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Harioudh MK, Perez J, So L, Maheshwari M, Ebert TS, Hornung V, Savan R, Rouf Banday A, Diamond MS, Rathinam VA, Sarkar SN. The canonical antiviral protein oligoadenylate synthetase 1 elicits antibacterial functions by enhancing IRF1 translation. Immunity 2024:S1074-7613(24)00309-1. [PMID: 38955184 DOI: 10.1016/j.immuni.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/11/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
An important property of the host innate immune response during microbial infection is its ability to control the expression of antimicrobial effector proteins, but how this occurs post-transcriptionally is not well defined. Here, we describe a critical antibacterial role for the classic antiviral gene 2'-5'-oligoadenylate synthetase 1 (OAS1). Human OAS1 and its mouse ortholog, Oas1b, are induced by interferon-γ and protect against cytosolic bacterial pathogens such as Francisella novicida and Listeria monocytogenes in vitro and in vivo. Proteomic and transcriptomic analysis showed reduced IRF1 protein expression in OAS1-deficient cells. Mechanistically, OAS1 binds and localizes IRF1 mRNA to the rough endoplasmic reticulum (ER)-Golgi endomembranes, licensing effective translation of IRF1 mRNA without affecting its transcription or decay. OAS1-dependent translation of IRF1 leads to the enhanced expression of antibacterial effectors, such as GBPs, which restrict intracellular bacteria. These findings uncover a noncanonical function of OAS1 in antibacterial innate immunity.
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Affiliation(s)
- Munesh K Harioudh
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joseph Perez
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lomon So
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Mayank Maheshwari
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Thomas S Ebert
- Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Veit Hornung
- Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Ram Savan
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - A Rouf Banday
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Vijay A Rathinam
- Department of Immunology, UConn Health School of Medicine, Farmington, CT, USA
| | - Saumendra N Sarkar
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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2
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Harioudh MK, Perez J, Chong Z, Nair S, So L, McCormick KD, Ghosh A, Shao L, Srivastava R, Soveg F, Ebert TS, Atianand MK, Hornung V, Savan R, Diamond MS, Sarkar SN. Oligoadenylate synthetase 1 displays dual antiviral mechanisms in driving translational shutdown and protecting interferon production. Immunity 2024; 57:446-461.e7. [PMID: 38423012 PMCID: PMC10939734 DOI: 10.1016/j.immuni.2024.02.002] [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: 06/15/2023] [Revised: 11/15/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
In response to viral infection, how cells balance translational shutdown to limit viral replication and the induction of antiviral components like interferons (IFNs) is not well understood. Moreover, how distinct isoforms of IFN-induced oligoadenylate synthetase 1 (OAS1) contribute to this antiviral response also requires further elucidation. Here, we show that human, but not mouse, OAS1 inhibits SARS-CoV-2 replication through its canonical enzyme activity via RNase L. In contrast, both mouse and human OAS1 protect against West Nile virus infection by a mechanism distinct from canonical RNase L activation. OAS1 binds AU-rich elements (AREs) of specific mRNAs, including IFNβ. This binding leads to the sequestration of IFNβ mRNA to the endomembrane regions, resulting in prolonged half-life and continued translation. Thus, OAS1 is an ARE-binding protein with two mechanisms of antiviral activity: driving inhibition of translation but also a broader, non-canonical function of protecting IFN expression from translational shutdown.
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Affiliation(s)
- Munesh K Harioudh
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA
| | - Joseph Perez
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA
| | - Zhenlu Chong
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sharmila Nair
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lomon So
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA; Division of Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Kevin D McCormick
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA
| | - Arundhati Ghosh
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA
| | - Lulu Shao
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA
| | - Rashmi Srivastava
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA
| | - Frank Soveg
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Thomas S Ebert
- Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Maninjay K Atianand
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Veit Hornung
- Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Ram Savan
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Saumendra N Sarkar
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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3
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Goldstein SA, Elde NC. Recurrent viral capture of cellular phosphodiesterases that antagonize OAS-RNase L. Proc Natl Acad Sci U S A 2024; 121:e2312691121. [PMID: 38277437 PMCID: PMC10835031 DOI: 10.1073/pnas.2312691121] [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: 07/25/2023] [Accepted: 11/20/2023] [Indexed: 01/28/2024] Open
Abstract
Phosphodiesterases (PDEs) encoded by viruses are putatively acquired by horizontal transfer of cellular PDE ancestor genes. Viral PDEs inhibit the OAS-RNase L antiviral pathway, a key effector component of the innate immune response. Although the function of these proteins is well-characterized, the origins of these gene acquisitions are less clear. Phylogenetic analysis revealed at least five independent PDE acquisition events by ancestral viruses. We found evidence that PDE-encoding genes were horizontally transferred between coronaviruses belonging to different genera. Three clades of viruses within Nidovirales: merbecoviruses (MERS-CoV), embecoviruses (HCoV-OC43), and toroviruses encode independently acquired PDEs, and a clade of rodent alphacoronaviruses acquired an embecovirus PDE via recent horizontal transfer. Among rotaviruses, the PDE of rotavirus A was acquired independently from rotavirus B and G PDEs, which share a common ancestor. Conserved motif analysis suggests a link between all viral PDEs and a similar ancestor among the mammalian AKAP7 proteins despite low levels of sequence conservation. Additionally, we used ancestral sequence reconstruction and structural modeling to reveal that sequence and structural divergence are not well-correlated among these proteins. Specifically, merbecovirus PDEs are as structurally divergent from the ancestral protein and the solved structure of human AKAP7 PDE as they are from each other. In contrast, comparisons of rotavirus B and G PDEs reveal virtually unchanged structures despite evidence for loss of function in one, suggesting impactful changes that lie outside conserved catalytic sites. These findings highlight the complex and volatile evolutionary history of viral PDEs and provide a framework to facilitate future studies.
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Affiliation(s)
- Stephen A. Goldstein
- Department of Human Genetics, University of Utah, School of Medicine, Salt Lake City, UT84112
- HHMI, Chevy Chase, MD20815
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, School of Medicine, Salt Lake City, UT84112
- HHMI, Chevy Chase, MD20815
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Olkova MV, Koshel SM, Petrushenko VS, Alimov AA. Features of Distribution of the Allelic Variant of the OAS1 Gene Associated with Severe Form of the Coronavirus Infection in the Russian and Global Populations. Bull Exp Biol Med 2023; 176:194-201. [PMID: 38191878 DOI: 10.1007/s10517-024-05994-4] [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: 04/30/2023] [Indexed: 01/10/2024]
Abstract
The study of the geographic distribution of the allelic variant of the OAS1 gene associated with severe form of the infections caused by RNA viruses was carried out using the rs10774671 polymorphic locus. The mutant allele encoding the p42 protein isoform was most prevalent in the Russian populations. A comparative analysis of the prevalence of the mutant allele in world populations showed that its frequency is 0.9 among the inhabitants of Northern Eurasia, while the allele encoding the p46 protein isoform is widespread among the population of West Central Africa. A cartographic analysis of the relationship between the population-frequency characteristics of the marker alleles and the geographical remoteness of the populations showed that the mutant allele is most often observed in the indigenous populations of the Far East, which suggests its East Asian origin.
