Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration [scATAC-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. Profiling of chromatin accessibility of liver hepatocytes by high throughput sequencing

成年肝脏具备极强的再生能力：即使在丢失三分之二组织质量的情况下，仍可完成再生并维持核心代谢功能。目前学界尚未明确肝脏如何在满足增殖活性提升与维持器官功能这双重需求间达成平衡，但该机制对预防肝功能衰竭至关重要。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ATAC测序（ATAC sequencing）技术，在肝脏再生过程中以单细胞分辨率对约13000个肝细胞的状态转变进行图谱绘制，并通过免疫组织化学（immunohistochemistry）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的机制。部分肝切除术后，肝细胞会快速且短暂地分化为多个功能特征各异的独特细胞群，呈现出明确的功能分叉：一部分细胞保留未受损成年肝脏中肝细胞的染色质景观与转录组特征，另一部分则发生转变，获得胎儿肝细胞的染色质景观与转录组特征。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的染色质景观中，受这些通路调控的转录因子结合位点显著富集。通过高通量测序对肝脏肝细胞的染色质可及性进行谱图分析。