Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration [RNA-Seq]

Adult liver has enormous regenerative capacity as it can regenerate after losing two-thirds of its mass while sustaining essential metabolic functions. How the liver balances dual demands for increased proliferative activity with maintenance of organ function is unknown, but essential to prevent liver failure. Using partial hepatectomy (PHx) in mice to model liver regeneration, we integrated single-cell RNA and ATAC sequencing to map state transitions in ~ 13,000 hepatocytes at single-cell resolution as livers regenerated, and validated key findings with immunohistochemistry, to uncover how the organ regenerates hepatocytes while simultaneously fulfilling its vital tissue-specific functions. After PHx, hepatocytes rapidly and transiently diversified into multiple distinct populations with distinct functional bifurcation: some retained the chromatin landscapes and transcriptomes of hepatocytes in undamaged adult livers while others transitioned to acquire chromatin landscapes and transcriptomes of fetal hepatocytes. Injury-related signaling pathways known to be critical for regeneration were activated in transitioning hepatocytes and the most fetal-like hepatocytes exhibited chromatin landscapes that were enriched with transcription factors regulated by those pathways. Overall design: Profiling of transcriptomes of liver hepatocytes by high throughput sequencing

成年肝脏具备极强的再生能力：即使在丧失三分之二的组织质量后，仍可完成再生并维持核心代谢功能。目前尚不明确肝脏如何平衡「增殖活动增强」与「维持器官功能」的双重需求，但该机制对预防肝衰竭至关重要。本研究以小鼠部分肝切除术（partial hepatectomy, PHx）构建肝脏再生模型，整合单细胞RNA测序（single-cell RNA sequencing）与转座酶可及性染色质测序（assay for transposase-accessible chromatin sequencing, ATAC-seq），在肝脏再生过程中以单细胞分辨率绘制约13000个肝细胞的状态转变轨迹，并通过免疫组织化学实验验证关键发现，以揭示肝脏在再生肝细胞的同时，如何维持其关键组织特异性功能。部分肝切除术后，肝细胞会快速且短暂地分化为多个存在功能分化差异的独特细胞群：一部分保留未受损成年肝脏肝细胞的染色质景观与转录组特征，另一部分则转变为具有胎儿肝细胞染色质景观与转录组特征的细胞群。已知对肝脏再生至关重要的损伤相关信号通路，在发生转变的肝细胞中被激活；且最接近胎儿表型的肝细胞，其染色质景观富集了受这些通路调控的转录因子。总体实验设计：通过高通量测序对肝脏肝细胞的转录组开展表征分析。