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Affiliation(s)
- M V Olkova
- Research Centre for Medical Genetics, Moscow, Russia.
| | - S M Koshel
- Research Centre for Medical Genetics, Moscow, Russia
- M. V. Lomonosov Moscow State University, Moscow, Russia
| | | | - A A Alimov
- Research Centre for Medical Genetics, Moscow, Russia
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5
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Sarkar SN, Harioudh MK, Shao L, Perez J, Ghosh A. The Many Faces of Oligoadenylate Synthetases. J Interferon Cytokine Res 2023; 43:487-494. [PMID: 37751211 PMCID: PMC10654648 DOI: 10.1089/jir.2023.0098] [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: 07/17/2023] [Accepted: 08/13/2023] [Indexed: 09/27/2023] Open
Abstract
2'-5' Oligoadenylate synthetases (OAS) are interferon-stimulated genes that are most well-known to protect hosts from viral infections. They are evolutionarily related to an ancient family of Nucleotidyltransferases, which are primarily involved in pathogen-sensing and innate immune response. Classical function of OAS proteins involves double-stranded RNA-stimulated polymerization of adenosine triphosphate in 2'-5' oligoadenylates (2-5A), which can activate the latent RNase (RNase L) to degrade RNA. However, accumulated evidence over the years have suggested alternative mode of antiviral function of several OAS family proteins. Furthermore, recent studies have connected some OAS proteins with wider function beyond viral infection. Here, we review some of the canonical and noncanonical functions of OAS proteins and their mechanisms.
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Affiliation(s)
- Saumendra N. Sarkar
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Munesh K. Harioudh
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lulu Shao
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Joseph Perez
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Arundhati Ghosh
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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6
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Goldstein SA, Elde NC. Recurrent Viral Capture of Cellular Phosphodiesterases that Antagonize OAS-RNase L. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.12.540623. [PMID: 37745432 PMCID: PMC10515750 DOI: 10.1101/2023.05.12.540623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Phosphodiesterases (PDEs) encoded by viruses are putatively acquired by horizontal transfer of cellular PDE ancestor genes. Viral PDEs inhibit the OAS-RNase L antiviral pathway, a key effector component of the innate immune response. Although the function of these proteins is well-characterized, the origins of these gene acquisitions is less clear. Phylogenetic analysis revealed at least five independent PDE acquisition events by ancestral viruses. We found evidence that PDE-encoding genes were horizontally transferred between coronavirus genera. Three clades of viruses within Nidovirales: merbecoviruses (MERS-CoV), embecoviruses (OC43), and toroviruses encode independently acquired PDEs, and a clade of rodent alphacoronaviruses acquired an embecovirus PDE via recent horizontal transfer. Among rotaviruses, the PDE of Rotavirus A was acquired independently from Rotavirus B and G PDEs, which share a common ancestor. Conserved motif analysis suggests a link between all viral PDEs and a similar ancestor among the mammalian AKAP7 proteins despite low levels of sequence conservation. Additionally, we used ancestral sequence reconstruction and structural modeling to reveal that sequence and structural divergence are not well-correlated among these proteins. Specifically, merbecovirus PDEs are as structurally divergent from the ancestral protein and the solved structure of human AKAP7 PDE as they are from each other. In contrast, comparisons of Rotavirus B and G PDEs reveal virtually unchanged structures despite evidence for loss of function in one, suggesting impactful changes that lie outside conserved catalytic sites. These findings highlight the complex and volatile evolutionary history of viral PDEs and provide a framework to facilitate future studies.
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Affiliation(s)
- Stephen A Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
| | - Nels C Elde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
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7
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Jiang S, Deng X, Luo M, Zhou L, Chai J, Tian C, Yan Y, Luo Z. Pan-cancer analysis identified OAS1 as a potential prognostic biomarker for multiple tumor types. Front Oncol 2023; 13:1207081. [PMID: 37746262 PMCID: PMC10511872 DOI: 10.3389/fonc.2023.1207081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Background 2',5'-oligoadenylate synthetase 1 (OAS1), has been reported as a tumor driver gene in breast carcinoma and pancreatic carcinoma. However, the role of OAS1 in most tumors has not been reported. Methods The original data of 35 tumor types were down load from the TCGA (The Cancer Genome Atlas) database and Human Protein Atlas (HPA) database. TIMER2, Kmplot, UALCAN, and TISIDB tools were used to investigate the expression and function of OAS1, and the role of OAS1 in prognosis, diagnostic value, and immune characteristics of pan-cancer. LUAD and PRAD cell lines, A549, H1975, PC-3 and C4-2 were utilized to perform cell function tests. Results OAS1 expression was up-regulated in 12 tumor types and down-regulated in 2 tumor types. High OAS1 expression was correlated with poor prognosis in 6 tumor types, while high OAS1 expression was correlated with good prognosis in 2 tumor types. OAS1 was correlated with molecular subtypes in 8 tumor types and immune subtypes in 12 tumor types. OAS1 was positively associated with the expression of numerous immune checkpoint genes and tumor mutational burden (TMB). OAS1 had potential diagnostic value in 15 tumor types. Silence of OAS1 significantly inhibited the cell proliferation ability, and promoted G2/M cell cycle arrest of LUAD and PRAD cells. Meanwhile, silence of OAS1 enhanced cisplatin-induced apoptosis of LUAD and PRAD cells, but weakened cell migration. Conclusion This pan-cancer study suggests that OAS1can be used as a molecular biomarker for prognosis in pan-cancer and may play an important role in tumor immune response.
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Affiliation(s)
- Shan Jiang
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xinzhou Deng
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
- Hubei Key Laboratory of Stem Cell Research, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Ming Luo
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Le Zhou
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Jingjing Chai
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Chao Tian
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yutao Yan
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zhiguo Luo
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
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8
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Chu L, Gong Z, Wang W, Han GZ. Origin of the OAS-RNase L innate immune pathway before the rise of jawed vertebrates via molecular tinkering. Proc Natl Acad Sci U S A 2023; 120:e2304687120. [PMID: 37487089 PMCID: PMC10400998 DOI: 10.1073/pnas.2304687120] [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: 03/22/2023] [Accepted: 06/26/2023] [Indexed: 07/26/2023] Open
Abstract
Discriminating self from nonself is fundamental to immunity. Yet, it remains largely elusive how the mechanisms of self and nonself discrimination originated. Sensing double-stranded RNA as nonself, the 2',5'-oligoadenylate synthetase (OAS)-ribonuclease L (RNase L) pathway represents a crucial component of innate immunity. Here, we combine phylogenomic and functional analyses to show that the functional OAS-RNase L pathway likely originated through tinkering with preexisting proteins before the rise of jawed vertebrates during or before the Silurian period (444 to 419 Mya). Multiple concerted losses of OAS and RNase L occurred during the evolution of jawed vertebrates, further supporting the ancient coupling between OAS and RNase L. Moreover, both OAS and RNase L genes evolved under episodic positive selection across jawed vertebrates, suggesting a long-running evolutionary arms race between the OAS-RNase L pathway and microbes. Our findings illuminate how an innate immune pathway originated via molecular tinkering.
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Affiliation(s)
- Lingyu Chu
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Zhen Gong
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Wenqiang Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu210023, China
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9
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Eckhart L, Sipos W. Differential Loss of OAS Genes Indicates Diversification of Antiviral Immunity in Mammals. Vaccines (Basel) 2023; 11:vaccines11020419. [PMID: 36851296 PMCID: PMC9964502 DOI: 10.3390/vaccines11020419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
One of the main mechanisms of inducing an antiviral response depends on 2'-5'-oligoadenylate synthetases (OAS), which sense double-stranded RNA in the cytoplasm and activate RNase L. Mutations leading to the loss of functional OAS1 and OAS2 genes have been identified as important modifiers of the human immune response against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we performed comparative genomics to search for inactivating mutations of OAS genes in other species of mammals and to establish a model for the diversifying evolution of the OAS gene family. We found that a recombination of the OAS and OAS-like (OASL) loci has led to the loss of OAS2 in camelids, which also lack OAS3. Both paralogs of OASL and OAS3 are absent in Asian pangolins. An evolutionarily ancient OAS paralog, which we tentatively name OAS4, has been lost in pangolins, bats and humans. A previously unknown OAS gene, tentatively named OAS5, is present in Yangochiroptera, a suborder of bats. These differences in the OAS gene repertoire may affect innate immune responses to coronaviruses and other RNA viruses.
