John E. Tavis, Ph.D.
Molecular Microbiology and Immunology
Ph.D. in Molecular Biology, Pennsylvania State University, 1990
Our lab studies Hepatitis B virus (HBV) and Hepatitis C virus (HCV). HBV and HCV are major causes of liver disease, including liver cancer, and together they cause nearly two millions of deaths each year world-wide. HBV is a Hepadnavirus with a DNA genome that replicates by reverse transcription using a virally-encoded reverse transcriptase. HCV is a non-vector borne Flavivirus and has a highly variable RNA genome.
Hepatitis B virus. The key enzyme in HBV replication is its reverse transcriptase. The reverse transcriptase is the main target of anti-HBV nucleoside analog drugs that are incorporated into the viral DNA and block viral replication. They are very good drugs, but they are not quite strong enough to eliminate the infection. Therefore, new drug targets that function by different mechanisms are needed to permit combination drug therapy. To identify such targets, we are studying the reverse transcriptase, using both HBV and the related animal virus, Duck Hepatitis B virus (DHBV).
We our primary focus is on the viral ribonuclease H activity that destroys the viral
RNA after it has been copied into DNA. We recently expressed the HBV RNAseH as an
active recombinant protein and found that it could be inhibited by antagonists of
the HIV RNAseH and integrase enzymes. We also demonstrated for the first time that
HBV viral replication could be pharmacologically inhibited using antagonists of the
RNAseH. These studies provide proof-of-concept that the HBV RNAseH is an attractive
target for antiviral drug development, and we are beginning drug discovery efforts.
We also work on the mechanism by which the reverse transcriptase binds to the viral
RNA that is the template for viral DNA synthesis. We identified two motifs on the
enzyme that directly bind to the RNA and have begun to characterize the enzyme’s complex,
two-stage RNA binding mechanism. We are extending these studies with the hope that
learning how to disrupt these RNA binding interfaces will lead to a new anti-HBV drug.
Figure 1. Inhibition of the HBV RNAseH by β-Thujaplicionol. An oligonucleotide-directed RNA cleavage assay was conducted using a uniformly-labeled RNA and a complementary DNA oligo (+) or a non-complementary oligo (-) as a control. Cutting the RNA:DNA heteroduplex substrate (S) cleaves the RNA into two products (P1 and P2). Plotting the data reveals that β-Thujaplicinol has an IC50 of ~6 μM against the HBV RNAseH.
Hepatitis C virus. HCV is very genetically variable, with six major genotypes and multiple subtypes. The genetic distance between two HCV isolates of the same subtype is larger than the difference between a typical mouse and human gene. We seek to understand how this viral genetic variation affects viral pathology and the response of HCV to antiviral therapy.
The backbone of HCV therapy is interferon alpha plus ribavirin, but this demanding therapy fails in about half of genotype 1 patients (the major genotype in the USA). We sequenced the HCV genome from 94 patients before therapy, stratified by response to the drugs. Viral genetic variability in patients where the virus was efficiently suppressed was much higher than in patients where suppression was minimal. This implies that the viruses in the patients who responded well were cleared due to the presence of many different variations that independently reduced their ability to counteract the strong interferon response induced by therapy, and that HCV in the poor responders survived because there are only a few ways to optimize activity of the viral proteins (and hence little genetic diversity). We are exploring the possibility that novel genome-wide genetic variation patterns we recently identified may provide a reliable clinical test to predict who will respond to interferon-based therapy, and are extending these concepts to other viruses.
HCV causes life-threatening illnesses such as cirrhosis or liver cancer in only about 25% of chronically-infected patients, but the reasons why some patients become seriously ill while disease in others is relatively mild are not understood. We hypothesized that this may be due to the presence of HCV genetic variants with varying degrees of virulence. We are conducting two studies to test this hypothesis. First, we sequenced 120 HCV genomes from 60 patients who had either rapid or slow progression of disease over a 3.5 year period. In the second study we asked whether there are oncogenic variants of HCV. Here, we sequenced the HCV genomes from 47 patients with or without liver cancer. In both cases the viral genetic analyses are being coupled to functional assays of the variant viral genes to provide biochemical evidence for or against virulence differences among the variants.
