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Mouzannar K, Schauer A, Liang TJ. The Post-Transcriptional Regulatory Element of Hepatitis B Virus: From Discovery to Therapy. Viruses 2024; 16:528. [PMID: 38675871 PMCID: PMC11055085 DOI: 10.3390/v16040528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The post-transcriptional regulatory element (PRE) is present in all HBV mRNAs and plays a major role in their stability, nuclear export, and enhancement of viral gene expression. Understanding PRE's structure, function, and mode of action is essential to leverage its potential as a therapeutic target. A wide range of PRE-based reagents and tools have been developed and assessed in preclinical and clinical settings for therapeutic and biotechnology applications. This manuscript aims to provide a systematic review of the characteristics and mechanism of action of PRE, as well as elucidating its current applications in basic and clinical research. Finally, we discuss the promising opportunities that PRE may provide to antiviral development, viral biology, and potentially beyond.
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Affiliation(s)
- Karim Mouzannar
- Liver Diseases Branch, National Institute of Diabetics and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | | | - T. Jake Liang
- Liver Diseases Branch, National Institute of Diabetics and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
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2
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Giosa D, Lombardo D, Musolino C, Chines V, Raffa G, Casuscelli di Tocco F, D'Aliberti D, Caminiti G, Saitta C, Alibrandi A, Aiese Cigliano R, Romeo O, Navarra G, Raimondo G, Pollicino T. Mitochondrial DNA is a target of HBV integration. Commun Biol 2023; 6:684. [PMID: 37400627 DOI: 10.1038/s42003-023-05017-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/05/2023] [Indexed: 07/05/2023] Open
Abstract
Hepatitis B virus (HBV) may integrate into the genome of infected cells and contribute to hepatocarcinogenesis. However, the role of HBV integration in hepatocellular carcinoma (HCC) development remains unclear. In this study, we apply a high-throughput HBV integration sequencing approach that allows sensitive identification of HBV integration sites and enumeration of integration clones. We identify 3339 HBV integration sites in paired tumour and non-tumour tissue samples from 7 patients with HCC. We detect 2107 clonally expanded integrations (1817 in tumour and 290 in non-tumour tissues), and a significant enrichment of clonal HBV integrations in mitochondrial DNA (mtDNA) preferentially occurring in the oxidative phosphorylation genes (OXPHOS) and D-loop region. We also find that HBV RNA sequences are imported into the mitochondria of hepatoma cells with the involvement of polynucleotide phosphorylase (PNPASE), and that HBV RNA might have a role in the process of HBV integration into mtDNA. Our results suggest a potential mechanism by which HBV integration may contribute to HCC development.
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Affiliation(s)
- Domenico Giosa
- Department of Clinical and Experimental Medicine, University Hospital of Messina, Messina, Italy
- Laboratory of Molecular Hepatology, University Hospital of Messina, Messina, Italy
| | - Daniele Lombardo
- Department of Clinical and Experimental Medicine, University Hospital of Messina, Messina, Italy
- Laboratory of Molecular Hepatology, University Hospital of Messina, Messina, Italy
| | - Cristina Musolino
- Laboratory of Molecular Hepatology, University Hospital of Messina, Messina, Italy
- Department of Human Pathology, University Hospital of Messina, Messina, Italy
| | - Valeria Chines
- Department of Clinical and Experimental Medicine, University Hospital of Messina, Messina, Italy
- Laboratory of Molecular Hepatology, University Hospital of Messina, Messina, Italy
| | - Giuseppina Raffa
- Department of Clinical and Experimental Medicine, University Hospital of Messina, Messina, Italy
- Laboratory of Molecular Hepatology, University Hospital of Messina, Messina, Italy
| | - Francesca Casuscelli di Tocco
- Department of Clinical and Experimental Medicine, University Hospital of Messina, Messina, Italy
- Laboratory of Molecular Hepatology, University Hospital of Messina, Messina, Italy
| | - Deborah D'Aliberti
- Department of Clinical and Experimental Medicine, University Hospital of Messina, Messina, Italy
- Laboratory of Molecular Hepatology, University Hospital of Messina, Messina, Italy
| | - Giuseppe Caminiti
- Laboratory of Molecular Hepatology, University Hospital of Messina, Messina, Italy
| | - Carlo Saitta
- Department of Clinical and Experimental Medicine, University Hospital of Messina, Messina, Italy
| | | | | | - Orazio Romeo
- Department of ChiBioFarAm, University of Messina, Messina, Italy
| | - Giuseppe Navarra
- Department of Human Pathology, University Hospital of Messina, Messina, Italy
| | - Giovanni Raimondo
- Department of Clinical and Experimental Medicine, University Hospital of Messina, Messina, Italy
| | - Teresa Pollicino
- Department of Clinical and Experimental Medicine, University Hospital of Messina, Messina, Italy.