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Affiliation(s)
- Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence:
| | - Wolfgang Sipos
- Clinical Department for Farm Animals and Herd Management, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
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10
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Mann JT, Riley BA, Baker SF. All differential on the splicing front: Host alternative splicing alters the landscape of virus-host conflict. Semin Cell Dev Biol 2023; 146:40-56. [PMID: 36737258 DOI: 10.1016/j.semcdb.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
Alternative RNA splicing is a co-transcriptional process that richly increases proteome diversity, and is dynamically regulated based on cell species, lineage, and activation state. Virus infection in vertebrate hosts results in rapid host transcriptome-wide changes, and regulation of alternative splicing can direct a combinatorial effect on the host transcriptome. There has been a recent increase in genome-wide studies evaluating host alternative splicing during viral infection, which integrates well with prior knowledge on viral interactions with host splicing proteins. A critical challenge remains in linking how these individual events direct global changes, and whether alternative splicing is an overall favorable pathway for fending off or supporting viral infection. Here, we introduce the process of alternative splicing, discuss how to analyze splice regulation, and detail studies on genome-wide and splice factor changes during viral infection. We seek to highlight where the field can focus on moving forward, and how incorporation of a virus-host co-evolutionary perspective can benefit this burgeoning subject.
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Affiliation(s)
- Joshua T Mann
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Brent A Riley
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Steven F Baker
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA.
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11
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Adaptive Evolution of the OAS Gene Family Provides New Insights into the Antiviral Ability of Laurasiatherian Mammals. Animals (Basel) 2023; 13:ani13020209. [PMID: 36670749 PMCID: PMC9854896 DOI: 10.3390/ani13020209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Many mammals risk damage from virus invasion due to frequent environmental changes. The oligoadenylate synthesis (OAS) gene family, which is an important component of the immune system, provides an essential response to the antiviral activities of interferons by regulating immune signal pathways. However, little is known about the evolutionary characteristics of OASs in Laurasiatherian mammals. Here, we examined the evolution of the OAS genes in 64 mammals to explore the accompanying molecular mechanisms of the antiviral ability of Laurasiatherian mammals living in different environments. We found that OAS2 and OAS3 were found to be pseudogenes in Odontoceti species. This may be related to the fact that they live in water. Some Antilopinae, Caprinae, and Cervidae species lacked the OASL gene, which may be related to their habitats being at higher altitudes. The OASs had a high number of positive selection sites in Cetartiodactyla, which drove the expression of strong antiviral ability. The OAS gene family evolved in Laurasiatherian mammals at different rates and was highly correlated with the species' antiviral ability. The gene evolution rate in Cetartiodactyla was significantly higher than that in the other orders. Compared to other species of the Carnivora family, the higher selection pressure on the OAS gene and the absence of positive selection sites in Canidae may be responsible for its weak resistance to rabies virus. The OAS gene family was relatively conserved during evolution. Conserved genes are able to provide better maintenance of gene function. The rate of gene evolution and the number of positively selected sites combine to influence the resistance of a species to viruses. The positive selection sites demonstrate the adaptive evolution of the OAS gene family to the environment. Adaptive evolution combined with conserved gene function improves resistance to viruses. Our findings offer insights into the molecular and functional evolution of the antiviral ability of Laurasian mammals.
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12
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Banday AR, Stanifer ML, Florez-Vargas O, Onabajo OO, Papenberg BW, Zahoor MA, Mirabello L, Ring TJ, Lee CH, Albert PS, Andreakos E, Arons E, Barsh G, Biesecker LG, Boyle DL, Brahier MS, Burnett-Hartman A, Carrington M, Chang E, Choe PG, Chisholm RL, Colli LM, Dalgard CL, Dude CM, Edberg J, Erdmann N, Feigelson HS, Fonseca BA, Firestein GS, Gehring AJ, Guo C, Ho M, Holland S, Hutchinson AA, Im H, Irby L, Ison MG, Joseph NT, Kim HB, Kreitman RJ, Korf BR, Lipkin SM, Mahgoub SM, Mohammed I, Paschoalini GL, Pacheco JA, Peluso MJ, Rader DJ, Redden DT, Ritchie MD, Rosenblum B, Ross ME, Anna HPS, Savage SA, Sharma S, Siouti E, Smith AK, Triantafyllia V, Vargas JM, Vargas JD, Verma A, Vij V, Wesemann DR, Yeager M, Yu X, Zhang Y, Boulant S, Chanock SJ, Feld JJ, Prokunina-Olsson L. Genetic regulation of OAS1 nonsense-mediated decay underlies association with COVID-19 hospitalization in patients of European and African ancestries. Nat Genet 2022; 54:1103-1116. [PMID: 35835913 PMCID: PMC9355882 DOI: 10.1038/s41588-022-01113-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 05/26/2022] [Indexed: 12/22/2022]
Abstract
The chr12q24.13 locus encoding OAS1-OAS3 antiviral proteins has been associated with coronavirus disease 2019 (COVID-19) susceptibility. Here, we report genetic, functional and clinical insights into this locus in relation to COVID-19 severity. In our analysis of patients of European (n = 2,249) and African (n = 835) ancestries with hospitalized versus nonhospitalized COVID-19, the risk of hospitalized disease was associated with a common OAS1 haplotype, which was also associated with reduced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance in a clinical trial with pegIFN-λ1. Bioinformatic analyses and in vitro studies reveal the functional contribution of two associated OAS1 exonic variants comprising the risk haplotype. Derived human-specific alleles rs10774671-A and rs1131454 -A decrease OAS1 protein abundance through allele-specific regulation of splicing and nonsense-mediated decay (NMD). We conclude that decreased OAS1 expression due to a common haplotype contributes to COVID-19 severity. Our results provide insight into molecular mechanisms through which early treatment with interferons could accelerate SARS-CoV-2 clearance and mitigate against severe COVID-19.
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Affiliation(s)
- A Rouf Banday
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Megan L Stanifer
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Oscar Florez-Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Olusegun O Onabajo
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Brenen W Papenberg
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Muhammad A Zahoor
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Lisa Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Timothy J Ring
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Chia-Han Lee
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Paul S Albert
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Evangelos Andreakos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Evgeny Arons
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Greg Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Leslie G Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - David L Boyle
- Altman Clinical & Translational Research Institute, UC San Diego Health Sciences, San Diego, CA, USA
| | - Mark S Brahier
- Georgetown University School of Medicine, Washington, DC, USA
| | | | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Euijin Chang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Leandro M Colli
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Clifton L Dalgard
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Carolynn M Dude
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeff Edberg
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nathan Erdmann
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Benedito A Fonseca
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Gary S Firestein
- Altman Clinical & Translational Research Institute, UC San Diego Health Sciences, San Diego, CA, USA
| | - Adam J Gehring
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Cuncai Guo
- Division of Cellular Polarity and Viral Infection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michelle Ho
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Steven Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Amy A Hutchinson
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Hogune Im
- Genome Opinion, Inc., Seoul, Republic of Korea
| | - Les'Shon Irby
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael G Ison
- Divisions of Infectious Diseases and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Naima T Joseph
- Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Robert J Kreitman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Steven M Lipkin
- Department of Medicine and Program in Mendelian Genetics, Weill Cornell Medicine, New York, NY, USA
| | - Siham M Mahgoub
- Department of Medicine, Infectious Diseases Division, Howard University Hospital, Howard University College of Medicine, Washington, DC, USA
| | - Iman Mohammed
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Guilherme L Paschoalini
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, CA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David T Redden
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brooke Rosenblum
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - M Elizabeth Ross
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Hanaisa P Sant Anna
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Sudha Sharma
- Department of Biochemistry and Molecular Biology, National Human Genome Center, Howard University College of Medicine, Washington, DC, USA
| | - Eleni Siouti
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Vasiliki Triantafyllia
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Joselin M Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jose D Vargas
- Veterans Affairs Medical Center, Washington, DC, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vibha Vij
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Duane R Wesemann
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Xu Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Steeve Boulant
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
- Division of Cellular Polarity and Viral Infection, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stephen J Chanock
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jordan J Feld
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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13
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Wang X, Hu J, Song L, Rong E, Yang C, Chen X, Pu J, Sun H, Gao C, Burt DW, Liu J, Li N, Huang Y. Functional divergence of oligoadenylate synthetase 1 (OAS1) proteins in Tetrapods. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1395-1412. [PMID: 34826092 DOI: 10.1007/s11427-021-2002-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
OASs play critical roles in immune response against virus infection by polymerizing ATP into 2-5As, which initiate the classical OAS/RNase L pathway and induce degradation of viral RNA. OAS members are functionally diverged in four known innate immune pathways (OAS/RNase L, OASL/IRF7, OASL/RIG-I, and OASL/cGAS), but how they functionally diverged is unclear. Here, we focus on evolutionary patterns and explore the link between evolutionary processes and functional divergence of Tetrapod OAS1. We show that Palaeognathae and Primate OAS1 genes are conserved in genomic and protein structures but differ in function. The former (i.e., ostrich) efficiently synthesized long 2-5A and activated RNase L, while the latter (i.e., human) synthesized short 2-5A and did not activate RNase L. We predicted and verified that two in-frame indels and one positively selected site in the active site pocket contributed to the functional divergence of Palaeognathae and Primate OAS1. Moreover, we discovered and validated that an in-frame indel in the C-terminus of Palaeognathae OAS1 affected the binding affinity of dsRNA and enzymatic activity, and contributed to the functional divergence of Palaeognathae OAS1 proteins. Our findings unravel the molecular mechanism for functional divergence and give insights into the emergence of novel functions in Tetrapod OAS1.
