Expression profile analysis of Differentially Expressed Genes in Human Coronary Artery Endothelial Cells Induced by Serum from Kawasaki Disease: A preliminary study

2020 ◽  
Author(s):  
Xue Fan ◽  
Meng Li ◽  
Min Xiao ◽  
Cong Liu ◽  
Mingguo Xu
Keyword(s):  
Endothelial Cells ◽  
Coronary Artery ◽  
Kawasaki Disease ◽  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Healthy Children ◽  
Rna Seq ◽  
Human Coronary Artery

Abstract Background: Kawasaki disease (KD) leads to coronary artery damage and the etiology of KD is unknown. The present study was designed to explore the differentially expressed genes (DEGs) in KD serum-induced human coronary artery endothelial cells (HCAECs) by RNA-sequence (RNA-seq). Methods: HCAECs were stimulated with serum (15% (v/v)), which were collected from 20 healthy children and 20 KD patients, for 24 hours. DEGs were then detected and analyzed by RNA-seq and bioinformatics analysis. Results: The expression of SMAD1, SMAD6, CD34, CXCL1, PITX2, and APLN was validated by qPCR. 102 genes, 59 up-regulated and 43 down-regulated genes, were significantly differentially expressed in KD groups. GO enrichment analysis showed that DEGs were enriched in cellular response to cytokines, cytokine-mediated signaling pathway, and regulation of immune cells migration and chemotaxis. KEGG signaling pathway analysis showed that DEGs were mainly involved in cytokine−cytokine receptor interaction, chemokine signaling pathway, and TGF−β signaling pathway. Besides, the mRNA expression levels of SMAD1, SMAD6, CD34, CXCL1, and APLN in the KD group were significantly up-regulated compared with the normal group, whilePITX2 was significantly down-regulated. Conclusion: 102 DEGs in KD serum-induced HCAECs were identified, and six new targets were proposed as potential indicators of KD.

scholarly journals Expression Profile Analysis of Differentially Expressed Genes in Human Coronary Artery Endothelial Cells Induced by Serum From Kawasaki Disease: A Preliminary Study

2021 ◽  
Author(s):  
Xue Fan ◽  
Meng Li ◽  
Min Xiao ◽  
Cong Liu ◽  
Mingguo Xu
Keyword(s):  
Endothelial Cells ◽  
Coronary Artery ◽  
Kawasaki Disease ◽  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Healthy Children ◽  
Rna Seq ◽  
Human Coronary Artery

Abstract Background: Kawasaki disease (KD) leads to coronary artery damage and the etiology of KD is unknown. The present study was designed to explore the differentially expressed genes (DEGs) in KD serum-induced human coronary artery endothelial cells (HCAECs) by RNA-sequence (RNA-seq). Methods: HCAECs were stimulated with serum (15% (v/v)), which were collected from 20 healthy children and 20 KD patients, for 24 hours. DEGs were then detected and analyzed by RNA-seq and bioinformatics analysis. Results: The expression of SMAD1, SMAD6, CD34, CXCL1, PITX2, and APLN was validated by qPCR. 102 genes, 59 up-regulated and 43 down-regulated genes, were significantly differentially expressed in KD groups. GO enrichment analysis showed that DEGs were enriched in cellular response to cytokines, cytokine-mediated signaling pathway, and regulation of immune cells migration and chemotaxis. KEGG signaling pathway analysis showed that DEGs were mainly involved in cytokine−cytokine receptor interaction, chemokine signaling pathway, and TGF−β signaling pathway. Besides, the mRNA expression levels of SMAD1, SMAD6, CD34, CXCL1, and APLN in the KD group were significantly up-regulated compared with the normal group, while PITX2 was significantly down-regulated. Conclusion: 102 DEGs in KD serum-induced HCAECs were identified, and six new targets may be closely associated with the pathogenesis of KD.

scholarly journals Identification of differentially expressed genes and the role of PDK4 in CD14+ monocytes of coronary artery disease

2021 ◽  
Author(s):  
Pei Du ◽  
Ren Guo ◽  
Keqin Gao ◽  
Shuang Yang ◽  
Baige Yao ◽  
...  
Keyword(s):  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
R Package ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Cell Periphery ◽  
Rna Seq ◽  
Artery Disease

