Multi-omic Analyses Reveal Complex Interactions Between HCVand Hepatocytes Demonstrating That the Red Queen IsUpand Running.

Abstract

See “Combined analysis of metabolomes, proteomes, and transcriptomes of hepatitis C virus–infected cells and liver to identify pathways associated with disease development,” by Lupberger J, Croonenborghs T, Roca Suarez AA, et al, on page 537. See “Combined analysis of metabolomes, proteomes, and transcriptomes of hepatitis C virus–infected cells and liver to identify pathways associated with disease development,” by Lupberger J, Croonenborghs T, Roca Suarez AA, et al, on page 537. Viruses lack the machineries for transcription and translation and thus subjugate cellular processes to their survival. Their genetically limited but efficient complexity allows them to develop a plethora of strategies to manipulate cellular pathways for maintaining a productive infection. In turn, cells respond to viral infections by inducing cellular defense mechanisms. This competition leads to co-evolution of the virus and the host, where each adapts to keep up with an ongoing “arms race”, exemplifying the “red queen hypothesis”1Van Valen L. A new evolutionary law.Evol Theory. 1973; 1: 1-30Google Scholar. In this issue of Gastroenterology, Lupberger et al,2Lupberger J. Croonenborghs T. Roca Suarez A.A. et al.Combined analysis of metabolomes, proteomes, and transcriptomes of hepatitis C virus–infected cells and liver to identify pathways associated with disease development.Gastroenterology. 2019; 157: 537-551Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar present a striking example for this interplay between hepatitis C virus (HCV) and the hepatocyte. HCV is the most common risk factor for hepatocellular carcinoma (HCC) in Western countries,3Perz J.F. Armstrong G.L. Farrington L.A. et al.The contributions of hepatitis B virus and hepatitis C virus infections to cirrhosis and primary liver cancer worldwide.J Hepatol. 2006; 45: 529-538Abstract Full Text Full Text PDF PubMed Scopus (1922) Google Scholar and a major public health problem with over 71 million infected people worldwide.4Polaris Observatory H.C.V.C. Global prevalence and genotype distribution of hepatitis C virus infection in 2015: a modelling study.Lancet Gastroenterol Hepatol. 2017; 2: 161-176Abstract Full Text Full Text PDF PubMed Scopus (1308) Google Scholar Using a multiomics approach and harnessing data obtained from cell culture and mouse models for HCV infection, as well as from human liver samples and data mining, this group discovered novel information on the complex interactions between the virus and the host and their consequences on HCV-associated liver disease (Figure 1). HCV infection is detected in the hepatocytes by pattern recognition receptors (PRRs) that induce interferon (INF) responses, thereby triggering interferon stimulated genes (ISGs) specifically targeting and inhibiting viral replication.5Heim M.H. Thimme R. Innate and adaptive immune responses in HCV infections.J Hepatol. 2014; 61: S14-S25Abstract Full Text Full Text PDF PubMed Scopus (190) Google Scholar Indeed, by transcriptome analysis, Lupberger et al,2Lupberger J. Croonenborghs T. Roca Suarez A.A. et al.Combined analysis of metabolomes, proteomes, and transcriptomes of hepatitis C virus–infected cells and liver to identify pathways associated with disease development.Gastroenterology. 2019; 157: 537-551Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar detected mRNA upregulation of genes downstream of the sensors RIG-I, MDA5, TLR3, as has been previously reported in cell culture models and liver biopsies.5Heim M.H. Thimme R. Innate and adaptive immune responses in HCV infections.J Hepatol. 2014; 61: S14-S25Abstract Full Text Full Text PDF PubMed Scopus (190) Google Scholar, 6Boldanova T. Suslov A. Heim M.H. et al.Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver.EMBO Mol Med. 2017; 9: 816-834Crossref PubMed Scopus (28) Google Scholar Gene Set Enrichment Analysis (GSEA) following comprehensive mining gene sets from multiples databases uncovered remarkable down regulation of host processes, with matched responses at both the mRNA and protein levels. However, unexpectedly, the small fraction of gene sets upregulated at the mRNA level was not consistently detected at the proteins level. The authors concluded that the host antiviral response is counteracted by the virus through actively halting protein translation, specifically of viral restrictions factors. The viral strategy of globally targeting host translation presented by Lupberger et al., adds another layer to our understanding of how HCV evades the host innate immune response to known mechanisms focusing mostly on specific factors in the IFN signaling pathway targeted by viral proteins.5Heim M.H. Thimme R. Innate and adaptive immune responses in HCV infections.J Hepatol. 