Dataset Information

Bioinformatic Analysis of Transcriptomic Data Reveals Novel Key Genes Regulating Osteogenic Differentiation of Human Adipose Stem Cells.

ABSTRACT: Adipose stem cells (ASCs) are an attractive cell source for treating many human diseases including osteoporosis. However, the molecular mechanisms accounting for ASC osteogenesis are poorly known. In this study, ASCs were first isolated from the fat tissues from the patients with osteoporosis. The global transcriptome profile between osteogenic differentiated ASCs and undifferentiated ASCs was compared using RNA sequencing (RNA-seq). Then, bioinformatic analysis was performed to reveal the central genes and pathways that regulated the osteogenic differentiation of ASCs. One of the interested genes C5AR1 was chosen for further investigation. A total of 1521 upregulated and 3020 downregulated genes were identified between the ASCs with osteogenic induction and controls. Functional gene ontology analysis revealed that these significantly differentially expressed genes (DEGs) were associated with cell cycle, protein binding, and nucleotide binding. Pathway analysis showed that many canonical pathways, such as the MAPK signaling pathway and the PI3K-AKT pathway, might actively be involved in regulating osteogenic differentiation of ASCs. A total of three subnetworks and 20 central nodes were identified by the protein-protein interaction analysis. In addition, the expression level of C5AR1 was significantly increased during osteogenic differentiation of ASCs. The downregulation of C5AR1 dramatically reduced the expression levels of osteogenic differentiation biomarkers and calcium nodule formation capacity. Collectively, we have provided a number of novel genes and pathways that might be indispensable for ASC osteogenic differentiation. Manipulating the levels of this candidate gene might contribute to the osteoporosis therapy.

SUBMITTER: Cheng J

PROVIDER: S-EPMC6701308 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Bioinformatic Analysis of Transcriptomic Data Reveals Novel Key Genes Regulating Osteogenic Differentiation of Human Adipose Stem Cells.

Cheng Jinluo J Zhao Xinyuan X Liu Juan J Cui Li L Zhu Yanfeng Y Yuan Xiaoqing X Gao Jianbo J Du Yunfeng Y Yan Xinmin X Hu Shen S

Stem cells international 20190731

Adipose stem cells (ASCs) are an attractive cell source for treating many human diseases including osteoporosis. However, the molecular mechanisms accounting for ASC osteogenesis are poorly known. In this study, ASCs were first isolated from the fat tissues from the patients with osteoporosis. The global transcriptome profile between osteogenic differentiated ASCs and undifferentiated ASCs was compared using RNA sequencing (RNA-seq). Then, bioinformatic analysis was performed to reveal the centr ...[more]

PMID: 31467558

Similar Datasets

Project description:BackgroundStem cell-based therapies show promise as a means of repairing the degenerate intervertebral disc, with growth factors often used alongside cells to help direct differentiation toward a nucleus pulposus (NP)-like phenotype. We previously demonstrated adipose-derived stem cell (ASC) differentiation with GDF6 as optimal for generating NP-like cells through evaluating end-stage differentiation parameters. Here we conducted a time-resolved transcriptomic characterization of ASCs response to GDF6 stimulation to understand the early drivers of differentiation to NP-like cells.MethodsHuman ASCs were treated with recombinant human GDF6 for 2, 6, and 12 h. RNA sequencing and detailed bioinformatic analysis were used to assess differential gene expression, gene ontology (GO), and transcription factor involvement during early differentiation. Quantitative polymerase chain reaction (qPCR) was used to validate RNA sequencing findings and inhibitors used to interrogate Smad and Erk signaling pathways, as well as identify primary and secondary response genes.ResultsThe transcriptomic response of ASCs to GDF6 stimulation was time-resolved and highly structured, with "cell differentiation" "developmental processes," and "response to stimulus" identified as key biological process GO terms. The transcription factor ERG1 was identified as a key early response gene. Temporal cluster analysis of differentiation genes identified positive regulation NP cell differentiation, as well as inhibition of osteogenesis and adipogenesis. A role for Smad and Erk signaling in the regulation of GDF6-induced early gene expression response was observed and both primary and secondary response genes were identified.ConclusionsThis study identifies a multifactorial early gene response that contributes to lineage commitment, with the identification of a number of potentially useful early markers of differentiation of ASCs to NP cells. This detailed insight into the molecular processes in response to GDF6 stimulation of ASCs is important for the development of an efficient and efficacious cell-based therapy for intervertebral disc degeneration-associated back pain.

Project description:Craniomaxillofacial bone defects can occur as a result of congenital, post-oncologic, and high-energy impact conditions. The scale and irregularity of such defects motivate new biomaterials to promote regeneration of the damaged bone. We have recently described a mineralized collagen scaffold capable of instructing stem cell osteogenic differentiation and new bone infill in the absence of traditional osteogenic supplements. Herein, we report the integration of a millimeter-scale reinforcing poly (lactic acid) frame fabricated via 3D-printing into the mineralized collagen scaffold with micron-scale porosity to form a multi-scale mineralized collagen-PLA composite. We describe modifications to the PLA frame design to increase the compressive strength (Young's Modulus, ultimate stress and strain) of the composite. A critical challenge beyond increasing the compressive strength of the collagen scaffold is addressing challenges inherent with the irregularity of clinical defects. As a result, we examined the potential for modifying the frame architecture to render the composite with increased compressive strength in one axis or radial compressibility and shape-fitting capacity in an orthogonal axis. A library of mineralized collagen-PLA composites was mechanically characterized via compression testing and push-out test to describe mechanical performance and shape-fitting capacity. We also report in vitro comparison of the bioactivity of porcine adipose derived stem cells in the mineralized collagen-PLA composite versus the mineralized collagen scaffold via metabolic activity, gene expression, and functional matrix synthesis. The results suggest that incorporation of the PLA reinforcing frame does not negatively influence the osteoinductive nature of the mineralized collagen scaffold. Together, these findings suggest a strategy to address often competing bioactivity, mechanical strength, and shape-fitting design requirements for biomaterials for craniomaxillofacial bone regeneration.

Dataset Information

Bioinformatic Analysis of Transcriptomic Data Reveals Novel Key Genes Regulating Osteogenic Differentiation of Human Adipose Stem Cells.

Publications

Bioinformatic Analysis of Transcriptomic Data Reveals Novel Key Genes Regulating Osteogenic Differentiation of Human Adipose Stem Cells.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets