scholarly journals Comparative proteomics analysis provides new insights into the haustorium development of Taxillus chinensis (DC.) Danser

2021 ◽  
Author(s):  
Limei Pan ◽  
Lingyun Wan ◽  
Lisha Song ◽  
Lili He ◽  
Ni Jiang ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Proteomics Analysis ◽  
Pathway Enrichment ◽  
Qrt Pcr ◽  
Protein Variation ◽  
Phenylpropanoid Biosynthesis ◽  
Itraq Proteomics ◽  
Differentially Abundant Proteins

Abstract Background Loranthus (Taxillus chinensis) is an important medicinal and parasitic plant that attacks other plants for living. To reveal the mechanisms of haustorium development, we employed an iTRAQ proteomics-based approach to identify differentially abundant proteins (DAPs) of fresh seeds (CK), baby (FB), and adult haustoria (FD). Results A total of 563 and 785 DAPs were successfully quantified in the early/later developmental stage, respectively. Pathway enrichment analysis indicated that the DAPs mainly associated with metabolic pathways, ribosome, phenylpropanoid biosynthesis and photosynthesis. In the meantime, DAPs associated with phytohormone signaling pathway changed markedly. Furthermore, we evaluated the contents change of phytohormone during the haustoria development. These results indicated that phytohormone is very important for haustorium development. qRT-PCR validation showed that the mRNA expression levels were consistent with the protein variation, suggesting that our result were reliable. Conclusions To the best of our knowledge, this is the first haustoria proteomes of loranthus, and our findings will improve our understanding of the molecular mechanism of haustoria development.

Identification of novel cardiovascular disease associated metabolites using untargeted metabolomics

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Shams Tabrez ◽  
Mohammed Razeeth Shait Mohammed ◽  
Nasimudeen R. Jabir ◽  
Mohammad Imran Khan
Keyword(s):  
Cardiovascular Disease ◽  
Metabolic Pathways ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Healthy Individuals ◽  
Great Opportunity ◽  
Pathway Enrichment ◽  
Pathophysiological Role ◽  
The World ◽  
Metabolomic Approach

Abstract Cardiovascular disease (CVD) remains the leading cause of morbidity and mortality around the world. Early diagnosis of CVD could provide the opportunity for sensible management and better clinical outcome along with the prevention of further progression of the disease. In the current study, we used an untargeted metabolomic approach to identify possible metabolite(s) that associate well with the CVD and could serve either as therapeutic target or disease-associated metabolite. We identified 26 rationally adjusted unique metabolites that were differentially present in the serum of CVD patients compared with healthy individuals, among them 15 were found to be statistically significant. Out of these metabolites, we identified some novel metabolites like UDP-l-rhamnose and N1-acetylspermidine that have not been reported to be linked with CVD directly. Further, we also found that some metabolites like ethanolamide, solanidine, dimethylarginine, N-acetyl-l-tyrosine, can act as a discriminator of CVD. Metabolites integrating pathway enrichment analysis showed enrichment of various important metabolic pathways like histidine metabolism, methyl histidine metabolism, carnitine synthesis, along with arginine and proline metabolism in CVD patients. Our study provides a great opportunity to understand the pathophysiological role and impact of the identified unique metabolites and can be extrapolated as specific CVD specific metabolites.

scholarly journals Metabolomic Links Between Sweetened Beverage Intake and Obesity (OR31-05-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Chao-Qiang Lai ◽  
Reiko Ichikawa ◽  
Bingjie Zhou ◽  
Laurence Parnell ◽  
Sabrina Noel ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Metabolic Pathways ◽  
Enrichment Analysis ◽  
Health Study ◽  
Pathway Enrichment Analysis ◽  
Linear Regression Models ◽  
Obesity Risk ◽  
Pathway Enrichment ◽  
Sweetened Beverage ◽  
Increased Risk

