Transcriptomic landscape of human induced pluripotent stem cell-derived osteogenic differentiation identifies a regulatory role of KLF16.
Transcriptomic landscape of human induced pluripotent stem cell-derived osteogenic differentiation identifies a regulatory role of KLF16.
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人类诱导多能干细胞来源的成骨分化的转录组景观确定了 KLF16 的调节作用。
DOI：
10.1101/2024.02.11.579844
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发表时间：
2024
期刊：
影响因子：
--
通讯作者：
Jabs,Ethyli
中科院分区：
文献类型：
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作者：
Ru,Ying;Ma,Meng;Zhou,Xianxiao;Kriti,Divya;Cohen,Ninette;D'Souza,Sunita;Schaniel,Christoph;MotchPerrine,SusanM;Kuo,Sharon;Pinto,Dalila;Housman,Genevieve;Wu,Meng;Holmes,Greg;Schadt,Eric;vanBakel,Harm;Zhang,Bin;Jabs,Ethyli
成骨分化对于骨发育、新陈代谢和修复是必不可少的；然而，基因之间潜在的调控关系仍然知之甚少。为了阐明转录水平的变化并寻找参与成骨分化的新的调控基因，我们将20株人IPSC来源的间充质干细胞(MSCs)分化为成骨前细胞(PreObs)和成骨细胞(OBS)。然后，我们对MSCs、前OB和OBS进行了转录组分析。IPSC来源的MSCs和OBS分别显示出与原代人MSCs和OBS相似的转录组图谱。基因差异表达分析显示，从MSCs到前OBS，再到OBS，转录本的整体变化，包括840个编码转录因子(TF)的基因的差异表达。信托基金监管网络分析揭示了一个由451个信托基金组成的网络，这些基金被组织成五个互动模块。多尺度嵌入式基因共表达网络分析(MEGENA)确定了基因共表达模块和关键网络调节因子(KNRs)。从这些分析来看，KLF16在成骨分化过程中是一个重要的转铁蛋白。我们证明，在体外过表达KLF16抑制了成骨分化和矿化，而KLF16+/−小鼠表现出骨密度、骨小梁数量和皮质骨面积增加。我们的研究强调了成骨分化的复杂性，并发现了新的调控基因，如KLF16，它在体外和体内都对成骨分化起抑制作用。
Osteogenic differentiation is essential for bone development, metabolism, and repair; however, the underlying regulatory relationships among genes remain poorly understood. To elucidate the transcriptomic changes and identify novel regulatory genes involved in osteogenic differentiation, we differentiated mesenchymal stem cells (MSCs) derived from 20 human iPSC lines into preosteoblasts (preOBs) and osteoblasts (OBs). We then performed transcriptome profiling of MSCs, preOBs and OBs. The iPSC-derived MSCs and OBs showed similar transcriptome profiles to those of primary human MSCs and OBs, respectively. Differential gene expression analysis revealed global changes in the transcriptomes from MSCs to preOBs, and then to OBs, including the differential expression of 840 genes encoding transcription factors (TFs). TF regulatory network analysis uncovered a network comprising 451 TFs, organized into five interactive modules. Multiscale embedded gene co-expression network analysis (MEGENA) identified gene co-expression modules and key network regulators (KNRs). From these analyses, KLF16 emerged as an important TF in osteogenic differentiation. We demonstrate that overexpression of Klf16 in vitro inhibited osteogenic differentiation and mineralization, while Klf16+/− mice exhibited increased bone mineral density, trabecular number, and cortical bone area. Our study underscores the complexity of osteogenic differentiation and identifies novel regulatory genes such as KLF16, which plays an inhibitory role in osteogenic differentiation both in vitro and in vivo.