Ru Ying, Ma Meng, Zhou Xianxiao, Kriti Divya, Cohen Ninette, D'Souza Sunita, Schaniel Christoph, Motch Perrine Susan M, Kuo Sharon, Pichurin Oksana, Pinto Dalila, Housman Genevieve, Holmes Greg, Schadt Eric, van Bakel Harm, Zhang Bin, Jabs Ethylin Wang, Wu Meng
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
Mount Sinai Genomics, Sema4, Stamford, CT, 06902, USA.
bioRxiv. 2025 Jan 27:2024.02.11.579844. doi: 10.1101/2024.02.11.579844.
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, emerged as an important TF in osteogenic differentiation. We demonstrate that overexpression of in vitro inhibited osteogenic differentiation and mineralization, while 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 , which plays an inhibitory role in osteogenic differentiation both in vitro and in vivo.
成骨分化对于骨骼发育、代谢和修复至关重要；然而，基因之间潜在的调控关系仍知之甚少。为了阐明转录组变化并鉴定参与成骨分化的新型调控基因，我们将源自20个人诱导多能干细胞（iPSC）系的间充质干细胞（MSC）分化为前成骨细胞（preOB）和成骨细胞（OB）。然后，我们对MSC、preOB和OB进行了转录组分析。iPSC衍生的MSC和OB分别显示出与原代人MSC和OB相似的转录组图谱。差异基因表达分析揭示了从MSC到preOB，再到OB的转录组的全局变化，包括840个编码转录因子（TF）的基因的差异表达。TF调控网络分析揭示了一个由451个TF组成的网络，该网络被组织成五个相互作用的模块。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（KNR）。通过这些分析，[具体基因名称未给出]在成骨分化中成为一个重要的TF。我们证明，在体外过表达[具体基因名称未给出]会抑制成骨分化和矿化，而[具体基因名称未给出]基因敲除小鼠表现出骨矿物质密度、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，并鉴定了新型调控基因，如[具体基因名称未给出]基因，其在体外和体内的成骨分化中均起抑制作用。
