Virology

 

Team

Aredia Francesca, Post Doc aredia@ingm.org
Bevilacqua Valeria, Post Doc bevilacqua@ingm.org
Cheroni Cristina, Post Doc cheroni@ingm.org
Donnici Lorena, Laboratory Technician donnici@ingm.org
Gelfo Sofia, Student gelfo@ingm.org
Vadalà Rebecca, Student vadala@ingm.org

Scientific Background

It is estimated that 3% of the world’s population are chronically infected by the hepatitis C virus (HCV). Most infections become chronic and over time evolve into chronic hepatitis. The most unwanted complication of chronic hepatitis is cirrhosis, a massive liver fibrosis, which can lead to liver failure and hepatocellular carcinoma.

The pathological outcome of HCV infection depends on viral- as well as host determinants. The development of in vitro cell culture systems has lead to significant progress in the understanding of the HCV life cycle, in particular viral replication, while viral entry and viral exit are still enigmatic. Upon infection, HCV subverts many different cellular pathways in favor of its own life cycle and virus-host interactions play a crucial role for the establishment of chronic infection. . One metabolic pathway drastically altered upon HCV infection is the phosphatidylinositol-4 phosphate (PI4P) pathway. HCV induces a specialized membranous compartment, called membranous web, which is highly enriched with phosphatidylinositol-4 phosphate (PI4P). Phosphatidylinositol 4-Kinase IIIα (PI4KIIIα), the cellular kinase crucially involved in the synthesis of the HCV membranous web, is recruited by the HCV nonstructural protein 5A (NS5A) and it is believed that this interaction stimulates PI4KIIIα kinase activity. Our laboratory is interested in understanding the molecular mechanisms of how HCV influences the PI4P pathway and how this subversion of PI4P metabolism influences the pathogenesis of chronic liver disease and progression to liver cancer.

Another focus of our laboratory is the identification of viral and host genetic determinants that influence liver disease progression and response to antiviral therapy. Whole-genome association studies identified host single nucleotide polymorphisms (SNPs) near the genomic region encoding IL28B as strongly associated with viral clearance in HCV genotype 1 subjects and we confirmed the role of IL28B genotype also in HCV genotype 4 patients in collaboration with the A.M. Migliavacca Center for Liver Disease (Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico).

Recently, HCV variants characterized by genomic deletions have been highlighted in the serum and liver of chronic HCV patients. These defective genomes contain large in-frame deletions affecting prevalently the Envelope proteins, and are efficiently packaged into infectious viral particles when co-expressed together with full-length viral genome. HCV carrying defective genomes will transduce self-replicating HCV subgenomes, resulting in the persistent expression of HCV proteins even in the absence of co-infection with the wild-type helper virus. To evaluate the hypothesis that HCV defective particles are cytopathogenic variants that could affect the severity of liver disease, we are employing a two-fold approach: (I) in-vitro dissection of the cythopathogenic effect of HCV defective variants and (II) ex-vivo evaluation of the association of HCV defective genomes with clinical features in chronic hepatitis C patients.

Ongoing Projects

  1. Role of phosphatidylinositol 4-phosphate metabolism and PI4K kinases in HCV replication and in the progression from of chronic liver disease to liver cancer.
  2. Identification of host and viral genetic determinants implicated in the progression of hepatic and extra-hepatic diseases associated with chronic hepatitis C (i.e. liver fibrosis, cirrhosis, hepatocellular carcinoma).
  3. Identification and characterization of short and long non-coding RNAs involved in the cellular response to viral infection and viral persistence of HCV and HBV.