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Affiliation(s)
- Xiaoxue Wang
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China
| | - Jiaxiang Hu
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China
| | - Linfei Song
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China
| | - Enguang Rong
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China
| | - Chenghuai Yang
- China Institute of Veterinary Drug Control, Beijing, 100081, China
| | - Xiaoyun Chen
- China Institute of Veterinary Drug Control, Beijing, 100081, China
| | - Juan Pu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100083, China
| | - Honglei Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100083, China
| | - Chuze Gao
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China
| | - David W Burt
- University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Jinhua Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100083, China
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China
| | - Yinhua Huang
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China.
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14
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Danziger O, Patel RS, DeGrace EJ, Rosen MR, Rosenberg BR. Inducible CRISPR activation screen for interferon-stimulated genes identifies OAS1 as a SARS-CoV-2 restriction factor. PLoS Pathog 2022; 18:e1010464. [PMID: 35421191 PMCID: PMC9041830 DOI: 10.1371/journal.ppat.1010464] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/26/2022] [Accepted: 03/23/2022] [Indexed: 11/19/2022] Open
Abstract
Interferons establish an antiviral state through the induction of hundreds of interferon-stimulated genes (ISGs). The mechanisms and viral specificities for most ISGs remain incompletely understood. To enable high-throughput interrogation of ISG antiviral functions in pooled genetic screens while mitigating potentially confounding effects of endogenous interferon and antiproliferative/proapoptotic ISG activities, we adapted a CRISPR-activation (CRISPRa) system for inducible ISG expression in isogenic cell lines with and without the capacity to respond to interferons. We used this platform to screen for ISGs that restrict SARS-CoV-2. Results included ISGs previously described to restrict SARS-CoV-2 and novel candidate antiviral factors. We validated a subset of these by complementary CRISPRa and cDNA expression experiments. OAS1, a top-ranked hit across multiple screens, exhibited strong antiviral effects against SARS-CoV-2, which required OAS1 catalytic activity. These studies demonstrate a high-throughput approach to assess antiviral functions within the ISG repertoire, exemplified by identification of multiple SARS-CoV-2 restriction factors.
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Affiliation(s)
- Oded Danziger
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Roosheel S. Patel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Emma J. DeGrace
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Mikaela R. Rosen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Brad R. Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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15
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Abstract
Upon infection, DNA viruses can be sensed by pattern recognition receptors (PRRs), leading to the activation of type I and III interferons to block infection. Therefore, viruses must inhibit these signaling pathways, avoid being detected, or both. Papillomavirus virions are trafficked from early endosomes to the Golgi apparatus and wait for the onset of mitosis to complete nuclear entry. This unique subcellular trafficking strategy avoids detection by cytoplasmic PRRs, a property that may contribute to the establishment of infection. However, as the capsid uncoats within acidic endosomal compartments, the viral DNA may be exposed to detection by Toll-like receptor 9 (TLR9). In this study, we characterized two new papillomaviruses from bats and used molecular archeology to demonstrate that their genomes altered their nucleotide compositions to avoid detection by TLR9, providing evidence that TLR9 acts as a PRR during papillomavirus infection. Furthermore, we showed that TLR9, like other components of the innate immune system, is under evolutionary selection in bats, providing the first direct evidence for coevolution between papillomaviruses and their hosts. Finally, we demonstrated that the cancer-associated human papillomaviruses show a reduction in CpG dinucleotides within a TLR9 recognition complex.
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16
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McCord JM, Hybertson BM, Cota-Gomez A, Gao B. Nrf2 activator PB125® as a carnosic acid-based therapeutic agent against respiratory viral diseases, including COVID-19. Free Radic Biol Med 2021; 175:56-64. [PMID: 34058321 PMCID: PMC8413148 DOI: 10.1016/j.freeradbiomed.2021.05.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/06/2021] [Accepted: 05/24/2021] [Indexed: 12/24/2022]
Abstract
PB125® is a phytochemical composition providing potent Nrf2 activation as well as a number of direct actions that do not involve Nrf2. Nrf2 is a transcription actor that helps maintain metabolic balance by providing redox-sensitive expression of numerous genes controlling normal day-to-day metabolic pathways. When ordinary metabolism is upset by extraordinary events such as injury, pathogenic infection, air or water pollution, ingestion of toxins, or simply by the slow but incessant changes brought about by aging and genetic variations, Nrf2 may also be called into action by the redox changes resulting from these events, whether acute or chronic. A complicating factor in all of this is that Nrf2 levels decline with aging, leaving the elderly less able to maintain proper redox balance. The dysregulated gene expression that results can cause or exacerbate a wide variety of pathological conditions, including susceptibility to viral infections. This review examines the characteristics desirable in Nrf2 activators that have therapeutic potential, as well as some of the patterns of dysregulated gene expression commonly observed during pulmonary infections and the normalizing effects possible by judicious use of phytochemicals to increase the activation level of available Nrf2.
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Affiliation(s)
- Joe M McCord
- Pathways Bioscience, Aurora, CO, 80045, USA; Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Brooks M Hybertson
- Pathways Bioscience, Aurora, CO, 80045, USA; Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Adela Cota-Gomez
- Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Bifeng Gao
- Pathways Bioscience, Aurora, CO, 80045, USA; Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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17
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Wickenhagen A, Sugrue E, Lytras S, Kuchi S, Noerenberg M, Turnbull ML, Loney C, Herder V, Allan J, Jarmson I, Cameron-Ruiz N, Varjak M, Pinto RM, Lee JY, Iselin L, Palmalux N, Stewart DG, Swingler S, Greenwood EJD, Crozier TWM, Gu Q, Davies EL, Clohisey S, Wang B, Trindade Maranhão Costa F, Freire Santana M, de Lima Ferreira LC, Murphy L, Fawkes A, Meynert A, Grimes G, Da Silva Filho JL, Marti M, Hughes J, Stanton RJ, Wang ECY, Ho A, Davis I, Jarrett RF, Castello A, Robertson DL, Semple MG, Openshaw PJM, Palmarini M, Lehner PJ, Baillie JK, Rihn SJ, Wilson SJ. A prenylated dsRNA sensor protects against severe COVID-19. Science 2021; 374:eabj3624. [PMID: 34581622 PMCID: PMC7612834 DOI: 10.1126/science.abj3624] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022]
Abstract
Inherited genetic factors can influence the severity of COVID-19, but the molecular explanation underpinning a genetic association is often unclear. Intracellular antiviral defenses can inhibit the replication of viruses and reduce disease severity. To better understand the antiviral defenses relevant to COVID-19, we used interferon-stimulated gene (ISG) expression screening to reveal that 2′-5′-oligoadenylate synthetase 1 (OAS1), through ribonuclease L, potently inhibits severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We show that a common splice-acceptor single-nucleotide polymorphism (Rs10774671) governs whether patients express prenylated OAS1 isoforms that are membrane-associated and sense-specific regions of SARS-CoV-2 RNAs or if they only express cytosolic, nonprenylated OAS1 that does not efficiently detect SARS-CoV-2. In hospitalized patients, expression of prenylated OAS1 was associated with protection from severe COVID-19, suggesting that this antiviral defense is a major component of a protective antiviral response.