- Laboratory of Molecular Hepatology, University Hospital of Messina, Messina, Italy.
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Seo JJ, Jung SJ, Yang J, Choi DE, Kim VN. Functional viromic screens uncover regulatory RNA elements. Cell 2023:S0092-8674(23)00675-X. [PMID: 37413987 DOI: 10.1016/j.cell.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 04/21/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023]
Abstract
The number of sequenced viral genomes has surged recently, presenting an opportunity to understand viral diversity and uncover unknown regulatory mechanisms. Here, we conducted a screening of 30,367 viral segments from 143 species representing 96 genera and 37 families. Using a library of viral segments in 3' UTR, we identified hundreds of elements impacting RNA abundance, translation, and nucleocytoplasmic distribution. To illustrate the power of this approach, we investigated K5, an element conserved in kobuviruses, and found its potent ability to enhance mRNA stability and translation in various contexts, including adeno-associated viral vectors and synthetic mRNAs. Moreover, we identified a previously uncharacterized protein, ZCCHC2, as a critical host factor for K5. ZCCHC2 recruits the terminal nucleotidyl transferase TENT4 to elongate poly(A) tails with mixed sequences, delaying deadenylation. This study provides a unique resource for virus and RNA research and highlights the potential of the virosphere for biological discoveries.
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Affiliation(s)
- Jenny J Seo
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Soo-Jin Jung
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jihye Yang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Da-Eun Choi
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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4
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Gorsuch CL, Nemec P, Yu M, Xu S, Han D, Smith J, Lape J, van Buuren N, Ramirez R, Muench RC, Holdorf MM, Feierbach B, Falls G, Holt J, Shoop W, Sevigny E, Karriker F, Brown RV, Joshi A, Goodwin T, Tam YK, Lin PJC, Semple SC, Leatherbury N, Delaney Iv WE, Jantz D, Rhoden Smith A. Targeting the hepatitis B cccDNA with a sequence-specific ARCUS nuclease to eliminate hepatitis B virus in vivo. Mol Ther 2022; 30:2909-2922. [PMID: 35581938 PMCID: PMC9481990 DOI: 10.1016/j.ymthe.2022.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/23/2022] Open
Abstract
Persistence of chronic hepatitis B (CHB) is attributed to maintenance of the intrahepatic pool of the viral covalently closed circular DNA (cccDNA), which serves as the transcriptional template for all viral gene products required for replication. Current nucleos(t)ide therapies for CHB prevent virus production and spread but have no direct impact on cccDNA or expression of viral genes. We describe a potential curative approach using a highly specific engineered ARCUS nuclease (ARCUS-POL) targeting the hepatitis B virus (HBV) genome. Transient ARCUS-POL expression in HBV-infected primary human hepatocytes produced substantial reductions in both cccDNA and hepatitis B surface antigen (HBsAg). To evaluate ARCUS-POL in vivo, we developed episomal adeno-associated virus (AAV) mouse and non-human primate (NHP) models containing a portion of the HBV genome serving as a surrogate for cccDNA. Clinically relevant delivery was achieved through systemic administration of lipid nanoparticles containing ARCUS-POL mRNA. In both mouse and NHP, we observed a significant decrease in total AAV copy number and high on-target indel frequency. In the case of the mouse model, which supports HBsAg expression, circulating surface antigen was durably reduced by 96%. Together, these data support a gene-editing approach for elimination of cccDNA toward an HBV cure.
