Microarray analysis identification of key pathways and interaction network of differential gene expressions during osteogenic differentiation

Abstract Background Adult bone marrow-derived mesenchymal stem cells (BM-MSCs) are multipotent stem cells that can differentiate into three lineages. They are suitable sources for cell-based therapy and regenerative medicine applications. This study aims to evaluate the hub genes and key pathways of differentially expressed genes (DEGs) related to osteogenesis by bioinformatics analysis in three different days. The DEGs were derived from the three different days compared with day 0. Results Gene expression profiles of GSE37558 were obtained from the Gene Expression Omnibus (GEO) database. A total of 4076 DEGs were acquired on days 8, 12, and 25. Gene ontology (GO) enrichment analysis showed that the non-canonical Wnt signaling pathway and lipopolysaccharide (LPS)-mediated signaling pathway were commonly upregulated DEGs for all 3 days. KEGG pathway analysis indicated that the PI3K-Akt and focal adhesion were also commonly upregulated DEGs for all 3 days. Ten hub genes were identified by CytoHubba on days 8, 12, and 25. Then, we focused on the association of these hub genes with the Wnt pathways that had been enriched from the protein-protein interaction (PPI) by the Cytoscape plugin MCODE. Conclusions These findings suggested further insights into the roles of the PI3K/AKT and Wnt pathways and their association with osteogenesis. In addition, the stem cell microenvironment via growth factors, extracellular matrix (ECM), IGF1, IGF2, LPS, and Wnt most likely affect osteogenesis by PI3K/AKT.

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Identification of key pathways and hub genes in the myogenic process of pluripotent stem cell: A bioinformatics study

10.21203/rs.3.rs-41291/v1 ◽

2020 ◽

Author(s):

Wenyong Fei ◽

Mingsheng Liu ◽

Yao Zhang ◽

Shichao Cao ◽

Xuanqi Wang ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Pluripotent Stem Cells ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Ppi Network ◽

Hub Genes ◽

Myogenic Stem Cells ◽

Key Pathways

Abstract Purpose: The study aims to determine the process of myoginc differentiation in human pluripotent stem cells and to figure out that the key pathways and hub genes in the process, which do helpful for the further research of muscular regeneration.Method: Three gene expression profiles, GSE131125, GSE148994, GSE149055, about the comparisons of pluripotent stem cells and myogenic stem cells from the Gene Expression Omnibus (GEO) data base. Common differentially expressed genes (DEGs) were obtained and for the further analysis as Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and GSEA analysis and protein‑protein interaction (PPI) network. In vitro cell research to verify the hub genes and key pathways.Result:824 DEGs were co-expressed in the three GSEs. 19 hub genes were identified from the PPI network. The GO and KEGG pathway analysis were performed to determine the functions of DEGs. GSEA analysis indicated the differentiated cells were enriched in muscle cell development and myogenesis.Conclusion: Our research revealed the main hub genes and modules in the myogeinc process of stem cells which contribute to further study about the molecular mechanism of myogenesis regeneration. Paving a way for more accurate treatment for muscle dysfunction.

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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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Meta-Analyses of Multiple Gene Expression Profiles to Screen Hub Genes Related to Osteoarthritis

Public Health Genomics ◽

10.1159/000517308 ◽

2021 ◽

Vol 24 (5-6) ◽

pp. 267-279

Author(s):

Xianyang Zhu ◽

Wen Guo

Keyword(s):

Gene Expression ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Meta Analysis ◽

