Thomas F Baumert

Institut de Recherche contre les Cancers de l'Appareil Digestif, Strasburg, Alsace, France

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Publications (254)1968.73 Total impact

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    ABSTRACT: Hepatitis C virus (HCV) remains a major global health burden, with more than 130 million individuals chronically infected and at risk for the development of hepatocellular carcinoma (HCC). The recent clinical licensing of direct-acting antivirals enables viral cure. However, limited access to therapy and treatment failure in patient subgroups warrants a continuing effort to develop complementary antiviral strategies. Furthermore, once fibrosis is established, curing HCV infection does not eliminate the risk for HCC. High-throughput approaches and screens have enabled the investigation of virus-host interactions on a genome-wide scale. Gain- and loss-of-function screens have identified essential host-dependency factors in the HCV viral life cycle, such as host cell entry factors or regulatory factors for viral replication and assembly. Network analyses of systems-scale data sets provided a comprehensive view of the cellular state following HCV infection, thus improving our understanding of the virus-induced responses of the target cell. Interactome, metabolomics and gene expression studies identified dysregulated cellular processes potentially contributing to HCV pathogenesis and HCC. Drug screens using chemical libraries led to the discovery of novel antivirals. Here, we review the contribution of high-throughput approaches for the investigation of virus-host interactions, viral pathogenesis and drug discovery.
    Virus Research 09/2015; DOI:10.1016/j.virusres.2015.09.013 · 2.32 Impact Factor
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    ABSTRACT: Background & aims: Efforts to develop an effective vaccine against hepatitis C virus (HCV) have been hindered by the propensity of the virus to evade host immune responses. HCV particles in serum and in cell culture (HCVcc) associate with lipoproteins, which contribute to viral entry. Lipoprotein association has also been proposed to mediate viral evasion of the humoral immune response, though the mechanisms are poorly defined. Methods: We used small interfering RNAs to reduce levels of apolipoprotein E (APOE) in HCVcc-producing Huh7.5-derived hepatoma cells and confirmed its depletion by immunoblot analyses of purified viral particles. Before infecting infection of naïve hepatoma cells, we exposed HCVcc strains of different genotypes, subtypes, and variants to serum and polyclonal and monoclonal antibodies isolated from patients with chronic HCV infection. We analyzed the interaction of APOE with viral envelope glycoprotein E2 and HCV virions by immunoprecipitation. Results: Through loss-of-function studies on patient-derived HCV variants of several genotypes and subtypes, we found that the HCV particle APOE allows the virus to avoid neutralization by patient-derived antibodies. Functional studies with human monoclonal antiviral antibodies showed that conformational epitopes of E2 envelope glycoprotein domains B and C were exposed following depletion of APOE. The level and conformation of virion-associated APOE affected the ability of the virus to escape neutralization by antibodies. Conclusions: In cell infection studies, we found that HCV-associated APOE helps the virus avoid neutralization by antibodies against HCV isolated from chronically infected patients. This method of immune evasion poses a challenge for the development of HCV vaccines.
    Gastroenterology 09/2015; DOI:10.1053/j.gastro.2015.09.014 · 16.72 Impact Factor
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    ABSTRACT: Cellular translation is down-regulated by host antiviral responses. Picornaviridae and Flaviviridae including hepatitis C virus (HCV) evade this process using internal ribosomal entry sequences (IRESs). Although HCV IRES translation is a prerequisite for HCV replication, only few host factors critical for IRES activity are known and the global regulator network remains largely unknown. Since signal transduction is an import regulator of viral infections and the host antiviral response we combined a functional RNAi screen targeting the human signaling network with a HCV IRES-specific reporter mRNA assay. We demonstrate that the HCV host cell cofactors PI4K and MKNK1 are positive regulators of HCV IRES translation representing a novel pathway with a functional relevance for the HCV life cycle and IRES-mediated translation of viral RNA.
