scholarly journals Identification of potential biomarkers or therapeutic targets of mesenchymal stem cells in multiple myeloma by bioinformatics analysis

2020 ◽  
Author(s):  
Zhi-Ran Li ◽  
Wen-Ke Cai ◽  
Qin Yang ◽  
Ming-Li Shen ◽  
Hua-Zhu Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Multiple Myeloma ◽  
Mesenchymal Stem Cells ◽  
Bioinformatics Analysis ◽  
Expression Profiles ◽  
Therapeutic Targets ◽  
Ppi Network ◽  
Key Genes ◽  
Potential Biomarkers

AbstractObjectivesMesenchymal stem cells (MSCs) play important roles in multiple myeloma (MM) pathogenesis. Previous studies have discovered a group of MM-associated potential biomarkers in MSCs derived from bone marrow (BM-MSCs). However, no study of the bioinformatics analysis was conducted to explore the key genes and pathways of MSCs derived from adipose (AD-MSCs) in MM. The aim of this study was to screen potential biomarkers or therapeutic targets of AD-MSCs and BM-MSCs in MM.MethodsThe gene expression profiles of AD-MSCs (GSE133346) and BM-MSCs (GSE36474) were downloaded from Gene Expression Omnibus (GEO) database. Gene Oncology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and protein-protein interaction (PPI) network of differentially expressed genes (DEGs) were performed.ResultsA total of 456 common downregulated DEGs in two datasets were identified and the remaining DEGs in GSE133346 were further identified as specific DEGs of AD-MSCs. Furthermore, a PPI network of common downregulated DEGs was constructed and seven hub genes were identified. Importantly, cell cycle was the most significantly enrichment pathway both in AD-MSCs and BM-MSCs from MM patients.ConclusionWe identified key genes and pathways closely related with MM progression, which may act as potential biomarkers or therapeutic targets of MM.

scholarly journals Identification of key genes and pathways of BMP-9-induced osteogenic differentiation of mesenchymal stem cells by integrated bioinformatics analysis

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Jia-qi Wu ◽  
Lin-bo Mao ◽  
Ling-feng Liu ◽  
Yong-mei Li ◽  
Jian Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Osteogenic Differentiation ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Pathway Enrichment ◽  
Key Genes

Abstract Background The purpose of present study was to identify the differentially expressed genes (DEGs) associated with BMP-9-induced osteogenic differentiation of mesenchymal stem cells (MSCs) by using bioinformatics methods. Methods Gene expression profiles of BMP-9-induced MSCs were compared between with GFP-induced MSCs and BMP-9-induced MSCs. GSE48882 containing two groups of gene expression profiles, 3 GFP-induced MSC samples and 3 from BMP-9-induced MSCs, was downloaded from the Gene Expression Omnibus (GEO) database. Then, DEGs were clustered based on functions and signaling pathways with significant enrichment analysis. Pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) demonstrated that the identified DEGs were potentially involved in cytoplasm, nucleus, and extracellular exosome signaling pathway. Results A total of 1967 DEGs (1029 upregulated and 938 downregulated) were identified from GSE48882 datasets. R/Bioconductor package limma was used to identify the DEGs. Further analysis revealed that there were 35 common DEGs observed between the samples. GO function and KEGG pathway enrichment analysis, among which endoplasmic reticulum, protein export, RNA transport, and apoptosis was the most significant dysregulated pathway. The result of protein-protein interaction (PPI) network modules demonstrated that the Hspa5, P4hb, Sec61a1, Smarca2, Pdia3, Dnajc3, Hyou1, Smad7, Derl1, and Surf4 were the high-degree hub nodes. Conclusion Taken above, using integrated bioinformatical analysis, we have identified DEGs candidate genes and pathways in BMP-9 induced MSCs, which could improve our understanding of the key genes and pathways for BMP-9-induced osteogenic of MSCs.