Wnt Signaling Pathway ◽

Gene Expression Profiles ◽

Enrichment Analysis ◽

Receptor Interaction ◽

Ppi Network ◽

Hub Genes

Background: This study aimed to screen and validate the crucial genes involved in osteoarthritis (OA) and explore its potential molecular mechanisms. Methods: Four expression profile datasets related to OA were downloaded from the Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) from 4 microarray patterns were identified by the meta-analysis method. The weighted gene co-expression network analysis (WGCNA) method was used to investigate stable modules most related to OA. In addition, a protein-protein interaction (PPI) network was built to explore hub genes in OA. Moreover, OA-related genes and pathways were retrieved from Comparative Toxicogenomics Database (CTD). Results: A total of 1,136 DEGs were identified from 4 datasets. Based on these DEGs, WGCNA further explored 370 genes included in the 3 OA-related stable modules. A total of 10 hub genes were identified in the PPI network, including AKT1, CDC42, HLA-DQA2, TUBB, TWISTNB, GSK3B, FZD2, KLC1, GUSB, and RHOG. Besides, 5 pathways including “Lysosome,” “Pathways in cancer,” “Wnt signaling pathway,” “ECM-receptor interaction” and “Focal adhesion” in CTD and enrichment analysis and 5 OA-related hub genes (including GSK3B, CDC42, AKT1, FZD2, and GUSB) were identified. Conclusion: In this study, the meta-analysis was used to screen the central genes associated with OA in a variety of gene expression profiles. Three OA-related modules (green, turquoise, and yellow) containing 370 genes were identified through WGCNA. It was discovered through the gene-pathway network that GSK3B, CDC42, AKT1, FZD2, and GUSB may be key genes related to the progress of OA and may become promising therapeutic targets.

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Potential genes and pathways associated with heterotopic ossification derived from analyses of gene expression profiles

Journal of Orthopaedic Surgery and Research ◽

10.1186/s13018-021-02658-1 ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Zhanyu Yang ◽

Delong Liu ◽

Rui Guan ◽

Xin Li ◽

Yiwei Wang ◽

...

Keyword(s):

Gene Expression ◽

Protein Kinase ◽

Heterotopic Ossification ◽

Signaling Pathway ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Differentially Expressed ◽

Heterotopic Bone ◽

Hub Genes ◽

Ppi Networks

Abstract Background Heterotopic ossification (HO) represents pathological lesions that refer to the development of heterotopic bone in extraskeletal tissues around joints. This study investigates the genetic characteristics of bone marrow mesenchymal stem cells (BMSCs) from HO tissues and explores the potential pathways involved in this ailment. Methods Gene expression profiles (GSE94683) were obtained from the Gene Expression Omnibus (GEO), including 9 normal specimens and 7 HO specimens, and differentially expressed genes (DEGs) were identified. Then, protein–protein interaction (PPI) networks and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed for further analysis. Results In total, 275 DEGs were differentially expressed, of which 153 were upregulated and 122 were downregulated. In the biological process (BP) category, the majority of DEGs, including EFNB3, UNC5C, TMEFF2, PTH2, KIT, FGF13, and WISP3, were intensively enriched in aspects of cell signal transmission, including axon guidance, negative regulation of cell migration, peptidyl-tyrosine phosphorylation, and cell-cell signaling. Moreover, KEGG analysis indicated that the majority of DEGs, including EFNB3, UNC5C, FGF13, MAPK10, DDIT3, KIT, COL4A4, and DKK2, were primarily involved in the mitogen-activated protein kinase (MAPK) signaling pathway, Ras signaling pathway, phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) signaling pathway, and Wnt signaling pathway. Ten hub genes were identified, including CX3CL1, CXCL1, ADAMTS3, ADAMTS16, ADAMTSL2, ADAMTSL3, ADAMTSL5, PENK, GPR18, and CALB2. Conclusions This study presented novel insight into the pathogenesis of HO. Ten hub genes and most of the DEGs intensively involved in enrichment analyses may be new candidate targets for the prevention and treatment of HO in the future.

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Multi-Omics Analysis to Examine Gene Expression and Metabolites From Multisite Adipose-Derived Mesenchymal Stem Cells

Frontiers in Genetics ◽

10.3389/fgene.2021.627347 ◽

2021 ◽

Vol 12 ◽

Author(s):

Chuanxi Yang ◽

Jing Zhang ◽

Tingting Wu ◽

Kun Zhao ◽

Xiaoguang Wu ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Mesenchymal Stem Cells ◽