Recent Publications

DEPDC5 variants increase fibrosis progression in Europeans with chronic HCV infection
Burza MA, Motta BM, Mancina RM, Pingitore P, Pirazzi C, Lepore SM, Spagnuolo R, Doldo P, Russo C, Lazzaro V,Fischer J, Berg T, Aghemo A, Cheroni C, De Francesco R, Fargion S, Colombo M, Datz C, Stickel F, Valenti L, Romeo S
Hepatology. 2015 Oct 30. doi: 10.1002/hep.28322. [Epub ahead of print]

Why is it so difficult to develop a hepatitis C virus preventive vaccine?
Zingaretti, C., De Francesco, R., and Abrignani, S.
Clin Microbiol Infect 2014; 20 Suppl 5: 103-109

Oxysterol-binding protein is a phosphatidylinositol 4-kinase effector required for HCV replication membrane integrity and cholesterol trafficking
Wang, H., Perry, J. W., Lauring, A. S., Neddermann, P., De Francesco, R., and Tai, A. W.
Gastroenterology 2014; 146: 1373-1385 e1371-1311

Photodynamic antibacterial and antibiofilm activity of RLP068/Cl against Staphylococcus aureus and Pseudomonas aeruginosa forming biofilms on prosthetic material
Vassena, C., Fenu, S., Giuliani, F., Fantetti, L., Roncucci, G., Simonutti, G., Romano, C. L., De Francesco, R., and Drago, L.
Int J Antimicrob Agents 2014; 44: 47-55

Genome-wide analysis of DNA methylation, copy number variation, and gene expression in monozygotic twins discordant for primary biliary cirrhosis
Selmi, C., Cavaciocchi, F., Lleo, A., Cheroni, C., De Francesco, R., Lombardi, S. A., De Santis, M., Meda, F., Raimondo, M. G., Crotti, C., Folci, M., Zammataro, L., Mayo, M. J., Bach, N., Shimoda, S., Gordon, S. C., Miozzo, M., Invernizzi, P., Podda, M., Scavelli, R., Martin, M. R., Lasalle, J. M., and Gershwin, M. E.
Front Immunol Front Immunol 2014; 5: 128

NS5A inhibitors impair NS5A- PI4KIIIalpha complex formation and cause a decrease of PI4P and cholesterol levels in HCV-associated membranes
Reghellin, V., Donnici, L., Fenu, S., Berno, V., Calabrese, V., Pagani, M., Abrignani, S., Peri, F., De Francesco, R., and Neddermann, P.
Antimicrob Agents Chemother 2014

Kinetic analyses reveal potent and early blockade of hepatitis C virus assembly by NS5A inhibitors
McGivern, D. R., Masaki, T., Williford, S., Ingravallo, P., Feng, Z., Lahser, F., Asante-Appiah, E., Neddermann, P., De Francesco, R., Howe, A. Y., and Lemon, S. M.
Gastroenterology 2014; 147: 453-462 e457

In vitro antibiofilm activity of bioactive glass S53P4
Drago, L., Vassena, C., Fenu, S., De Vecchi, E., Signori, V., De Francesco, R., and Romano, C. L.
Future Microbiol 2014; 9: 593-601

Interleukin 28B genotype and insulin resistance in chronic hepatitis C patients
Degasperi, E., Valenti, L., Aghemo, A., De Francesco, R., Rumi, M., Soffredini, R., Donnici, L., Cheroni, C., Fargion, S., Zanoni, V., Orsi, E., and Colombo, M.
Antivir Ther 2014

Interaction between PNPLA3 I148M Variant and Age at Infection in Determining Fibrosis Progression in Chronic Hepatitis C
De Nicola, S., Dongiovanni, P., Aghemo, A., Cheroni, C., D’Ambrosio, R., Pedrazzini, M., Marabita, F., Donnici, L., Maggioni, M., Fargion, S., Colombo, M., De Francesco, R., and Valenti, L.
PLoS One 2014; 9: e106022

The association of IL28B genotype with the histological features of chronic hepatitis C is HCV genotype dependent
D’Ambrosio, R., Aghemo, A., De Francesco, R., Rumi, M. G., Galmozzi, E., De Nicola, S., Cheroni, C., Clark, P. J., Ronchi, G., Lampertico, P., and Colombo, M.
Int J Mol Sci 2014; 15: 7213-7224

Daclatasvir: a team player rather than a prima donna in the treatment of hepatitis C
Aghemo, A., and De Francesco, R.
Gut 2014

