Comprehensive analysis of long noncoding RNAs and mRNAs expression profiles and functional networks during chondrogenic differentiation of murine ATDC5 cells

2019 ◽  
Vol 51 (8) ◽  
pp. 778-790
Author(s):  
Wei Wang ◽  
Yu Ding ◽  
Yanhua Xu ◽  
Hefeng Yang ◽  
Wenjing Liu ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Pathway Analysis ◽  
Chondrogenic Differentiation ◽  
Kegg Pathway ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Receptor Interaction ◽  
Messenger Rnas ◽  
Kegg Pathway Analysis

AbstractChondrogenic differentiation is a coordinated biological process orchestrated by various cell signaling pathways, involving complex pathways regulated at both transcriptional and post-transcriptional levels. Long noncoding RNAs (lncRNAs) are emerging as important regulators in the modulation of multiple cell processes. However, the potential roles of lncRNAs and their regulatory mechanisms in chondrogenic differentiation remain largely unclear. In this study, microarray was performed to detect the expression profiles of lncRNAs and messenger RNAs (mRNAs) during chondrogenic differentiation of murine chondrogenic cell line ATDC5. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to explore their functions. Coding-noncoding co-expression (CNC) and competing endogenous RNA (ceRNA) networks were also constructed with bioinformatics methods. The results revealed that 1009 lncRNAs and 1206 mRNAs were differentially regulated during chondrogenic differentiation. GO and KEGG pathway analysis indicated that the principal functions of the transcripts were associated with system development and extracellular matrix-receptor interaction, TGF-β signaling, and PI3K-Akt signaling pathways. The CNC network showed that lncRNA AK136902 was positively correlated with prostaglandin F receptor (FP). The ceRNA network covered 3 lncRNAs, 121 miRNAs and 241 edges. The upregulated lncRNA AK136902, AK016344, and ENSMUST00000180767 might promote chondrogenic differentiation by acting as ceRNAs. Knockdown of lncRNA AK136902 could inhibit the mRNA expression of FP and other chondrogenic related genes, including Aggrecan and Col2a1 during chondrogenic differentiation. Our results provide a new perspective on the modulation of lncRNAs during chondrogenic differentiation.

scholarly journals Expression profiles of long noncoding RNAs and messenger RNAs in the border zone of myocardial infarction in rats

2019 ◽  
Vol 24 (1) ◽  
Author(s):  
Qingkun Meng ◽  
Zhijun Sun ◽  
Hui Gu ◽  
Jiaying Luo ◽  
Jingjing Wang ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
Signaling Pathway ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Cytokine Receptor ◽  
Border Zone ◽  
Receptor Interaction ◽  
Messenger Rnas ◽  
Chromosomal Distribution

Abstract Background The participation of long noncoding RNAs (lncRNAs) in myocardial infarction has recently been noted. However, their underlying roles in the border zone of myocardial infarction remain unclear. This study uses microarrays to determine the profiles of lncRNAs and mRNAs in the border zone. Methods Bioinformatics methods were employed to uncover their underlying roles. Highly dysregulated lncRNAs was further validated via PCR. Results Four hundred seven lncRNAs and 752 mRNAs were upregulated, while 132 lncRNAs and 547 mRNAs were downregulated in the border zone of myocardial infarction. A circos graph was constructed to visualize the chromosomal distribution and classification of the dysregulated lncRNAs and mRNAs. The upregulated mRNAs in the border zone were most highly enriched in cytokine activity, binding, cytokine receptor binding and related processes, as ascertained through Go analysis. Pathway analysis of the upregulated mRNAs showed the most significant changes were in the TNF signaling pathway, cytokine–cytokine receptor interaction and chemokine signaling pathway and similar pathways and interactions. An lncRNA–mRNA co-expression network was established to probe into the underlying functions of the 10 most highly dysregulated lncRNAs based on their co-expressed mRNAs. In the co-expression network, we found 16 genes directly involved in myocardial infarction, including Alox5ap, Itgb2 and B4galt1. The lncRNAs AY212271, EF424788 and MRAK088538, among others, might be associated with myocardial infarction. BC166504 is probably a key lncRNA in the border zone of myocardial infarction. Conclusions The results may have revealed some aberrantly expressed lncRNAs and mRNAs that contribute to the underlying pathophysiological mechanisms of myocardial infarction.

