Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden.
Metab Eng. 2019 Mar;52:263-272. doi: 10.1016/j.ymben.2019.01.001. Epub 2019 Jan 4.
The pathogenesis of non-alcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC) has been associated with altered expression of liver-specific genes including pyruvate kinase liver and red blood cell (PKLR), patatin-like phospholipase domain containing 3 (PNPLA3) and proprotein convertase subtilisin/kexin type 9 (PCSK9). Here, we inhibited and overexpressed the expression of these three genes in HepG2 cells, generated RNA-seq data before and after perturbation and revealed the altered global biological functions with the modulation of these genes using integrated network (IN) analysis. We found that modulation of these genes effects the total triglycerides levels within the cells and viability of the cells. Next, we generated IN for HepG2 cells, identified reporter transcription factors based on IN and found that the modulation of these genes affects key metabolic pathways associated with lipid metabolism (steroid biosynthesis, PPAR signalling pathway, fatty acid synthesis and oxidation) and cancer development (DNA replication, cell cycle and p53 signalling) involved in the progression of NAFLD and HCC. Finally, we observed that inhibition of PKLR lead to decreased glucose uptake and decreased mitochondrial activity in HepG2 cells. Hence, our systems level analysis indicated that PKLR can be targeted for development efficient treatment strategy for NAFLD and HCC.
非酒精性脂肪性肝病 (NAFLD) 和肝细胞癌 (HCC) 的发病机制与肝脏特异性基因的表达改变有关，包括丙酮酸激酶肝和红细胞 (PKLR)、亲脂酶结构域包含 3 (PNPLA3) 和前蛋白转化酶枯草溶菌素/柯萨奇蛋白酶 9 (PCSK9)。在这里，我们在 HepG2 细胞中抑制和过表达这三个基因的表达，在扰动前后生成 RNA-seq 数据，并使用集成网络 (IN) 分析揭示这些基因调节后的全局生物学功能。我们发现这些基因的调节会影响细胞内总甘油三酯水平和细胞活力。接下来，我们为 HepG2 细胞生成了 IN，根据 IN 确定了报告转录因子，并发现这些基因的调节会影响与脂质代谢（甾体生物合成、PPAR 信号通路、脂肪酸合成和氧化）和癌症发展（DNA 复制、细胞周期和 p53 信号通路）相关的关键代谢途径，这些途径与 NAFLD 和 HCC 的进展有关。最后，我们观察到 PKLR 的抑制导致 HepG2 细胞中葡萄糖摄取减少和线粒体活性降低。因此，我们的系统水平分析表明，PKLR 可以作为开发针对 NAFLD 和 HCC 的有效治疗策略的靶点。
