shown that multiple factors, including genetic, environmental, and autoimmune factors, were involved in the pathogenesis of the disease, but the exact mechanisms were not yet clear. The aim of this study was to identify differentially expressed genes (DEGs) by comprehensive analysis and to provide specific insights into HT. MethodsTwo gene expression profiles (GSE6339, GSE138198) about HT were downloaded from the Gene Expression Omnibus (GEO) database. The DEGs were assessed between the HT and normal groups using the GEO2R. The DEGs were then sent to the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The hub genes were discovered using Cytoscape and CytoHubba. Finally, NetworkAnalyst was utilized to create the hub genes' targeted microRNAs (miRNAs). ResultsA total of 62 DEGs were discovered, including 60 up-regulated and 2 down-regulated DEGs. The signaling pathways were mainly engaged in cytokine interaction and cytotoxicity, and the DEGs were mostly enriched in immunological and inflammatory responses. IL2RA, CXCL9, IL10RA, CCL3, CCL4, CCL2, STAT1, CD4, CSF1R, and ITGAX were chosen as hub genes based on the results of the protein-protein interaction (PPI) network and CytoHubba. Five miRNAs, including mir-24-3p, mir-223-3p, mir-155-5p, mir-34a-5p, mir-26b-5p, and mir-6499-3p, were suggested as likely important miRNAs in HT. ConclusionsThese hub genes, pathways and miRNAs contribute to a better understanding of the pathophysiology of HT and offer potential treatment options for HT.

scholarly journals Bioinformatics Analysis Reveals the Potential Diagnostic Biomarkers for Abdominal Aortic Aneurysm

2021 ◽  
Vol 8 ◽  
Author(s):  
Xinsheng Xie ◽  
En ci Wang ◽  
Dandan Xu ◽  
Xiaolong Shu ◽  
Yu fei Zhao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Bioinformatics Analysis ◽  
Inflammatory Responses ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Aortic Aneurysms ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Abdominal Aortic

Objectives: Abdominal aortic aneurysms (AAAs) are associated with high mortality rates. The genes and pathways linked with AAA remain poorly understood. This study aimed to identify key differentially expressed genes (DEGs) linked to the progression of AAA using bioinformatics analysis.Methods: Gene expression profiles of the GSE47472 and GSE57691 datasets were acquired from the Gene Expression Omnibus (GEO) database. These datasets were merged and normalized using the “sva” R package, and DEGs were identified using the limma package in R. The functions of these DEGs were assessed using Cytoscape software. We analyzed the DEGs using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Protein–protein interaction networks were assembled using Cytoscape, and crucial genes were identified using the Cytoscape plugin, molecular complex detection. Data from GSE15729 and GSE24342 were also extracted to verify our findings.Results: We found that 120 genes were differentially expressed in AAA. Genes associated with inflammatory responses and nuclear-transcribed mRNA catabolic process were clustered in two gene modules in AAA. The hub genes of the two modules were IL6, RPL21, and RPL7A. The expression levels of IL6 correlated positively with RPL7A and negatively with RPL21. The expression of RPL21 and RPL7A was downregulated, whereas that of IL6 was upregulated in AAA.Conclusions: The expression of RPL21 or RPL7A combined with IL6 has a diagnostic value for AAA. The novel DEGs and pathways identified herein might provide new insights into the underlying molecular mechanisms of AAA.

scholarly journals EXPRESS: Metabolic Endophenotype Associated with Right Ventricular Glucose Uptake in Pulmonary Hypertension

2021 ◽  
pp. 204589402110543
Author(s):  
Samar Farha ◽  
Suzy Comhair ◽  
Yuan Hou ◽  
Margaret Park ◽  
Jacqueline Sharp ◽  
...  
Keyword(s):  
Pulmonary Hypertension ◽  
Glucose Uptake ◽  
Global Longitudinal Strain ◽  
Hypoxia Inducible Factor ◽  
Enrichment Analysis ◽  
Tca Cycle ◽  
Pathway Enrichment Analysis ◽  
Nitric Oxide Metabolism ◽  
Positron Emission ◽  
Interactome Network

