Single-Cell Transcriptomics of Bone Marrow Stromal Cells in Diversity Outbred Mice: A Model for Population-Level scRNA-Seq Studies.
Single-Cell Transcriptomics of Bone Marrow Stromal Cells in Diversity Outbred Mice: A Model for Population-Level scRNA-Seq Studies.
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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。
DOI：
10.1002/jbmr.4882
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Farber,CharlesR
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文献类型：
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作者：
Dillard,LukeJ;Rosenow,WillT;Calabrese,GinaM;Mesner,LarryD;Al-Barghouthi,BaselM;Abood,Abdullah;Farber,EmilyA;Onengut-Gumuscu,Suna;Tommasini,StevenM;Horowitz,MarkA;Rosen,CliffordJ;Yao,Lutian;Qin,Ling;Farber,CharlesR
全基因组关联研究(GWAS)促进了我们对骨质疏松症遗传学的理解；然而，挑战一直是将关联转化为因果基因。研究利用转录组数据将疾病相关变异与基因联系起来，但在单细胞水平上在骨骼上生成的群体转录组很少。为了应对这一挑战，我们使用单细胞RNA-seq(scRNA-seq)分析了在成骨条件下培养的五种多样性近交系(DO)小鼠的骨髓基质细胞(BMSCs)的转录本。这项研究的目标是确定骨髓间充质干细胞是否可以作为一种模型，从大量小鼠中产生特定细胞类型的间充质系细胞转录图谱，为遗传学研究提供信息。通过在体外丰富间充质系细胞，再加上多个样本的汇集和下游的基因反卷积，我们证明了该模型在种群水平研究中的可扩展性。我们证明，骨髓间充质干细胞从高度矿化的基质中分离出来对其活性或其转录特征几乎没有影响。此外，我们发现在成骨条件下培养的BMSCs是多样的，由具有间充质祖细胞特征的细胞、骨髓成脂前体细胞(MALPs)、成骨细胞、骨样细胞和免疫细胞组成。重要的是，从转录学的角度来看，所有细胞都与体内分离的细胞相似。我们使用scRNA-seq分析工具来确认所描述的细胞类型的生物学特性。Senic被用来重建基因调控网络(GRN)，我们观察到细胞类型显示出成骨和成脂前谱系细胞所期望的GRN。此外，CELLECT分析表明，成骨细胞、骨样细胞和MALP捕获了骨密度(BMD)遗传力的重要组成部分。综上所述，这些数据表明，在成骨条件下培养的BMSCs与scRNA-seq相结合，可以作为一种可扩展的生物学信息模型，在大量人群中产生间充质系细胞的细胞类型特异性转录图谱。作者：《骨与矿物研究杂志》，由Wiley期刊有限责任公司代表美国骨与矿物研究学会(ASBMR)出版。
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 Researchpublished by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).