MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, Tsinghua University, Beijing, China; School of Life Sciences, Tsinghua University, Beijing 100084, China.
School of Life Sciences, Tsinghua University, Beijing 100084, China.
Cell Rep. 2016 May 17;15(7):1467-1480. doi: 10.1016/j.celrep.2016.04.043. Epub 2016 May 5.
The growth plate (GP) comprising sequentially differentiated cell layers is a critical structure for bone elongation and regeneration. Although several key regulators in GP development have been identified using genetic perturbation, systematic understanding is still limited. Here, we used single-cell RNA-sequencing (RNA-seq) to determine the gene expression profiles of 217 single cells from GPs and developed a bioinformatics pipeline named Sinova to de novo reconstruct physiological GP development in both temporal and spatial high resolution. Our unsupervised model not only confirmed prior knowledge, but also enabled the systematic discovery of genes, potential signal pathways, and surface markers CD9/CD200 to precisely depict development. Sinova further identified the effective combination of transcriptional factors (TFs) that regulates GP maturation, and the result was validated using an in vitro EGFP-Col10a screening system. Our case systematically reconstructed molecular cascades in GP development through single-cell profiling, and the bioinformatics pipeline is applicable to other developmental processes. VIDEO ABSTRACT.
生长板（GP）由顺序分化的细胞层组成，是骨骼伸长和再生的关键结构。尽管已经使用遗传干扰鉴定了几个 GP 发育中的关键调节因子，但系统的理解仍然有限。在这里，我们使用单细胞 RNA 测序（RNA-seq）来确定来自 GP 的 217 个单细胞的基因表达谱，并开发了一个名为 Sinova 的生物信息学管道，以在时间和空间高分辨率上从头重建生理 GP 发育。我们的无监督模型不仅证实了先前的知识，还能够系统地发现基因、潜在的信号通路和表面标记物 CD9/CD200，以准确描绘发育过程。Sinova 进一步确定了调节 GP 成熟的转录因子（TFs）的有效组合，并且使用体外 EGFP-Col10a 筛选系统验证了该结果。我们的案例通过单细胞分析系统地重建了 GP 发育中的分子级联反应，并且该生物信息学管道适用于其他发育过程。
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