Comparative transcriptome analysis of human adipose-derived stem cells undergoing osteogenesis in 2d and 3d culture conditions

Byung Chul Kim, Kyu Hwan Kwack, Jeewan Chun, Jae Hyung Lee

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Human adipose-derived stem cells (hADSCs) are types of mesenchymal stem cells (MSCs) that have been used as tissue engineering models for bone, cartilage, muscle, marrow stroma, tendon, fat and other connective tissues. Tissue regeneration materials composed of hADSCs have the potential to play an important role in reconstituting damaged tissue or diseased mesenchymal tissue. In this study, we assessed and investigated the osteogenesis of hADSCs in both two-dimensional (2D) and three-dimensional (3D) culture conditions. We confirmed that the hADSCs successfully differentiated into bone tissues by ARS staining and quantitative RT–PCR. To gain insight into the detailed biological difference between the two culture conditions, we profiled the overall gene expression by analyzing the whole transcriptome sequencing data using various bioinformatic methods. We profiled the overall gene expression through RNA-Seq and further analyzed this using various bioinformatic methods. During differential gene expression testing, significant differences in the gene expressions between hADSCs cultured in 2D and 3D conditions were observed. The genes related to skeletal development, bone development and bone remodeling processes were overexpressed in the 3D culture condition as compared to the 2D culture condition. In summary, our RNA-Seq-based study proves effective in providing new insights that contribute toward achieving a genome-wide understanding of gene regulation in mesenchymal stem cell osteogenic differentiation and bone tissue regeneration within the 3D culture system.

Original languageEnglish
Article number7939
JournalInternational Journal of Molecular Sciences
Issue number15
Publication statusPublished - 1 Aug 2021


  • Bioinformatics
  • Human adipose-derived stem cells (hADSCs)
  • Osteogenic differentiation
  • RNA-Seq
  • Three-dimensional (3D) culture


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