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

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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Data for the gene expression profiling and alternative splicing events during the chondrogenic differentiation of human cartilage endplate-derived stem cells under hypoxia

Data in Brief ◽

10.1016/j.dib.2016.04.037 ◽

2016 ◽

Vol 7 ◽

pp. 1438-1442 ◽

Cited By ~ 2

Author(s):

Yuan Yao ◽

Jin Shang ◽

Weilin Song ◽

Qiyue Deng ◽

Huan Liu ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Alternative Splicing ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Chondrogenic Differentiation ◽

Human Cartilage ◽

Cartilage Endplate ◽

Alternative Splicing Events

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Global profiling of the gene expression and alternative splicing events during hypoxia-regulated chondrogenic differentiation in human cartilage endplate-derived stem cells

Genomics ◽

10.1016/j.ygeno.2016.03.003 ◽

2016 ◽

Vol 107 (5) ◽

pp. 170-177 ◽

Cited By ~ 9

Author(s):

Yuan Yao ◽

Jin Shang ◽

Weilin Song ◽

Qiyue Deng ◽

Huan Liu ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Alternative Splicing ◽

Chondrogenic Differentiation ◽

Human Cartilage ◽

Cartilage Endplate ◽

Alternative Splicing Events

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Screening and Functional Prediction of Key Candidate Genes in Hepatitis B Virus-Associated Hepatocellular Carcinoma

BioMed Research International ◽

10.1155/2020/7653506 ◽

2020 ◽

Vol 2020 ◽

pp. 1-13

Author(s):

Xia Chen ◽

Ling Liao ◽

Yuwei Li ◽

Hengliu Huang ◽

Qing Huang ◽

...

Keyword(s):

Gene Expression ◽

Hepatocellular Carcinoma ◽

Hepatitis B Virus ◽

Hepatitis B ◽

Pathway Analysis ◽

Kegg Pathway ◽

Metabolic Process ◽

Hub Genes ◽

Kegg Pathway Analysis ◽

B Virus

Background. The molecular mechanism by which hepatitis B virus (HBV) induces hepatocellular carcinoma (HCC) is still unknown. The genomic expression profile and bioinformatics methods were used to investigate the potential pathogenesis and therapeutic targets for HBV-associated HCC (HBV-HCC). Methods. The microarray dataset GSE55092 was downloaded from the Gene Expression Omnibus (GEO) database. The data was analyzed by the bioinformatics software to find differentially expressed genes (DEGs). Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, ingenuity pathway analysis (IPA), and protein-protein interaction (PPI) network analysis were then performed on DEGs. The hub genes were identified using Centiscape2.2 and Molecular Complex Detection (MCODE) in the Cytoscape software (Cytoscape_v3.7.2). The survival data of these hub genes was downloaded from the Gene Expression Profiling Interactive Analysis (GEPIA). Results. A total of 2264 mRNA transcripts were differentially expressed, including 764 upregulated and 1500 downregulated in tumor tissues. GO analysis revealed that these DEGs were related to the small-molecule metabolic process, xenobiotic metabolic process, and cellular nitrogen compound metabolic process. KEGG pathway analysis revealed that metabolic pathways, complement and coagulation cascades, and chemical carcinogenesis were involved. Diseases and biofunctions showed that DEGs were mainly associated with the following diseases or biological function abnormalities: cancer, organismal injury and abnormalities, gastrointestinal disease, and hepatic system disease. The top 10 upstream regulators were predicted to be activated or inhibited by Z-score and identified 25 networks. The 10 genes with the highest degree of connectivity were defined as the hub genes. Cox regression revealed that all the 10 genes (CDC20, BUB1B, KIF11, TTK, EZH2, ZWINT, NDC80, TPX2, MELK, and KIF20A) were related to the overall survival. Conclusion. Our study provided a registry of genes that play important roles in regulating the development of HBV-HCC, assisting us in understanding the molecular mechanisms that underlie the carcinogenesis and progression of HCC.

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A genome-wide analysis of the gene expression profiles and alternative splicing events during the hypoxia-regulated osteogenic differentiation of human cartilage endplate-derived stem cells

Molecular Medicine Reports ◽

10.3892/mmr.2017.6846 ◽

2017 ◽

Vol 16 (2) ◽

pp. 1991-2001 ◽

Cited By ~ 2

Author(s):

Yuan Yao ◽

Qiyue Deng ◽

Chao Sun ◽

Weiling Song ◽

Huan Liu ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Alternative Splicing ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Human Cartilage ◽

Genome Wide Analysis ◽

Cartilage Endplate ◽

Genome Wide ◽

A Genome

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

10.21203/rs.2.15313/v1 ◽

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.

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Gene expression profiling of chondrogenic differentiation by dexamethasone-conjugated polyethyleneimine with SOX trio genes in stem cells

Stem Cell Research & Therapy ◽

10.1186/s13287-018-0998-7 ◽

2018 ◽

Vol 9 (1) ◽

Cited By ~ 7

Author(s):

Se Won Yi ◽

Hye Jin Kim ◽

Hyun Jyung Oh ◽

Heejun Shin ◽

Jung Sun Lee ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Chondrogenic Differentiation

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General regulatory effects of hypoxia on human cartilage endplate-derived stem cells: A genome-wide analysis of differential gene expression and alternative splicing events

Molecular Medicine Reports ◽

10.3892/mmr.2017.6907 ◽

2017 ◽

Vol 16 (3) ◽

pp. 3001-3009

Author(s):

Yuan Yao ◽

Weilin Song ◽

Qiyue Deng ◽

Huiyu Zhang ◽

Jian Wang ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Alternative Splicing ◽

Human Cartilage ◽

Genome Wide Analysis ◽

Cartilage Endplate ◽

Genome Wide ◽

A Genome ◽

Differential Gene ◽

Regulatory Effects

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

Acta Biochimica et Biophysica Sinica ◽

10.1093/abbs/gmz064 ◽

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.

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Gene-expression profile and postpartum transition of bovine endometrial side population cells†

Biology of Reproduction ◽

10.1093/biolre/ioab004 ◽

2021 ◽

Author(s):

Ryoki Tatebayashi ◽

Sho Nakamura ◽

Shiori Minabe ◽

Tadashi Furusawa ◽

Ryoya Abe ◽

...

Keyword(s):

Gene Expression ◽

Progenitor Cells ◽

Pathway Analysis ◽

Kegg Pathway ◽

Side Population ◽

Gene Set Enrichment Analysis ◽

Stem Cell Marker ◽

Endometrial Cells ◽

Kegg Pathway Analysis ◽

Upregulated Genes

Abstract The mechanism of bovine endometrial regeneration after parturition remains unclear. Here, we hypothesized that bovine endometrial stem/progenitor cells participate in the postpartum regeneration of the endometrium. Flow cytometry analysis identified the presence of side population (SP) cells among endometrial stromal cells. Endometrial SP cells were shown to differentiate into osteoblasts and adipocytes. RNA-seq data showed that the gene expression pattern was different between bovine endometrial SP cells and main population cells. Gene Set Enrichment Analysis identified the enrichment of stemness genes in SP cells. Significantly (false discovery rate < 0.01) upregulated genes in SP cells contained several stem cell marker genes. Gene ontology (GO) analysis of the upregulated genes in SP cells showed enrichment of terms related to RNA metabolic process and transcription. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of upregulated genes in SP cells revealed enrichment of signaling pathways associated with maintenance and differentiation of stem/progenitor cells. The terms involved in TCA cycles were enriched in GO and KEGG pathway analysis of downregulated genes in SP cells. These results support the assumption that bovine endometrial SP cells exhibit characteristics of somatic stem/progenitor cells. The ratio of SP cells to endometrial cells was lowest on days 9–11 after parturition, which gradually increased thereafter. SP cells were shown to differentiate into epithelial cells. Collectively, these results suggest that bovine endometrial SP cells were temporarily reduced immediately after calving possibly due to their differentiation to provide new endometrial cells.

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