scholarly journals Prognostic Implication of the Expression Level of PECAM-1 in Non-small Cell Lung Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Shuhui Cao ◽  
Yue Wang ◽  
Jingwen Li ◽  
Xuxinyi Ling ◽  
Yao Zhang ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Survival Analysis ◽  
Cell Motility ◽  
Pathway Analysis ◽  
Kinase Inhibitor ◽  
Kegg Pathway ◽  
Expression Profiles ◽  
The Cancer Genome Atlas ◽  
Kegg Pathway Analysis ◽  
Low Expression

Background: Lung cancer is a malignant disease that threatens human health. Hence, it is crucial to identify effective prognostic factors and treatment targets. Single-cell RNA sequencing can quantify the expression profiles of transcripts in individual cells.Methods:GSE117570 profiles were downloaded from the Gene Expression Omnibus database. Key ligand-receptor genes in the tumor and the normal groups were screened to identify integrated differentially expressed genes (DEGs) from the GSE118370 and The Cancer Genome Atlas Lung Adenocarcinoma databases. DEGs associated with more ligand-receptor pairs were selected as candidate DEGs for Gene Ontology (GO) functional annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and survival analysis. In addition, we conducted validation immunohistochemical experiments on postoperative specimens of 30 patients with lung cancer.Results: A total of 18 candidate DEGs were identified from the tumor and the normal groups. The analysis of the GO biological process revealed that these DEGs were mainly enriched in wound healing, in response to wounding, cell migration, cell motility, and regulation of cell motility, while the KEGG pathway analysis found that these DEGs were mainly enriched in proteoglycans in cancer, bladder cancer, malaria, tyrosine kinase inhibitor resistance in Epidermal Growth Factor Receptor (EGFR), and the ERBB signaling pathway. Survival analysis showed that a high, rather than a low, expression of platelet endothelial cell adhesion molecule-1 (PECAM-1) was associated with improved survival. Similarly, in postoperative patients with lung cancer, we found that the overall survival of the PECAM-1 high-expression group shows a better trend than the PECAM-1 low-expression group (p = 0.172).Conclusions: The candidate DEGs identified in this study may play some important roles in the occurrence and development of lung cancer, especially PECAM-1, which may present potential prognostic biomarkers for the outcome.

scholarly journals Long Noncoding RNAs and Messenger RNAs Expression Profiles Potentially Regulated by ZBTB7A in Nasopharyngeal Carcinoma

2019 ◽  
Vol 2019 ◽  
pp. 1-16
Author(s):  
Fei Liu ◽  
Jiazhang Wei ◽  
Yanrong Hao ◽  
Fengzhu Tang ◽  
Wei Jiao ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Fatty Acid Synthase ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Messenger Rnas ◽  
Regulatory Pathways ◽  
Different Levels

Our previous studies showed that ZBTB7A played an important role in promoting nasopharyngeal carcinoma (NPC) progression. However, molecular mechanisms of different levels of ZBTB7A are still unclear. It is necessary to search molecular markers which are closely connected with ZBTB7A. We selected NPC sublines CNE2 with stably transfecting empty plasmid (negative control, NC) and short hair RNA (shRNA) plasmid targeting ZBTB7A as research objectives. Microarray was used to screen differentially expressed long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) via shRNA-CNE2 versus NC-CNE2. Quantitative PCR (qPCR) was used to validate lncRNAs and mRNAs from the sublines, chronic rhinitis, and NPC tissues. Bioinformatics was used to analyze regulatory pathways which were connected with ZBTB7A. The 1501 lncRNAs (long noncoding RNAs) and 1275 differentially expressed mRNAs were upregulated or downregulated over 2-fold. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the upregulated or downregulated carbohydrate and lipid metabolisms probably involved in carcinogenicity of shRNA-CNE2 (P-value cut-off was 0.05). In order to find the molecular mechanisms of ZBTB7A, we validated 12 differentially expressed lncRNAs and their nearby mRNAs by qPCR. Most of the differentially expressed mRNAs are closely connected with carbohydrate and lipid metabolisms in multiply cancers. Furthermore, part of them were validated in NPC and rhinitis tissues by qPCR. As a result, NR_047538, ENST00000442852, and fatty acid synthase (FASN) were closely associated with NPC. ZBTB7A had a positive association with NR_047538 and negative associations with ENST00000442852 and FASN. The results probably provide novel candidate biomarkers for NPC progression with different levels of ZBTB7A.