Abstract Objectives Sweetened beverage (SB) consumption is highly associated with obesity, but the mechanism underlying this correlation is not understood. Our objective was to examine metabolomic links between SB intake and obesity to understand metabolic mechanisms. Methods We examined the association of plasma metabolomic profiles with SB intake and obesity risk in 782 participants, aged 45–75y, in the Boston Puerto Rican Health Study (BPRHS) using linear regression models, controlling for potential confounding factors. Based on identified metabolites, we conducted pathway enrichment analysis to identify potential metabolic pathways that link SB intake and obesity risk. Genetic variants in identified metabolic pathways were examined for their interaction with SB intake on metabolites of interest and obesity. Interactions between SB and genotypes on obesity were evaluated for replication in the Framingham Heart Study (FHS). Results In BPRHS, SB intake was highly correlated with BMI (β = 0.455, P < 0.05). Among 526 measurable metabolites, 109 metabolites showed significant correlation with SB intake and 170 metabolites with BMI (P < 0.05); and 43 were correlated with both SB intake and BMI. Pathway enrichment analysis identified two metabolic pathways: phosphatidylethanolamine (PE) and lysophospholipid pathways linking SB intake and obesity, after correction for multiple testing. Focusing on the PE pathway, we identified 12 SNPs in nine genes that were significantly associated with BMI. At least four genetic variants showed suggestive interaction with SB intake on obesity risk and obesity-associated metabolites. In particular, CC carriers of rs4646360 in the PEMT (Phosphatidylethanolamine N-Methyltransferase) gene had increased risk of obesity when consuming SB. We replicated this finding in the FHS study. Conclusions We identified two key metabolic pathways linking SB intake to obesity, revealing potential mechanisms by which SB intake increases the risk of obesity. The interaction between genetic variants in the identified pathway and SB intake on obesity and obesity-associated metabolites further supports the mechanism. Funding Sources This work was funded by the US Department of Agriculture, under agreement no. 8050-51,000-098-00D, and NIH grants P01 AG023394, P50 HL105185, and R01 AG027087.

scholarly journals Comprehensive Circulatory Metabolomics in ME/CFS Reveals Disrupted Metabolism of Acyl Lipids and Steroids

Metabolites ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 34 ◽  
Author(s):  
Arnaud Germain ◽  
Dinesh K. Barupal ◽  
Susan M. Levine ◽  
Maureen R. Hanson
Keyword(s):  
Metabolic Pathways ◽  
Acid Metabolism ◽  
Enrichment Analysis ◽  
Chronic Fatigue ◽  
Organ System ◽  
Pathway Enrichment Analysis ◽  
Pathway Enrichment ◽  
Fatigue Syndrome ◽  
Organ Systems ◽  
Acyl Lipids

The latest worldwide prevalence rate projects that over 65 million patients suffer from myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), an illness with known effects on the functioning of the immune and nervous systems. We performed an extensive metabolomics analysis on the plasma of 52 female subjects, equally sampled between controls and ME/CFS patients, which delivered data for about 1750 blood compounds spanning 20 super-pathways, subdivided into 113 sub-pathways. Statistical analysis combined with pathway enrichment analysis points to a few disrupted metabolic pathways containing many unexplored compounds. The most intriguing finding concerns acyl cholines, belonging to the fatty acid metabolism sub-pathway of lipids, for which all compounds are consistently reduced in two distinct ME/CFS patient cohorts. We compiled the extremely limited knowledge about these compounds and regard them as promising in the quest to explain many of the ME/CFS symptoms. Another class of lipids with far-reaching activity on virtually all organ systems are steroids; androgenic, progestin, and corticosteroids are broadly reduced in our patient cohort. We also report on lower dipeptides and elevated sphingolipids abundance in patients compared to controls. Disturbances in the metabolism of many of these molecules can be linked to the profound organ system symptoms endured by ME/CFS patients.

scholarly journals Metabolomic Links between Sugar-Sweetened Beverage Intake and Obesity

2020 ◽  
Vol 2020 ◽  
pp. 1-10 ◽  
Author(s):  
Bingjie Zhou ◽  
Reiko Ichikawa ◽  
Laurence D. Parnell ◽  
Sabrina E. Noel ◽  
Xiyuan Zhang ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Multiple Testing ◽  
Enrichment Analysis ◽  
Health Study ◽  
Pathway Enrichment Analysis ◽  
Obesity Risk ◽  
Sugar Sweetened Beverage ◽  
Pathway Enrichment ◽  
Sweetened Beverage ◽  
Increased Risk