    Scientific Reports 09/2015; 5:13344. DOI:10.1038/srep13344 · 5.58 Impact Factor
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    ABSTRACT: Hepatitis B virus (HBV) infection is a major cause of chronic liver disease, including liver cirrhosis, liver failure and hepatocellular carcinoma (HCC)-the second leading and fastest rising cause of cancer death world-wide. While de novo infection can be efficiently prevented by vaccination and chronic infection can be controlled using antivirals targeting the viral polymerase, the development of efficient antiviral strategies to eliminate the virus and thus to cure infection remains a key unmet medical need. The recent progress in the development of robust infectious HBV cell culture models now enables the investigation of the full viral life cycle, including a more detailed study of the molecular mechanisms of virus-host interactions responsible for viral persistence. The understanding of these virus-host interactions will be instrumental for the development of curative treatments. Host-dependency factors have recently emerged as promising candidates to treat and prevent infection by various pathogens. This review focuses on the potential of host-targeting agents (HTAs) as novel antivirals to treat and cure HBV infection. These include HTAs that inhibit de novo and re-infection, synthesis and spread of cccDNA as well as development of immune-based approaches eliminating or curing infected hepatocytes, including the eradication of viral cccDNA. Copyright © 2015 Elsevier B.V. All rights reserved.
    08/2015; 14:41-46. DOI:10.1016/j.coviro.2015.07.009
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    Dataset: GPC5 screen
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    ABSTRACT: Lipoprotein components are crucial factors for hepatitis C virus (HCV) assembly and entry. As hepatoma cells producing cell culture-derived HCV particles (HCVcc) are impaired in some aspects of lipoprotein metabolism, it is of upmost interest to biochemically and functionally characterize the in vivo-produced viral particles, particularly regarding how lipoprotein components modulate HCV entry by lipid transfer receptors such as scavenger receptor BI (SR-BI). Sera from HCVcc-infected liver humanized FRG mice were separated by density gradients. Viral subpopulations, termed HCVfrg particles, were characterized for their physical properties, apolipoprotein association and infectivity. We demonstrate that in contrast to the widely-spread distribution of apolipoproteins across the different HCVcc subpopulations, the most infectious HCVfrg particles are highly enriched in ApoE, suggesting that such apolipoprotein enrichment plays a role for entry of in vivo-derived infectious particles, likely via usage of apolipoprotein receptors. Consistent with this salient feature, we further reveal previously undefined functionalities of SR-BI in promoting entry of in vivo-produced HCV. First, unlike HCVcc, SR-BI is a particularly limiting factor for entry of HCVfrg subpopulations of very low density. Second, HCVfrg entry involves SR-BI lipid transfer activity, but not its binding capacity to the viral glycoprotein E2. In conclusion, we demonstrate that composition and biophysical properties of the different subpopulations of in vivo-produced HCVfrg particles modulate their levels of infectivity and receptor usage, hereby featuring divergences with in vitro-produced HCVcc particles and highlighting the powerfulness of this in vivo model for the functional study of the interplay between HCV and liver components. Copyright © 2015, The American Society for Biochemistry and Molecular Biology.
    Journal of Biological Chemistry 07/2015; DOI:10.1074/jbc.M115.662999 · 4.57 Impact Factor
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    ABSTRACT: Chronic hepatitis B and D infections are major causes of liver disease and hepatocellular carcinoma worldwide. Efficient therapeutic approaches for cure are absent. Sharing the same envelope proteins, hepatitis B virus (HBV) and hepatitis D virus (HDV) use the sodium taurocholate co-transporting polypeptide (NTCP, a bile acid transporter) as a receptor to enter hepatocytes. However, the detailed mechanisms of the viral entry process are still poorly understood. Here, we established a high-throughput infectious cell culture model enabling functional genomics of HDV entry and infection. Using a targeted RNAi entry screen we identified glypican 5 (GPC5) as a common host cell entry factor for HBV and HDV. These findings advance our understanding of virus cell entry and open new avenues for curative therapies. Since glypicans have been shown to play a role in the control of cell division and growth regulation, virus-GPC5 interactions may also play a role in the pathogenesis of virus-induced liver disease and cancer. This article is protected by copyright. All rights reserved. © 2015 by the American Association for the Study of Liver Diseases.