scholarly journals Network analyses of circular RNAs expression profiles and their hub genes in pancreatic ductal adenocarcinoma

2019 ◽  
Author(s):  
Yanyan Tang ◽  
Ping Zhang
Keyword(s):  
Gene Expression ◽  
Pancreatic Ductal Adenocarcinoma ◽  
Signaling Pathway ◽  
Pathway Analysis ◽  
Kegg Pathway ◽  
Expression Profiles ◽  
Ductal Adenocarcinoma ◽  
Ppi Network ◽  
Hub Genes ◽  
Kegg Pathway Analysis

Abstract Pancreatic ductal adenocarcinoma (PDAC) is one of the most common malignant tumor in digestive system. CircRNAs involve in lots of biological processes through interacting with miRNAs and their targeted mRNA. We obtained the circRNA gene expression profiles from Gene Expression Omnibus (GEO) and identified differentially expressed genes (DEGs) between PDAC samples and paracancerous tissues. Bioinformatics analyses, including GO analysis, KEGG pathway analysis and PPI network analysis, were conducted for further investigation. We also constructed circRNA‑microRNA-mRNA co-expression network. A total 291 differentially expressed circRNAs were screened out. The GO enrichment analysis revealed that up-regulated DEGs were mainly involved metabolic process, biological regulation, and gene expression, and down-regulated DEGs were involved in cell communication, single-organism process, and signal transduction. The KEGG pathway analysis, the upregulated circRNAs were enriched cGMP-PKG signaling pathway, and HTLV-I infection, while the downregulated circRNAs were enriched in protein processing in endoplasmic reticulum, insulin signaling pathway, regulation of actin cytoskeleton, etc. Four genes were identified from PPI network as both hub genes and module genes, and their circRNA‑miRNA-mRNA regulatory network also be constructed. Our study indicated possible involvement of dysregulated circRNAs in the development of PDAC and promoted our understanding of the underlying molecular mechanisms.

scholarly journals PSXII-25 Isolation and identification of bovine preadipocytes and screening of miRNAs associated with adipogenesis

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 244-245
Author(s):  
Xiang Yu ◽  
Xibi Fang ◽  
Runjun Yang
Keyword(s):  
Lipid Metabolism ◽  
Pathway Analysis ◽  
Kegg Pathway ◽  
Expression Profiles ◽  
Marker Gene ◽  
Control Group ◽  
Small Rna Sequencing ◽  
Fatty Tissue ◽  
Isolation And Identification ◽  
Kegg Pathway Analysis

Abstract Introduction: In the breeding of beef cattle, the adipogenesis is a significant process to fat deposition. Thus isolating and identifying bovine preadipocytes in vitro is a basis for investigating mechanism of adipogenesis. As important transcriptional regulators, miRNAs play a pivotal role in adipogenesis. Materials and methods: Bovine preadipocytes were isolated from subcutaneous fatty tissue and induced to differentiate into adipocytes. The verification of preadipocytes and adipocytes was performed by qPCR, Oil Red O stain and triglycerides detection. Total RNAs were extracted from bovine preadipocytes and adipocytes and proceeded small-RNA sequencing. KEGG pathway analysis and GO analysis were used to screen differently expressed miRNAs associated with adipogenesis. Results: The result showed that more lipid drops in induced group were observed and stained red compared with control group. The expression levels of key genes (pparγ, c/ebpα, fabp4, fasn and leptin) associated with adipogenesis were increased. Dlk1, as a marker gene of preadipocytes, was scarcely expressed in adipocytes. The content of cellar triglycerides detected in adipocytes was significantly upgraded. 131 miRNAs were found to be highly expressed in bovine adipocytes, and 119 miRNAs were highly expressed in bovine preadipocytes. KEGG pathway analysis showed that 4.76% of the differentially expressed genes were enriched in lipid metabolism. Discussion and conclusion: Previous studies have found that some miRNAs could regulate lipid metabolism. But few studies have explored the relationship between miRNAs and adipogenesis. In our study, we characterized the miRNAs associated with adipogenesis in bovine preadipocytes. The expression profiles of 11 miRNAs verified by q-PCR, including miR-149-5p, miR-199a-3p, miR-199a-5p, miR-148a and miR-449a were the same to sequencing data. Based on the KEGG pathway analysis, the predicted target genes were mainly enriched in signal transduction, catabolism and lipid metabolism. This work contributes to existing knowledge by providing an understanding of bovine adipogenesis at the molecular level.