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Affiliation(s)
- Arthur Wickenhagen
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Elena Sugrue
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Spyros Lytras
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Srikeerthana Kuchi
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Marko Noerenberg
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Matthew L. Turnbull
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Colin Loney
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Vanessa Herder
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Jay Allan
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Innes Jarmson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Natalia Cameron-Ruiz
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Margus Varjak
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Rute M. Pinto
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Jeffrey Y. Lee
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Louisa Iselin
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Natasha Palmalux
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Douglas G. Stewart
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Simon Swingler
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Edward J. D. Greenwood
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Thomas W. M. Crozier
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Quan Gu
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Emma L. Davies
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Fabio Trindade Maranhão Costa
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paolo, Brazil
| | - Monique Freire Santana
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Amazonas, Brazil
| | - Luiz Carlos de Lima Ferreira
- Postgraduate Program in Tropical Medicine, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Alison Meynert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Graeme Grimes
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - ISARIC4C Investigators
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paolo, Brazil
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Amazonas, Brazil
- Postgraduate Program in Tropical Medicine, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
- Division of Infection & Immunity, Cardiff University, Cardiff, UK
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare, National Health Service Trust London, London, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Joao Luiz Da Silva Filho
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Matthias Marti
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | | | - Eddie C. Y. Wang
- Division of Infection & Immunity, Cardiff University, Cardiff, UK
| | - Antonia Ho
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ruth F. Jarrett
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Alfredo Castello
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - David L. Robertson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, UK
| | - Peter J. M. Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare, National Health Service Trust London, London, UK
| | - Massimo Palmarini
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Paul J. Lehner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - J. Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Suzannah J. Rihn
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Sam J. Wilson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
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18
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Palmer S, Chappidi S, Pinkham C, Hancks DC. Evolutionary profile for (host and viral) MLKL indicates its activities as a battlefront for extensive counteradaptation. Mol Biol Evol 2021; 38:5405-5422. [PMID: 34436583 PMCID: PMC8662602 DOI: 10.1093/molbev/msab256] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Pathogen infection triggers host innate defenses which may result in the activation of regulated cell death (RCD) pathways such as apoptosis. Given a vital role in immunity, apoptotic effectors are often counteracted by pathogen-encoded antagonists. Mounting evidence indicates that programmed necrosis, which is mediated by the RIPK3/MLKL axis and termed necroptosis, evolved as a countermeasure to pathogen-mediated inhibition of apoptosis. Yet, it is unclear whether components of this emerging RCD pathway display signatures associated with pathogen conflict that are rare in combination but common to key host defense factors, namely, rapid evolution, viral homolog (virolog), and cytokine induction. We leveraged evolutionary sequence analysis that examines rates of amino acid replacement, which revealed: 1) strong and recurrent signatures of positive selection for primate and bat RIPK3 and MLKL, and 2) elevated rates of amino acid substitution on multiple RIPK3/MLKL surfaces suggestive of past antagonism with multiple, distinct pathogen-encoded inhibitors. Furthermore, our phylogenomics analysis across poxvirus genomes illuminated volatile patterns of evolution for a recently described MLKL viral homolog. Specifically, poxviral MLKLs have undergone numerous gene replacements mediated by duplication and deletion events. In addition, MLKL protein expression is stimulated by interferons in human and mouse cells. Thus, MLKL displays all three hallmarks of pivotal immune factors of which only a handful of factors like OAS1 exhibit. These data support the hypothesis that over evolutionary time MLKL functions—which may include execution of necroptosis—have served as a major determinant of infection outcomes despite gene loss in some host genomes.
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Affiliation(s)
- Suzette Palmer
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Sruthi Chappidi
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Chelsea Pinkham
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Dustin C Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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19
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Soveg FW, Schwerk J, Gokhale NS, Cerosaletti K, Smith JR, Pairo-Castineira E, Kell AM, Forero A, Zaver SA, Esser-Nobis K, Roby JA, Hsiang TY, Ozarkar S, Clingan JM, McAnarney ET, Stone AEL, Malhotra U, Speake C, Perez J, Balu C, Allenspach EJ, Hyde JL, Menachery VD, Sarkar SN, Woodward JJ, Stetson DB, Baillie JK, Buckner JH, Gale M, Savan R. Endomembrane targeting of human OAS1 p46 augments antiviral activity. eLife 2021; 10:e71047. [PMID: 34342578 PMCID: PMC8357416 DOI: 10.7554/elife.71047] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 12/14/2022] Open
Abstract
Many host RNA sensors are positioned in the cytosol to detect viral RNA during infection. However, most positive-strand RNA viruses replicate within a modified organelle co-opted from intracellular membranes of the endomembrane system, which shields viral products from cellular innate immune sensors. Targeting innate RNA sensors to the endomembrane system may enhance their ability to sense RNA generated by viruses that use these compartments for replication. Here, we reveal that an isoform of oligoadenylate synthetase 1, OAS1 p46, is prenylated and targeted to the endomembrane system. Membrane localization of OAS1 p46 confers enhanced access to viral replication sites and results in increased antiviral activity against a subset of RNA viruses including flaviviruses, picornaviruses, and SARS-CoV-2. Finally, our human genetic analysis shows that the OAS1 splice-site SNP responsible for production of the OAS1 p46 isoform correlates with protection from severe COVID-19. This study highlights the importance of endomembrane targeting for the antiviral specificity of OAS1 and suggests that early control of SARS-CoV-2 replication through OAS1 p46 is an important determinant of COVID-19 severity.