2014; 61: S14-S25Abstract Full Text Full Text PDF PubMed Scopus (190) Google Scholar In contrast to innate immunity genes that were transcriptionally, but not translationally, upregulated, extensive profiling of transcriptome, protein products and the downstream accumulation of their metabolites, demonstrated impaired expression and function of peroxisome-related genes, and a consequential accumulation of very long chain fatty acids (VLCFs). These observations were proposed to be a consequence of impaired expression of genes induced by the peroxisome activator, the nuclear receptor peroxisomal proliferator activated receptor alpha (PPARA), as well as down regulation of the PPARA protein itself following HCV infection. In addition, the authors identified an increase in glucose metabolism in HCV-infected cells which impairs PPARA activity.7Roduit R. Morin J. Masse F. et al.Glucose down-regulates the expression of the peroxisome proliferator-activated receptor-alpha gene in the pancreatic beta -cell.J Biol Chem. 2000; 275: 35799-35806Crossref PubMed Scopus (146) Google Scholar Computational network analysis underscored the HCV-altered IL-6/STAT3 signaling pathway as regulating the change in peroxisome function as confirmed by functional assays. Collectively, the data suggest a model where HCV-driven activation of the IL-6/STAT3 pathway shifts from fatty acids to glucose metabolism. These alterations may result in HCV-induced lipotoxicity, oxidative stress, production of ROS, Warburg-like metabolic shift of metabolism, and induction of inflammation, all of which are hallmarks of cancer.8Vescovo T. Refolo G. Vitagliano G. et al.Molecular mechanisms of hepatitis C virus-induced hepatocellular carcinoma.Clin Microbiol Infect. 2016; 22: 853-861Abstract Full Text Full Text PDF PubMed Scopus (89) Google Scholar The authors clearly demonstrated an association between their findings and liver pathogenesis in HCV-infected patients, including liver injury, cirrhosis and steatohepatitis. Indeed, lipid accumulation in the liver leads to chronic inflammation and non-alcoholic steatohepatitis (NASH), which are associated with chronic HCV infection and contribute to HCV-related cirrhosis and HCC.8Vescovo T. Refolo G. Vitagliano G. et al.Molecular mechanisms of hepatitis C virus-induced hepatocellular carcinoma.Clin Microbiol Infect. 2016; 22: 853-861Abstract Full Text Full Text PDF PubMed Scopus (89) Google Scholar Recent report demonstrated lower replication efficiency of HCV in cancer cells compared to neighboring non-cancer cells in HCC.9Harouaka D. Engle R.E. Wollenberg K. et al.Diminished viral replication and compartmentalization of hepatitis C virus in hepatocellular carcinoma tissue.Proc Natl Acad Sci U S A. 2016; 113: 1375-1380Crossref PubMed Scopus (44) Google Scholar Why is then the virus promoting these processes that lead to progression towards an unfavorable environment? Clearly, these alterations must promote the viral life cycle, at least for the short term. Indeed, the dependency of HCV on lipids in each step of its life cycle, and the consequent manipulation of host lipid metabolism by the virus, is well established.10Felmlee D.J. Hafirassou M.L. Lefevre M. et al.Hepatitis C virus, cholesterol and lipoproteins--impact for the viral life cycle and pathogenesis of liver disease.Viruses. 2013; 5: 1292-1324Crossref PubMed Scopus (98) Google Scholar The data presented by Lupberger et al,2Lupberger J. Croonenborghs T. Roca Suarez A.A. et al.Combined analysis of metabolomes, proteomes, and transcriptomes of hepatitis C virus–infected cells and liver to identify pathways associated with disease development.Gastroenterology. 2019; 157: 537-551Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar provide evidence for the role of peroxisome impairment in this process. It also establishes a beneficial impact of increasing glucose metabolism on the virus replication by promoting peroxisome dysfunction and VLCFs accumulation. Importantly, the fact that IL-6/STAT3 regulates the downstream accumulation of lipids provides a reasonable explanation for the previously reported activation of STAT3 by HCV core protein.11Yoshida T. Hanada T. Tokuhisa T. et al.Activation of STAT3 by the hepatitis C virus core protein leads to cellular transformation.J Exp Med. 2002; 196: 641-653Crossref PubMed Scopus (218) Google Scholar This contributes to the hypothesis that maintaining an inflammatory state is not merely a consequence of the infection, but also promotes viral propagation, and is therefore actively manipulated by HCV.12Virzi A. Roca Suarez A.A. Baumert T.F. et al.Oncogenic signaling induced by HCV infection.Viruses. 2018; 10Crossref PubMed Scopus (12) Google Scholar Despite the success of DAAs in high rates of SVR, many challenges still remain.13Hayes C.N. Chayama K. Why highly effective drugs are not enough: the need for an affordable solution to eliminating HCV.Expert Rev Clin Pharmacol. 2017; 10: 583-594Crossref PubMed Scopus (16) Google Scholar Importantly, it recently became evident that these drugs do not prevent HCC development.14van der Meer A.J. Feld J.J. Hofer H. et al.Risk of cirrhosis-related complications in patients with advanced fibrosis following hepatitis C virus eradication.J Hepatol. 