Gene Expression Regulation underlying Osteo-, Adipo-, and Chondro-Genic Lineage Commitment of Human Mesenchymal Stem Cells

2013 ◽  
pp. 76-94 ◽  
Author(s):  
Ana M. Sotoca ◽  
Michael Weber ◽  
Everardus J. J. van Zoelen
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Gene Expression Regulation ◽  
Expression Profiles ◽  
Human Mesenchymal Stem Cells ◽  
Gene Expression Profiles ◽  
Stem Cell Differentiation ◽  
Cell Types ◽  
Lineage Commitment

Human mesenchymal stem cells have a high potential in regenerative medicine. They can be isolated from a variety of adult tissues, including bone marrow, and can be differentiated into multiple cell types of the mesodermal lineage, including adipocytes, osteocytes, and chondrocytes. Stem cell differentiation is controlled by a process of interacting lineage-specific and multipotent genes. In this chapter, the authors use full genome microarrays to explore gene expression profiles in the process of Osteo-, Adipo-, and Chondro-Genic lineage commitment of human mesenchymal stem cells.

Gene expression profiles of early adipogenesis in human mesenchymal stem cells

Gene ◽  
2004 ◽  
Vol 340 (1) ◽  
pp. 141-150 ◽  
Author(s):  
Shih-Chieh Hung ◽  
Ching-Fang Chang ◽  
Hsiao-Li Ma ◽  
Tain-Hsiung Chen ◽  
Larry Low-Tone Ho
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Expression Profiles ◽  
Human Mesenchymal Stem Cells ◽  
Gene Expression Profiles

257 EXPRESSION OF DEVELOPMENTAL GENES IN PORCINE NUCLEAR TRANSFER EMBRYOS RECONSTRUCTED WITH BONE MARROW MESENCHYMAL STEM CELLS

2006 ◽  
Vol 18 (2) ◽  
pp. 236
Author(s):  
B. Mohana Kumar ◽  
H.-F. Jin ◽  
J.-G. Kim ◽  
S. Balasubramanian ◽  
S.-Y. Choe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Bone Marrow ◽  
Mesenchymal Stem Cells ◽  
Nuclear Transfer ◽  
Expression Profiles ◽  
Donor Cells ◽  
Fetal Fibroblasts ◽  
Marrow Mesenchymal Stem Cells

Abnormal gene expression is frequently observed in nuclear transfer (NT) embryos and is one of the suggested causes of the low success rates of this approach. Recent study has suggested that adult stem cells may be better donor cells for NT, as their less differentiated state may ease epigenetic reprogramming by the oocyte (Kato et al. 2004 Biol. Reprod. 70, 415-418). In the present study, we investigated the expression profile of some selected genes involved in the development of the pre-implantation embryos of in vivo- and NT-derived origin using bone marrow mesenchymal stem cells (MSCs) and porcine fetal fibroblasts (pFF) as donors. Isolated population of MSCs from porcine bone marrow were characterized by cell-surface antigen profile (CD13pos, CD105pos, CD45neg, and CD133neg) and by their extensive consistent differentiation to multiple mesenchymal lineages (adipocytic, osteocytic and chondrocytic) under controlled in vitro conditions (Pittenger et al. 1999 Science 284, 143-147). Primary cultures of pFF from a female fetus at <30 days of gestation were established. for NT, donor cells at 3-4 passages were employed. Embryos cloned from MSCs showed enhanced developmental potential compared to pFF cloned embryos, indicated by higher rates of blastocyst formation (15.3% � 4.8 and 9.0% � 3.9, respectively) and total cell number (31.5 � 7.2 and 20.5 � 5.4, respectively) in Day 7 blastocysts. Total RNA was extracted from pools (triplicates) of 10 embryos each of 8-cell, morula, and blastocyst stages of in vivo and NT origin using Dynabeads� mRNA DIRECT" kit (Dynal, Oslo, Norway). Reverse transcription was performed with a Superscript" III cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA). Real-time PCR was performed on a Light cycler� using FastStart DNA Master SYBR Green I (Roche Diagnostics, Mannheim, Germany). The expression profiles of genes involved in transcription (Oct-4, Stat3), DNA methylation (Dnmt1), de novo methylation (Dnmt3a), histone deacetylation (Hdac2), anti-apoptosis (Bcl-xL), and embryonic growth (Igf2r) were determined. The mRNA of H2a was employed to normalize the levels. Significant differences (P < 0.05) in the relative abundance of Stat3, Dnmt1, Dnmt3a, Bcl2, and Igf2r were observed in pFF NT embryos compared with in vivo-produced embryos, whereas embryos derived from MSCs showed expression patterns similar to those of in vivo-produced embryos. However, Oct-4 and Hdac2 revealed similar expression profiles in NT- and in vivo-produced embryos. These results indicate that MSC-derived NT embryos had enhanced embryonic development and their gene expression pattern more closely resembled that of in vivo-produced embryos. Hence, less differentiated MSCs may have a more flexible potential in improving the efficiency of the porcine NT technique. This work was supported by Grant No. R05-2004-000-10702-0 from KOSEF, Republic of Korea.

