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Xia Y, Cheng X, Nilsson T, Zhang M, Zhao G, Inuzuka T, Teng Y, Li Y, Anderson DE, Holdorf M, Liang TJ. Nucleolin binds to and regulates transcription of hepatitis B virus covalently closed circular DNA minichromosome. Proc Natl Acad Sci U S A 2023; 120:e2306390120. [PMID: 38015841 DOI: 10.1073/pnas.2306390120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/03/2023] [Indexed: 11/30/2023] Open
Abstract
Hepatitis B virus (HBV) remains a major public health threat with nearly 300 million people chronically infected worldwide who are at a high risk of developing hepatocellular carcinoma. Current therapies are effective in suppressing HBV replication but rarely lead to cure. Current therapies do not affect the HBV covalently closed circular DNA (cccDNA), which serves as the template for viral transcription and replication and is highly stable in infected cells to ensure viral persistence. In this study, we aim to identify and elucidate the functional role of cccDNA-associated host factors using affinity purification and protein mass spectrometry in HBV-infected cells. Nucleolin was identified as a key cccDNA-binding protein and shown to play an important role in HBV cccDNA transcription, likely via epigenetic regulation. Targeting nucleolin to silence cccDNA transcription in infected hepatocytes may be a promising therapeutic strategy for a functional cure of HBV.
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Affiliation(s)
- Yuchen Xia
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Xiaoming Cheng
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Tobias Nilsson
- Department of Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, CA 94608
| | - Min Zhang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892
| | - Gaihong Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Tadashi Inuzuka
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892
| | - Yan Teng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Yao Li
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892
| | - D Eric Anderson
- Advanced Mass Spectrometry Core, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892
| | - Meghan Holdorf
- Department of Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, CA 94608
| | - T Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892
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Hyrina A, Jones C, Chen D, Clarkson S, Cochran N, Feucht P, Hoffman G, Lindeman A, Russ C, Sigoillot F, Tsang T, Uehara K, Xie L, Ganem D, Holdorf M. A Genome-wide CRISPR Screen Identifies ZCCHC14 as a Host Factor Required for Hepatitis B Surface Antigen Production. Cell Rep 2020; 29:2970-2978.e6. [PMID: 31801065 DOI: 10.1016/j.celrep.2019.10.113] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/23/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022] Open
Abstract
A hallmark of chronic hepatitis B (CHB) virus infection is the presence of high circulating levels of non-infectious small lipid HBV surface antigen (HBsAg) vesicles. Although rare, sustained HBsAg loss is the idealized endpoint of any CHB therapy. A small molecule, RG7834, has been previously reported to inhibit HBsAg expression by targeting terminal nucleotidyltransferase proteins 4A and 4B (TENT4A and TENT4B). In this study, we describe a genome-wide CRISPR screen to identify other potential host factors required for HBsAg expression and to gain further insights into the mechanism of RG7834. We report more than 60 genes involved in regulating HBsAg and identify additional factors involved in RG7834 activity, including a zinc finger CCHC-type containing 14 (ZCCHC14) protein. We show that ZCCHC14, together with TENT4A/B, stabilizes HBsAg expression through HBV RNA tailing, providing a potential new therapeutic target to achieve functional cure in CHB patients.
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Affiliation(s)
- Anastasia Hyrina
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA.
| | - Christopher Jones
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Darlene Chen
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Scott Clarkson
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Nadire Cochran
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Paul Feucht
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Gregory Hoffman
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Alicia Lindeman
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Carsten Russ
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | - Tiffany Tsang
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Kyoko Uehara
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Lili Xie
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Don Ganem
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Meghan Holdorf
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
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Publicover J, Gaggar A, Jespersen JM, Halac U, Johnson AJ, Goodsell A, Avanesyan L, Nishimura SL, Holdorf M, Mansfield KG, Judge JB, Koshti A, Croft M, Wakil AE, Rosenthal P, Pai E, Cooper S, Baron JL. An OX40/OX40L interaction directs successful immunity to hepatitis B virus. Sci Transl Med 2019; 10:10/433/eaah5766. [PMID: 29563320 DOI: 10.1126/scitranslmed.aah5766] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 01/03/2018] [Indexed: 12/19/2022]
Abstract
Depending on age of acquisition, hepatitis B virus (HBV) can induce a cell-mediated immune response that results in either cure or progressive liver injury. In adult-acquired infection, HBV antigens are usually cleared, whereas in infancy-acquired infection, they persist. Individuals infected during infancy therefore represent the majority of patients chronically infected with HBV (CHB). A therapy that can promote viral antigen clearance in most CHB patients has not been developed and would represent a major health care advance and cost mitigator. Using an age-dependent mouse model of HBV clearance and persistence in conjunction with human blood and liver tissue, we studied mechanisms of viral clearance to identify new therapeutic targets. We demonstrate that age-dependent expression of the costimulatory molecule OX40 ligand (OX40L) by hepatic innate immune cells is pivotal in determining HBV immunity, and that treatment with OX40 agonists leads to improved HBV antigen clearance in young mice, as well as increased strength of T cell responses in young mice and adult mice that were exposed to HBV when they were young and developed a CHB serological profile. Similarly, in humans, we show that hepatic OX40L transcript expression is age-dependent and that increased OX40 expression on peripheral CD4+ T cells in adults is associated with HBV clearance. These findings provide new mechanistic understanding of the immune pathways and cells necessary for HBV immunity and identify potential therapeutic targets for resolving CHB.