Alterations in metabolism and bioenergetics are hypothesized in the mechanisms leading to pulmonary vascular remodeling and heart failure in pulmonary hypertension (PH). To test this, we performed metabolomic analyses on 30 PH individuals and 12 controls. Furthermore, using 2-[18F]fluoro-2-deoxy-D-glucose positron emission tomography (FDG-PET), we dichotomized PH patients into metabolic phenotypes of high and low right ventricle (RV) glucose uptake and followed them longitudinally. In support of metabolic alterations in PH and its progression, the high RV glucose group had higher RVSP (p < 0.001), worse RV function as measured by RV fractional area change and peak global longitudinal strain (both p < 0.05) and may be associated with poorer outcomes (33% death or transplantation in the high glucose RV uptake group compared to 7% in the low RV glucose uptake group at 5 years follow up, log-ranked p = 0.07). Pathway enrichment analysis identified key metabolic pathways including fructose catabolism, arginine-nitric oxide metabolism, tricarboxylic acid (TCA) cycle, and ketones metabolism. Integrative human protein-protein interactome network analysis of metabolomic and transcriptomic data identified key pathobiological pathways: arginine biosynthesis, TCA cycle, purine metabolism, hypoxia-inducible factor 1 and apelin signaling. These findings identify a PH metabolomic endophenotype, and for the first time link this to disease severity and outcomes.

scholarly journals Combination of Systems Pharmacology and Experimental Evaluation to Explore the Mechanism of Synergistic Action of Frankincense-Myrrh in the Treatment of Cerebrovascular Diseases

2022 ◽  
Vol 12 ◽  
Author(s):  
Yucheng Liao ◽  
Jingwen Wang ◽  
Chao Guo ◽  
Min Bai ◽  
Bowei Ju ◽  
...  
Keyword(s):  
Target Genes ◽  
Inflammatory Responses ◽  
Infarct Volume ◽  
Blood Stasis ◽  
Enrichment Analysis ◽  
Cerebrovascular Diseases ◽  
Pathway Enrichment Analysis ◽  
Systems Pharmacology

Frankincense-Myrrh is a classic drug pair that promotes blood circulation, and eliminates blood stasis. The combination of the two drugs has a definite clinical effect on the treatment of cerebrovascular diseases (CBVDs), but its mechanism of action and compatibility have not been elucidated. In this study, the bioactive components, core targets, and possible synergistic mechanisms of Frankincense-Myrrh in the treatment of CBVDs are explored through systems pharmacology combined with in vivo and in vitro experiments. Comparing target genes of components in Frankincense and Myrrh with CBVD-related genes, common genes were identified; 15 core target genes of Frankincense-Myrrh for the treatment of CBVDs were then identified using protein-protein interaction (PPI) analysis. It was also predicted through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis that the molecular mechanism of Frankincense-Myrrh action on CBVDs was mainly related to the regulation of neurotrophic factors and inflammatory responses. Frankincense-Myrrh significantly improved neurological function, decreased infarct volume, alleviated histopathological damage, inhibited microglial expression, and promoted the expression of neurons in middle cerebral artery occlusion (MCAO)-induced rats. The results of this study not only provide important theoretical support and experimental basis for the synergistic effect of Frankincense-Myrrh, but also provide new ideas for the prevention and treatment of cerebral ischemic injuries.

scholarly journals Investigating the Multi-Target Pharmacological Mechanism of Rhodiola Wallichiana Var. Cholaensis Acting on Angina Pectoris by Combined Network Pharmacology and Molecular Docking

2021 ◽  
Author(s):  
Haitao Zhang ◽  
Xudong Zhuang ◽  
Zhixiong Li ◽  
Xinrui Wang
Keyword(s):  
Molecular Docking ◽  
Angina Pectoris ◽  
Inflammatory Responses ◽  
Experimental Studies ◽  
Enrichment Analysis ◽  
Microvascular Dysfunction ◽  
Binding Potential ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Systematic Analysis

