Comparative Transcriptome Analysis of Human Adipose-Derived Stem Cells Undergoing Osteogenesis in 2D and 3D Culture Conditions

Abstract

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.

Revolutionizing Disease Modeling: The Emergence of Organoids in Cellular Systems

“…Despite these limitations, 2D cell culture remains a valuable tool in the laboratory, and many advances were made in recent years to improve the system, such as techniques for analyzing and characterizing cells, such as high-content imaging and transcriptomics. These techniques allow for a more detailed understanding of the behavior and characteristics of cells in culture [ 104 , 105 ].…”

Advanced Nanofiber-Based Scaffolds for Achilles Tendon Regenerative Engineering

“…Since they are stem cells, it is crucial to provide them with the proper signals so that they differentiate toward tendinocyte lines, and they do not differentiate toward osteogenic lines resulting in ECM characteristics of bone tissue rather than tendon tissue ( Loebel and Burdick, 2018 ). The most commonly used stem cells in tendon tissue engineering are MSCs ( Kim et al, 2021 ), TSPCs ( Zhang et al, 2019 ), and IPSCs ( Tsutsumi et al, 2022 ), which can also give rise to tendinocytes or fibroblasts after differentiation.…”

Mesenchymal Stem/Progenitor Cells and Their Derivates in Tissue Regeneration

“…Molecular and transcriptomic background of osteogenesis of hADSCs was studied by Kim and co-workers in two-dimensional (2D) and three-dimensional (3D) culture conditions [ 7 ]. The comprehensive transcriptome expression profiles during osteogenic differentiation of hADSCs under different culture conditions revealed that the genes related to bone development and bone remodeling processes were overexpressed in the 3D culture condition.…”