Signaling Pathway ◽

Malignant Tumors ◽

Ras Signaling ◽

Sprague Dawley ◽

Hub Genes ◽

P53 Signaling ◽

Omics Analysis

This study aimed at exploring the gene expression and metabolites among multisite adipose-derived mesenchymal stem cells (ASCs) and investigate the metabolic pathway using a multi-omics analysis. Subcutaneous adipose-derived mesenchymal stem cells (SASCs), perirenal adipose-derived mesenchymal stem cells (PASCs), and epididymal adipose-derived mesenchymal stem cells (EASCs) were isolated from Sprague Dawley rats. RNA and metabolites were extracted and sequenced using transcriptomics and metabolomics analyses, respectively. There were 720 differentially expressed genes (DEGs) in EASCs and 688 DEGs in PASCs compared with SASCs; there were 166 unique DEGs in EASCs, 134 unique DEGs in PASCs, and 554 common DEGs between EASCs and PASCs. Furthermore, there were 226 differential metabolites in EASCs, 255 differential metabolites in PASCs, 83 unique differential metabolites in EASCs, 112 unique differential metabolites in PASCs, and 143 common differential metabolites between EASCs and PASCs. The transcriptomics and metabolomics analyses identified four hub genes, one in EASCs and three in PASCs. There are functional differences among multisite ASCs that may be related to the hub genes Atac2, Rrm1, Rrm2, and Gla. The relevant signaling pathways are the Ras signaling pathway, HIF-1 signaling pathway, and the p53 signaling pathway. In conclusion, compared with SASCs, our multi-omics analysis identified that EASCs with higher Acat2 expression may be more correlated to fat metabolism and insulin resistance, while PASCs with abnormal expression of Rrm1/2 and Gla may be more correlated with some malignant tumors and cardiac-cerebral vascular disease.

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Potential Genes and Pathways Associated with Heterotopic Ossification, Derived from Analyses of Gene Expression Profiles

10.21203/rs.3.rs-572774/v1 ◽

2021 ◽

Author(s):

Zhanyu Yang ◽

Delong Liu ◽

Rui Guan ◽

Xin Li ◽

Yiwei Wang ◽

...

Keyword(s):

Gene Expression ◽

Protein Kinase ◽

Heterotopic Ossification ◽

Signaling Pathway ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Differentially Expressed ◽

Heterotopic Bone ◽

Hub Genes ◽

Ppi Networks

Abstract Background: Heterotopic ossification (HO) represents pathological lesions, referred to the development of heterotopic bone in extraskeletal tissues around joints. This study will investigate the genetic characteristics of bone marrow mesenchymal stem cells (BMSCs) from HO tissues and explore the potential pathways involved. Methods: The gene expression profiles (GSE94683) was obtained from the Gene Expression Omnibus (GEO), including 9 normal specimens and 7 HO specimens, and differentially expressed genes (DEGs) were identified. Then, the protein‑protein interaction (PPI) networks, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis were performed for further analysis. Results: Totally 275 DEGs were differentially expressed, of which 153 were upregulated and 122 were downregulated. In the biological process (BP), the majority of DEGs, including EFNB3, UNC5C, TMEFF2, PTH2, KIT, FGF13 and WISP3, were intensively enriched in cell signal transmission items, including axon guidance, negative regulation of cell migration, peptidyl-tyrosine phosphorylation and cell-cell signaling. Moreover, KEGG analysis indicated that the majority of DEGs, including EFNB3, UNC5C, FGF13, MAPK10, DDIT3, KIT, COL4A4 and DKK2, primarily involved in mitogen-activated protein kinase (MAPK) signaling pathway, Ras signaling pathway, phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) signaling pathway and Wnt signaling pathway. 10 hub genes were identified, including CX3CL1, CXCL1, ADAMTS3, ADAMTS16, ADAMTSL2, ADAMTSL3, ADAMTSL5, PENK, GPR18, CALB2.Conclusions: This study presents a novel insight into the pathogenesis of HO. 10 hub genes and most of the DEGs intensively involved in enrichment analyses may be the new candidate targets for the prevention and treatment of HO in the future.

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An Investigation about Gene Modules Associated with hDPSC Differentiation for Adolescents

Stem Cells International ◽

10.1155/2019/8913287 ◽

2019 ◽

Vol 2019 ◽

pp. 1-8

Author(s):

Wenjing Xu ◽

Jianqiang Li ◽

Juan Li ◽

Ji-Jiang Yang ◽

Qing Wang ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Signaling Pathway ◽

Wnt Signaling Pathway ◽

Gene Expression Omnibus ◽

Regenerative Therapy ◽

Kegg Pathways ◽

Significant Gene ◽

Gene Modules ◽

Neurotrophin Signaling

Dental pulp stem cells (DPSCs) have the property of self-renewal and multidirectional differentiation so that they have the potential for future regenerative therapy of various diseases. The latest breakthrough in the biology of stem cells and the development of regenerative biology provides an effective strategy for regenerative therapy. However, in the medium promoting differentiation during long-term passage, DPSCs would lose their differentiation capability. Some efforts have been made to find genes influencing human DPSC (hDPSC) differentiation based on hDPSCs isolated from adults. However, hDPSC differentiation is a very complex process, which involves multiple genes and multielement interactions. The purpose of this study is to detect sets of correlated genes (i.e., gene modules) that are associated to hDPSC differentiation at the crown-completed stage of the third molars, by using weighted gene coexpression network analysis (WGCNA). Based on the gene expression dataset GSE10444 from Gene Expression Omnibus (GEO), we identified two significant gene modules: yellow module (742 genes) and salmon module (9 genes). The WEB-based Gene SeT AnaLysis Toolkit showed that the 742 genes in the yellow module were enriched in 59 KEGG pathways (including Wnt signaling pathway), while the 9 genes in the salmon module were enriched in one KEGG pathway (neurotrophin signaling pathway). There were 660 (7) genes upregulated at P10 and 82 (2) genes downregulated at P10 in the yellow (salmon) module. Our results provide new insights into the differentiation capability of hDPSCs.

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Identification of key pathways and hub genes in the myogenic differentiation of pluripotent stem cell: A bioinformatics and experimental study

10.21203/rs.3.rs-41291/v2 ◽

2020 ◽

Author(s):

Wenyong Fei ◽

Mingsheng Liu ◽

Yao Zhang ◽

Shichao Cao ◽

Xuanqi Wang ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Actin Cytoskeleton ◽

Myogenic Differentiation ◽

Ppi Network ◽

Hub Genes ◽

Differentiated Cells ◽

Key Genes ◽

Key Pathways

Abstract Background: The regeneration of muscle cells from stem cells is an intricate process and various genes are included in the process as myoD, mf5, mf6 etc. The key genes and pathways in the differentiating stages is various. Therefore, the differential expression of key genes after 4weeks of differentiation were investigated in our study. Method: Three published gene expression profiles, GSE131125, GSE148994, GSE149055, about the comparisons of pluripotent stem cells to differentiated cells after 4 weeks were obtained from the Gene Expression Omnibus (GEO) database. Common differentially expressed genes (DEGs) were obtained for further analysis as proteinprotein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and GSEA analysis. After hub genes and key pathways were obtained, we manipulated in vitro cell research for substantiation as immunohistochemical staining and semi-quantitative analysis and quantitative real-time PCR. Results: A total of 824 DEGs including 350 up-regulated genes and 474 down-regulated genes were identified in the three GSEs. 19 hub genes were identified from the PPI network. The GO and KEGG pathway analysis confirmed that myogenic differentiation at 4 weeks was strongly associated with pathway in cancer, PI3K pathway, actin cytoskeleton regulation and metabolic pathway, biosynthesis of antibodies and cell cycle. GSEA analysis indicated the differentiated cells were enriched in muscle cell development and myogenesis. Meanwhile, the core genes in each pathway were identified from the GSEA analysis. The in vitro cell research revealed that actin cytoskeleton and myoD were up-regulated after 4 weeks differentiation. Conclusions: The research revealed the potential hub genes and key pathways after 4 weeks differentiation of stem cells which contribute to further study about the molecular mechanism of myogenesis regeneration. Paving a way for more accurate treatment for muscle dysfunction.