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Affiliation(s)
| | - Paige Nemec
- Precision BioSciences Inc, Durham, NC 27701, USA
| | - Mei Yu
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Simin Xu
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Dong Han
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Jeff Smith
- Precision BioSciences Inc, Durham, NC 27701, USA
| | - Janel Lape
- Precision BioSciences Inc, Durham, NC 27701, USA
| | | | | | | | | | | | - Greg Falls
- Precision BioSciences Inc, Durham, NC 27701, USA
| | - Jason Holt
- Precision BioSciences Inc, Durham, NC 27701, USA
| | - Wendy Shoop
- Precision BioSciences Inc, Durham, NC 27701, USA
| | - Emma Sevigny
- Precision BioSciences Inc, Durham, NC 27701, USA
| | | | | | - Amod Joshi
- Precision BioSciences Inc, Durham, NC 27701, USA
| | | | - Ying K Tam
- Acuitas Therapeutics, Vancouver, BC V6T 1Z3, Canada
| | | | | | | | | | - Derek Jantz
- Precision BioSciences Inc, Durham, NC 27701, USA.
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Veatch JR, Lee SM, Shasha C, Singhi N, Szeto JL, Moshiri AS, Kim TS, Smythe K, Kong P, Fitzgibbon M, Jesernig B, Bhatia S, Tykodi SS, Hall ET, Byrd DR, Thompson JA, Pillarisetty VG, Duhen T, McGarry Houghton A, Newell E, Gottardo R, Riddell SR. Neoantigen-specific CD4 + T cells in human melanoma have diverse differentiation states and correlate with CD8 + T cell, macrophage, and B cell function. Cancer Cell 2022; 40:393-409.e9. [PMID: 35413271 PMCID: PMC9011147 DOI: 10.1016/j.ccell.2022.03.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/23/2021] [Accepted: 03/14/2022] [Indexed: 12/29/2022]
Abstract
CD4+ T cells that recognize tumor antigens are required for immune checkpoint inhibitor efficacy in murine models, but their contributions in human cancer are unclear. We used single-cell RNA sequencing and T cell receptor sequences to identify signatures and functional correlates of tumor-specific CD4+ T cells infiltrating human melanoma. Conventional CD4+ T cells that recognize tumor neoantigens express CXCL13 and are subdivided into clusters expressing memory and T follicular helper markers, and those expressing cytolytic markers, inhibitory receptors, and IFN-γ. The frequency of CXCL13+ CD4+ T cells in the tumor correlated with the transcriptional states of CD8+ T cells and macrophages, maturation of B cells, and patient survival. Similar correlations were observed in a breast cancer cohort. These results identify phenotypes and functional correlates of tumor-specific CD4+ T cells in melanoma and suggest the possibility of using such cells to modify the tumor microenvironment.
