Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of Hepatitis C Virus-Infected Cells and Liver to Identify Pathways Associated With Disease Development.
Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of Hepatitis C Virus-Infected Cells and Liver to Identify Pathways Associated With Disease Development.
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DOI：
10.1053/j.gastro.2019.04.003
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发表时间：
2019-08
期刊：
影响因子：
29.4
通讯作者：
Baumert TF
中科院分区：
文献类型：
--
作者：
Lupberger J;Croonenborghs T;Roca Suarez AA;Van Renne N;Jühling F;Oudot MA;Virzì A;Bandiera S;Jamey C;Meszaros G;Brumaru D;Mukherji A;Durand SC;Heydmann L;Verrier ER;El Saghire H;Hamdane N;Bartenschlager R;Fereshetian S;Ramberger E;Sinha R;Nabian M;Everaert C;Jovanovic M;Mertins P;Carr SA;Chayama K;Dali-Youcef N;Ricci R;Bardeesy NM;Fujiwara N;Gevaert O;Zeisel MB;Hoshida Y;Pochet N;Baumert TF
丙型肝炎病毒 (HCV) 感染、肝病进展和肝癌发生的机制尚不完全清楚。我们对 HCV 感染的细胞和嵌合小鼠进行了基因组、蛋白质组和代谢组分析，以了解有关这些过程的更多信息。 Huh7.5.1dif（肝细胞样细胞）被培养物来源的 HCV 感染，并用于 RNA-Seq、蛋白质组学、代谢组学和综合基因组分析。 uPA/SCID小鼠被注射HCV感染患者的血清； 8周后，收集肝组织并通过RNA-seq和蛋白质组学进行分析。通过差异表达、基因集富集分析和蛋白质相互作用图谱，我们确定了因 HCV 感染而发生变化的途径。我们对 216 名 HCV 感染和早期肝硬化患者的肝组织以及 99 名肝细胞癌患者（包括 17 名具有脂肪性肝炎组织学特征的患者）的配对活检进行了研究，验证了我们的研究结果。 HCV感染患者的肝硬化肝组织根据相对过氧化物酶体功能分为2组；评估的结果包括Child-Pugh分级、肝细胞癌的发展、生存和脂肪性肝炎。肝细胞癌根据脂肪性肝炎进行分类；结果是相对过氧化物酶体功能。我们定量了 HCV 感染细胞中的 21,950 个 mRNA 和 8297 个蛋白质。 HCV感染肝细胞样细胞和嵌合小鼠后，我们观察到参与代谢和肝癌发生的mRNA和蛋白质水平发生显着变化。 HCV 感染肝细胞样细胞显着增加了调节先天免疫反应的 mRNA 水平，但没有增加蛋白质水平，我们认为这是由于这些细胞中的翻译受到抑制。 HCV感染肝细胞样细胞增加葡萄糖消耗和代谢以及STAT3信号通路并降低过氧化物酶体功能。过氧化物酶体介导极长链脂肪酸 (VLCFA) 的 β 氧化；我们发现 HCV 感染的细胞中存在 VLCFA 的细胞内积聚，这在脂肪肝患者中也观察到。 HCV 感染小鼠肝脏细胞中与过氧化物酶体功能相关的 mRNA 和蛋白质水平显着降低，表明过氧化物酶体受到干扰。我们将过氧化物酶体功能缺陷与患者 HCV 相关肝硬化、脂肪肝和肝细胞癌的结果和特征相关联。我们对 HCV 感染的肝细胞样细胞和 HCV 感染的小鼠的肝组织进行了联合转录组、蛋白质组和代谢组分析。我们发现HCV感染会增加葡萄糖代谢和STAT3信号通路，从而降低过氧化物酶体功能；过氧化物酶体基因表达的改变与肝病患者的预后相关。这些发现提供了对肝病发病机制的见解，并可用于确定新的治疗靶点。
The mechanisms of hepatitis C virus (HCV) infection, liver disease progression, and hepatocarcinogenesis are only partially understood. We performed genomic, proteomic, and metabolomic analyses of HCV-infected cells and chimeric mice to learn more about these processes. Huh7.5.1dif (hepatocyte-like cells) were infected with culture-derived HCV and used in RNA-Seq, proteomic, metabolomic, and integrative genomic analyses. uPA/SCID mice were injected with serum from HCV-infected patients; 8 weeks later, liver tissues were collected and analyzed by RNA-seq and proteomics. Using differential expression, gene set enrichment analyses, and protein interaction mapping, we identified pathways that changed in response to HCV infection. We validated our findings in studies of liver tissues from 216 patients with HCV infection and early-stage cirrhosis and paired biopsies from 99 patients with hepatocellular carcinoma, including 17 patients with histologic features of steatohepatitis. Cirrhotic liver tissues from patients with HCV infection were classified into 2 groups based on relative peroxisome function; outcomes assessed included Child-Pugh class, development of hepatocellular carcinoma, survival and steatohepatitis. Hepatocellular carcinomas were classified according to steatohepatitis; the outcome was relative peroxisomal function. We quantified 21,950 mRNAs and 8297 proteins in HCV-infected cells. Upon HCV infection of hepatocyte-like cells and chimeric mice, we observed significant changes in levels of mRNAs and proteins involved in metabolism and hepatocarcinogenesis. HCV infection of hepatocyte-like cells significantly increased levels of mRNAs, but not proteins, that regulate the innate immune response—we believe this was due to the inhibition of translation in these cells. HCV infection of hepatocyte-like cells increased glucose consumption and metabolism and the STAT3 signaling pathway and reduced peroxisome function. Peroxisomes mediate beta-oxidation of very long-chain fatty acids (VLCFAs); we found intracellular accumulation of VLCFAs in HCV-infected cells, which is also observed in patients with fatty liver disease. Cells in livers from HCV-infected mice had significant reductions in levels of mRNAs and proteins associated with peroxisome function, indication perturbation of peroxisomes. We associated defects in peroxisome function with outcomes and features of HCV-associated cirrhosis, fatty liver disease, and hepatocellular carcinoma in patients. We performed combined transcriptome, proteome, and metabolome analyses of liver tissues from HCV-infected hepatocyte-like cells and HCV-infected mice. We found that HCV infection increases glucose metabolism and the STAT3 signaling pathway and thereby reduces peroxisome function; alterations in expression of peroxisome genes were associated with outcomes of patients with liver diseases. These findings provide insights into liver disease pathogenesis and might be used to identify new therapeutic targets.
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影响因子：
82.9
作者：
Friedman SL;Neuschwander-Tetri BA;Rinella M;Sanyal AJ
通讯作者：
Sanyal AJ
影响因子：
8
作者：
Buzzai, M;Bauer, DE;Thompson, CB
通讯作者：
Thompson, CB
影响因子：
29.4
作者：
Bauhofer, Oliver;Ruggieri, Alessia;Bartenschlager, Ralf
通讯作者：
Bartenschlager, Ralf
影响因子：
25.7
作者：
Anjani, Kavya;Lhomme, Marie;Tordjman, Joan
通讯作者：
Tordjman, Joan
DOI：
10.1007/978-981-10-8684-7_3
发表时间：
2018-01-01
期刊：
OBESITY, FATTY LIVER AND LIVER CANCER
影响因子：
--
作者：
Farrell, Geoffrey C.;Haczeyni, Fahrettin;Chitturi, Shivakumar
通讯作者：
Chitturi, Shivakumar