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Identification of key pathways and hub genes in the myogenic differentiation of pluripotent stem cell: a bioinformatics and experimental study

Journal of Orthopaedic Surgery and Research ◽

10.1186/s13018-020-01979-x ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Wenyong Fei ◽

Mingsheng Liu ◽

Yao Zhang ◽

Shichao Cao ◽

Xuanqi Wang ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Actin Cytoskeleton ◽

Myogenic Differentiation ◽

Ppi Network ◽

Hub Genes ◽

Differentiated Cells ◽

Key Genes ◽

Key Pathways

Abstract Background The regeneration of muscle cells from stem cells is an intricate process, and various genes are included in the process such as myoD, mf5, mf6, etc. The key genes and pathways in the differentiating stages are various. Therefore, the differential expression of key genes after 4 weeks of differentiation were investigated in our study. Method Three published gene expression profiles, GSE131125, GSE148994, and GSE149055, about the comparisons of pluripotent stem cells to differentiated cells after 4 weeks were obtained from the Gene Expression Omnibus (GEO) database. Common differentially expressed genes (DEGs) were obtained for further analysis such as protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and GSEA analysis. After hub genes and key pathways were obtained, we manipulated in vitro cell research for substantiation such as immunohistochemical staining and semi-quantitative analysis and quantitative real-time PCR. Results A total of 824 DEGs including 350 upregulated genes and 474 downregulated genes were identified in the three GSEs. Nineteen hub genes were identified from the PPI network. The GO and KEGG pathway analyses confirmed that myogenic differentiation at 4 weeks was strongly associated with pathway in cancer, PI3K pathway, actin cytoskeleton regulation and metabolic pathway, biosynthesis of antibodies, and cell cycle. GSEA analysis indicated the differentiated cells were enriched in muscle cell development and myogenesis. Meanwhile, the core genes in each pathway were identified from the GSEA analysis. The in vitro cell research revealed that actin cytoskeleton and myoD were upregulated after 4-week differentiation. Conclusions The research revealed the potential hub genes and key pathways after 4-week differentiation of stem cells which contribute to further study about the molecular mechanism of myogenesis regeneration, paving a way for more accurate treatment for muscle dysfunction.

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Effect of Uniaxial Tensile Cyclic Loading Regimes on Matrix Organization and Tenogenic Differentiation of Adipose-Derived Stem Cells Encapsulated within 3D Collagen Scaffolds

Stem Cells International ◽

10.1155/2017/6072406 ◽

2017 ◽

Vol 2017 ◽

pp. 1-16 ◽

Cited By ~ 5

Author(s):

Gayathri Subramanian ◽

Alexander Stasuk ◽

Mostafa Elsaadany ◽

Eda Yildirim-Ayan

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Expression Profiles ◽

Three Dimensional ◽

Uniaxial Tensile ◽

Adipose Derived Stem Cells ◽

Collagen Scaffolds ◽

Differentiation Potential ◽

Tenogenic Differentiation ◽

Matrix Organization

Adipose-derived mesenchymal stem cells have become a popular cell choice for tendon repair strategies due to their relative abundance, ease of isolation, and ability to differentiate into tenocytes. In this study, we investigated the solo effect of different uniaxial tensile strains and loading frequencies on the matrix directionality and tenogenic differentiation of adipose-derived stem cells encapsulated within three-dimensional collagen scaffolds. Samples loaded at 0%, 2%, 4%, and 6% strains and 0.1 Hz and 1 Hz frequencies for 2 hours/day over a 7-day period using a custom-built uniaxial tensile strain bioreactor were characterized in terms of matrix organization, cell viability, and musculoskeletal gene expression profiles. The results displayed that the collagen fibers of the loaded samples exhibited increased matrix directionality with an increase in strain values. Gene expression analyses demonstrated that ASC-encapsulated collagen scaffolds loaded at 2% strain and 0.1 Hz frequency showed significant increases in extracellular matrix genes and tenogenic differentiation markers. Importantly, no cross-differentiation potential to osteogenic, chondrogenic, and myogenic lineages was observed at 2% strain and 0.1 Hz frequency loading condition. Thus, 2% strain and 0.1 Hz frequency were identified as the appropriate mechanical loading regime to induce tenogenic differentiation of adipose-derived stem cells cultured in a three-dimensional environment.

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