scholarly journals Analysis of Long Noncoding RNA and mRNA Expression Profiles in IL-9-Activated Astrocytes and EAE Mice

2018 ◽  
Vol 45 (5) ◽  
pp. 1986-1998 ◽  
Author(s):  
Xiaomei Liu ◽  
Qing Zhang ◽  
Weixiao Wang ◽  
Dongjiao Zuo ◽  
Jing Wang ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Pathway Analysis ◽  
Kegg Pathway ◽  
Expression Profiles ◽  
Astrocyte Activation ◽  
Kegg Pathway Analysis ◽  
The Brain ◽  
Brain Tissues

Background/Aims: Multiple sclerosis (MS) is an autoimmune disease in the central nervous system associated with demyelination and axonal injury. Astrocyte activation is involved in the pathogenesis of MS and experimental autoimmune encephalomyelitis (EAE), an animal model of MS. This study was designed to find potential lncRNAs in EAE mice and activated astrocytes. Methods: we performed microarray analysis of lncRNAs from the brain tissues of EAE mice and primary mouse astrocytes treated with IL-9(50 ng/ml). 12 lncRNAs were validated through real-time PCR. Gene ontology and KEGG pathway analysis were applied to explore the potential functions of lncRNAs. Results: Differentially expressed 3300 lncRNAs and 3250 mRNAs were in the brain tissues of EAE mice, and 3748 lncRNAs and 3332 mRNAs were in activated astrocytes. Notably, there were 2 co-up-regulated lncRNAs and 3 co-down-regulated lncRNAs both in the brain tissues of EAE mice and in activated astrocytes, including Gm14005, Gm12478, mouselincRNA1117, AK080435, and mouselincRNA0681, which regulate the ER calcium flux kinetics, zinc finger protein and cell apoptosis. Similarly, there were 7 mRNAs co-up-regulated and 2 mRNAs co-down-regulated both in vivo and in vitro. Gene ontology and KEGG pathway analysis showed that the biological functions of differentially expressed mRNAs were associated with metabolism, development and inflammation. The results of realtime PCR validation were consistent with the data from the microarrays. Conclusions: Our data uncovered the expression profiles of lncRNAs and mRNAs in vivo and in vitro, which may help delineate the mechanisms of astrocyte activation during MS/EAE process.

scholarly journals Global Gene Expression Profiling and Alternative Splicing Events during the Chondrogenic Differentiation of Human Cartilage Endplate-Derived Stem Cells

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Jin Shang ◽  
Xin Fan ◽  
Lei Shangguan ◽  
Huan Liu ◽  
Yue Zhou
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Alternative Splicing ◽  
Pathway Analysis ◽  
Expression Profiling ◽  
Chondrogenic Differentiation ◽  
Kegg Pathway ◽  
Cartilage Endplate ◽  
Kegg Pathway Analysis ◽  
Alternatively Spliced

Low back pain (LBP) is a very prevalent disease and degenerative disc diseases (DDDs) usually account for the LBP. However, the pathogenesis of DDDs is complicated and difficult to elucidate. Alternative splicing is a sophisticated regulatory process which greatly increases cellular complexity and phenotypic diversity of eukaryotic organisms. In addition, the cartilage endplate-derived stem cells have been discovered and identified by our research group. In this paper, we continue to investigate gene expression profiling and alternative splicing events during chondrogenic differentiation of cartilage endplate-derived stem cells. We adopted Affymetrix Human Transcriptome Array 2.0 (HTA 2.0) to compare the transcriptional and splicing changes between the control and differentiated samples. RT-PCR and quantitative PCR are used to validate the microarray results. The GO and KEGG pathway analysis was also performed. After bioinformatics analysis of the data, we detected 1953 differentially expressed genes. In terms of alternative splicing, the Splicing Index algorithm was used to select alternatively spliced genes. We detected 4411 alternatively spliced genes. GO and KEGG pathway analysis also revealed several functionally involved biological processes and signaling pathways. To our knowledge, this is the first study to investigate the alternative splicing mechanisms in chondrogenic differentiation of stem cells on a genome-wide scale.

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