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Affiliation(s)
- Joshua R Veatch
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Sylvia M Lee
- Department of Medical Oncology, University of Washington, Seattle, WA, USA
| | - Carolyn Shasha
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Naina Singhi
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Julia L Szeto
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ata S Moshiri
- Department of Dermatology, University of Washington, Seattle, WA, USA
| | - Teresa S Kim
- Department of Surgery, University of Washington, Seattle, WA, USA
| | - Kimberly Smythe
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul Kong
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Matthew Fitzgibbon
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Brenda Jesernig
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Shailender Bhatia
- Department of Medical Oncology, University of Washington, Seattle, WA, USA
| | - Scott S Tykodi
- Department of Medical Oncology, University of Washington, Seattle, WA, USA
| | - Evan T Hall
- Department of Medical Oncology, University of Washington, Seattle, WA, USA
| | - David R Byrd
- Department of Surgery, University of Washington, Seattle, WA, USA
| | - John A Thompson
- Department of Medical Oncology, University of Washington, Seattle, WA, USA
| | | | - Thomas Duhen
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - A McGarry Houghton
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Evan Newell
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Raphael Gottardo
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stanley R Riddell
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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6
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Broennimann K, Ricardo-Lax I, Adler J, Michailidis E, de Jong YP, Reuven N, Shaul Y. RNR-R2 Upregulation by a Short Non-Coding Viral Transcript. Biomolecules 2021; 11:biom11121822. [PMID: 34944466 PMCID: PMC8698843 DOI: 10.3390/biom11121822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 01/12/2023] Open
Abstract
DNA viruses require dNTPs for replication and have developed different strategies to increase intracellular dNTP pools. Hepatitis B virus (HBV) infects non-dividing cells in which dNTPs are scarce and the question is how viral replication takes place. Previously we reported that the virus induces the DNA damage response (DDR) pathway culminating in RNR-R2 expression and the generation of an active RNR holoenzyme, the key regulator of dNTP levels, leading to an increase in dNTPs. How the virus induces DDR and RNR-R2 upregulation is not completely known. The viral HBx open reading frame (ORF) was believed to trigger this pathway. Unexpectedly, however, we report here that the production of HBx protein is dispensable. We found that a small conserved region of 125 bases within the HBx ORF is sufficient to upregulate RNR-R2 expression in growth-arrested HepG2 cells and primary human hepatocytes. The observed HBV mRNA embedded regulatory element is named ERE. ERE in isolation is sufficient to activate the ATR-Chk1-E2F1-RNR-R2 DDR pathway. These findings demonstrate a non-coding function of HBV transcripts to support its propagation in non-cycling cells.
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Affiliation(s)
- Karin Broennimann
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel; (K.B.); (I.R.-L.); (J.A.); (N.R.)
| | - Inna Ricardo-Lax
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel; (K.B.); (I.R.-L.); (J.A.); (N.R.)
- Laboratory of Virology and Infectious Disease, Rockefeller University, New York, NY 10065, USA; (E.M.); (Y.P.d.J.)
| | - Julia Adler
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel; (K.B.); (I.R.-L.); (J.A.); (N.R.)
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, Rockefeller University, New York, NY 10065, USA; (E.M.); (Y.P.d.J.)
| | - Ype P. de Jong
- Laboratory of Virology and Infectious Disease, Rockefeller University, New York, NY 10065, USA; (E.M.); (Y.P.d.J.)
- Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Nina Reuven
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel; (K.B.); (I.R.-L.); (J.A.); (N.R.)
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel; (K.B.); (I.R.-L.); (J.A.); (N.R.)
- Correspondence: ; Tel.: +972-8-934-2320
