Objective: To analyze and compare the differentially expressed genes (DEGs) of Yes-associated protein (YAP)-positive and negative hepatocytes and further understand the preliminary functional characteristics of YAP-positive hepatocytes in an early mouse model of nonalcoholic steatohepatitis (NASH) with transcriptome sequence (RNA-Seq). Methods: C57BL/6 mice were fed with methionine-choline deficiency (MCD) diet for 2 weeks to establish an early NASH model, and the control group was fed with normal diet. Liver tissue was stained with hematoxylin-eosin (HE) and Sirius red, and the pathological score was recorded. The expression of YAP and P-YAP were determined by immunohistochemistry (IHC) in liver tissues. Primary hepatocytes with viability greater than 90% were isolated and purified by collagenase perfusion combined with Percoll density gradient centrifugation. YAP-positive and negative hepatocytes were assessed by YAP antibody, flow cytometry and RNA-Seq analyses. Sequencing results were screened by GO, KEGG and interaction network analysis methods. RT-PCR was used to verify the expression levels of YAP and some DEGs in liver tissue model group. Two samples mean was compared by independent samples t-test. Results: Compared with the control group, the HE-stained liver tissue of MCD-induced mice at 2 weeks showed steatosis (pathological score 1.07±0.21), accompanied by lobular inflammation (pathological score 1.13±0.32) and ballooned hepatocyte (pathological score 0.80) ±0.20). Sirius red staining showed non-significant liver fibrosis (pathological score 0.40±0.40). IHC showed partial YAP-positive hepatocytes expression in an early stage of NASH. RNA-Seq analysis showed that clean reads of YAP-positive and negative hepatocytes were 49 310 604 and 5 4820 036, respectively. Compared with YAP-negative hepatocytes, YAP-positive hepatocytes had differential expression of 5 565 genes, including 1 662 up-regulated genes and 3 903 down-regulated genes. GO analysis of up-regulated genes showed that the metabolic processes related to mitochondrial functions, such as purine nucleoside triphosphate and nucleoside triphosphate were significantly enriched in biological processes (BP), while down-regulated gene analysis showed that olfactory-related receptor were significantly enriched in BP. KEGG analysis showed that DEGs were enriched in 292 pathways, and oxidative phosphorylation (OXPHOS) pathway was significantly enriched in signaling pathway. RT-PCR validated that inflammatory factors (interleukin-1β, interleukin-6), YAP and its target genes (Cyr61, Ankrd1), and Cox5b and Sdhc genes were significantly up-regulated in the OXPHOS pathway, which was consistent with the sequencing results. In addition, eight key genes with interaction network analysis were predicted. Conclusion: Changes in hepatocyte metabolic levels may be associated with increased YAP activity in an early stage of NASH.
目的： 基于转录组测序（RNA-Seq），分析比较非酒精性脂肪性肝炎（NASH）早期小鼠模型中Yes相关蛋白（YAP）阳性肝细胞和YAP阴性肝细胞的差异表达基因（DEGs），初步了解此类YAP阳性肝细胞的功能学特征。 方法： 蛋氨酸-胆碱缺乏（MCD）饲喂C57BL/6小鼠2周构建NASH早期模型，对照组为正常饮食。肝组织行苏木精-伊红（HE）、天狼星红染色和病理学评分；免疫组织化学（IHC）观察YAP、p-YAP在肝组织的表达。胶原酶灌注联合Percoll密度梯度离心获取活率大于90%的原代肝细胞。进行YAP抗体标记、流式分选获得YAP阳性和YAP阴性肝细胞并进行RNA-Seq。测序结果用GO、KEGG和相互作用网路的分析方法筛选DEGs。RT-PCR验证模型组肝组织中YAP以及部分DEGs的表达水平。两样本均数比较采用独立样本t检验。 结果： 与对照组相比，MCD诱导小鼠2周的HE染色肝组织可见脂肪变（病理评分1.07±0.21），伴有小叶炎症（病理评分1.13±0.32）和肝细胞气球样变（病理评分0.80±0.20），天狼星红染色未见明显肝纤维化（病理学评分0.40±0.40）。IHC显示NASH早期的部分肝细胞YAP表达为阳性。RNA-Seq分析，YAP阳性和YAP阴性的肝细胞分别得到Clean reads为49 310 604条、54 820 036条。与YAP阴性肝细胞相比，YAP阳性肝细胞导致5 565个基因差异表达，包括上调基因1 662个，下调基因3 903个。上调基因的GO分析显示，嘌呤三磷酸核苷和三磷酸核苷等线粒体功能相关的代谢过程为显著富集的生物学过程（BP）；下调基因分析到显著富集的BP为嗅觉受体相关过程。KEGG分析显示，DEGs富集到292条通路，氧化磷酸化（OXPHOS）通路为显著富集信号通路。RT-PCR确认炎症因子（白细胞介素-1β、白细胞介素-6）、YAP及其靶基因（Cyr61、Ankrd1）以及OXPHOS通路的Cox5b、Sdhc基因水平显著上调，与测序结果一致。相互作用网络分析预测到8个关键基因。 结论： NASH早期肝细胞代谢水平的变化可能与YAP活性增加有关。.