2017; 66: 485-493Abstract Full Text Full Text PDF PubMed Scopus (171) Google Scholar Our recent study, 15Perez S. Kaspi A. Domovitz T. et al.Hepatitis C virus leaves an epigenetic signature post cure of infection by direct-acting antivirals.PLoS Genet. 2019; 15e1008181Crossref PubMed Scopus (66) Google Scholar as well as a recent study by the authors,16Hamdane N. Juhling F. Crouchet E. et al.HCV-induced epigenetic changes associated with liver cancer risk persist after sustained virologic response.Gastroenterology. 2019; 156: 2313-2329Abstract Full Text Full Text PDF PubMed Scopus (115) Google Scholar both demonstrated an epigenetic signature that remains following HCV cure by DAAs and maintains pathogenic gene expression. These new findings highlight the importance of continuing the quest for understanding and targeting host factors activated by HCV to prevent liver diseases, even after SVR. Therefore, an important aspect of this study is identifying opportunities for new avenues for novel etiology-specific therapeutic approaches for HCV-associated liver disease and NASH. The uncovered mechanisms of pathogenesis shared by HCV infection and fatty liver, two known etiologies of cirrhosis and HCC, identify new host targets for liver diseases on the background of these etiologies. These mechanisms are fundamentally different from hepatitis B virus (HBV)-associated liver diseases and HCC. Interference with the innate immune response is unique to HCV, as HBV infection is not sensed by PRRs and does not induce expression of innate immunity genes in the liver.17Suslov A. Boldanova T. Wang X. et al.Hepatitis B virus does not interfere with innate immune responses in the human liver.Gastroenterology. 2018; 154: 1778-1790Abstract Full Text Full Text PDF PubMed Scopus (97) Google Scholar Importantly, the authors demonstrated that while HCV impairs peroxisome function, HBV increases it, correlating with clinical data that in contrast to HCV, HBV does not show a strong correlation with fatty liver disease.18Pais R. Rusu E. Zilisteanu D. et al.Prevalence of steatosis and insulin resistance in patients with chronic hepatitis B compared with chronic hepatitis C and non-alcoholic fatty liver disease.Eur J Intern Med. 2015; 26: 30-36Abstract Full Text Full Text PDF PubMed Scopus (35) Google Scholar This study highlights the potential of drugs stimulating PPARA or inhibiting STAT3 as new targets for prevention of lipotoxicity.19Friedman S.L. Neuschwander-Tetri B.A. Rinella M. et al.Mechanisms of NAFLD development and therapeutic strategies.Nat Med. 2018; 24: 908-922Crossref PubMed Scopus (1188) Google Scholar It will be interesting to explore whether the mechanisms of lipotoxicity shown here persist after viral eradication, and whether specific drugs can reverse it. In summary, Lupberger et al,2Lupberger J. Croonenborghs T. Roca Suarez A.A. et al.Combined analysis of metabolomes, proteomes, and transcriptomes of hepatitis C virus–infected cells and liver to identify pathways associated with disease development.Gastroenterology. 2019; 157: 537-551Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar provide valuable insights into the mechanisms of HCV immune evasion and HCV-induced progression to steatohepatitis and HCC, which may lead to new targets of preventing liver diseases. This study is an elegant example of how global mechanistic insights can be achieved by integrating transcriptomics, proteomics, metabolomics as well as data mining, providing a multilayered atlas leading to novel information which may not be identified by a single omics approach. This multiomics approach is of particular value for studying multifactorial diseases as HCC, and an evasive and devious pathogen such as HCV.20Wooden B. Goossens N. Hoshida Y. et al.Using big data to discover diagnostics and therapeutics for gastrointestinal and liver diseases.Gastroenterology. 2017; 152: 53-67 e3Abstract Full Text Full Text PDF PubMed Scopus (45) Google Scholar, 21Perez S. Gevor M. Davidovich A. et al.Dysregulation of the cohesin subunit RAD21 by Hepatitis C virus mediates host-virus interactions.Nucleic Acids Res. 2019; 47: 2455-2471Crossref PubMed Scopus (4) Google Scholar This study confirms that the “red queen” is still in the running in the case of HCV and HCV-associated diseases are still a topic of high priority. The answer to the question of who will win will be determined not only by the ability to eradicate the virus by DAAs, but also by the ability to prevent HCV-induced pathogenesis pre- and post-SVR. Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of Hepatitis C Virus–Infected Cells and Liver to Identify Pathways Associated With Disease DevelopmentGastroenterologyVol. 157Issue 2PreviewThe 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. Full-Text PDF Covering the CoverGastroenterologyVol. 157Issue 2PreviewA randomized control trial showed that pantoprazole did not reduce upper gastrointestinal events among patients taking aspirin or rivaroxaban Full-Text PDF