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Host Poly(A) Polymerases PAPD5 and PAPD7 Provide Two Layers of Protection That Ensure the Integrity and Stability of Hepatitis B Virus RNA. J Virol 2021; 95:e0057421. [PMID: 34191584 PMCID: PMC8387043 DOI: 10.1128/jvi.00574-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Noncanonical poly(A) polymerases PAPD5 and PAPD7 (PAPD5/7) stabilize hepatitis B virus (HBV) RNA via the interaction with the viral posttranscriptional regulatory element (PRE), representing new antiviral targets to control HBV RNA metabolism, hepatitis B surface antigen (HBsAg) production, and viral replication. Inhibitors targeting these proteins are being developed as antiviral therapies; therefore, it is important to understand how PAPD5/7 coordinate to stabilize HBV RNA. Here, we utilized a potent small-molecule AB-452 as a chemical probe, along with genetic analyses to dissect the individual roles of PAPD5/7 in HBV RNA stability. AB-452 inhibits PAPD5/7 enzymatic activities and reduces HBsAg both in vitro (50% effective concentration [EC50] ranged from 1.4 to 6.8 nM) and in vivo by 0.94 log10. Our genetic studies demonstrate that the stem-loop alpha sequence within PRE is essential for both maintaining HBV poly(A) tail integrity and determining sensitivity toward the inhibitory effect of AB-452. Although neither single knockout (KO) of PAPD5 nor PAPD7 reduces HBsAg RNA and protein production, PAPD5 KO does impair poly(A) tail integrity and confers partial resistance to AB-452. In contrast, PAPD7 KO did not result in any measurable changes within the HBV poly(A) tails, but cells with both PAPD5 and PAPD7 KO show reduced HBsAg production and conferred complete resistance to AB-452 treatment. Our results indicate that PAPD5 plays a dominant role in stabilizing viral RNA by protecting the integrity of its poly(A) tail, while PAPD7 serves as a second line of protection. These findings inform PAPD5-targeted therapeutic strategies and open avenues for further investigating PAPD5/7 in HBV replication. IMPORTANCE Chronic hepatitis B affects more than 250 million patients and is a major public health concern worldwide. HBsAg plays a central role in maintaining HBV persistence, and as such, therapies that aim at reducing HBsAg through destabilizing or degrading HBV RNA have been extensively investigated. Besides directly degrading HBV transcripts through antisense oligonucleotides or RNA silencing technologies, small-molecule compounds targeting host factors such as the noncanonical poly(A) polymerase PAPD5 and PAPD7 have been reported to interfere with HBV RNA metabolism. Herein, our antiviral and genetic studies using relevant HBV infection and replication models further characterize the interplays between the cis element within the viral sequence and the trans elements from the host factors. PAPD5/7-targeting inhibitors, with oral bioavailability, thus represent an opportunity to reduce HBsAg through destabilizing HBV RNA.
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Lim CS, Sozzi V, Littlejohn M, Yuen LK, Warner N, Betz-Stablein B, Luciani F, Revill PA, Brown CM. Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes. Microb Genom 2021; 7:mgen000492. [PMID: 33439114 PMCID: PMC8115900 DOI: 10.1099/mgen.0.000492] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Hepatitis B virus (HBV) is a major human pathogen that causes liver diseases. The main HBV RNAs are unspliced transcripts that encode the key viral proteins. Recent studies have shown that some of the HBV spliced transcript isoforms are predictive of liver cancer, yet the roles of these spliced transcripts remain elusive. Furthermore, there are nine major HBV genotypes common in different regions of the world, these genotypes may express different spliced transcript isoforms. To systematically study the HBV splice variants, we transfected human hepatoma cells, Huh7, with four HBV genotypes (A2, B2, C2 and D3), followed by deep RNA-sequencing. We found that 13-28 % of HBV RNAs were splice variants, which were reproducibly detected across independent biological replicates. These comprised 6 novel and 10 previously identified splice variants. In particular, a novel, singly spliced transcript was detected in genotypes A2 and D3 at high levels. The biological relevance of these splice variants was supported by their identification in HBV-positive liver biopsy and serum samples, and in HBV-infected primary human hepatocytes. Interestingly the levels of HBV splice variants varied across the genotypes, but the spliced pregenomic RNA SP1 and SP9 were the two most abundant splice variants. Counterintuitively, these singly spliced SP1 and SP9 variants had a suboptimal 5' splice site, supporting the idea that splicing of HBV RNAs is tightly controlled by the viral post-transcriptional regulatory RNA element.
