Genome-wide association studies (GWASs) have advanced our understanding of the genetics of osteoporosis; however, the challenge has been converting associations to causal genes. Studies have utilized transcriptomics data to link disease-associated variants to genes, but few population transcriptomics data sets have been generated on bone at the single-cell level. To address this challenge, we profiled the transcriptomes of bone marrow–derived stromal cells (BMSCs) cultured under osteogenic conditions from five diversity outbred (DO) mice using single-cell RNA-seq (scRNA-seq). The goal of the study was to determine if BMSCs could serve as a model to generate cell type–specific transcriptomic profiles of mesenchymal lineage cells from large populations of mice to inform genetic studies. By enriching for mesenchymal lineage cells in vitro, coupled with pooling of multiple samples and downstream genotype deconvolution, we demonstrate the scalability of this model for population-level studies. We demonstrate that dissociation of BMSCs from a heavily mineralized matrix had little effect on viability or their transcriptomic signatures. Furthermore, we show that BMSCs cultured under osteogenic conditions are diverse and consist of cells with characteristics of mesenchymal progenitors, marrow adipogenic lineage precursors (MALPs), osteoblasts, osteocyte-like cells, and immune cells. Importantly, all cells were similar from a transcriptomic perspective to cells isolated in vivo. We employed scRNA-seq analytical tools to confirm the biological identity of profiled cell types. SCENIC was used to reconstruct gene regulatory networks (GRNs), and we observed that cell types show GRNs expected of osteogenic and pre-adipogenic lineage cells. Further, CELLECT analysis showed that osteoblasts, osteocyte-like cells, and MALPs captured a significant component of bone mineral density (BMD) heritability. Together, these data suggest that BMSCs cultured under osteogenic conditions coupled with scRNA-seq can be used as a scalable and biologically informative model to generate cell type–specific transcriptomic profiles of mesenchymal lineage cells in large populations. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

中文翻译：

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多样性远交小鼠骨髓基质细胞的单细胞转录组学：群体水平 scRNA 测序研究的模型

全基因组关联研究（GWAS）增进了我们对骨质疏松症遗传学的理解；然而，挑战是将关联转化为因果基因。研究利用转录组学数据将疾病相关变异与基因联系起来，但很少在单细胞水平上在骨骼上生成群体转录组学数据集。为了应对这一挑战，我们使用单细胞 RNA-seq (scRNA-seq) 对五只多样性远交 (DO) 小鼠在成骨条件下培养的骨髓源性基质细胞 (BMSC) 的转录组进行了分析。该研究的目的是确定 BMSC 是否可以作为模型来生成来自大量小鼠的间充质谱系细胞的细胞类型特异性转录组图谱，为遗传研究提供信息。通过体外富集间充质谱系细胞，再加上多个样本的汇集和下游基因型反卷积，我们证明了该模型在群体水平研究中的可扩展性。我们证明，BMSC 从高度矿化的基质中解离对其活力或其转录组特征几乎没有影响。此外，我们发现在成骨条件下培养的骨髓间充质干细胞是多样化的，由具有间充质祖细胞、骨​​髓成脂谱系前体（MALP）、成骨细胞、骨细胞样细胞和免疫细胞特征的细胞组成。重要的是，从转录组学的角度来看，所有细胞都与体内分离的细胞相似。我们采用 scRNA-seq 分析工具来确认分析细胞类型的生物学特性。SCENIC 用于重建基因调控网络 (GRN)，我们观察到细胞类型显示出预期的成骨和前脂肪形成谱系细胞的 GRN。此外，CELLECT 分析表明，成骨细胞、骨细胞样细胞和 MALP 捕获了骨矿物质密度 (BMD) 遗传力的重要组成部分。总之，这些数据表明，在成骨条件下培养的 BMSC 与 scRNA-seq 相结合，可用作可扩展且具有生物学信息的模型，以生成大量间充质谱系细胞的细胞类型特异性转录组谱。© 2023 作者。《Journal of Bone and Mineral Research》由 Wiley periodicals LLC 代表美国骨与矿物研究学会 (ASBMR) 出版。