Background. Sugar-sweetened beverage (SSB) consumption is highly associated with obesity, but the metabolic mechanism underlying this correlation is not understood. Objective. Our objective was to examine metabolomic links between SSB intake and obesity to understand metabolic mechanisms. Design. We examined the association of plasma metabolomic profiles with SSB intake and obesity risk in 781 participants, aged 45–75 y, in the Boston Puerto Rican Health Study (BPRHS) using generalized linear models, controlling for potential confounding factors. Based on identified metabolites, we conducted pathway enrichment analysis to identify potential metabolic pathways that link SSB intake and obesity risk. Variants in genes encoding enzymes known to function in identified metabolic pathways were examined for their interactions with SSB intake on obesity. Results. SSB intake was correlated with BMI (β = 0.607, P=0.045). Among 526 measured metabolites, 86 showed a significant correlation with SSB intake and 148 with BMI (P≤0.05); 28 were correlated with both SSB intake and BMI (P≤0.05). Pathway enrichment analysis identified the phosphatidylcholine and lysophospholipid pathways as linking SSB intake to obesity, after correction for multiple testing. Furthermore, 8 of 10 genes functioning in these two pathways showed strong interaction with SSB intake on BMI. Our results further identified participants who may exhibit an increased risk of obesity when consuming SSB. Conclusions. We identified two key metabolic pathways that link SSB intake to obesity, revealing the potential of phosphatidylcholine and lysophospholipid to modulate how SSB intake can increase obesity risk. The interaction between genetic variants related to these pathways and SSB intake on obesity further supports the mechanism.

scholarly journals Identification of an EMT-Related Gene Signature for Predicting Overall Survival in Gastric Cancer

2021 ◽  
Vol 12 ◽  
Author(s):  
Weiyu Dai ◽  
Yizhi Xiao ◽  
Weimei Tang ◽  
Jiaying Li ◽  
Linjie Hong ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Cox Regression ◽  
External Validation ◽  
Enrichment Analysis ◽  
Gene Signature ◽  
Time Dependent ◽  
Pathway Enrichment Analysis ◽  
Related Gene ◽  
Pathway Enrichment ◽  
Qrt Pcr

BackgroundIt has been widely reported that epithelial-mesenchymal transition (EMT) is associated with malignant progression in gastric cancer (GC). Integration of the molecules related to EMT for predicting overall survival (OS) is meaningful for understanding the role of EMT in GC. Here, we aimed to establish an EMT-related gene signature in GC.MethodsTranscriptional profiles and clinical data of GC were downloaded from The Cancer Genome Atlas (TCGA). We constructed EMT-related gene signature for predicting OS by using univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses. Time-dependent receiver operating characteristic (ROC), Kaplan-Meier analysis were performed to assess its predictive value. A nomogram combining the prognostic signature with clinical characteristics for OS prediction was established. And its predictive power was estimated by concordance index (C-index), time-dependent ROC curve, calibration curve and decision curve analysis (DCA). GSE62254 dataset from Gene Expression Omnibus (GEO) was used for external validation. Quantitative real-time PCR (qRT-PCR) was used to detected the mRNA expression of the five EMT-related genes in human normal gastric mucosal and GC cell lines. To further understand the potential mechanisms of the signature, Gene Set Enrichment Analysis (GSEA), pathway enrichment analysis, predictions of transcription factors (TFs)/miRNAs were performed.ResultsA novel EMT-related gene signature (including ITGAV, DAB2, SERPINE1, MATN3, PLOD2) was constructed for OS prediction of GC. With external validation, ROC curves indicated the signature’s good performance. Patients stratified into high- and low-risk groups based on the signature yielded significantly different prognosis. Univariate and multivariate Cox regression suggested that the signature was an independent prognostic variable. Nomogram for prognostication including the signature presented better predictive accuracy and clinical usefulness than the similar model without risk score to some extent with external validation. The qRT-PCR assays suggested that high expression of the five EMT-related genes could be found in human GC cell lines compared with normal gastric mucosal cell line. GSEA and pathway enrichment analysis revealed that focal adhesion and ECM-receptor interaction might be the two important pathways to the signature.ConclusionOur EMT-related gene signature may have practical application as an independent prognostic factor in GC.