Figure 1. Select HCV genes in sequences from patients who responded well to therapy (marked) are more diverse than from the patients who responded poorly to therapy. Importantly, each of these genes can counteract the function of interferon alpha in vitro.
Labs and Facilities
Left to right: Nathan Ponzar, Juan Villa Torrecilla, Tiffany Edwards, John Tavis, Jil Daw, Elena Lomonosova, Qilan Li, and Mikhail Ryzhikov
Lomonosova, E., and Tavis, J.E. In vitro enzymatic and cell culture-based assays for measuring activity of HBV RNaseH inhibitors. Chapter 14 in Hepatitis B Virus: Methods and Protocols (H. Guo and A. Cuconati, eds.). Springer, New York, New York.
Ireland, P.J., Tavis, J.E., D’Erasmo, M.P., Hirsch, D.R., Murelli, R.P., Cadiz, M.M., Patel, B.S., Gupta, A.K., Edwards, T.C., Korom, M., Moran, E.A., and Morrison, L.A. (2016). Synthetic a-hydroxytropolones inhibit replication of wild-type and acyclovir-resistant herpes simplex viruses. Antimicrob. Agents and Chemother. 60:2140-2149. PMCID: PMC4808205.
Luo, X. Huang, Y., Chen, Y., Tu, Z., Hu, J., Tavis, J.E., Huang, A., and Hu, Y. (2016). Association of Hepatitis B Virus Covalently Closed Circular DNA and Human APOBEC3B in Hepatitis B Virus-Related Hepatocellular Carcinoma. PLoS One, 11:e0157708.
Villa, J.A., Pike, D.P., Patel, K.B., Lomonosova, E., Lu, G., Abdulqader, R., and Tavis, J.E. (2016). Purification and enzymatic characterization of the hepatitis B virus ribonuclease H, a new target for antiviral inhibitors. Antiviral Research, 132:186-195. PMCID in progress.
Lu, G., Villa, J.A., Donlin, M.J., Edwards, T.C., Cheng, X., Heier, R.F., Meyers, M.J. and Tavis, J.E. (2016). Hepatitis B virus genetic diversity has minimal impact on sensitivity of the viral ribonuclease H to inhibitors. Antiviral Research, 135:24-30. PMCID in progress.
Lomonosova, L., Zlotnick, A., and Tavis, J.E. (2016). Synergistic interactions between Hepatitis B Virus ribonuclease H antagonists and other inhibitors. Antimicrob. Agents and Chemother. In Press.
Donlin, M.J., Zunica, A., Lipnicky, A., Garimallaprabhakaran, A.K., Berkowitz, A.J., Grigoryan, A., Meyers, M.J., Tavis, J.E., and Murelli, R.P. (2017). Troponoids can inhibit growth of the human fungal pathogen Cryptococcus neoformans. Antimicrob. Agents and Chemother. In Press.
Ireland, P.J., Tavis, J.E., D’Erasmo, M.P., Hirsch, D.R., Murelli, R.P., Cadiz, M.M., Patel, B.S., Gupta, A.K., Edwards, T.C., Korom, M., Moran, E.A., and Morrison, L.A. (2016). Synthetic α-hydroxytropolones inhibit replication of wild-type and acyclovir-resistant herpes simplex viruses. Antimicrob. Agents and Chemother. In Press.
Lu G., Lomonosova E., Cheng X., Moran E.A., Meyers M.J., Le Grice S.F., Thomas C.J.,
Jiang J.K., Meck C., Hirsch D.R., D'Erasmo M.P., Suyabatmaz D.M., Murelli R.P., Tavis J.E.(2015).
Hydroxylated Tropolones Inhibit Hepatitis B Virus Replication by Blocking the Viral Ribonuclease H Activity.
Antimicrob. Agents and Chemother. 2015 59:1070-7079.
Pubmed Abstract link: 25451058
Cai, C.W., Lomonosova, E., Moran, E.A., Cheng, X. Patel, K.B., Bailly, F., Cotelle,
P., Meyers, M.J., and Tavis, J.E.
