Elucidating Novel Hepatitis C Virus–Host Interactions Using Combined Mass Spectrometry and Functional Genomics Approaches

Germain, Marie-Anne; Chatel‐Chaix, Laurent; Gagné, Bridget; Bonneil, Éric; Thibault, Pierre; Pradezynski, Fabrine; Chassey, Benoı̂t de; Meyniel-Schicklin, Laurène; Lotteau, Vincent; Baril, Martin; Lamarre, Daniel

doi:10.1074/mcp.m113.030155

Cited by 67 publications

(76 citation statements)

References 69 publications

(59 reference statements)

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“…Here, no overlap in datasets was found (Fisher's exact test; P value50.70). On the other hand, the overlap between our data and that in Germain et al (2014) using N-terminal FLAG-tagged NS5B in distantly related HCV was far more significant (P value57.2|10 29 ), underlining the importance of tag size. While our list was enriched in cytosolic proteins, Carpp et al (2014) showed enrichment in nuclear import and transport system proteins.…”

Section: Tap-tagged Dengue Virus and Host-virus Interactionsmentioning

confidence: 66%

“…In particular, large ribosomal subunit members (RPL6, RPL7, RPL13, RPL14, RPL19 and RPL31) were identified as NS5 interaction partners, with only low levels of other ribosome proteins found in the control group. Though translational elongation and viral replication are processes that, logically, cannot occur simultaneously, Germain et al (2014) also found ribosomal proteins interacting with the HCV polymerase.…”

Section: Tap-tagged Dengue Virus and Host-virus Interactionsmentioning

confidence: 99%

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Development of viable TAP-tagged dengue virus for investigation of host–virus interactions in viral replication

Poyomtip

Hodge

Matangkasombut

et al. 2016

Journal of General Virology

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Dengue virus (DENV) is a mosquito-borne flavivirus responsible for life-threatening dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS). The viral replication machinery containing the core non-structural protein 5 (NS5) is implicated in severe dengue symptoms but molecular details remain obscure. To date, studies seeking to catalogue and characterize interaction networks between viral NS5 and host proteins have been limited to the yeast twohybrid system, computational prediction and co-immunoprecipitation (IP) of ectopically expressed NS5. However, these traditional approaches do not reproduce a natural course of infection in which a number of DENV NS proteins colocalize and tightly associate during the replication process. Here, we demonstrate the development of a recombinant DENV that harbours a TAP tag in NS5 to study host-virus interactions in vivo. We show that our engineered DENV was infective in several human cell lines and that the tags were stable over multiple viral passages, suggesting negligible structural and functional disturbance of NS5. We further provide proof-of-concept for the use of rationally tagged virus by revealing a high confidence NS5 interaction network in human hepatic cells. Our analysis uncovered previously unrecognized hnRNP complexes and several low-abundance fatty acid metabolism genes, which have been implicated in the viral life cycle. This study sets a new standard for investigation of host-flavivirus interactions.

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Section: Tap-tagged Dengue Virus and Host-virus Interactionsmentioning

confidence: 66%

Section: Tap-tagged Dengue Virus and Host-virus Interactionsmentioning

confidence: 99%

Development of viable TAP-tagged dengue virus for investigation of host–virus interactions in viral replication

Poyomtip

Hodge

Matangkasombut

et al. 2016

Journal of General Virology

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“…This method is also used by Davis et al to decipher host-pathogen interactions of Kaposi's sarcoma-associated herpesvirus reported in the current issue of Molecular Cell . Similar AP-MS approaches have partially been used in HCV research (Germain et al, 2014; Pichlmair et al, 2012). However, these studies were performed in HEK293T cells and lacked the full set of HCV proteins.…”

Section: Introductionmentioning

confidence: 99%

A Combined Proteomics/Genomics Approach Links Hepatitis C Virus Infection with Nonsense-Mediated mRNA Decay

et al. 2015

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SUMMARY Hepatitis C virus (HCV) is a leading cause of liver disease, but insight into virus-host interactions remains limited. We systematically used affinity purification/mass spectrometry to define the host interactions of all 10 HCV proteins in hepatoma cells. We combined these studies with RNAi knockdown of corresponding genes using a two-step scoring approach to generate a map of 139 high-confidence HCV-host protein-protein interactions. We found mitochondrial proteins highly involved in HCV infection and characterized a new interaction between the viral core protein and host protein within bgcn homolog (WIBG). Expression of core prevents WIBG from binding its regular interaction partners Y14 and Magoh, two known mediators of the nonsense-mediated mRNA decay pathway. We discovered that this surveillance pathway is disrupted in HCV-infected cells, causing potentially harmful transcripts to accumulate. Our study provides the first comprehensive view of HCV-host interactions and uncovers new mechanisms for how HCV perturbs host functions during infection.

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“…Because NS3 protease is essential for viral replication, protease inhibitors usually exert robust antiviral activity against HCV. Protein NS3 also exerts ATPase/helicase activity and plays a role in inhibiting the transport of interferon signaling and therefore in HCV viral immune escape 65,66…”

Section: Mechanism Of Actionmentioning

confidence: 99%

Asunaprevir, a protease inhibitor for the treatment of hepatitis C infection

Gentile¹,

Buonomo²,

Zappulo³

et al. 2014

TCRM

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According to the World Health Organization, approximately 150 million people worldwide are chronic carriers of hepatitis C virus (HCV). HCV infection can evolve into cirrhosis of the liver and its complications, which are ultimately responsible for more than 350,000 deaths every year. Antiviral therapy, when successful, is able to decrease the rate of progression and increase survival. Two types of therapies are currently available, ie, interferon-based therapies and interferon-free ones. The latter have several advantages in terms of safety and tolerability, and could be used even in the most advanced stages of the disease. However, their use is restricted to some viral genotypes (genotype 2 and 3) and they are expensive. Several molecules are in an advanced phase of development. This review deals with the pharmacokinetics, pharmacodynamics, tolerability, and safety of asunaprevir, an inhibitor of HCV nonstructural 3 protease. Asunaprevir exerts optimal in vitro activity particularly against HCV genotypes 1 and 4, and its pharmacokinetic profile enables twice daily administration. The drawback of asunaprevir, and of all protease inhibitors, is its low barrier to resistance. Consequently, it is used in association with other drugs to prevent resistance. Specifically, when combined with daclatasvir, an NS5A inhibitor, asunaprevir results in a very high rate of viral eradication in both treatment-naïve and treatment-experienced patients, with a sustained virological response rate of 80%–90%. Tolerability is fair; in fact, asunaprevir is associated with a transient increase in aminotransferase levels, which is mild in most cases. In conclusion, asunaprevir is a good candidate component of interferon-free combinations and may revolutionize the treatment of chronic HCV infection in the near future.

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Elucidating Novel Hepatitis C Virus–Host Interactions Using Combined Mass Spectrometry and Functional Genomics Approaches

Cited by 67 publications

References 69 publications

Development of viable TAP-tagged dengue virus for investigation of host–virus interactions in viral replication

Development of viable TAP-tagged dengue virus for investigation of host–virus interactions in viral replication

A Combined Proteomics/Genomics Approach Links Hepatitis C Virus Infection with Nonsense-Mediated mRNA Decay

Asunaprevir, a protease inhibitor for the treatment of hepatitis C infection

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