RNA-Sequencing analysis of liver tissue from female Foxa3-Cre YAP1 knockout mice, Foxa3-Cre YAP1 KO TAZ heterozygous mice, and WT littermate controls, at 3-4 months of age

We developed a mouse model of bile duct paucity by deleting Yes-associated protein 1 (YAP1) in foregut endoderm progenitors, using the Foxa3 promoter to drive Cre expression. YAP1 KO mice are viable postnatally and survive long-term despite a complete failure of intrahepatic bile duct development, resembling the liver phenotype of Alagille syndrome. Adult YAP1 KO mice suffer from severe chronic cholestasis, but show minimal hepatocellular injury, suggesting that the hepatocytes have adapted to preserve liver function and reduce damage from the toxicity of bile acids and bilirubin. We next bred Foxa3-Cre YAP1 KO TAZ heterozygote and Foxa3-Cre YAP1 KO TAZ KO (DKO) mice to assess the role of TAZ in this model. DKO mice and male YAP KO TAZ heterozygotes died around time of birth. The survivors, YAP1 KO TAZ heterozygote females, were overall phenotypically similar to YAP1 KO mice, with absence of intrahepatic bile ducts and long-term survival. We used RNA-seq to analyze the gene expression patterns of whole liver tissue of female adult YAP1 KO mice compared to WT controls (C57BL/6 background), and female adult YAP1 KO TAZ heterozygote (YKTH) mice compared to WT controls (mixed C57BL/6 - FVB background). We found that both YAP1 KO and YAP1 KO TAZ heterozygote female mice were overall very similar and showed similar alterations in gene expression compared to WT. There were a few differences in pathways involved in cell cycling and monocyte recruitment. We analyzed 6 healthy WT female liver tissue samples (3 C57BL/6 background, 3 mixed C57BL/6-FVB background), 3 female YAP1 KO liver tissue samples (C57BL/6 background), and 3 female YAP1 KO TAZ heterozygote (YKTH) liver tissue samples (mixed C57BL/6-FVB background).本研究通过Foxa3启动子驱动Cre重组酶表达，在前肠内胚层祖细胞中敲除Yes相关蛋白1（Yes-associated protein 1, YAP1），构建了胆管稀少症小鼠模型。YAP1敲除（YAP1 KO）小鼠在出生后可存活且能长期生存，尽管其肝内胆管发育完全失败，该表型与阿拉吉尔综合征（Alagille syndrome）的肝脏表型高度相似。成年YAP1 KO小鼠会出现严重慢性胆汁淤积，但肝细胞损伤极轻微，提示肝细胞已发生适应性改变，以维持肝脏功能并减轻胆汁酸与胆红素毒性所致的损伤。随后我们繁育了Foxa3-Cre YAP1 KO TAZ杂合子小鼠与Foxa3-Cre YAP1 KO TAZ敲除（DKO）小鼠，以探究TAZ在该模型中的作用。DKO小鼠与雄性YAP1 KO TAZ杂合子小鼠在围产期死亡，存活的雌性YAP1 KO TAZ杂合子小鼠整体表型与YAP1 KO小鼠相似，同样表现为肝内胆管缺失且可长期生存。我们采用RNA测序（RNA-seq）技术，分别分析了成年雌性YAP1 KO小鼠（背景为C57BL/6品系）与同背景野生型（wild type, WT）对照小鼠的全肝组织基因表达谱，以及成年雌性YAP1 KO TAZ杂合子（YKTH）小鼠与C57BL/6-FVB混合背景野生型对照小鼠的全肝组织基因表达谱。研究发现，与野生型对照相比，雌性YAP1 KO小鼠与雌性YAP1 KO TAZ杂合子小鼠的整体基因表达谱极为相似，基因表达改变模式也高度一致，仅在细胞周期与单核细胞募集中相关的通路上存在少量差异。本研究共分析了6例健康雌性野生型小鼠肝组织样本（其中3例为C57BL/6背景，3例为C57BL/6-FVB混合背景）、3例雌性YAP1 KO小鼠肝组织样本（C57BL/6背景）以及3例雌性YAP1 KO TAZ杂合子（YKTH）小鼠肝组织样本（C57BL/6-FVB混合背景）。