Hepatitis B virus replication is blocked by a 2-hydroxyisoquinoline-1,3(2H,4H)-dione (HID) inhibitor of the viral ribonuclease H activity.
Antiviral Research 2014 108:48-55.
Pubmed Abstract link: 24858512
Donlin, M.J., Lomonosova, E., Kiss, A., Cheng, X., Cao, F., Curto, T.M., Di Bisceglie,
A., and Tavis, J.E.
HCV genome-wide genetic analyses in context of disease progression and hepatocellular carcinoma.
PLoS One 2014 9:e103748.
Pubmed Abstract link: 25079603
Tavis, J.E., Wang, H. Tollefson, A.E., Ying, B., Korom, M., Cheng, X. Cao, F., Davis, K.L., Wold,
W.S.M, and Morrison, L.A.
Inhibitors of nucleotidyl transferase superfamily enzymes suppress herpes simplex virus replication.
Antimicrobial Agents and Chemotherapy 2014 58:7451-7461.
Pubmed Abstract link: 25267681
Jones, S.A., Clark, D.N., Cao, F., Tavis, J.E., and Hu, J.
Comparative analyses of Hepatitis B Virus polymerase sequences required for viral RNA binding, packaging and protein priming.
Journal of Virology 2014 88:1564-1572.
Pubmed Abstract link: 24227865
Chowdhury, A.Y., Tavis J.E., and George, S.L.
Human pegivirus (GB virus C) NS3 protease activity inhibits induction of the type I interferon response and is not inhibited by HCV NS3 protease inhibitors.
Virology 2014 456-457:300-309.
Pubmed Abstract link: 24889249
Cao, F., Jones, S.A., Li, W., Cheng, X., Hu, Y., Hu, J., and Tavis, J.E.
Sequences in the terminal protein and reverse transcriptase domains of the hepatitis B virus polymerase contribute to RNA binding and encapsidation.
Journal of Viral Hepatitis 2014 21:882-893.
Pubmed Abstract link: 24401091
Hu, Y., Cheng, X., Cao, F., Huang, A. and Tavis, J.E.
β-Thujaplicinol Inhibits Hepatitis B Virus Replication by Blocking the Viral Ribonuclease H Activity.
Antiviral Research 2013 99:221-229.
Pubmed Abstract link: 23796982
Tavis, J.E., Cheng, X., Hu, Y., Totten, M., Cao, F., Michailidis, E., Aurora, R., Meyers, M.J.,
Jacobsen, J., Parniak, M.A., and Sarafianos, S.G.
The hepatitis B virus ribonuclease H is sensitive to inhibitors of the human immunodeficiency virus ribonuclease H and integrase enzymes.
PLos Pathogens; 2013. 9:e1003125.
Pubmed Abstract link:23349632
Terrault, N.A., Dodge, J.L., Murphy, E.L., Tavis, J.E., Kiss, A., Levin, T.R., Gish, R., Busch, M., Reingold, A.L., and Alter, M.J.
Sexual transmission of HCV among monogamous heterosexual couples: The HCV Partners Study.
Hepatology; 2013. 9:e1003125.
Pubmed Abstract link:23175457
Schvoerer, E., Moenne-Loccoz, R., Murray, J.M., Velay, A., Turek, M., Fofana, I.,
Fafi-Kremer, S., Erba, A.C., Habersetzer, F., Foffoel, M., Gut, J.P., Donlin, M.D.,
Tavis, J.E., Zeisel, M.D., Stoll-Keller, F., and Baumert, T.F.
Hepatitis C virus envelope glycoprotein signatures are associated with treatment failure and modulation of viral entry and neutralization.
J. Infect. Dis.; 2013. 9:e1003125.
Pubmed Abstract link:23335805
Lara, J., Tavis, J.E.,Donlin, M.J., Lee, W., Yuan, H.J., Pearlman, B., Vaughan, G., Forbi, J., Xia, G.L.,
and Khudyakov, Y.
Coordinated evolution among hepatitis C virus genomic sites is coupled to host factors and resistance to interferon.
In Silico Biology; 2012. 11:213-224.
Pubmed Abstract link:23202423
Donlin, M.J., Szeto, B., Gohara, D.W., Aurora, R., and Tavis, J.E.
