Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Computer Science, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.
Cell Stem Cell. 2019 Jul 3;25(1):149-164.e9. doi: 10.1016/j.stem.2019.05.020. Epub 2019 Jun 20.
Direct cellular reprogramming provides a powerful platform to study cell plasticity and dissect mechanisms underlying cell fate determination. Here, we report a single-cell transcriptomic study of human cardiac (hiCM) reprogramming that utilizes an analysis pipeline incorporating current data normalization methods, multiple trajectory prediction algorithms, and a cell fate index calculation we developed to measure reprogramming progression. These analyses revealed hiCM reprogramming-specific features and a decision point at which cells either embark on reprogramming or regress toward their original fibroblast state. In combination with functional screening, we found that immune-response-associated DNA methylation is required for hiCM induction and validated several downstream targets of reprogramming factors as necessary for productive hiCM reprograming. Collectively, this single-cell transcriptomics study provides detailed datasets that reveal molecular features underlying hiCM determination and rigorous analytical pipelines for predicting cell fate conversion.
直接细胞重编程为研究细胞可塑性和剖析细胞命运决定的机制提供了一个强大的平台。在这里,我们报告了一项利用整合了当前数据标准化方法、多个轨迹预测算法以及我们开发的细胞命运指数计算的单细胞转录组学研究,用于测量重编程进展。这些分析揭示了 hiCM 重编程特有的特征和一个决策点,在此决策点处,细胞要么开始重编程,要么向其原始成纤维细胞状态倒退。与功能筛选相结合,我们发现免疫反应相关的 DNA 甲基化对于 hiCM 的诱导是必需的,并验证了几个重编程因子的下游靶标作为高效 hiCM 重编程所必需的。总的来说,这项单细胞转录组学研究提供了详细的数据集,揭示了 hiCM 决定的分子特征和用于预测细胞命运转换的严格分析管道。