scholarly journals Bioinformatics analysis and identification of genes and molecular pathways in steroid-induced osteonecrosis of the femoral head

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Tianye Lin ◽  
Weijian Chen ◽  
Peng Yang ◽  
Ziqi Li ◽  
Qiushi Wei ◽  
...  
Keyword(s):  
Femoral Head ◽  
Signaling Pathways ◽  
Signaling Pathway ◽  
Peripheral Blood ◽  
Bioinformatics Analysis ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Ppi Network ◽  
Pathway Enrichment ◽  
Qrt Pcr

Abstract Background Steroid-induced osteonecrosis of the femoral head (ONFH) is a common hip joint disease and is difficult to be diagnosed early. At present, the pathogenesis of steroid-induced ONFH remains unclear, and recognized and effective diagnostic biomarkers are deficient. The present study aimed to identify potentially important genes and signaling pathways involved in steroid-induced ONFH and investigate their molecular mechanisms. Methods Microarray data sets GSE123568 (peripheral blood) and GSE74089 (cartilage) were obtained from the Gene Expression Omnibus database, including 34 ONFH samples and 14 control samples. Morpheus software and Venn diagram were used to identify DEGs and co-expressed DEGs, respectively. Besides, we conducted Kyoto Encyclopedia of Genome (KEGG) and gene ontology (GO) pathway enrichment analysis. We construct a protein-protein interaction (PPI) network through GEO2R and used cytoHubba to divide the PPI network into multiple sub-networks. Additionally, quantitative real-time polymerase chain reaction (qRT-PCR) was performed to verify the bioinformatics analysis results. Results A total of 118 intersecting DEGs were obtained between the peripheral blood and cartilage samples, including 40 upregulated genes and 78 downregulated genes. Then, GO and KEGG pathway enrichment analysis revealed that upregulated DEGs focused on the signaling pathways related to staphylococcus aureus infection, leishmaniasis, antigen processing, and presentation, as well as asthma and graft-versus-host disease. Downregulated genes were concentrated in the FoxO signaling pathway, AMPK signaling pathway, signaling pathway regulating stem cell pluripotency, and mTOR signaling pathway. Some hub genes with high interactions such as CXCR1, FPR1, MAPK1, FOXO3, FPR2, CXCR2, and TYROBP were identified in the PPI network. The results of qRT-PCR demonstrated that CXCR1, FPR1, and TYROBP were upregulated while MAPK1 was downregulated in peripheral blood of steroid-induced ONFH patients. This was consistent with the bioinformatics analysis. Conclusions The present study would provide novel insight into the genes and associated pathways involved in steroid-induced ONFH. CXCR1, FPR1, TYROBP, and MAPK1 may be used as potential drug targets and biomarkers for the diagnosis and prognosis of steroid-induced ONFH.

scholarly journals Microbiome-Metabolome Analyze The Immune Microenvironment of Cecal Contents, Soft and Hard Feces of Hyplus Rabbits

2021 ◽  
Author(s):  
Zhichao Li ◽  
Hui He ◽  
Mengke Ni ◽  
Zhouyan Wang ◽  
Chaohui Guo ◽  
...  
Keyword(s):  
Immune Regulation ◽  
Metabolic Pathways ◽  
Enrichment Analysis ◽  
Short Chain Fatty Acids ◽  
Vital Role ◽  
Pathway Enrichment Analysis ◽  
Immune Microenvironment ◽  
Pathway Enrichment ◽  
Host Growth ◽  
Growth Development