Background. Coronary artery disease (CAD) is a chronic inflammatory disease caused by development of atherosclerosis, which is the leading cause of mortality and disability. Our study aimed to identify the differentially expressed genes (DEGs) in CD14+ monocytes from CAD patients compared with those from non-CAD controls, which might pave the way to diagnosis and treatment for CAD. Methods. The RNA-seq was performed by BGISEQ-500, followed by analyzing with R package to screening differentially expressed genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed by R package. In addition, we validated the results of RNA-seq using RT-qPCR. Furthermore, we explored the function of selected ten genes in LDL-treated CD14+ monocytes by RT-qPCR. Results. a total of 2897 DEGs were identified, including 753 up- and 2144 down-regulated genes in CD14+ monocytes from CAD patients. These DEGs were mainly enriched in plasma membrane and cell periphery of cell component, immune system process of biological process, NF-kappa B signaling pathway, cell adhesion molecules signaling pathway and cytokine-cytokine receptor interaction signaling pathway. In LDL-treated CD14+ monocytes, the mRNA expression of PDK4 was significantly up-regulated. Conclusion. In this study, we suggested that PDK4 might play a role in progression of CAD. The study will provide some pieces of evidence to investigate the role and mechanism of key genes in the pathogenesis of CAD.

scholarly journals Identification of critical pathways and potential therapeutic targets in Poorly differentiated duodenal papilla adenocarcinoma

2020 ◽  
Author(s):  
Yuanxiang Lu ◽  
Wensen Li ◽  
Ge Liu ◽  
Erwei Xiao ◽  
Senmao Mu ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Therapeutic Targets ◽  
Malignant Neoplasm ◽  
Differentially Expressed ◽  
High Recurrence Rate ◽  
Rna Seq ◽  
Duodenal Papilla ◽  
Ppi Network ◽  
Hub Genes

Abstract Background: Duodenal papilla carcinoma (DPC) is a rare malignancy of the gastrointestinal tract with high recurrence rate, and the pathogenesis of this highly malignant neoplasm is yet to be fully elucidated. This study aims to identify key genes to further understand the biology and pathogenesis underlying the molecular alterations driving DPC, which could be potential diagnostic or therapeutic targets.Methods: Tumor samples of three DPC patients were collected and integrating RNA-seq analysis of tumor tissues and matched normal tissues were performed to discover differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were carried out to understand the potential bio-functions of the DPC differentially expressed genes (DEGs) and protein–protein interaction (PPI) network was constructed for functional modules analysis and dentification of hub genes. Results: A total of 110 DEGs were identified from our RNA-Seq data, GO and KEGG analyses showed that the DEGs were mainly enriched in multiple cancer-related functions and pathways, such as cell proliferation, IL-17signaling pathway, Jak-STAT signaling pathway, PPAR signaling pathway. The PPI network screened out six hub genes including IL-6, LEP, LCN2, CCND1, FABP4 and MMP1, which were identified as core genes in the network and potential therapeutic targets of DPC. Discussion: The current study provides new insight into the exploration of DPC pathogenesis and the screened hub genes may serve as potential diagnostic indicator and novel therapeutic target.

scholarly journals RNA-Seq Analysis Identifies Differentially Expressed Genes in Subcutaneous Adipose Tissue in Qaidaford Cattle, Cattle-Yak, and Angus Cattle

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1077 ◽  
Author(s):  
Chengchuang Song ◽  
Yongzhen Huang ◽  
Zhaoxin Yang ◽  
Yulin Ma ◽  
Buren Chaogetu ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Meat Quality ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Cell Metabolism ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Control Group ◽  
Rna Seq ◽  
Angus Cattle

