Our laboratory is committed to understanding how positive-sense RNA viruses enter human host cells, replicate, and evade the immune response. Toward this overarching goal we are (1) determining how hepatitis C virus (HCV) glycoproteins with host cell receptors and broadly neutralizing antibodies, (2) exploring the mechanisms of viral polyprotein processing, and (3) examining how the innate immune system distinguishes self versus viral RNAs. Our long-term goal is to discover and develop an effective HCV vaccine, novel antiviral drugs, and RIG-I immunomodulators for use as broad-based antiviral agents.

HCV represents an important public health problem, infecting an estimated 2% of the world’s population, approximately 150 million people. There is no vaccine against HCV and it is estimated that an additional 3-4 million individuals become newly infected each year worldwide. Several direct acting antivirals for HCV have recently been FDA approved; however, there is still a need for an HCV vaccine as these drugs are prohibitively expensive. HCV is an enveloped virus with an outer shell composed of many copies of two glycoproteins, E1 and E2. Mechanistic studies aimed at providing a detailed understanding of HCV entry have lagged behind due to an inability to produce properly folded HCV glycoproteins. To circumvent this obstacle, my laboratory has developed a cost-, labor-, and time-efficient method for the large-scale production of recombinant glycoproteins in mammalian cell lines with native, post-translational modifications. This production system enabled the first determination of the core domain of HCV E2 structure in complex with an Fab (Khan et al. Nature 2014). This structure revealed that HCV E2 does not share any similarity to other viral glycoproteins, including those from closely related viruses, suggesting that HCV may use a novel entry mechanism.

Numerous viruses, many of which severely impact human health around the globe (e.g. HIV, Zika virus, Dengue virus, West Nile virus, chikungunya virus, and SARS virus), utilize a gene expression mechanism wherein one gene encodes a single polyprotein that is post-translationally cleaved into individual proteins. Proteolytic processing occurs in a highly regulated and coordinated manner with intermediates having distinct functions and playing important roles during viral infection. Remarkably, viral proteases found within the polyprotein are capable of performing multiple cleavages that can be separated by long distances in linear sequence. Despite the commonality of polyprotein processing as a means of regulating the viral life cycle, very little is known about the higher order complexes of replication proteins post-processing, and even less about the structural properties of the precursor forms. Much of the existing biochemical and biophysical information on viral proteins stems from structural results of individual domains or mature forms of the viral proteins. To fully understand the biology and the regulation behind each step of the viral life cycle, it is absolutely necessary to examine the changes in the properties of viral proteins before and after polyprotein processing. We have determined the structure of the precleavage form of a portion of the Alphavirus replication machinery, helping to illuminate these critical steps in the virus life cycle (Shin et al. PNAS 2012). Our results have provided unprecedented insights into viral polyprotein processing and pathogenesis, which may be applicable to other important human viruses that undergo polyprotein processing.

The innate immune system is an evolutionarily ancient component of the host defense mechanisms. The innate immune receptors can efficiently distinguish general features of pathogens in a background of related self-molecules. The RIG-I (retinoic-acid-inducible gene-I) like receptors (RLR) consist of three cytoplasmic proteins (RIG-I, MDA5 and LGP2) that detect the presence of viral RNA in infected cells. A major goal of our research is to understand the mechanism of self versus non-self recognition and immune signaling actions of the RLR family receptors. To understand the synergy between the various domains of RIG-I for RNA binding and activation, my laboratory determined the structure of the RNA binding domains of human RIG-I in complex with dsRNA and an ATP analogue (Jiang et al. Nature, 2011). Recently, we established that the 2’O-methyl group on the first nucleotide adjacent to the 7-methyl guanosine cap is an important self versus non-self marker for RIG-I and demonstrated that RNAs with only 7-methyl guanosine caps are PAMPs (Devarkar et al. PNAS 2016).

Dr. Joseph Marcotrigiano pursued graduate studies at Rockefeller University in the laboratory of Dr. Stephen K. Burley, determining the first structures of proteins involved in eukaryotic translation initiation. After receiving a Ph.D., Dr. Marcotrigiano became a Merck Fellow of the Life Sciences Research Foundation at the Center for the Study of Hepatitis C under the direction of Dr. Charles Rice. As a postdoctoral fellow, he determined the structures of HCV nonstructural protein (NS) 5A and NS2. In 2007, he began an independent tenure-track position at the Center for Advanced Biotechnology and Medicine at Rutgers University and was awarded tenure in July 2013. In September 2016, he was selected as a Howard Hughes Medical Institute Faculty Scholar. Dr. Marcotrigiano became chief of the Structural Virology Section in the Laboratory of Infectious Diseases in January 2017.

Jennifer Casino-Matos
Chen Wang
Yuanyuan Wang

Devarkar S, Wang C, Miller MT, Ramanathan A, Jiang F, Khan AG, Patel S, Marcotrigiano J. Structural basis for m7G recognition and 2’-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I. Proceedings of the National Academy of Sciences USA. 2016 Jan 19;113(3):596-601.

Khan A, Whidby J, Miller M, Scarborough H, Zatorski A, Cygan A, Price A, Yost S, Bohannon C, Jacob J, Grakoui A, Marcotrigiano J. Structure of the core ectodomain of the hepatitis C virus envelope glycoprotein 2. Nature. 2014 May 15;509(7500):381-4.

