1
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Cousineau SE, Camargo C, Sagan SM. Poly(rC)-Binding Protein 2 Does Not Directly Participate in HCV Translation or Replication, but Rather Modulates Genome Packaging. Viruses 2024; 16:1220. [PMID: 39205194 PMCID: PMC11359930 DOI: 10.3390/v16081220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
The hepatitis C virus (HCV) co-opts many cellular factors-including proteins and microRNAs-to complete its life cycle. A cellular RNA-binding protein, poly(rC)-binding protein 2 (PCBP2), was previously shown to bind to the hepatitis C virus (HCV) genome; however, its precise role in the viral life cycle remained unclear. Herein, using the HCV cell culture (HCVcc) system and assays that isolate each step of the viral life cycle, we found that PCBP2 does not have a direct role in viral entry, translation, genome stability, or HCV RNA replication. Rather, our data suggest that PCBP2 depletion only impacts viral RNAs that can undergo genome packaging. Taken together, our data suggest that endogenous PCBP2 modulates the early steps of genome packaging, and therefore only has an indirect effect on viral translation and RNA replication, likely by increasing the translating/replicating pool of viral RNAs to the detriment of virion assembly.
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Affiliation(s)
- Sophie E. Cousineau
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Carolina Camargo
- Department of Microbiology & Immunology, University of British Columbia, 2350 Health Science Mall, Room 4.520, Vancouver, BC V6T 1Z3, Canada
| | - Selena M. Sagan
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4, Canada
- Department of Microbiology & Immunology, University of British Columbia, 2350 Health Science Mall, Room 4.520, Vancouver, BC V6T 1Z3, Canada
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2
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Bhattarai K, Holcik M. Diverse roles of heterogeneous nuclear ribonucleoproteins in viral life cycle. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.1044652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the host-virus interactions helps to decipher the viral replication strategies and pathogenesis. Viruses have limited genetic content and rely significantly on their host cell to establish a successful infection. Viruses depend on the host for a broad spectrum of cellular RNA-binding proteins (RBPs) throughout their life cycle. One of the major RBP families is the heterogeneous nuclear ribonucleoproteins (hnRNPs) family. hnRNPs are typically localized in the nucleus, where they are forming complexes with pre-mRNAs and contribute to many aspects of nucleic acid metabolism. hnRNPs contain RNA binding motifs and frequently function as RNA chaperones involved in pre-mRNA processing, RNA splicing, and export. Many hnRNPs shuttle between the nucleus and the cytoplasm and influence cytoplasmic processes such as mRNA stability, localization, and translation. The interactions between the hnRNPs and viral components are well-known. They are critical for processing viral nucleic acids and proteins and, therefore, impact the success of the viral infection. This review discusses the molecular mechanisms by which hnRNPs interact with and regulate each stage of the viral life cycle, such as replication, splicing, translation, and assembly of virus progeny. In addition, we expand on the role of hnRNPs in the antiviral response and as potential targets for antiviral drug research and development.
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3
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Leppek K, Byeon GW, Kladwang W, Wayment-Steele HK, Kerr CH, Xu AF, Kim DS, Topkar VV, Choe C, Rothschild D, Tiu GC, Wellington-Oguri R, Fujii K, Sharma E, Watkins AM, Nicol JJ, Romano J, Tunguz B, Diaz F, Cai H, Guo P, Wu J, Meng F, Shi S, Participants E, Dormitzer PR, Solórzano A, Barna M, Das R. Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics. Nat Commun 2022; 13:1536. [PMID: 35318324 PMCID: PMC8940940 DOI: 10.1038/s41467-022-28776-w] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 02/07/2022] [Indexed: 02/07/2023] Open
Abstract
Therapeutic mRNAs and vaccines are being developed for a broad range of human diseases, including COVID-19. However, their optimization is hindered by mRNA instability and inefficient protein expression. Here, we describe design principles that overcome these barriers. We develop an RNA sequencing-based platform called PERSIST-seq to systematically delineate in-cell mRNA stability, ribosome load, as well as in-solution stability of a library of diverse mRNAs. We find that, surprisingly, in-cell stability is a greater driver of protein output than high ribosome load. We further introduce a method called In-line-seq, applied to thousands of diverse RNAs, that reveals sequence and structure-based rules for mitigating hydrolytic degradation. Our findings show that highly structured “superfolder” mRNAs can be designed to improve both stability and expression with further enhancement through pseudouridine nucleoside modification. Together, our study demonstrates simultaneous improvement of mRNA stability and protein expression and provides a computational-experimental platform for the enhancement of mRNA medicines. The authors develop an RNA sequencing-based platform, PERSIST-seq, to simultaneously delineate in-cell mRNA stability, ribosome load, and in-solution stability of a diverse mRNA library to derive design principles for improved mRNA therapeutics.