    Hepatology 07/2015; DOI:10.1002/hep.28013 · 11.06 Impact Factor
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    ABSTRACT: Hepatitis C virus (HCV) enters human hepatocytes through a multistep mechanism involving, among other host proteins, the virus receptor CD81. How CD81 governs HCV entry is poorly characterized, and CD81 protein interactions after virus binding remain elusive. We have developed a quantitative proteomics protocol to identify HCV-triggered CD81 interactions and found 26 dynamic binding partners. At least six of these proteins promote HCV infection, as indicated by RNAi. We further characterized serum response factor binding protein 1 (SRFBP1), which is recruited to CD81 during HCV uptake and supports HCV infection in hepatoma cells and primary human hepatocytes. SRFBP1 facilitates host cell penetration by all seven HCV genotypes, but not of vesicular stomatitis virus and human coronavirus. Thus, SRFBP1 is an HCV-specific, pan-genotypic host entry factor. These results demonstrate the use of quantitative proteomics to elucidate pathogen entry and underscore the importance of host protein-protein interactions during HCV invasion. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
    Cell Reports 07/2015; 12(5). DOI:10.1016/j.celrep.2015.06.063 · 8.36 Impact Factor
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    Eloi R Verrier · Stefan Wieland · Thomas F Baumert
    Hepatology 06/2015; 62(3). DOI:10.1002/hep.27935 · 11.06 Impact Factor
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    ABSTRACT: In our study, we characterized the effect of monensin, an ionophore that is known to raise the intracellular pH, on the hepatitis C virus (HCV) life cycle. We showed that monensin inhibits HCV entry in a pangenotypic and dose-dependent manner. Monensin induces an alkalization of intracellular organelles, leading to an inhibition of the fusion step between viral and cellular membranes. Interestingly, we demonstrated that HCV cell-to-cell transmission is dependent on the vesicular pH. Using the selective pressure of monensin, we selected a monensin-resistant virus which has evolved to use a new entry route that is partially pH and clathrin independent. Characterization of this mutant led to the identification of two mutations in envelope proteins, the Y297H mutation in E1 and the I399T mutation in hypervariable region 1 (HVR1) of E2, which confer resistance to monensin and thus allow HCV to use a pH-independent entry route. Interestingly, the I399T mutation introduces an N-glycosylation site within HVR1 and increases the density of virions and their sensitivity to neutralization with anti-apolipoprotein E (anti-ApoE) antibodies, suggesting that this mutation likely induces conformational changes in HVR1 that in turn modulate the association with ApoE. Strikingly, the I399T mutation dramatically reduces HCV cell-to-cell spread. In summary, we identified a mutation in HVR1 that overcomes the vesicular pH dependence, modifies the biophysical properties of particles, and drastically reduces cellto- cell transmission, indicating that the regulation by HVR1 of particle association with ApoE might control the pH dependence of cell-free and cell-to-cell transmission. Thus, HVR1 and ApoE are critical regulators of HCV propagation.
    Journal of Virology 06/2015; 89(16). DOI:10.1128/JVI.00192-15 · 4.44 Impact Factor
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    Che C. Colpitts · Eloi R. Verrier · Thomas F. Baumert
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    ABSTRACT: Hepatitis B virus (HBV) and hepatitis C virus (HCV) infections remain major health problems worldwide, with 400-500 million chronically infected people worldwide. Chronic infection results in liver cirrhosis and hepatocellular carcinoma, the second leading cause of cancer death. Current treatments for HBV limit viral replication without efficiently curing infection. HCV treatment has markedly progressed with the licensing of direct-acting antivirals (DAAs) for HCV cure, yet limited access for the majority of patients is a major challenge. Preventative and curative treatment strategies, aimed at novel targets, are needed for both viruses. Viral entry represents one such target, although detailed knowledge of the entry mechanisms is a prerequisite. For HBV, the recent discovery of the NTCP cell entry factor enabled the establishment of an HBV cell culture model and showed that cyclosporin A and Myrcludex B are NTCP-targeting entry inhibitors. Advances in the understanding of HCV entry revealed it to be a complex process involving many factors, offering several antiviral targets. These include viral envelope proteins E1 and E2, virion-associated lipoprotein ApoE, and cellular factors CD81, SR-BI, EGFR, claudin-1, occludin, and the cholesterol transporter NPC1L1. Small molecules targeting SR-BI, EGFR and NPC1L1 have entered clinical trials, whereas other viral- and host-targeted small molecules, peptides and antibodies show promise in preclinical models. This review summarizes our current understanding of HBV and HCV entry, and describes novel antiviral targets and compounds in different stages of clinical development. Overall, proof-of-concept studies indicate that entry inhibitors are a promising class of antivirals to prevent and treat HBV and HCV infections.
