间充质干细胞(MSC)是多能干细胞,可以分化为多种细胞类型,包括成骨细胞,软骨细胞,和脂肪细胞。成骨细胞分化在骨质疏松发展过程中减少,导致骨形成减少。Further,从不同供体分离的MSC具有不同的成骨能力。在这项研究中,我们使用单细胞多组分析对来自4名健康供体的MSC的转录组和表观基因组进行了分析.对于每个供体,从〜1300至1600个细胞获得数据。这些细胞分为四组,表明来自不同供体的MSC具有不同的染色质可接近的调节元件来调节基因表达。为了研究MSC进行成骨分化的机制,我们使用来自单细胞多体组数据的染色质可及性数据来鉴定个体特异性增强子-启动子对,并评估了转录调节因子的表达水平和活性.来自四个供体的MSC显示出不同的分化为成骨细胞的潜能。供体1的MSC显示出最大的平均基序活动,表明来自供体1的MSC最有可能分化为成骨细胞。我们的验证实验结果与生物信息学预测一致。我们还测试了单细胞多体组数据中确定的患者特异性染色质可访问区域中几种肌肉骨骼疾病特征的全基因组关联研究(GWAS)信号的富集,包括骨质疏松症,骨质减少,和骨关节炎。我们发现骨关节炎相关变体仅在从供体4鉴定的区域中富集。相比之下,骨质疏松和骨质减少变异体在供体1的区域富集,而在供体4的区域富集最少.由于骨质疏松和骨质减少与骨细胞密度有关,来自这些性状的变体的富集应该与MSC的成骨潜力相关。总之,这项研究提供了大规模数据,将调控元件与其靶基因联系起来,以研究间充质干细胞分化过程中的调控关系,并为基因调控机制提供更深入的见解。
Mesenchymal stem cells (MSC) are multipotent stem cells that can differentiate into multiple cell types, including osteoblasts, chondrocytes, and adipocytes. Osteoblast differentiation is reduced during osteoporosis development, resulting in reduced bone formation. Further, MSC isolated from different donors possess distinct osteogenic capacity. In this study, we used single-cell multiomic analysis to profile the transcriptome and epigenome of MSC from four healthy donors. Data were obtained from ~1300 to 1600 cells for each donor. These cells were clustered into four groups, indicating that MSC from different donors have distinct chromatin accessible regulatory elements for regulating gene expression. To investigate the mechanism by which MSC undergo osteogenic differentiation, we used the chromatin accessibility data from the single-cell multiome data to identify individual-specific enhancer-promoter pairs and evaluated the expression levels and activities of the transcriptional regulators. The MSC from four donors showed distinct differentiation potential into osteoblasts. MSC of donor 1 showed the largest average motif activities, indicating that MSC from donor 1 was most likely to differentiate into osteoblasts. The results of our validation experiments were consistent with the bioinformatics prediction. We also tested the enrichment of genome-wide association study (GWAS) signals of several musculoskeletal disease traits in the patient-specific chromatin accessible regions identified in the single-cell multiome data, including osteoporosis, osteopenia, and osteoarthritis. We found that osteoarthritis-associated variants were only enriched in the regions identified from donor 4. In contrast, osteoporosis and osteopenia variants were enriched in regions from donor 1 and least enriched in donor 4. Since osteoporosis and osteopenia are related to the density of bone cells, the enrichment of variants from these traits should be correlated with the osteogenic potential of MSC. In summary, this study provides large-scale data to link regulatory elements with their target genes to study the regulatory relationships during the differentiation of mesenchymal stem cells and provide a deeper insight into the gene regulatory mechanism.