Genome-wide networks of amino acid covariances are common among viruses .
J. Virol.; 2012. Mar; 86:3050-3063.
Pubmed Abstract link:22238298.
George, S.L., Varmaz, D.,Tavis, J.E., and Chowdhury, A..
The GB virus C (GBV-C) NS3 serine protease inhibits HIV-1 replication in a CD4+ T lymphocyte cell line without decreasing HIV receptor expression..
PLoS One; 2011. Jan; 7:e30653.
Pubmed Abstract link:22292009.
Cao, F., and Tavis, J.E.
RNA elements needed for translation of the duck Hepatitis B virus polymerase via ribosomal shunting.
J. Virol.; 2011. May; 85:6463-6352.
Pubmed Abstract link:21507974.
Cao, F., Donlin, M.J., Turner, K., Cheng, X., and Tavis, J.E.
Genetic and biochemical diversity in the HCV NS5B RNA polymerase in the context of interferon α plus ribavirin therapy.
J. Viral Hepat; 2011. May; 18:349-357.
Pubmed Abstract link:20529202
Wagoner, J., Morishima, C., Graf, T.N., Oberlies, N.H., Teissier, E., Pecheur, E.I.,
Tavis, J.E., and Polyak S.J.
Differential in vitro effects of intravenous versus oral formulations of silibinin on the HCV life cycle and inflammation.
PLoS One; 2011. Jan; 6:e16464.
Pubmed Abstract link:21297922.
Wagoner, J., Negash, A., Kane, O.J., Martinez, L.E., Nahmias, Y., Bourne, N., Owen,
D.M., Grove, J., Brimacombe, C., McKeating, J.A., Pecheur, E.-I., Graf, T.N,., Oberlies,
N.H., Lohmann, V., Cao, F., Tavis, J.E., and Polyak, S.J.
Multiple effects of silymarin on the Hepatitis C virus lifecycle.
Hepatology; 2010. Jun; 51:1912-1921.
Pubmed Abstract link:20512985.
Donlin, M.J., Cannon, N.A., Aurora, R., Li, J., Wahed, A.S., Di Bisceglie, A., and
Contribution of genome-wide HCV genetic differences to outcome of interferon-based therapy in Caucasian American and African American patients.
PLoS One; 2010. Feb; 5:e9032.
Pubmed Abstract link:20140258.
Cano-Monreal, G.L., Wylie, K.M., Cao, F., Tavis, J.E., and Morrison, L.M.
Herpes simplex virus 2 UL13 protein kinase disrupts nuclear lamins.
Virology, 2009. Sep; 392:137-147.
Pubmed Abstract link:19640559.
Cannon, N.A., Donlin, M.J., Mayes, L.M., Castro, A.L., Di Bisceglie, A.M., and Tavis, J.E.
Evidence for action of ribavirin through the hepatitis C virus RNA polymerase.
J. Viral Hepat. 2009 Aug; 16:595-604.
Pubmed Abstract link:19243495.
Badtke, M.P., Khan, I., Cao, F., Hu, J., and Tavis, J.E.
An inter-domain RNA binding site on the hepadnaviral polymerase that is essential for reverse transcription.
Virology 2009 Jul 30; 390:130-138.
Pubmed Abstract link:19467554.
Dazert, E., Neumann-Haefelin, C., Bressanelli, S., Fitzmaurice, K., Kort, J., Timm,
J., McKiernan, S., Kelleher, D., Gruener N., Tavis, J.E., Rosen, H., Shaw, J., Bowness, P., Blum, H.E., Klenerman P., Bartenschlager, R.,
and Thimme, R.
Loss of viral fitness and cross-recognition by CD8+ T cells limit HCV escape from a protective HLA-B27-restricted human immune response.
J. Clin. Invest. 2009 Feb; 119:376-386.
Pubmed Abstract link: 19139562.
Tavis, J.E., and Badtke, M.P. (2009). Hepadnaviral Genomic Replication. Chapter 7 in Viral Genomic Replication, M. Gotte, K. Raney, and C.E. Cameron, eds. Springer, New York, New York. In Press. PMCID: In Process.