Effect of cell source and osteoblast differentiation on gene expression profiles of mesenchymal stem cells derived from bone marrow or adipose tissue

2019 ◽  
Vol 120 (7) ◽  
pp. 11842-11852 ◽  
Author(s):  
Simone Ortiz Moura Fideles ◽  
Adriana Cassia Ortiz ◽  
Amanda Freire Assis ◽  
Max Jordan Duarte ◽  
Fabiola Singaretti Oliveira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Bone Marrow ◽  
Mesenchymal Stem Cells ◽  
Adipose Tissue ◽  
Osteoblast Differentiation ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cell Source

scholarly journals Gene Expression Profiles of Human Adipose Tissue-Derived Mesenchymal Stem Cells Are Modified by Cell Culture Density

PLoS ONE ◽  
2014 ◽  
Vol 9 (1) ◽  
pp. e83363 ◽  
Author(s):  
Dae Seong Kim ◽  
Myoung Woo Lee ◽  
Keon Hee Yoo ◽  
Tae-Hee Lee ◽  
Hye Jin Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Cell Culture ◽  
Mesenchymal Stem Cells ◽  
Adipose Tissue ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Human Adipose Tissue ◽  
Culture Density

scholarly journals Integrated analysis of DNA methylome and transcriptome reveals the differences in biological characteristics of porcine mesenchymal stem cells from bone marrow and umbilical cord

2019 ◽  
Author(s):  
Yalan Yang ◽  
Zhiguo Liu ◽  
Weimin Zhao ◽  
Lei Huang ◽  
Tianwen Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Stem Cells ◽  
Bone Marrow ◽  
Mesenchymal Stem Cells ◽  
Umbilical Cord ◽  
Expression Profiles ◽  
Biological Characteristics ◽  
Integrated Analysis ◽  
Differentiation Potential

Abstract Background Bone marrow (BM) and umbilical cord (UC) are the main sources of mesenchymal stem cells (MSCs). These two MSCs display significant differences in many biological characteristics, yet the underlying molecular mechanisms need to be explored. Results In this study, to better understanding the biological features of MSCs, we isolated BMMSCs and UCMSCs from inbred Wuzhishan miniature pigs and generated the first global DNA methylation and gene expression profiles of porcine MSCs. The results showed that the osteogenic and adipogenic differentiation ability of porcine BMMSCs is stronger than that of UCMSCs. Stem cell surface marker CD90 were positively detected in both BMMSCs and UCMSCs. 587 genes were differentially methylated (280 hypermethylated and 307 hypomethylated) at the promoter regions between BMMSCs and UCMSCs. Meanwhile, 1,979 differentially expressed genes (1,407 up-regulated and 572 down-regulated) were identified between BMMSCs and UCMSCs. Integrative analysis reveals that 120 genes displayed differences in both gene expression and promoter methylation. Gene Ontology enrichment analysis revealed that these differential genes were associated with cell differentiation, cell migration, and immunogenicity properties. Remarkably, skeletal system development related genes were significantly hypomethylated and up-regulated in UCMSCs, while cell cycle genes were significantly higher down-regulated and hypermethylated, implying UCMSCs have higher cell proliferative activity and lower osteogenic differentiation potential than BMMSCs. Conclusions Our results indicate that DNA methylation plays an important role in regulating the biological characteristics differences between BMMSCs and UCMSCs. The study might provide a molecular theory basis for the application of porcine MSCs in human.

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