Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.
Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA.
Hepatology. 2021 Jul;74(1):444-457. doi: 10.1002/hep.31704. Epub 2021 Jul 12.
Following liver injury, a fraction of hepatocytes adopt features of biliary epithelial cells (BECs) in a process known as biliary reprogramming. The aim of this study was to elucidate the molecular events accompanying this dramatic shift in cellular identity.
We applied the techniques of bulk RNA-sequencing (RNA-seq), single-cell RNA-seq, and assay for transposase-accessible chromatin with high-throughput sequencing to define the epigenetic and transcriptional changes associated with biliary reprogramming. In addition, we examined the role of TGF-β signaling by profiling cells undergoing reprogramming in mice with hepatocyte-specific deletion in the downstream TGF-β signaling component mothers against decapentaplegic homolog 4 (Smad4). Biliary reprogramming followed a stereotyped pattern of altered gene expression consisting of robust induction of biliary genes and weaker repression of hepatocyte genes. These changes in gene expression were accompanied by corresponding modifications at the chromatin level. Although some reprogrammed cells had molecular features of "fully differentiated" BECs, most lacked some biliary characteristics and retained some hepatocyte characteristics. Surprisingly, single-cell analysis of Smad4 mutant mice revealed a dramatic increase in reprogramming.
Hepatocytes undergo widespread chromatin and transcriptional changes during biliary reprogramming, resulting in epigenetic and gene expression profiles that are similar to, but distinct from, native BECs. Reprogramming involves a progressive accumulation of biliary molecular features without discrete intermediates. Paradoxically, canonical TGF-β signaling through Smad4 appears to constrain biliary reprogramming, indicating that TGF-β can either promote or inhibit biliary differentiation depending on which downstream components of the pathway are engaged. This work has implications for the formation of BECs and bile ducts in the adult liver.
肝损伤后，部分肝细胞在胆管重编程过程中获得胆管上皮细胞（BEC）的特征。本研究旨在阐明伴随细胞身份急剧转变的分子事件。
我们应用批量 RNA 测序（RNA-seq）、单细胞 RNA-seq 和高通量测序的转座酶可及染色质分析技术，定义与胆管重编程相关的表观遗传和转录变化。此外，我们通过对具有肝细胞特异性 Smad4（TGF-β 信号下游成分）缺失的小鼠中发生重编程的细胞进行分析，研究了 TGF-β 信号的作用。胆管重编程遵循改变基因表达的刻板模式，包括胆管基因的强烈诱导和肝细胞基因的较弱抑制。这些基因表达的变化伴随着染色质水平的相应修饰。尽管一些重编程细胞具有“完全分化”BEC 的分子特征，但大多数缺乏一些胆管特征并保留一些肝细胞特征。令人惊讶的是，Smad4 突变小鼠的单细胞分析显示重编程急剧增加。
肝细胞在胆管重编程过程中经历广泛的染色质和转录变化，导致表观遗传和基因表达谱与天然 BEC 相似但又不同。重编程涉及胆管分子特征的逐渐积累，而没有离散的中间产物。矛盾的是，通过 Smad4 的经典 TGF-β 信号似乎限制了胆管重编程，表明 TGF-β 可以促进或抑制胆管分化，具体取决于所涉及的途径下游成分。这项工作对成人肝脏中 BEC 和胆管的形成具有重要意义。