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Affiliation(s)
- Frank W Soveg
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Johannes Schwerk
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Nandan S Gokhale
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | | | - Julian R Smith
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | | | - Alison M Kell
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
- Department of Molecular Genetics and Microbiology, School of Medicine, University of New MexicoAlbuquerqueUnited States
| | - Adriana Forero
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State UniversityColumbusUnited States
| | - Shivam A Zaver
- Department of Microbiology, School of Medicine, University of WashingtonSeattleUnited States
| | - Katharina Esser-Nobis
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Justin A Roby
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Tien-Ying Hsiang
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Snehal Ozarkar
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Jonathan M Clingan
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Eileen T McAnarney
- Department of Microbiology and Immunology, University of Texas Medical CenterGalvestonUnited States
| | - Amy EL Stone
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University NevadaHendersonUnited States
| | - Uma Malhotra
- Department of Infectious Disease, Virginia Mason Medical CenterSeattleUnited States
- Department of Medicine, Section of Infectious Diseases, University of WashingtonSeattleUnited States
| | - Cate Speake
- Benaroya Research Institute at Virginia MasonSeattleUnited States
| | - Joseph Perez
- Cancer Virology Program, University of Pittsburgh Cancer Institute, University of PittsburghPittsburghUnited States
| | - Chiraag Balu
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Eric J Allenspach
- Center for Immunity and Immunotherapies, Seattle Children's Research InstituteSeattleUnited States
| | - Jennifer L Hyde
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State UniversityColumbusUnited States
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical CenterGalvestonUnited States
| | - Saumendra N Sarkar
- Cancer Virology Program, University of Pittsburgh Cancer Institute, University of PittsburghPittsburghUnited States
| | - Joshua J Woodward
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
- Department of Microbiology, School of Medicine, University of WashingtonSeattleUnited States
| | - Daniel B Stetson
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - John Kenneth Baillie
- Roslin Institute, University of EdinburghEdinburghUnited Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General HospitalEdinburghUnited Kingdom
| | - Jane H Buckner
- Benaroya Research Institute at Virginia MasonSeattleUnited States
| | - Michael Gale
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Ram Savan
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
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20
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Magg T, Okano T, Koenig LM, Boehmer DFR, Schwartz SL, Inoue K, Heimall J, Licciardi F, Ley-Zaporozhan J, Ferdman RM, Caballero-Oteyza A, Park EN, Calderon BM, Dey D, Kanegane H, Cho K, Montin D, Reiter K, Griese M, Albert MH, Rohlfs M, Gray P, Walz C, Conn GL, Sullivan KE, Klein C, Morio T, Hauck F. Heterozygous OAS1 gain-of-function variants cause an autoinflammatory immunodeficiency. Sci Immunol 2021; 6:eabf9564. [PMID: 34145065 PMCID: PMC8392508 DOI: 10.1126/sciimmunol.abf9564] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/06/2021] [Indexed: 12/13/2022]
Abstract
Analysis of autoinflammatory and immunodeficiency disorders elucidates human immunity and fosters the development of targeted therapies. Oligoadenylate synthetase 1 is a type I interferon-induced, intracellular double-stranded RNA (dsRNA) sensor that generates 2'-5'-oligoadenylate to activate ribonuclease L (RNase L) as a means of antiviral defense. We identified four de novo heterozygous OAS1 gain-of-function variants in six patients with a polymorphic autoinflammatory immunodeficiency characterized by recurrent fever, dermatitis, inflammatory bowel disease, pulmonary alveolar proteinosis, and hypogammaglobulinemia. To establish causality, we applied genetic, molecular dynamics simulation, biochemical, and cellular functional analyses in heterologous, autologous, and inducible pluripotent stem cell-derived macrophages and/or monocytes and B cells. We found that upon interferon-induced expression, OAS1 variant proteins displayed dsRNA-independent activity, which resulted in RNase L-mediated RNA cleavage, transcriptomic alteration, translational arrest, and dysfunction and apoptosis of monocytes, macrophages, and B cells. RNase L inhibition with curcumin modulated and allogeneic hematopoietic cell transplantation cured the disorder. Together, these data suggest that human OAS1 is a regulator of interferon-induced hyperinflammatory monocyte, macrophage, and B cell pathophysiology.
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Affiliation(s)
- Thomas Magg
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tsubasa Okano
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Lars M Koenig
- Division of Clinical Pharmacology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Daniel F R Boehmer
- Division of Clinical Pharmacology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Samantha L Schwartz
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, USA
| | - Kento Inoue
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Jennifer Heimall
- Department of Allergy Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Francesco Licciardi
- Department of Pediatric and Public Health Sciences, University of Torino, Regina Margherita Children's Hospital, AOU Città della Salute e della Scienza di Torino, Turin, Italy
| | - Julia Ley-Zaporozhan
- Department of Radiology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ronald M Ferdman
- Division of Clinical Immunology and Allergy, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Andrés Caballero-Oteyza
- Centre for Chronic Immunodeficiency (CCI) and Institute for Immunodeficiency (IFI), University Hospital Freiburg, Freiburg, Germany
| | - Esther N Park
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Brenda M Calderon
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Hirokazu Kanegane
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kazutoshi Cho
- Maternity and Perinatal Care Center, Hokkaido University Hospital, Hokkaido, Japan
| | - Davide Montin
- Department of Pediatric and Public Health Sciences, University of Torino, Regina Margherita Children's Hospital, AOU Città della Salute e della Scienza di Torino, Turin, Italy
| | - Karl Reiter
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Matthias Griese
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Lung Research (DZL), Munich, Germany
| | - Michael H Albert
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Meino Rohlfs
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paul Gray
- Department of Immunology and Infectious Disease, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Christoph Walz
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, USA
| | - Kathleen E Sullivan
- Department of Allergy Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- German Centre for Infection Research (DZIF), Munich, Germany
- Munich Centre for Rare Diseases (M-ZSE), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
| | - Fabian Hauck
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.
- German Centre for Infection Research (DZIF), Munich, Germany
- Munich Centre for Rare Diseases (M-ZSE), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
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21
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Zeberg H, Pääbo S. A genomic region associated with protection against severe COVID-19 is inherited from Neandertals. Proc Natl Acad Sci U S A 2021; 118:e2026309118. [PMID: 33593941 PMCID: PMC7936282 DOI: 10.1073/pnas.2026309118] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
It was recently shown that the major genetic risk factor associated with becoming severely ill with COVID-19 when infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is inherited from Neandertals. New, larger genetic association studies now allow additional genetic risk factors to be discovered. Using data from the Genetics of Mortality in Critical Care (GenOMICC) consortium, we show that a haplotype at a region on chromosome 12 associated with requiring intensive care when infected with the virus is inherited from Neandertals. This region encodes proteins that activate enzymes that are important during infections with RNA viruses. In contrast to the previously described Neandertal haplotype that increases the risk for severe COVID-19, this Neandertal haplotype is protective against severe disease. It also differs from the risk haplotype in that it has a more moderate effect and occurs at substantial frequencies in all regions of the world outside Africa. Among ancient human genomes in western Eurasia, the frequency of the protective Neandertal haplotype may have increased between 20,000 and 10,000 y ago and again during the past 1,000 y.
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Affiliation(s)
- Hugo Zeberg
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany;
- Department of Neuroscience, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany;
- Human Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
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22
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A Neanderthal OAS1 isoform protects individuals of European ancestry against COVID-19 susceptibility and severity. Nat Med 2021; 27:659-667. [PMID: 33633408 DOI: 10.1038/s41591-021-01281-1] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 02/05/2021] [Indexed: 12/15/2022]
Abstract
To identify circulating proteins influencing Coronavirus Disease 2019 (COVID-19) susceptibility and severity, we undertook a two-sample Mendelian randomization (MR) study, rapidly scanning hundreds of circulating proteins while reducing bias due to reverse causation and confounding. In up to 14,134 cases and 1.2 million controls, we found that an s.d. increase in OAS1 levels was associated with reduced COVID-19 death or ventilation (odds ratio (OR) = 0.54, P = 7 × 10-8), hospitalization (OR = 0.61, P = 8 × 10-8) and susceptibility (OR = 0.78, P = 8 × 10-6). Measuring OAS1 levels in 504 individuals, we found that higher plasma OAS1 levels in a non-infectious state were associated with reduced COVID-19 susceptibility and severity. Further analyses suggested that a Neanderthal isoform of OAS1 in individuals of European ancestry affords this protection. Thus, evidence from MR and a case-control study support a protective role for OAS1 in COVID-19 adverse outcomes. Available pharmacological agents that increase OAS1 levels could be prioritized for drug development.