Abstract Background: Angina pectoris is a kind of cardiovascular disease, which is caused by epicardial stenosis, microvascular dysfunction, dynamic stenosis area contraction or more comprehensive factors, eventually leading to Coronary artery disease. Rhodiola wallichiana var. cholaensis, which is one of the most well-known Traditional Chinese Medicine, is widely used to treat angina pectoris. However, the possible underlying mechanisms remain to be elucidated.Methods: In this study, systematic and comprehensive network pharmacology and molecular docking were utilized for the first time to reveal the potential pharmacological mechanisms of RW on AP. Firstly, the relative compounds were obtained by mining literature and potential targets of these compounds by target predicting were collected. Then, We built the AP target database using the DigSee and GeneCards Database. Based on the data, GO and KEGG pathway enrichment analysis, protein-protein interaction (PPI) analysis were performed and screen the hub targets by topology. Furthermore, evaluation of the binding potential of key targets and compounds through molecular docking.Results: The results indicate that 218 known RW therapeutic targets were selected. By systematic analysis, identified 9 hub targets (VEGFA, GAPDH, TP53, AKT1, CASP3, STAT3, TNF, MAPK1 and JUN) mainly involved in the complex treating effects associated with the protection of vascular endothelium, as well as the regulation of glucose metabolism, cellular processes, inflammatory responses, and cellular signal transduction.Conclusion: The results of this study preliminarily explain the potential targets and signaling pathways of RW in AP therapy and lay a good foundation for further experimental studies and clinical trials.

scholarly journals Dysregulated paired related homeobox 1 impacts on hepatocellular carcinoma phenotypes

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Weronika Piorońska ◽  
Zeribe Chike Nwosu ◽  
Mei Han ◽  
Michael Büttner ◽  
Matthias Philip Ebert ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Overall Survival ◽  
Cell Lines ◽  
Transcriptional Control ◽  
Epithelial Mesenchymal Transition ◽  
Enrichment Analysis ◽  
Tca Cycle ◽  
Pathway Enrichment Analysis ◽  
Mesenchymal Transition ◽  
Cancer Hallmarks

Abstract Background Hepatocellular carcinoma (HCC) is a major cause of cancer-related death. Paired related homeobox 1 (PRRX1) is a transcription factor that regulates cell growth and differentiation, but its importance in HCC is unclear. Methods We examined the expression pattern of PRRX1 in nine microarray datasets of human HCC tumour samples (n > 1100) and analyzed its function in HCC cell lines. In addition, we performed gene set enrichment, Kaplan-Meier overall survival analysis, metabolomics and functional assays. Results PRRX1 is frequently upregulated in human HCC. Pathway enrichment analysis predicted a direct correlation between PRRX1 and focal adhesion and epithelial-mesenchymal transition. High expression of PRRX1 and low ZEB1 or high ZEB2 significantly predicted better overall survival in HCC patients. In contrast, metabolic processes correlated inversely and transcriptional analyses revealed that glycolysis, TCA cycle and amino acid metabolism were affected. These findings were confirmed by metabolomics analysis. At the phenotypic level, PRRX1 knockdown accelerated proliferation and clonogenicity in HCC cell lines. Conclusions Our results suggest that PRRX1 controls metabolism, has a tumour suppressive role, and may function in cooperation with ZEB1/2. These findings have functional relevance in HCC, including in understanding transcriptional control of distinct cancer hallmarks.

scholarly journals Metabolomic Analysis of Aqueous Humor Identifies Aberrant Amino Acid and Fatty Acid Metabolism in Vogt-Koyanagi-Harada and Behcet’s Disease

2021 ◽  
Vol 12 ◽  
Author(s):  
Jing Xu ◽  
Guannan Su ◽  
Xinyue Huang ◽  
Rui Chang ◽  
Zhijun Chen ◽  
...  
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Behçet’S Disease ◽  
Aqueous Humor ◽  
Behcet’S Disease ◽  
Behçet's Disease ◽  
Enrichment Analysis ◽  
Control Group ◽  
Pathway Enrichment Analysis ◽  
Behcet's Disease