Abstract Background: Intestinal microbiota and its metabolites play a vital role in host growth, development and immune regulation. Methods: This study analyzed the microbial community distribution, cytokines and short chain fatty acids (SCFAs) content of cecal contents (Con) group, soft feces (SF) group and hard feces (HF) group of 140-day-old Hyplus rabbits, and verified the effect of soft feces on cecal immune microenvironment by fasting soft feces.Results: The results showed that there were significant differences in the levels of phylum and genus composition, cytokines and SCFAs among Con group, SF group and HF group. In addition, metabolic pathway enrichment analysis found that there were two significantly up-regulated differential metabolic pathways in SF group and HF group compared with con group, P125-PWY, namely the super pathway of (R, R) - butanediol biosynthesis and P341-PWY, namely the glycolysis V pathway. At the same time, Christensenellaceae_R-7_Group and Lachnoclostridium are significantly enriched in the above two pathways. The correlation analysis of cytokines and SCFAs with differential microbial communities showed that Muribaculaceae and Ruminococcaceae_UCG-014, Ruminococcaceae_NK4A214_group and Christensenellaceae_R-7_Group are closely related to cytokines and SCFAs. After fasting soft feces (CP), the contents of SCFAs and cytokines (IL-4, IL-10) in cecum decreased significantly, while cytokines (TNF-a, IL-1β) increased significantly. The results of multiple immunofluorescence showed that the expression of claudin-1, occludin and ZO-1 related to intestinal immune barrier increased significantly in CP Group. Conclusions: In conclusion, soft feces are not only rich in probiotics and SCFAs, but also play a very important role in improving the immune microenvironment of cecum. This study may provide a valuable reference for the treatment of inflammatory intestinal diseases.

A Method of Pathway Enrichment Analysis Based Gene Expression Variability

2013 ◽  
Vol 40 (12) ◽  
pp. 1256
Author(s):  
XiaoDong JIA ◽  
XiuJie CHEN ◽  
Xin WU ◽  
JianKai XU ◽  
FuJian TAN ◽  
...  
Keyword(s):  
Gene Expression ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Expression Variability ◽  
Pathway Enrichment

Systematic Investigation of Quercetin for Treating Cardiovascular Disease Based on Network Pharmacology

2019 ◽  
Vol 22 (6) ◽  
pp. 411-420 ◽  
Author(s):  
Xian-Jun Wu ◽  
Xin-Bin Zhou ◽  
Chen Chen ◽  
Wei Mao
Keyword(s):  
Cardiovascular Disease ◽  
Cardiovascular Diseases ◽  
Signaling Pathway ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Therapeutic Effects ◽  
Pathway Enrichment ◽  
Compound Target

Aim and Objective: Cardiovascular disease is a serious threat to human health because of its high mortality and morbidity rates. At present, there is no effective treatment. In Southeast Asia, traditional Chinese medicine is widely used in the treatment of cardiovascular diseases. Quercetin is a flavonoid extract of Ginkgo biloba leaves. Basic experiments and clinical studies have shown that quercetin has a significant effect on the treatment of cardiovascular diseases. However, its precise mechanism is still unclear. Therefore, it is necessary to exploit the network pharmacological potential effects of quercetin on cardiovascular disease. Materials and Methods: In the present study, a novel network pharmacology strategy based on pharmacokinetic filtering, target fishing, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, compound-target-pathway network structured was performed to explore the anti- cardiovascular disease mechanism of quercetin. Results:: The outcomes showed that quercetin possesses favorable pharmacokinetic profiles, which have interactions with 47 cardiovascular disease-related targets and 12 KEGG signaling pathways to provide potential synergistic therapeutic effects. Following the construction of Compound-Target-Pathway (C-T-P) network, and the network topological feature calculation, we obtained top 10 core genes in this network which were AKT1, IL1B, TNF, IL6, JUN, CCL2, FOS, VEGFA, CXCL8, and ICAM1. KEGG pathway enrichment analysis. These indicated that quercetin produced the therapeutic effects against cardiovascular disease by systemically and holistically regulating many signaling pathways, including Fluid shear stress and atherosclerosis, AGE-RAGE signaling pathway in diabetic complications, TNF signaling pathway, MAPK signaling pathway, IL-17 signaling pathway and PI3K-Akt signaling pathway.

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