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23
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Huijser E, Versnel MA. Making Sense of Intracellular Nucleic Acid Sensing in Type I Interferon Activation in Sjögren's Syndrome. J Clin Med 2021; 10:532. [PMID: 33540529 PMCID: PMC7867173 DOI: 10.3390/jcm10030532] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/13/2022] Open
Abstract
Primary Sjögren's syndrome (pSS) is a systemic autoimmune rheumatic disease characterized by dryness of the eyes and mucous membranes, which can be accompanied by various extraglandular autoimmune manifestations. The majority of patients exhibit persistent systemic activation of the type I interferon (IFN) system, a feature that is shared with other systemic autoimmune diseases. Type I IFNs are integral to anti-viral immunity and are produced in response to stimulation of pattern recognition receptors, among which nucleic acid (NA) receptors. Dysregulated detection of endogenous NAs has been widely implicated in the pathogenesis of systemic autoimmune diseases. Stimulation of endosomal Toll-like receptors by NA-containing immune complexes are considered to contribute to the systemic type I IFN activation. Accumulating evidence suggest additional roles for cytosolic NA-sensing pathways in the pathogenesis of systemic autoimmune rheumatic diseases. In this review, we will provide an overview of the functions and signaling of intracellular RNA- and DNA-sensing receptors and summarize the evidence for a potential role of these receptors in the pathogenesis of pSS and the sustained systemic type I IFN activation.
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Affiliation(s)
| | - Marjan A. Versnel
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands;
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24
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Yang E, Li MMH. All About the RNA: Interferon-Stimulated Genes That Interfere With Viral RNA Processes. Front Immunol 2020; 11:605024. [PMID: 33362792 PMCID: PMC7756014 DOI: 10.3389/fimmu.2020.605024] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022] Open
Abstract
Interferon (IFN) signaling induces the expression of a wide array of genes, collectively referred to as IFN-stimulated genes (ISGs) that generally function to inhibit viral replication. RNA viruses are frequently targeted by ISGs through recognition of viral replicative intermediates and molecular features associated with viral genomes, or the lack of molecular features associated with host mRNAs. The ISGs reviewed here primarily inhibit viral replication in an RNA-centric manner, working to sense, degrade, or repress expression of viral RNA. This review focuses on dissecting how these ISGs exhibit multiple antiviral mechanisms, often through use of varied co-factors, highlighting the complexity of the type I IFN response. Specifically, these ISGs can mediate antiviral effects through viral RNA degradation, viral translation inhibition, or both. While the OAS/RNase L pathway globally degrades RNA and arrests translation, ISG20 and ZAP employ targeted RNA degradation and translation inhibition to block viral replication. Meanwhile, SHFL targets translation by inhibiting -1 ribosomal frameshifting, which is required by many RNA viruses. Finally, a number of E3 ligases inhibit viral transcription, an attractive antiviral target during the lifecycle of negative-sense RNA viruses which must transcribe their genome prior to translation. Through this review, we aim to provide an updated perspective on how these ISGs work together to form a complex network of antiviral arsenals targeting viral RNA processes.
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Affiliation(s)
- Emily Yang
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Melody M. H. Li
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
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25
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Yan S, Fang J, Zhu Y, Xie Y, Fang F. Comprehensive analysis of prognostic immune-related genes associated with the tumor microenvironment of pancreatic ductal adenocarcinoma. Oncol Lett 2020; 20:366. [PMID: 33133266 PMCID: PMC7590433 DOI: 10.3892/ol.2020.12228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 09/04/2020] [Indexed: 12/21/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a malignant tumor with a specific tumor immune microenvironment (TIME). Therefore, investigating prognostic immune-related genes (IRGs) that are closely associated with TIME to predict PDAC clinical outcomes is necessary. In the present study, 459 samples of PDAC from the Genotype-Tissue Expression database, The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO) were included and a survival-associated module was identified using weighted gene co-expression network analysis. Based on the Cox regression analysis and least absolute shrinkage and selection operator analysis, four IRGs (2′-5′-oligoadenylate synthetase 1, MET proto-oncogene, receptor tyrosine kinase, interleukin 1 receptor type 2 and interleukin 20 receptor subunit β) were included in the prognostic model to calculate the risk score (RS), and patients with PDAC were divided into high- and low-RS groups. Kaplan-Meier survival and receiver operating characteristic curve analyses demonstrated that the low-RS group had significantly improved survival conditions compared with the high-RS group in TCGA training set. The prognostic function of the model was also validated using ICGC and GEO cohorts. To investigate the mechanism of different overall survival between the high- and low-RS groups, the present study included Estimation of Stromal and Immune Cells in Malignant Tumor Tissues Using Expression Data and Cell Type Identification by Estimating Relative Subset of Known RNA Transcripts algorithms to investigate the state of the tumor microenvironment and immune infiltration inpatients in the cohort from TCGA. In summary, four genes associated with the TIME of PDAC were identified, which may provide a reference for clinical treatment.
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Affiliation(s)
- Shibai Yan
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Juntao Fang
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Yuanqiang Zhu
- Department of Infertility and Sexual Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Yong Xie
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
| | - Feng Fang
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
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26
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Luo Y, Chen L, Zhou Q, Xiong Y, Wang G, Liu X, Xiao Y, Ju L, Wang X. Identification of a prognostic gene signature based on an immunogenomic landscape analysis of bladder cancer. J Cell Mol Med 2020; 24:13370-13382. [PMID: 33048468 PMCID: PMC7701570 DOI: 10.1111/jcmm.15960] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 06/27/2020] [Accepted: 08/05/2020] [Indexed: 12/22/2022] Open
Abstract
Cancer immune plays a critical role in cancer progression. Tumour immunology and immunotherapy are one of the exciting areas in bladder cancer research. In this study, we aimed to develop an immune‐related gene signature to improve the prognostic prediction of bladder cancer. Firstly, we identified 392 differentially expressed immune‐related genes (IRGs) based on TCGA and ImmPort databases. Functional enrichment analysis revealed that these genes were enriched in inflammatory and immune‐related pathways, including in ‘regulation of signaling receptor activity’, ‘cytokine‐cytokine receptor interaction’ and ‘GPCR ligand binding’. Then, we separated all samples in TCGA data set into the training cohort and the testing cohort in a ratio of 3:1 randomly. Data set GSE13507 was set as the validation cohort. We constructed a prognostic six‐IRG signature with LASSO Cox regression in the training cohort, including AHNAK, OAS1, APOBEC3H, SCG2, CTSE and KIR2DS4. Six IRGs reflected the microenvironment of bladder cancer, especially immune cell infiltration. The prognostic value of six‐IRG signature was further validated in the testing cohort and the validation cohort. The results of multivariable Cox regression and subgroup analysis revealed that six‐IRG signature was a clinically independent prognostic factor for bladder cancer patients. Further, we constructed a nomogram based on six‐IRG signature and other clinicopathological risk factors, and it performed well in predict patients' survival. Finally, we found six‐IRG signature showed significant difference in different molecular subtypes of bladder cancer. In conclusions, our research provided a novel immune‐related gene signature to estimate prognosis for patients' survival with bladder cancer.
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Affiliation(s)
- Yongwen Luo
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
| | - Liang Chen
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiang Zhou
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yaoyi Xiong
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Gang Wang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China.,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.,Cancer Precision Diagnosis and Treatment and Translational Medicine, Hubei Engineering Research Center, Wuhan, China
| | - Xuefeng Liu
- Department of Pathology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington, DC, USA
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China.,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lingao Ju
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China.,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China.,Cancer Precision Diagnosis and Treatment and Translational Medicine, Hubei Engineering Research Center, Wuhan, China
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27
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Constitutive immune mechanisms: mediators of host defence and immune regulation. Nat Rev Immunol 2020; 21:137-150. [PMID: 32782357 PMCID: PMC7418297 DOI: 10.1038/s41577-020-0391-5] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2020] [Indexed: 02/07/2023]
Abstract
The immune system enables organisms to combat infections and to eliminate endogenous challenges. Immune responses can be evoked through diverse inducible pathways. However, various constitutive mechanisms are also required for immunocompetence. The inducible responses of pattern recognition receptors of the innate immune system and antigen-specific receptors of the adaptive immune system are highly effective, but they also have the potential to cause extensive immunopathology and tissue damage, as seen in many infectious and autoinflammatory diseases. By contrast, constitutive innate immune mechanisms, including restriction factors, basal autophagy and proteasomal degradation, tend to limit immune responses, with loss-of-function mutations in these pathways leading to inflammation. Although they function through a broad and heterogeneous set of mechanisms, the constitutive immune responses all function as early barriers to infection and aim to minimize any disruption of homeostasis. Supported by recent human and mouse data, in this Review we compare and contrast the inducible and constitutive mechanisms of immunosurveillance.