In the beef industry, fat tissue is closely related to meat quality. In this study, high-throughput RNA sequencing was utilized for adipose tissue transcriptome analysis between cattle-yak, Qaidamford cattle, and Angus cattle. The screening and identification of differentially expressed genes (DEGs) between different breeds of cattle would facilitate cattle breeding. Compared to Angus cattle adipose tissue, a total of 4167 DEGs were identified in cattle-yak adipose tissue and 3269 DEGs were identified in Qaidamford cattle adipose tissue. Considering cattle-yak as a control group, 154 DEGs were identified in Qaidamford cattle adipose tissue. GO analysis indicated the significant enrichment of some DEGs related to lipid metabolism. The KEGG pathway database was also used to map DEGs and revealed that most annotated genes were involved in ECM-receptor interaction and the PI3K-Akt signal pathway, which are closely related to cell metabolism. Eight selected DEGs related to adipose tissue development or metabolism were verified by RT-qPCR, indicating the reliability of the RNA-seq data. The results of this comparative transcriptome analysis of adipose tissue and screening DEGs suggest several candidates for further investigations of meat quality in different cattle breeds.

scholarly journals Differential Analysis of Expressed Genes in Diabetic Nephropathy Based on Bioinformatics Technology

2021 ◽  
Author(s):  
Yu Liu ◽  
Jundong Wang ◽  
wencheng Chi ◽  
Jing Xie ◽  
LaiKuan Teh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Diabetic Nephropathy ◽  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Biological Effects ◽  
Cytokine Receptor ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Differential Analysis ◽  
Core Genes

Abstract Objective: Bioinformatics technology was used in this study to analyze the expression data of patients with diabetic nephropathy (DN) and normal subjects from the microarray. The purpose of this study was to screen the differentially expressed genes in DN and to explore the pathogenesis and potential therapeutic targets of DN. Methods: The data of gene expression in the gse142153 gene chip was downloaded from the gene expression database (GEO). The up-regulated and down-regulated expressed genes were analyzed by R language. The core genes of differentially expressed genes were analyzed by string database, Cytoscape software and its plug-in. The differentially expressed genes were analyzed by gene ontology and Kyoto Encyclopedia of genes and genomes. Results: A total of 112 differentially expressed genes were screened, including 50 down-regulated genes and 62 up-regulated genes. There are 10 up-regulated core genes including CXCL8, MMP9, IL1B, IL6, IL10, CXCL2, CCL20, ATF3, CXCL3, F3. Their biological effects are mainly concentrated in the IL-17 signaling pathway, rheumatoid arthritis, viral protein interaction with cytokine and cytokine receptor, Amoebiasis, TNF signaling pathway, Legionellosis, Cytokine-cytokine receptor interaction, Lipid, and atherosclerosis, Malaria, NOD-like receptor signaling pathway, etc. Conclusion: Analysis of differentially expressed genes and core genes enhanced the understanding of the pathogenesis of DN and provided a potential train of thought for the treatment of DN.

scholarly journals Network Analyses of Differentially Expressed Genes in Osteoarthritis to Identify Hub Genes

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Zhaoyan Li ◽  
Lei Zhong ◽  
Zhenwu Du ◽  
Gaoyang Chen ◽  
Jing Shang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Hub Genes ◽  
Expression Levels ◽  
Network Analyses ◽  
Synovial Membranes

Background. Osteoarthritis (OA) is the most common degenerative disease in orthopedics. However, the cause and underlying molecular mechanisms are not clear. This study aims to identify the hub genes and pathways involved in the occurrence of osteoarthritis. Methods. The raw data of GSE89408 were downloaded from the Gene Expression Omnibus (GEO) database, and the differentially expressed genes (DEGs) were identified by R software. The DAVID database was used for pathway and gene ontology analysis, and p<0.05 and gene count >2 were set as the cut-off point. Moreover, protein-protein interaction (PPI) network construction was applied for exploring the hub genes in osteoarthritis. The expression levels of the top ten hub genes in knee osteoarthritis synovial membranes and controls were detected by quantitative real-time PCR system. Results. A total of 229 DEGs were identified in osteoarthritis synovial membranes compared with normal synovial membranes, including 145 upregulated and 84 downregulated differentially expressed genes. The KEGG pathway analysis results showed that up-DEGs were enriched in proteoglycans in cytokine-cytokine receptor interaction, chemokine signaling pathway, rheumatoid arthritis, and TNF signaling pathway, whereas down-DEGs were enriched in the PPAR signaling pathway and AMPK signaling pathway. The qRT-PCR results showed that the expression levels of ADIPOQ, IL6, and CXCR1 in the synovium of osteoarthritis were significantly increased (p <0.05).

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