Potential landscape decomposes the cell identity conversion in liver regeneration and tumorigenesis [scRNA-seq]

Tumorigenesis, accompanied by tissue regenerative responses, always occurs during mammalian organ injury. In liver, injury context promotes dedifferentiated liver progenitor-like cells (LPLCs) from hepatocytes for regeneration, and also increases the occurrence of hepatocellular carcinoma (HCC). However, little is known about the contribution of injury specific LPLCs to tumorigenesis. Here, by using lineage tracing model, we have demonstrated that LPLCs are highly susceptible to oncogene-induced tumorigenesis. By using quantitative landscape of differentiation dynamics (LDD) model, we have constructed potential landscape of liver regeneration and tumorigenesis via scRNA-seq data, in order to predict distinct regulations of cell fate decisions. Applying this landscape with in vivo validation by transgenic mouse model, we have found blocking Wnt activation not only inhibits tumorigenesis, but also decreases LPLCs. Surprisingly, by using least action pathway analysis, we have decomposed regeneration and tumorigenesis routes, and found EP300 is specifically involved in tumorigenesis, which is further supported by in vivo EP300-knockout model and EP300 inhibitor assays. These findings might be applied as a framework to find tumor-specific regulators and develop strategies specifically inhibiting tumor initiation while leaving tissue regeneration unaffected. Overall design: Single-cell RNA sequencing of hepatocytes, LPLCs and DDC&cMet induced HCC cells in liver

肿瘤发生这一过程，在哺乳动物器官损伤期间总会伴随组织再生反应一同发生。在肝脏中，损伤微环境可促使肝细胞向去分化肝祖细胞样细胞（liver progenitor-like cells, LPLCs）转化以完成再生，同时也会提升肝细胞癌（hepatocellular carcinoma, HCC）的发生风险。然而，目前学界对于损伤特异性肝祖细胞样细胞在肿瘤发生中的作用贡献仍知之甚少。本研究借助谱系示踪模型，证实肝祖细胞样细胞对癌基因诱导的肿瘤发生具有高度易感性。通过分化动力学定量景观模型（quantitative landscape of differentiation dynamics, LDD model），我们基于单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）数据构建了肝脏再生与肿瘤发生的潜在景观，以此预测细胞命运决定的不同调控机制。结合转基因小鼠模型的体内验证对该景观进行分析后，我们发现阻断Wnt信号激活不仅可抑制肿瘤发生，还能减少肝祖细胞样细胞的数量。令人意外的是，本研究通过最小作用路径分析解析了再生与肿瘤发生的细胞通路，并发现EP300特异性参与肿瘤发生过程，这一结论进一步得到了EP300基因敲除小鼠模型及EP300抑制剂实验的体内验证。上述研究结果可作为寻找肿瘤特异性调控因子的研究框架，用于开发在不影响组织再生的前提下特异性抑制肿瘤起始的治疗策略。整体实验设计：对肝脏中的肝细胞、肝祖细胞样细胞及DDC联合cMet诱导的肝细胞癌细胞进行单细胞RNA测序。