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28
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Frankiw L, Mann M, Li G, Joglekar A, Baltimore D. Alternative splicing coupled with transcript degradation modulates OAS1g antiviral activity. RNA (NEW YORK, N.Y.) 2020; 26:126-136. [PMID: 31740586 PMCID: PMC6961538 DOI: 10.1261/rna.073825.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/13/2019] [Indexed: 05/17/2023]
Abstract
At the heart of an innate immune response lies a tightly regulated gene expression program. This precise regulation is crucial because small changes can shift the balance from protective to destructive immunity. Here we identify a frequently used alternative splice site in the gene oligoadenylate synthetase 1g (Oas1g), a key component of the 2-5A antiviral system. Usage of this splice site leads to the generation of a transcript subject to decay, and removal of the site leads to increased expression of Oas1g and an improved antiviral response. However, removal of the splice site also leads to an increase in apoptotic cell death, suggesting this splicing event exists as a compromise between the pathogen protective benefits and collateral damage associated with OAS1g activity. Across the innate immune response, we show that a multitude of alternative splicing events predicted to lead to decay exist, and thus have the potential to play a significant role in the regulation of gene expression in innate immunity.
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Affiliation(s)
- Luke Frankiw
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Mati Mann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Guideng Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Alok Joglekar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
- Center for Systems Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
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29
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Di H, Elbahesh H, Brinton MA. Characteristics of Human OAS1 Isoform Proteins. Viruses 2020; 12:v12020152. [PMID: 32013110 PMCID: PMC7077331 DOI: 10.3390/v12020152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/23/2022] Open
Abstract
The human OAS1 (hOAS1) gene produces multiple possible isoforms due to alternative splicing events and sequence variation among individuals, some of which affect splicing. The unique C-terminal sequences of the hOAS1 isoforms could differentially affect synthetase activity, protein stability, protein partner interactions and/or cellular localization. Recombinant p41, p42, p44, p46, p48, p49 and p52 hOAS1 isoform proteins expressed in bacteria were each able to synthesize trimer and higher order 2'-5' linked oligoadenylates in vitro in response to poly(I:C). The p42, p44, p46, p48 and p52 isoform proteins were each able to induce RNase-mediated rRNA cleavage in response to poly(I:C) when overexpressed in HEK293 cells. The expressed levels of the p42 and p46 isoform proteins were higher than those of the other isoforms, suggesting increased stability in mammalian cells. In a yeast two-hybrid screen, Fibrillin1 (FBN1) was identified as a binding partner for hOAS1 p42 isoform, and Supervillin (SVIL) as a binding partner for the p44 isoform. The p44-SVIL interaction was supported by co-immunoprecipitation data from mammalian cells. The data suggest that the unique C-terminal regions of hOAS1 isoforms may mediate the recruitment of different partners, alternative functional capacities and/or different cellular localization.
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Affiliation(s)
- Han Di
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (H.D.); (H.E.)
| | - Husni Elbahesh
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (H.D.); (H.E.)
- Research Center for Emerging Infections and Zoonosis (RIZ), University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Margo A. Brinton
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (H.D.); (H.E.)
- Correspondence:
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30
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Kranzusch PJ. cGAS and CD-NTase enzymes: structure, mechanism, and evolution. Curr Opin Struct Biol 2019; 59:178-187. [PMID: 31593902 PMCID: PMC7127440 DOI: 10.1016/j.sbi.2019.08.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/25/2019] [Accepted: 08/25/2019] [Indexed: 01/22/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS) is a signaling enzyme in human cells that controls immune-sensing of cytosolic DNA. The recent discoveries of diverse structural homologs of cGAS in animals and bacteria reveal that cGAS-like signaling is surprisingly ancient and widespread in biology. Together with the Vibrio cholerae protein dinucleotide cyclase in Vibrio (DncV), cGAS and DncV homologs comprise a family of cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzymes that synthesize noncanonical RNA signals including cyclic dinucleotides, cyclic trinucleotides, and linear oligonucleotides. Structural and biochemical breakthroughs provide a framework to understand how CD-NTase signaling allows cells to respond to changing environmental conditions. The CD-NTase family also includes uncharacterized human genes like MB21D2 and Mab21L1, highlighting emerging functions of cGAS-like signaling beyond innate immunity.
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Affiliation(s)
- Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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31
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Liu Q, Rao Y, Tian M, Zhang S, Feng P. Modulation of Innate Immune Signaling Pathways by Herpesviruses. Viruses 2019; 11:E572. [PMID: 31234396 PMCID: PMC6630988 DOI: 10.3390/v11060572] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/16/2019] [Accepted: 06/18/2019] [Indexed: 12/25/2022] Open
Abstract
Herpesviruses can be detected by pattern recognition receptors (PRRs), which then activate downstream adaptors, kinases and transcription factors (TFs) to induce the expression of interferons (IFNs) and inflammatory cytokines. IFNs further activate the Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway, inducing the expression of interferon-stimulated genes (ISGs). These signaling events constitute host innate immunity to defeat herpesvirus infection and replication. A hallmark of all herpesviruses is their ability to establish persistent infection in the presence of active immune response. To achieve this, herpesviruses have evolved multiple strategies to suppress or exploit host innate immune signaling pathways to facilitate their infection. This review summarizes the key host innate immune components and their regulation by herpesviruses during infection. Also we highlight unanswered questions and research gaps for future perspectives.
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Affiliation(s)
- Qizhi Liu
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W 34th Street, Los Angeles, CA 90089, USA.
| | - Youliang Rao
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W 34th Street, Los Angeles, CA 90089, USA.
| | - Mao Tian
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W 34th Street, Los Angeles, CA 90089, USA.
| | - Shu Zhang
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W 34th Street, Los Angeles, CA 90089, USA.
| | - Pinghui Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W 34th Street, Los Angeles, CA 90089, USA.
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32
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Schwartz SL, Conn GL. RNA regulation of the antiviral protein 2'-5'-oligoadenylate synthetase. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1534. [PMID: 30989826 DOI: 10.1002/wrna.1534] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 12/25/2022]
Abstract
The innate immune system is a broad collection of critical intra- and extra-cellular processes that limit the infectivity of diverse pathogens. The 2'-5'-oligoadenylate synthetase (OAS) family of enzymes are important sensors of cytosolic double-stranded RNA (dsRNA) that play a critical role in limiting viral infection by activating the latent ribonuclease (RNase L) to halt viral replication and establish an antiviral state. Attesting to the importance of the OAS/RNase L pathway, diverse viruses have developed numerous distinct strategies to evade the effects of OAS activation. How OAS proteins are regulated by viral or cellular RNAs is not fully understood but several recent studies have provided important new insights into the molecular mechanisms of OAS activation by dsRNA. Other studies have revealed unanticipated features of RNA sequence and structure that strongly enhance activation of at least one OAS family member. While these discoveries represent important advances, they also underscore the fact that much remains to be learned about RNA-mediated regulation of the OAS/RNase L pathway. In particular, defining the full complement of RNA molecular signatures that activate OAS is essential to our understanding of how these proteins maximize their protective role against pathogens while still accurately discriminating host molecules to avoid inadvertent activation by cellular RNAs. A more complete knowledge of OAS regulation may also serve as a foundation for the development of novel antiviral therapeutic strategies and lead the way to a deeper understanding of currently unappreciated cellular functions of the OAS/RNase L pathway in the absence of infection. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation.
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Affiliation(s)
- Samantha L Schwartz
- Department of Biochemistry, Emory University School of Medicine and Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Atlanta, Georgia
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine and Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Atlanta, Georgia
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