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Affiliation(s)
- Jean Publicover
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA.,UCSF Liver Center, UCSF, San Francisco, CA 94143, USA
| | - Anuj Gaggar
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA.,UCSF Liver Center, UCSF, San Francisco, CA 94143, USA
| | - Jillian M Jespersen
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA.,UCSF Liver Center, UCSF, San Francisco, CA 94143, USA
| | - Ugur Halac
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA.,UCSF Liver Center, UCSF, San Francisco, CA 94143, USA
| | - Audra J Johnson
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA.,UCSF Liver Center, UCSF, San Francisco, CA 94143, USA
| | - Amanda Goodsell
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA.,UCSF Liver Center, UCSF, San Francisco, CA 94143, USA
| | - Lia Avanesyan
- Liver Immunology Laboratory, California Pacific Medical Center Research Institute, San Francisco, CA 94115, USA.,Division of General and Transplant Hepatology, California Pacific Medical Center Research Institute, San Francisco, CA 94115, USA
| | | | - Meghan Holdorf
- Novartis Institute for Biomedical Research, Emeryville, CA 94619, USA
| | - Keith G Mansfield
- Discovery and Investigative Pathology, Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Joyce Bousquet Judge
- Discovery and Investigative Pathology, Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Arya Koshti
- Novartis Institute for Biomedical Research, Emeryville, CA 94619, USA
| | - Michael Croft
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Adil E Wakil
- Liver Immunology Laboratory, California Pacific Medical Center Research Institute, San Francisco, CA 94115, USA.,Division of General and Transplant Hepatology, California Pacific Medical Center Research Institute, San Francisco, CA 94115, USA
| | - Philip Rosenthal
- UCSF Liver Center, UCSF, San Francisco, CA 94143, USA.,Department of Pediatrics, UCSF, San Francisco, CA 94143, USA.,Department of Surgery, UCSF, San Francisco, CA 94143, USA
| | - Eric Pai
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA.,UCSF Liver Center, UCSF, San Francisco, CA 94143, USA
| | - Stewart Cooper
- UCSF Liver Center, UCSF, San Francisco, CA 94143, USA.,Liver Immunology Laboratory, California Pacific Medical Center Research Institute, San Francisco, CA 94115, USA.,Division of General and Transplant Hepatology, California Pacific Medical Center Research Institute, San Francisco, CA 94115, USA
| | - Jody L Baron
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA. .,UCSF Liver Center, UCSF, San Francisco, CA 94143, USA
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Arias C, Weisburd B, Stern-Ginossar N, Mercier A, Madrid AS, Bellare P, Holdorf M, Weissman JS, Ganem D. KSHV 2.0: a comprehensive annotation of the Kaposi's sarcoma-associated herpesvirus genome using next-generation sequencing reveals novel genomic and functional features. PLoS Pathog 2014; 10:e1003847. [PMID: 24453964 PMCID: PMC3894221 DOI: 10.1371/journal.ppat.1003847] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 10/20/2013] [Indexed: 01/08/2023] Open
Abstract
Productive herpesvirus infection requires a profound, time-controlled remodeling of the viral transcriptome and proteome. To gain insights into the genomic architecture and gene expression control in Kaposi's sarcoma-associated herpesvirus (KSHV), we performed a systematic genome-wide survey of viral transcriptional and translational activity throughout the lytic cycle. Using mRNA-sequencing and ribosome profiling, we found that transcripts encoding lytic genes are promptly bound by ribosomes upon lytic reactivation, suggesting their regulation is mainly transcriptional. Our approach also uncovered new genomic features such as ribosome occupancy of viral non-coding RNAs, numerous upstream and small open reading frames (ORFs), and unusual strategies to expand the virus coding repertoire that include alternative splicing, dynamic viral mRNA editing, and the use of alternative translation initiation codons. Furthermore, we provide a refined and expanded annotation of transcription start sites, polyadenylation sites, splice junctions, and initiation/termination codons of known and new viral features in the KSHV genomic space which we have termed KSHV 2.0. Our results represent a comprehensive genome-scale image of gene regulation during lytic KSHV infection that substantially expands our understanding of the genomic architecture and coding capacity of the virus. Kaposi's sarcoma-associated herpesvirus (KSHV) is a cancer-causing agent in immunocompromised patients that establishes long-lasting infections in its hosts. Initially described in 1994 and extensively studied ever since, KSHV molecular biology is understood in broad outline, but many detailed questions are still to be resolved. After almost two decades, specific aspects pertaining to the organization of the KSHV genome as well as the fate of the viral transcripts during the productive stages of infection remain unexplored. Here we use a systematic genome-wide approach to investigate changes in gene and protein expression during the productive stage of infection known as the lytic cycle. We found that the viral genome has a large coding capacity, capable of generating at least 45% more products than initially anticipated by bioinformatic analyses alone, and that it uses multiple strategies to expand its coding capacity well beyond what is determined solely by the DNA sequence of its genome. We also provide an expanded and highly detailed annotation of known and new genomic features in KSHV. We have termed this new architectural and functional annotation KSHV 2.0. Our results indicate that viral genomes are more complex than anticipated, and that they are subject to tight mechanisms of regulation to ensure correct gene expression.
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Affiliation(s)
- Carolina Arias
- Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America
- * E-mail:
| | - Ben Weisburd
- Novartis Vaccines and Diagnostics, Bioinformatics, Emeryville, California, United States of America
| | - Noam Stern-Ginossar
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Alexandre Mercier
- Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America
| | - Alexis S. Madrid
- Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America
| | - Priya Bellare
- Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America
| | - Meghan Holdorf
- Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America
| | - Jonathan S. Weissman
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Don Ganem
- Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America
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