Cao, F., Scougall, C.A., Jilbert, A.R., and Tavis, J.E.
Pre-P is a secreted glycoprotein encoded as an N-terminal extension of the duck hepatitis B virus polymerase gene.
J. Virol. 2009 Jul 20; 83:1368-1378.
Pubmed Abstract link: 19004940.
Aurora, R., Donlin, M.J., Cannon, N.A., and Tavis, J.E. for the Virahep-C Study Group. Genome-wide hepatitis C virus amino acid covariance
networks can predict response to antiviral therapy in humans.
J. Clin. Invest. 2009 Jan; 119:225-236.
Pubmed Abstract link: 19104147.
Oh, T.S. and Rice, C.M.
Predicting response to hepatitis C therapy.
J. Clin Invest. 2009 Jan; 119:5-7.
Pubmed Abstract link: 19104144.
R21 AI124672 (Tavis, P.I.) 01/01/17 – 12/31/18
Defining approaches for improving HID and HPD compounds as HBV RNaseH antagonists The goal of this project is to conduct very early hit-to-lead optimization of HID and HPD inhibitors of the HBV RNaseH in order to define the best strategies for a subsequent large-scale medicinal chemistry campaign.
R03AI123689 (Tavis, PI) 03/17/16 – 02/28/18
Structural studies of the HBV ribonuclease H
The goal of this project is to identify crystallization conditions for the HBV RNaseH that are suitable for X-ray crystallographic structural studies.
R01 GM105414 (Blackard, P.I.) 05/02/13 – 04/30/18
Genotypic & phenotypic characterization of the HCV polymerase (NS5B) in HIV
The major goal of this grant is to determine how HIV-induced sequence changes in HCV affect function of the HCV NS5B RNA polymerase. Dr. Tavis will conduct Aim3 of this grant, which involves purifying and biochemically evaluating a collection of variant HCV RNA polymerases.
SLU eRS 2-92309 (Tavis, PI) 07/01/16 – 06/30/17
Friends of the Saint Louis University Liver Center
The HBV e RNA stem loop as a novel anti-HBV drug target
The goal of this seed grant is to measure anti-HBV efficacy of compounds that bind to the HBV e RNA stem loop.
U01 DK082871 (Di Bisceglie, P.I.; Tavis, project P.I.) 09/01/14 – 08/31/15
Prospects for HBV ribonuclease H inhibitors as practical antiviral drugs
The goals of this ancillary study within the Hepatitis B Virus Research Network are to determine if our existing anti-RNaseH compounds and nuclos(t)ide analog inhibitors act synergistically against HBV replication and if RNaseH genes from viral isolates that are relatively resistant to nucleos(t)ide analogs retain full sensitivity to RNaseH inhibitors. Note: the only αHT covered by this grant is #46, which is not proposed to be studied in the current R01 application.
R01 AI104494 (Tavis, P.I.) 12/01/13 – 11/30/16
A screen for antiviral compounds targeting the Hepatitis B Virus ribonuclease H
The goal of this project is to adapt our low-throughput assay for HBV ribonuclease H activity to a high-throughput format and to conduct a proof-of-principle screen for inhibitors.
R03 AI109460 (Tavis, P.I.) 03/15/14 – 03/14/16
Hepatitis B Virus diversity and ribonuclease H inhibitor efficacy
The goal of this project is to determine the degree to which HBV’s natural genetic variation will affect its sensitivity to newly-discovered inhibitors of the viral ribonuclease H activity.
R44 GM088948 (Zhang, P.I.; Tavis, co-investigator) 04/01/14 – 03/31/16
Direct RT-PCR detection of RNA pathogens and mRNA expression in crude samples
The major goal of this project is to determine whether PCR additives and specialized Taq polymerases produced by DNA Polymerase Technology, Inc. permit robust direct RT-PCR amplification RNAs from serum or plasma. Dr. Tavis is P.I. of a subcontract from DNA Polymerase Technology to perform the testing of patient samples under approved biosafety conditions.