Shin G, Yost S, Miller M, Elrod E, Grakoui A, Marcotrigiano J. Structural and Functional Insights into Alphavirus Polyprotein Processing and Pathogenesis. Proceedings of the National Academy of Sciences (PNAS) USA. 2012 Oct 9;109(41):16534-9.

Jiang F, Ramanathan A, Miller MT, Tang G-Q, Gale M Jr., Patel SS, Marcotrigiano J. Structural basis of RNA recognition and activation by innate immune receptor RIG-I. Nature. 2011 Sep 25;479(7373):423-7.

Whidby J, Mateu G, Scarborough H, Demeler B, Grakoui A, Marcotrigiano J. Blocking hepatitis C virus infection with recombinant form of envelope protein 2 ectodomain. Journal of Virology. 2009 Nov;83(21):11078-89.

Saito T, Owen DM, Jiang F, Marcotrigiano J, Gale M Jr. Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA. Nature. 2008 Jul 24;454(7203):523-7.

The Hepatic Pathogenesis Section (HPS) was established in 2010 to conduct translational research in the field of liver diseases, particularly in the study of pathogenesis of acute and chronic viral hepatitis, with the main goal of merging clinical medicine with basic research. Acute and chronic inflammatory liver diseases, especially viral hepatitis, are a major cause of morbidity and mortality both in the United States and in the rest of the world. A significant proportion of patients die of long-term sequelae of chronic liver disease, primarily cirrhosis and liver cancer.

Although there has been considerable progress in the control and treatment of acute and chronic viral hepatitis, future advances will depend on a more thorough knowledge of the mechanisms of pathogenesis. HPS has developed a comprehensive research program to study the molecular mechanisms of pathogenesis of acute liver failure and acute and chronic hepatitis especially of viral etiology, as well as the long-term sequelae of chronic hepatitis, cirrhosis, and hepatocellular carcinoma. Current research efforts also include the search for new hepatitis agents that may be implicated in the etiology of other forms of acute and chronic inflammatory liver diseases. New knowledge gained from these studies will pave the way toward the development of better means of preventing, diagnosing, and treating these illnesses.

Dr. Farci earned her M.D. at the University of Cagliari Medical School, Italy, and then became a board-certified specialist in infectious diseases and gastroenterology at the same university. She was trained at the department of gastroenterology of the Molinette Hospital in Torino under Dr. Mario Rizzetto and at the department of medicine of the Royal Free Hospital School of Medicine in London under Professor Sheila Sherlock. In 1989, she joined the laboratory of Dr. Robert H. Purcell in the Laboratory of Infectious Diseases (LID) as a visiting scientist. In 1992, she became associate professor of medicine and, in 2000, full professor of medicine and director of the liver unit and of the postgraduate school of gastroenterology at the University of Cagliari. In 2007, she returned to LID, where in 2010 she became chief of the Hepatic Pathogenesis Section.

Farah Alayli, Zhaochun Chen, Emily J Danoff, Teresa Pollicino, Anna Pomerenke

Melis M, Diaz G,  Kleiner DE, Zamboni F, Kabat J, Lai J, Mogavero G, Tice A, Engle RE, Becker S, Brown CR, Hanson JC, Rodrigues-Canales J, Emmert-Buck M, Govindarajan S, Kew M, Farci P. Viral expression and molecular profiling in liver tissue versus microdissected hepatocytes in hepatitis B virus-associated hepatocellular carcinoma. J Transl Med. 2014 Aug 21;12:230.

Diaz G, Melis M, Tice A, Kleiner DE, Mishra L, Zamboni F, Farci P. Identification of microRNAs specifically expressed in hepatitis C virus-associated hepatocellular carcinoma. Int J Cancer. 2013 Aug 15;133(4):816-24.

Farci P, Wollenberg K, Diaz G, Engle RE, Lai ME, Klenerman P, Purcell RH, Pybus OG, Alter HJ. Profibrogenic chemokines and viral evolution predict rapid progression of hepatitis C to cirrhosis. Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14562-7.

Farci P, Diaz G, Chen Z, Govindarajan S, Tice A, Agulto L, Pittaluga S, Boon D, Yu C, Engle RE, Haas M, Simon R, Purcell RH, Zamboni F. B-cell gene signature with massive intrahepatic production of antibodies to hepatitis B core antigen in hepatitis B virus-associated acute liver failure. Proc Natl Acad Sci U S A. 2010 May 11;107(19):8766-71.

Farci P, Quinti I, Farci S, Alter HJ, Strazzera R, Palomba E, Coiana A, Cao D, Casadei AM, Ledda R, Iorio R, Vegnente A, Diaz G, Tovo PA. Evolution of hepatitis C viral quasispecies and hepatic injury in perinatally infected children followed prospectively. Proc Natl Acad Sci U S A. 2006 May 30;103(22):8475-80.

Farci P, Shimoda A, Coiana A, Diaz G, Peddis G, Melpolder JC, Strazzera A, Chien DY, Munoz SJ, Balestrieri A, Purcell RH, Alter HJ. The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies. Science. 2000 Apr 14;288(5464):339-44.

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