    05/2015; DOI:10.1021/acsinfecdis.5b00039
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    ABSTRACT: Since their discovery, tremendous progress has been made in our understanding of the roles of claudins in tight junction physiology. In addition, interactions between claudins and other cellular proteins have highlighted their novel roles in cell physiology. Moreover, the importance of claudins is becoming apparent in the pathophysiology of several diseases, including viral infections. Notable is the discovery of CLDN1 as an essential host factor for hepatitis C virus (HCV) entry, which led to detailed characterization of CLDN1 and its association with tetraspanin CD81 for the initiation of HCV infection. CLDN1 has also been shown to facilitate dengue virus entry. Furthermore, owing to the roles of claudins in forming anatomical barriers, several viruses have been shown to alter claudin expression at the tight junction. This review summarizes the role of claudins in viral infection, with particular emphasis on HCV. Copyright © 2015. Published by Elsevier Ltd.
    Seminars in Cell and Developmental Biology 05/2015; 42. DOI:10.1016/j.semcdb.2015.04.011 · 6.27 Impact Factor
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    ABSTRACT: Hepatitis C virus (HCV) causes persistent infection in the majority of infected individuals. The mechanisms of persistence and clearance are only partially understood. Antibodies against host cell entry receptors have been shown to inhibit HCV infection in cell culture and animal models. In this study we aimed to investigate whether anti-receptor antibodies are induced during infection in humans in vivo and whether their presence is associated with outcome of infection. We established an ELISA using a recombinant CD81- claudin-1 (CLDN1) fusion protein to detect and quantify antibodies directed against extracellular epitopes of the HCV CD81-CLDN1 co-receptor complex. The presence of anti-receptor antibodies was studied in serum of patients from a well-defined cohort of a single-source HCV outbreak of pregnant women and several control groups including uninfected pregnant women, patients with chronic hepatitis B and D virus (HBV/HDV) infection and healthy individuals. The virus-neutralizing activity of antibodies was determined using recombinant cell culture-derived HCV (HCVcc). Our results demonstrate that HCV infected patients have statistically significantly higher anti-CD81/CLDN1 antibody titers during the early phase of infection than controls, the titers being significantly higher in resolvers compared to persisters. Functional studies using immunoadsorption and HCV cell culture models demonstrate that HCV-neutralizing anti-receptor antibodies are induced in early phase of HCV infection but not in control groups. The virus-neutralizing properties of these antibodies suggest a role for control of viral infection in conjunction with anti-viral responses. Characterization of these anti-receptor antibodies opens new avenues to prevent and treat HCV infection. This article is protected by copyright. All rights reserved. © 2015 by the American Association for the Study of Liver Diseases.
    Hepatology 05/2015; 62(3). DOI:10.1002/hep.27906 · 11.06 Impact Factor
  • Medecine sciences: M/S 05/2015; 31(5):469-72. DOI:10.1051/medsci/20153105003 · 0.67 Impact Factor
  • Che C Colpitts · Mirjam B Zeisel · Thomas F Baumert
    Hepatology 04/2015; DOI:10.1002/hep.27876 · 11.06 Impact Factor
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    ABSTRACT: Hepatitis C virus (HCV) infection relies on virus-host interactions with human hepatocytes, a context in which host cell kinases play critical roles in every step of the HCV life cycle. During viral entry, cellular kinases, including EGFR, EphA2 and PKA, regulate the localization of host HCV entry factors and induce receptor complex assembly. Following virion internalization, viral genomes replicate on endoplasmic reticulum-derived membranous webs. The formation of membranous webs depends on interactions between the HCV NS5a protein and PI4KIIIα. The phosphorylation status of NS5a, regulated by PI4KIIIα, CKI and other kinases, also acts as a molecular switch to virion assembly, which takes place on lipid droplets. The formation of lipid droplets is enhanced by HCV activation of IKKα. In view of the multiple crucial steps in the viral life cycle that are mediated by host cell kinases, these enzymes also represent complementary targets for antiviral therapy. This article is part of a Special Issue entitled:Inhibitors of Protein Kinases. Copyright © 2015. Published by Elsevier B.V.