Human CD1c+ dendritic cells secrete high levels of IL-12 and potently prime cytotoxic T-cell responses
Nizzoli, G., Krietsch, J., Weick, A., Steinfelder, S., Facciotti, F., Gruarin, P., Bianco, A., Steckel, B., Moro, M., Crosti, M., Romagnani, C., Stolzel, K., Torretta, S., Pignataro, L., Scheibenbogen, C., Neddermann, P., De Francesco, R., Abrignani, S., and Geginat, J.
Blood 2013; 122: 932-942

IL28B polymorphisms predict interferon-related hepatitis B surface antigen seroclearance in genotype D hepatitis B e antigen-negative patients with chronic hepatitis B
Lampertico, P., Vigano, M., Cheroni, C., Facchetti, F., Invernizzi, F., Valveri, V., Soffredini, R., Abrignani, S., De Francesco, R., and Colombo, M.
Hepatology 2013; 57: 890-896

Hepatitis C virus-specific directly acting antiviral drugs
Delang, L., Neyts, J., Vliegen, I., Abrignani, S., Neddermann, P., and De Francesco, R.
Curr Top Microbiol Immunol 2013; 369: 289-320

Cirrhosis and rapid virological response to peginterferon plus ribavirin determine treatment outcome in HCV-1 IL28B rs12979860 CC patients
Aghemo, A., Degasperi, E., Rumi, M. G., Galmozzi, E., Valenti, L., De Francesco, R., De Nicola, S., Cheroni, C., Grassi, E., and Colombo, M.
Biomed Res Int 2013; 2013: 580796

New horizons in hepatitis C antiviral therapy with direct-acting antivirals
Aghemo, A., and De Francesco, R.
Hepatology 2013; 58: 428-438

Identification of new autoantigens by protein array indicates a role for IL4 neutralization in autoimmune hepatitis
Zingaretti, C., Arigo, M., Cardaci, A., Moro, M., Crosti, M., Sinisi, A., Sugliano, E., Cheroni, C., Marabita, F., Nogarotto, R., Bonnal, R. J., Marcatili, P., Marconi, M., Zignego, A., Muratori, P., Invernizzi, P., Colombatto, P., Brunetto, M., Bonino, F., De Francesco, R., Geginat, J., Pagani, M., Muratori, L., Abrignani, S., and Bombaci, M.
Mol Cell Proteomics 2012; 11: 1885-1897

Interleukin 28B polymorphism predicts pegylated interferon plus ribavirin treatment outcome in chronic hepatitis C genotype 4
De Nicola, S., Aghemo, A., Rumi, M. G., Galmozzi, E., Valenti, L., Soffredini, R., De Francesco, R., Prati, G. M., D’Ambrosio, R., Cheroni, C., Donato, M. F., and Colombo, M.
Hepatology 2012; 55: 336-342

Metabolism of phosphatidylinositol 4-kinase IIIalpha-dependent PI4P Is subverted by HCV and is targeted by a 4-anilino quinazoline with antiviral activity
Bianco, A., Reghellin, V., Donnici, L., Fenu, S., Alvarez, R., Baruffa, C., Peri, F., Pagani, M., Abrignani, S., Neddermann, P., and De Francesco, R.
PLoS Pathog 2012; 8: e1002576

Distinct microRNA signatures in human lymphocyte subsets and enforcement of the naive state in CD4+ T cells by the microRNA miR-125b
Rossi, R. L., Rossetti, G., Wenandy, L., Curti, S., Ripamonti, A., Bonnal, R. J., Birolo, R. S., Moro, M., Crosti, M. C., Gruarin, P., Maglie, S., Marabita, F., Mascheroni, D., Parente, V., Comelli, M., Trabucchi, E., De Francesco, R., Geginat, J., Abrignani, S., and Pagani, M.
Nat Immunol 2011; 12: 796-803

Genetic variation in the interleukin-28B gene is not associated with fibrosis progression in patients with chronic hepatitis C and known date of infection
Marabita, F., Aghemo, A., De Nicola, S., Rumi, M. G., Cheroni, C., Scavelli, R., Crimi, M., Soffredini, R., Abrignani, S., De Francesco, R., and Colombo, M.
Hepatology 2011; 54: 1127-1134

INGM researches are supported by