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Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Vitina Sozzi
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lilly K.W. Yuen
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nadia Warner
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Brigid Betz-Stablein
- Systems Medicine, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Present address: Dermatology Research Centre, Diamantina Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Fabio Luciani
- Systems Medicine, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter A. Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chris M. Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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9
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The Dihydroquinolizinone Compound RG7834 Inhibits the Polyadenylase Function of PAPD5 and PAPD7 and Accelerates the Degradation of Matured Hepatitis B Virus Surface Protein mRNA. Antimicrob Agents Chemother 2020; 65:AAC.00640-20. [PMID: 33046485 DOI: 10.1128/aac.00640-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
Hepatitis B virus (HBV) mRNA metabolism is dependent upon host proteins PAPD5 and PAPD7 (PAPD5/7). PAPD5/7 are cellular, noncanonical, poly(A) polymerases (PAPs) whose main function is to oligoadenylate the 3' end of noncoding RNA (ncRNA) for exosome degradation. HBV seems to exploit these two ncRNA quality-control factors for viral mRNA stabilization, rather than degradation. RG7834 is a small-molecule compound that binds PAPD5/7 and inhibits HBV gene production in both tissue culture and animal study. We reported that RG7834 was able to destabilize multiple HBV mRNA species, ranging from the 3.5-kb pregenomic/precore mRNAs to the 2.4/2.1-kb hepatitis B virus surface protein (HBs) mRNAs, except for the smallest 0.7-kb X protein (HBx) mRNA. Compound-induced HBV mRNA destabilization was initiated by a shortening of the poly(A) tail, followed by an accelerated degradation process in both the nucleus and cytoplasm. In cells expressing HBV mRNA, both PAPD5/7 were found to be physically associated with the viral RNA, and the polyadenylating activities of PAPD5/7 were susceptible to RG7834 repression in a biochemical assay. Moreover, in PAPD5/7 double-knockout cells, viral transcripts with a regular length of the poly(A) sequence could be initially synthesized but became shortened in hours, suggesting that participation of PAPD5/7 in RNA 3' end processing, either during adenosine oligomerization or afterward, is crucial for RNA stabilization.
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10
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Osteopetrosis-Associated Transmembrane Protein 1 Recruits RNA Exosome To Restrict Hepatitis B Virus Replication. J Virol 2020; 94:JVI.01800-19. [PMID: 32188736 DOI: 10.1128/jvi.01800-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/22/2020] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) chronically infects approximately 350 million people worldwide, and 600,000 deaths are caused by HBV-related hepatic failure, liver cirrhosis, and hepatocellular carcinoma annually. It is important to reveal the mechanism underlying the regulation of HBV replication. This study demonstrated that osteopetrosis-associated transmembrane protein 1 (Ostm1) plays an inhibitory role in HBV replication. Ostm1 represses the levels of HBeAg and HBsAg proteins, HBV 3.5-kb and 2.4/2.1-kb RNAs, and core-associated DNA in HepG2, Huh7, and NTCP-HepG2 cells. Notably, Ostm1 has no direct effect on the activity of HBV promoters or the transcription of HBV RNAs; instead, Ostm1 binds to HBV RNA to facilitate RNA decay. Detailed studies further demonstrated that Ostm1 binds to and recruits the RNA exosome complex to promote the degradation of HBV RNAs, and knockdown of the RNA exosome component exonuclease 3 (Exosc3) leads to the elimination of Ostm1-mediated repression of HBV replication. Mutant analyses revealed that the N-terminal domain, the transmembrane domain, and the C-terminal domain are responsible for the repression of HBV replication, and the C-terminal domain is required for interaction with the RNA exosome complex. Moreover, Ostm1 production is not regulated by interferon-α (IFN-α) or IFN-γ, and the expression of IFN signaling components is not affected by Ostm1, suggesting that Ostm1 anti-HBV activity is independent of the IFN signaling pathway. In conclusion, this study revealed a distinct mechanism underlying the repression of HBV replication, in which Ostm1 binds to HBV RNA and recruits RNA exosomes to degrade viral RNA, thereby restricting HBV replication.IMPORTANCE Hepatitis B virus (HBV) is a human pathogen infecting the liver to cause a variety of diseases ranging from acute hepatitis to advanced liver diseases, fulminate hepatitis, liver cirrhosis, and hepatocellular carcinoma, thereby causing a major health problem worldwide. In this study, we demonstrated that Ostm1 plays an inhibitory role in HBV protein production, RNA expression, and DNA replication. However, Ostm1 has no effect on the activities of the four HBV promoters; instead, it binds to HBV RNA and recruits RNA exosomes to promote HBV RNA degradation. We further demonstrated that the anti-HBV activity of Ostm1 is independent of the interferon signaling pathway. In conclusion, this study reveals a distinct mechanism underlying the repression of HBV replication and suggests that Ostm1 is a potential therapeutic agent for HBV infection.
