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Transcriptomic Landscape of Human iPSCs-derived Osteogenic Differentiation Identifies a Key Regulator, KLF16

ABSTRACT: The osteogenic differentiation process is essential for bone development and metabolism, but the underlying gene regulatory networks have not been well investigated. In this study, we performed RNA-seq analysis of mesenchymal stem cell differentiation to preosteoblasts and osteoblasts, derived from normal human induced pluripotent stem cell (iPSC) lines. Systematic analyses revealed potential transcription factor (TF) - TF regulatory networks, regulatory roles of long noncoding RNAs (lncRNAs), and differential splicing of extracellular matrix, TF, lncRNA, and splicing factor genes. TF-TF regulatory and gene co-expression network analyses predicted a key role for KLF16 in osteogenesis. In vitro and in vivo biological functional studies further established the inhibitory role of Klf16 in osteogenesis. Our model system and transcriptomic approach identify novel osteogenic genes and highlight the regulatory complexity of osteogenesis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE200492 | GEO | 2024/03/06

REPOSITORIES: GEO

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Project description:The intriThe intricate balance between MSCs differentiation to osteoblasts or adipocytes is finely regulated. To explore novel participating molecules, we screened for early-stage osteogenesis- or adipogenesis-based MSCs protein expression profile using TMT-based quantitative proteomic analysis. Protein annotation, hierarchical clustering, functional stratification, and protein-protein association assessments were performed. Moreover, two upregulated proteins, namely, FBLN2 and NPR3, were validated to participate in the osteogenic differentiation process of MSCs. Subsequently, we independently downregulated FBLN2 and NPR3 during 7 days of osteogenic differentiation, and conducted quantitative proteomics analysis to assess the differential protein regulation between knockdown and control cells. Based on gene ontology (GO) and network analyses, FBLN2 deficiency induced functional alterations associated with biological regulation and stimulus response, whereas, NPR3 deficiency induced functional alterations related to cellular and metabolic processes, and so on. These results demonstrated that proteomics is still an effective tool for the comprehensive exploration of the MSCs differentiation process. cate balance between MSCs differentiation to osteoblasts or adipocytes is finely regulated. To explore novel participating molecules, we screened for early-stage osteogenesis- or adipogenesis-based MSCs protein expression profile using TMT-based quantitative proteomic analysis. Protein annotation, hierarchical clustering, functional stratification, and protein-protein association assessments were performed. Moreover, two upregulated proteins, namely, FBLN2 and NPR3, were validated to participate in the osteogenic differentiation process of MSCs. Subsequently, we independently downregulated FBLN2 and NPR3 during 7 days of osteogenic differentiation, and conducted quantitative proteomics analysis to assess the differential protein regulation between knockdown and control cells. Based on gene ontology (GO) and network analyses, FBLN2 deficiency induced functional alterations associated with biological regulation and stimulus response, whereas, NPR3 deficiency induced functional alterations related to cellular and metabolic processes, and so on. These results demonstrated that proteomics is still an effective tool for the comprehensive exploration of the MSCs differentiation process.

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Transcriptomic Landscape of Human iPSCs-derived Osteogenic Differentiation Identifies a Key Regulator, KLF16

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