To investigate aqueous metabolic profiles in Vogt-Koyanagi-Harada (VKH) and Behcet’s disease (BD), we applied ultra-high-performance liquid chromatography equipped with quadrupole time-of flight mass spectrometry in aqueous humor samples collected from these patients and controls. Metabolite levels in these three groups were analyzed by univariate logistic regression. The differential metabolites were subjected to subsequent pathway analysis by MetaboAnalyst. The results showed that both partial-least squares discrimination analysis and hierarchical clustering analysis showed specific aqueous metabolite profiles when comparing VKH, BD, and controls. There were 28 differential metabolites in VKH compared to controls and 29 differential metabolites in BD compared to controls. Amino acids and fatty acids were the two most abundant categories of differential metabolites. Furthermore, pathway enrichment analysis identified several perturbed pathways, including pantothenate and CoA biosynthesis when comparing VKH with the control group, and D-arginine and D-ornithine metabolism and phenylalanine metabolism when comparing BD with the control group. Aminoacyl-tRNA biosynthesis was altered in both VKH and BD when compared to controls. Our findings suggest that amino acids metabolism as well as two fatty acids, palmitic acid and oleic acid, may be involved in the pathogenesis of BD and VKH.

scholarly journals Metabolomic and Proteomic Analyses of Persistent Valvular Atrial Fibrillation and Non-Valvular Atrial Fibrillation

2021 ◽  
Vol 12 ◽  
Author(s):  
Bo Hu ◽  
Wen Ge ◽  
Yuliang Wang ◽  
Xiaobin Zhang ◽  
Tao Li ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Enrichment Analysis ◽  
Heart Rhythm ◽  
Tca Cycle ◽  
Inorganic Pyrophosphatase ◽  
Pathway Enrichment Analysis ◽  
Increased Risk ◽  
Novel Biomarkers ◽  
Glycerol 3 Phosphate Dehydrogenase ◽  
Altered Proteins

Atrial fibrillation (AF) is an abnormal heart rhythm related to an increased risk of heart failure, dementia, and stroke. The distinction between valvular and non-valvular AF remains a debate. In this study, proteomics and metabolomics were integrated to describe the dysregulated metabolites and proteins of AF patients relative to sinus rhythm (SR) patients. Totally 47 up-regulated and 41 down-regulated proteins in valvular AF, and 59 up-regulated and 149 down-regulated proteins in non-valvular AF were recognized in comparison to SR patients. Moreover, 58 up-regulated and 49 significantly down-regulated metabolites in valvular AF, and 47 up-regulated and 122 down-regulated metabolites in persistent non-valvular AF patients were identified in comparison to SR patients. Based on analysis of differential levels of metabolites and proteins, 15 up-regulated and 22 down-regulated proteins, and 13 up-regulated and 122 down-regulated metabolites in persistent non-valvular AF were identified relative to valvular AF. KEGG pathway enrichment analysis showed the altered proteins and metabolites were significantly related to multiple metabolic pathways, such as Glycolysis/Gluconeogenesis. Interestingly, the enrichment pathways related to non-valvular AF were obviously different from those in valvular AF. For example, valvular AF was significantly related to Glycolysis/Gluconeogenesis, but non-valvular AF was more related to Citrate cycle (TCA cycle). Correlation analysis between the differentially expressed proteins and metabolites was also performed. Several hub proteins with metabolites were identified in valvular AF and non-valvular AF. For example, Taurine, D-Threitol, L-Rhamnose, and DL-lactate played crucial roles in valvular AF, while Glycerol-3-phosphate dehydrogenase, Inorganic pyrophosphatase 2, Hydroxymethylglutaryl-CoAlyase, and Deoxyuridine 5-triphosphate nucleotidohydrolase were crucial in non-valvular AF. Then two hub networks were recognized as potential biomarkers, which can effectively distinguish valvular AF and non-valvular persistent AF from SR samples, with areas under curve of 0.75 and 0.707, respectively. Hence, these metabolites and proteins can be used as potential clinical molecular markers to discriminate two types of AF from SR samples. In summary, this study provides novel insights to understanding the mechanisms of AF progression and identifying novel biomarkers for prognosis of non-valvular AF and valvular AF by using metabolomics and proteomics analyses.

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