3-20264(Tavis, P.I.) 06/01/13 – 05/31/14
Washington University Institute of Clinical and Translational Sciences
Repurposing HIV integrase drugs as HBV RNAseH inhibitors
The goal of this grant is to determine whether analogs of the HIV integrase drugs Raltegravir and Elvitegravir can inhibit the HBV RNAseH.
R01 CA126807 (Tavis, P.I.) 01/14/08 – 12/31/13
HCV genetic variation and hepatocellular carcinoma
The major goal of this project is to determine how natural sequence variation in the full-length HCV genome affects its oncogenic potential through a combination of genetic and functional analyses.
R01 DK080711 (Fan, P.I.) 03/01/08 – 02/28/14
Hepatitis C Virus Quasispecies in the Resistance to Antiviral Therapy
The major goal of this project is to evaluate patterns of genetic variation in the full-length HCV quasispecies during antiviral therapy.
2-30076 (Tavis, P.I.) 09/01/11 – 02/28/13
Saint Louis University President’s Research Fund
Biochemical characterization of the HBV RNAseH as a novel drug target
The major goal of this institutional seed grant is to perform a basic biochemical characterization of recombinant Hepatitis B virus RNAseH proteins from divergent HBV genotypes in preparation for drug screening.
R01 DK074515 (Tavis, P.I.) 07/15/07 – 06/30/12
Role of HCV sequence variation in pathology
The major goal of this project was to determine how natural sequence variation in the full-length HCV genome affect its virulence in collaboration with the HALT-C clinical study.
3-07813 (Tavis, P.I.) 01/01/10 – 02/28/11
Saint Louis University President’s Research Fund
HCV covariance networks as biomarkers of non-response to therapy
The goal of this seed grant was to provide preliminary validation in an external patient cohort of the ability of HCV amino acid covariance networks to predict non-response to interferon α- based therapy.
R43 AI84232 (Cao, P.I.) 08/01/09 – 07/31/10
An HBV polymerase RNA binding assay suitable for inhibito screening.
The major goal of this project was to identify the form of recombinant HBV reverse transrciptase best suited for use in a screen for therapeutic inhibitors of RNA binding by the enzyme. Dr. Tavis relinquished the role of P.I. on this project to Dr. Cao when the NIAID converted the application from an R41 STTR to an R43 SBIR grant.
R01 AI057573 (Morrison, P.I.) 05/01/04 – 01/30/10
Functional analysis of HSV2 tegument proteins in mice
The major goal of this project was to examine the function and contribution to pathogenesis of the HSV2 tegument proteins UL13 and VP22 in cultured cells and in mice.
R21 CA125321 (Tavis, P.I.) 06/07/07 – 05/31/09
Variation in NTP use by the HCV polymerase and response to therapy
The major goal of this project was to determine how natural variation in the HCV RNA polymerase affects its use of ribavirin triphosphate.
R01 AI38447 (Tavis, P.I.) 07/01/96 – 04/30/08
Analysis of the hepadnaviral reverse transcriptase
The major goal of this project was to obtain a molecular understanding of the hepatitis B virus reverse transcriptase, using the duck hepatitis B virus enzyme as a model. We studied the activity of the enzyme, its structure, and its interaction with cells.
R03 AI059050 (Morrison, P.I.) 03/01/05 – 02/28/08
Substrate recognition motif of the HSV-2 UL13 kinase
The major goal of this project was to identify the substrate recognition motif of the HSV-2 UL13 protein kinase to guide subsequent efforts to determine the role of UL13 in viral replication and pathology.
No Project Number (Tavis, P.I.) 09/01/05 – 08/31/07
Friends of the St. Louis University Liver Center
Mechanism of ribavirin action through the HCV NS5B RNA polymerase
The goal of this project was to determine if natural variation in the HCV NS5B RNA-dependent RNA polymerase modulates incorporation of the antiviral nucleoside analog ribavirin, hence modulating its effectiveness.
U01 DK60345 (Tavis, P.I.) 07/01/01 – 04/30/07
Response of HCV to therapy in African Americans
The major goal of this project was to analyze genetic variation in HCV associated with success or failure of antiviral therapy with pegylated interferon alpha plus ribavirin in African Americans and Caucasian Americans.