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Hu B, Yu L, Zhu N, Xie J. Cellular UAP56 interacts with the HBx protein of the hepatitis B virus and is involved in viral RNA nuclear export in hepatocytes. Exp Cell Res 2020; 390:111929. [DOI: 10.1016/j.yexcr.2020.111929] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 01/29/2023]
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Veatch JR, Jesernig BL, Kargl J, Fitzgibbon M, Lee SM, Baik C, Martins R, Houghton AM, Riddell SR. Endogenous CD4 + T Cells Recognize Neoantigens in Lung Cancer Patients, Including Recurrent Oncogenic KRAS and ERBB2 ( Her2) Driver Mutations. Cancer Immunol Res 2019; 7:910-922. [PMID: 31043415 PMCID: PMC6584616 DOI: 10.1158/2326-6066.cir-18-0402] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/12/2018] [Accepted: 04/24/2019] [Indexed: 12/20/2022]
Abstract
T cells specific for neoantigens encoded by mutated genes in cancers are increasingly recognized as mediators of tumor destruction after immune-checkpoint inhibitor therapy or adoptive cell transfer. Much of the focus has been on identifying epitopes presented to CD8+ T cells by class I MHC. However, CD4+ class II MHC-restricted T cells have been shown to have an important role in antitumor immunity. Unfortunately, the vast majority of neoantigens recognized by CD8+ or CD4+ T cells in cancer patients result from random mutations and are patient-specific. Here, we screened the blood of 5 non-small cell lung cancer (NSCLC) patients for T-cell responses to candidate mutation-encoded neoepitopes. T-cell responses were detected to 8.8% of screened antigens, with 1 to 7 antigens identified per patient. A majority of responses were to random, patient-specific mutations. However, CD4+ T cells that recognized the recurrent KRAS G12V and the ERBB2 (Her2) internal tandem duplication (ITD) oncogenic driver mutations, but not the corresponding wild-type sequences, were identified in two patients. Two different T-cell receptors (TCR) specific for KRAS G12V and one T-cell receptor specific for Her2-ITD were isolated and conferred antigen specificity when transfected into T cells. Deep sequencing identified the Her2-ITD-specific TCR in the tumor but not nonadjacent lung. Our results showed that CD4+ T-cell responses to neoantigens, including recurrent driver mutations, can be derived from the blood of NSCLC patients. These data support the use of adoptive transfer or vaccination to augment CD4+ neoantigen-specific T cells and elucidate their role in human antitumor immunity.
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Affiliation(s)
- Joshua R Veatch
- Immunotherapy Integrated Research Center, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
| | - Brenda L Jesernig
- Immunotherapy Integrated Research Center, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Julia Kargl
- Immunotherapy Integrated Research Center, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Otto Loewi Research Center, Pharmacology, Medical University of Graz, Graz, Austria
| | - Matthew Fitzgibbon
- Immunotherapy Integrated Research Center, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Sylvia M Lee
- Division of Medical Oncology, University of Washington, Seattle, Washington
| | - Christina Baik
- Division of Medical Oncology, University of Washington, Seattle, Washington
| | - Renato Martins
- Division of Medical Oncology, University of Washington, Seattle, Washington
| | - A McGarry Houghton
- Immunotherapy Integrated Research Center, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stanley R Riddell
- Immunotherapy Integrated Research Center, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
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Mitra B, Thapa RJ, Guo H, Block TM. Host functions used by hepatitis B virus to complete its life cycle: Implications for developing host-targeting agents to treat chronic hepatitis B. Antiviral Res 2018; 158:185-198. [PMID: 30145242 PMCID: PMC6193490 DOI: 10.1016/j.antiviral.2018.08.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 02/06/2023]
Abstract
Similar to other mammalian viruses, the life cycle of hepatitis B virus (HBV) is heavily dependent upon and regulated by cellular (host) functions. These cellular functions can be generally placed in to two categories: (a) intrinsic host restriction factors and innate defenses, which must be evaded or repressed by the virus; and (b) gene products that provide functions necessary for the virus to complete its life cycle. Some of these functions may apply to all viruses, but some may be specific to HBV. In certain cases, the virus may depend upon the host function much more than does the host itself. Knowing which host functions regulate the different steps of a virus' life cycle, can lead to new antiviral targets and help in developing novel treatment strategies, in addition to improving a fundamental understanding of viral pathogenesis. Therefore, in this review we will discuss known host factors which influence key steps of HBV life cycle, and further elucidate therapeutic interventions targeting host-HBV interactions.