    Biochimica et Biophysica Acta 04/2015; DOI:10.1016/j.bbapap.2015.04.011 · 4.66 Impact Factor
  • Journal of Hepatology 04/2015; 62:S196. DOI:10.1016/S0168-8278(15)30021-0 · 11.34 Impact Factor
  • Journal of Hepatology 04/2015; 62:S203-S204. DOI:10.1016/S0168-8278(15)30035-0 · 11.34 Impact Factor
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    ABSTRACT: Direct-acting antivirals (DAAs) inhibit hepatitis C virus (HCV) infection by targeting viral proteins that play essential roles in the replication process. However, selection of resistance-associated variants (RAVs) during DAA therapy has been a cause of therapeutic failure. In this study, we wished to address whether such RAVs could be controlled by the co-administration of host-targeting entry inhibitors that prevent intrahepatic viral spread. We investigated the effect of adding an entry inhibitor (the anti-scavenger receptor class B type I mAb1671) to a DAA monotherapy (the protease inhibitor ciluprevir) in human-liver mice chronically infected with HCV of genotype 1b. Clinically relevant non-laboratory strains were used to achieve viraemia consisting of a cloud of related viral variants (quasispecies) and the emergence of RAVs was monitored at high resolution using next-generation sequencing. HCV-infected human-liver mice receiving DAA monotherapy rapidly experienced on-therapy viral breakthrough. Deep sequencing of the HCV protease domain confirmed the manifestation of drug-resistant mutants upon viral rebound. In contrast, none of the mice treated with a combination of the DAA and the entry inhibitor experienced on-therapy viral breakthrough, despite detection of RAV emergence in some animals. This study provides preclinical in vivo evidence that addition of an entry inhibitor to an anti-HCV DAA regimen restricts the breakthrough of DAA-resistant viruses. Our approach is an excellent strategy to prevent therapeutic failure caused by on-therapy rebound of DAA-RAVs. Inclusion of an entry inhibitor to the newest DAA combination therapies may further increase response rates, especially in difficult-to-treat patient populations. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to
    Journal of Hepatology 04/2015; 62:S214. DOI:10.1016/S0168-8278(15)30058-1 · 11.34 Impact Factor

Publication Stats

6k Citations
1,968.73 Total Impact Points


  • 2015
    • Institut de Recherche contre les Cancers de l'Appareil Digestif
      Strasburg, Alsace, France
  • 2008–2015
    • French Institute of Health and Medical Research
      Lutetia Parisorum, Île-de-France, France
  • 2007–2015
    • University of Strasbourg
      • Laboratoire de BioVectorologie
      Strasburg, Alsace, France
    • Institut Pasteur de Lille
      Lille, Nord-Pas-de-Calais, France
  • 2014
    • Harvard University
      Cambridge, Massachusetts, United States
  • 2009–2014
    • Unité Inserm U1077
      Caen, Lower Normandy, France
    • CHRU de Strasbourg
      Strasburg, Alsace, France
  • 1998–2014
    • Harvard Medical School
      Boston, Massachusetts, United States
  • 2013
    • Imperial College London
      Londinium, England, United Kingdom
    • Institut de France
      Lutetia Parisorum, Île-de-France, France
  • 2012
    • Johns Hopkins University
      • Department of Medicine
      Baltimore, Maryland, United States
  • 2010–2012
    • University of Birmingham
      • • School of Biosciences
      • • Institute for Biomedical Research
      Birmingham, England, United Kingdom
    • Stanford University
      • Department of Pathology
      Palo Alto, California, United States
    • Institut de Génétique et de Biologie Moléculaire et Cellulaire
      • Department of Biology and Stem Cell Development
      Strasburg, Alsace, France
  • 2011
    • Cancer Research Center of Lyon
      Lyons, Rhône-Alpes, France
  • 2001–2009
    • University of Freiburg
      • • Faculty of Biology
      • • Department of Internal Medicine
      Freiburg, Baden-Württemberg, Germany
  • 2006–2007
    • Humboldt-Universität zu Berlin
      Berlín, Berlin, Germany
    • Rensselaer Polytechnic Institute
      • Department of Chemical and Biological Engineering
      Troy, New York, United States
  • 2004
    • Technische Universität München
      München, Bavaria, Germany
  • 1998–2001
    • National Institutes of Health
      • National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
      Maryland, United States
  • 1996
    • Massachusetts General Hospital
      • Department of Medicine
      Boston, Massachusetts, United States