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Affiliation(s)
- Bidisha Mitra
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Haitao Guo
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA.
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Lim CS, Brown CM. Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs. Front Microbiol 2018; 8:2582. [PMID: 29354101 PMCID: PMC5758548 DOI: 10.3389/fmicb.2017.02582] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/11/2017] [Indexed: 12/14/2022] Open
Abstract
Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community.
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Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Chris M Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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15
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Zhou T, Block T, Liu F, Kondratowicz AS, Sun L, Rawat S, Branson J, Guo F, Steuer HM, Liang H, Bailey L, Moore C, Wang X, Cuconatti A, Gao M, Lee ACH, Harasym T, Chiu T, Gotchev D, Dorsey B, Rijnbrand R, Sofia MJ. HBsAg mRNA degradation induced by a dihydroquinolizinone compound depends on the HBV posttranscriptional regulatory element. Antiviral Res 2017; 149:191-201. [PMID: 29133129 DOI: 10.1016/j.antiviral.2017.11.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 11/01/2017] [Accepted: 11/07/2017] [Indexed: 12/23/2022]
Abstract
In pursuit of novel therapeutics targeting the hepatitis B virus (HBV) infection, we evaluated a dihydroquinolizinone compound (DHQ-1) that in the nanomolar range reduced the production of virion and surface protein (HBsAg) in tissue culture. This compound also showed broad HBV genotype coverage, but was inactive against a panel of DNA and RNA viruses of other species. Oral administration of DHQ-1 in the AAV-HBV mouse model resulted in a significant reduction of serum HBsAg as soon as 4 days following the commencement of treatment. Reduction of HBV markers in both in vitro and in vivo experiments was related to the reduced amount of viral RNA including pre-genomic RNA (pgRNA) and 2.4/2.1 kb HBsAg mRNA. Nuclear run-on and subcellular fractionation experiments indicated that DHQ-1 mediated HBV RNA reduction was the result of accelerated viral RNA degradation in the nucleus, rather than the consequence of inhibition of transcription initiation. Through mutagenesis of HBsAg gene sequences, we found induction of HBsAg mRNA decay by DHQ-1 required the presence of the HBV posttranscriptional regulatory element (HPRE), with a 109 nucleotides sequence within the central region of the HPRE alpha sub-element being the most critical. Taken together, the current study shows that a small molecule can reduce the overall levels of HBV RNA, especially the HBsAg mRNA, and viral surface proteins. This may shed light on the development of a new class of HBV therapeutics.
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Affiliation(s)
- Tianlun Zhou
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States.
| | - Timothy Block
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Fei Liu
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Andrew S Kondratowicz
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Liren Sun
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Siddhartha Rawat
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Jeffrey Branson
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Fang Guo
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | | | - Hongyan Liang
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Lauren Bailey
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Chris Moore
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Xiaohe Wang
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Andy Cuconatti
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Min Gao
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Amy C H Lee
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Troy Harasym
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Tim Chiu
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Dimitar Gotchev
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Bruce Dorsey
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Rene Rijnbrand
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Michael J Sofia
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States.
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