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Affiliation(s)
- Kathrin Leppek
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Gun Woo Byeon
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | | | - Craig H Kerr
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Adele F Xu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Do Soon Kim
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Ved V Topkar
- Program in Biophysics, Stanford University, Stanford, CA, 94305, USA
| | - Christian Choe
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Daphna Rothschild
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Gerald C Tiu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | | | - Kotaro Fujii
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Eesha Sharma
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - John J Nicol
- Eterna Massive Open Laboratory, Stanford University, Stanford, CA, 94305, USA
| | - Jonathan Romano
- Eterna Massive Open Laboratory, Stanford University, Stanford, CA, 94305, USA.,Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, New York, 14260, USA
| | - Bojan Tunguz
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.,NVIDIA Corporation, 2788 San Tomas Expy, Santa Clara, CA, 95051, USA
| | - Fernando Diaz
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Hui Cai
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Pengbo Guo
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Jiewei Wu
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Fanyu Meng
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Shuai Shi
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Eterna Participants
- Eterna Massive Open Laboratory, Stanford University, Stanford, CA, 94305, USA
| | - Philip R Dormitzer
- Pfizer Vaccine Research and Development, Pearl River, NY, USA.,GlaxoSmithKline, 1000 Winter St., Waltham, MA, 02453, USA
| | | | - Maria Barna
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA. .,Program in Biophysics, Stanford University, Stanford, CA, 94305, USA. .,Eterna Massive Open Laboratory, Stanford University, Stanford, CA, 94305, USA.
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4
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Babaei G, Massah A, Koohi Habibi M. Efficient translation of Eggplant mottled dwarf nucleorhabdovirus N and X genes requires both 5' and 3' UTRs. Virol J 2021; 18:129. [PMID: 34174907 PMCID: PMC8236180 DOI: 10.1186/s12985-021-01601-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background Circularization of RNA mediated by association of translation factors and RNA elements in 5′ and 3′ UTRs is a common feature for translation control in eukaryotes. There is no information about translation in plant rhabdoviruses and little information is known in animal rhabdoviruses.
Methods The role of 5′ and 3′ UTRs in two genes of EMDV in translation were studied using luciferase constructs and RNA structures of these sequences were analyzed by SHAPE and Inline probing. Results We have found that efficient translation of N and X mRNAs of nucleorhabdovirus Eggplant mottled dwarf virus (EMDV) requires elements present in both 5′ and 3′ UTRs. Luciferase reporter constructs containing precise 5′ and 3′ UTRs of the N and X genes had substantially higher translational activity compared with constructs containing only the 5′ or 3′ UTR. The 3′UTR of carmovirus Turnip crinkle virus, which contains a well-characterized cap-independent translation enhancer, was unable to complement the lack of EMDV 3′ UTR. Addition of cap analog to luciferase constructs containing the UTRs of the N gene did not restore translation, and translation of the reporter construct in the absence of the 5′ cap was higher than the capped construct. No RNA-RNA interactions between 5′ and 3′ UTRs were detected by EMSA or in-line cleavage structural assays. Deletion of 11 nucleotides from the 3′ terminus negated the synergistic activity of the 3′UTR. Conclusions The results with RNA-RNA interaction suggesting that translational synergy between the UTRs may utilize alternative means. Mutation analysis in 3′UTR suggesting that the polyadenylation signal sequence contained in this location may play a critical role in translation.
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Affiliation(s)
- Ghobad Babaei
- Plant Protection Research Department, Chaharmahal and Bakhtiari Agricultural and Natural Resources Research and Education Center, AREEO, Shahrekord, Iran.
| | - Amir Massah
- Department of Plant Protection, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Mina Koohi Habibi
- Department of Plant Protection, Faculty of Agricultural Sciences and Engineering, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
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5
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Leppek K, Byeon GW, Kladwang W, Wayment-Steele HK, Kerr CH, Xu AF, Kim DS, Topkar VV, Choe C, Rothschild D, Tiu GC, Wellington-Oguri R, Fujii K, Sharma E, Watkins AM, Nicol JJ, Romano J, Tunguz B, Participants E, Barna M, Das R. Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.29.437587. [PMID: 33821271 PMCID: PMC8020971 DOI: 10.1101/2021.03.29.437587] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Therapeutic mRNAs and vaccines are being developed for a broad range of human diseases, including COVID-19. However, their optimization is hindered by mRNA instability and inefficient protein expression. Here, we describe design principles that overcome these barriers. We develop a new RNA sequencing-based platform called PERSIST-seq to systematically delineate in-cell mRNA stability, ribosome load, as well as in-solution stability of a library of diverse mRNAs. We find that, surprisingly, in-cell stability is a greater driver of protein output than high ribosome load. We further introduce a method called In-line-seq, applied to thousands of diverse RNAs, that reveals sequence and structure-based rules for mitigating hydrolytic degradation. Our findings show that "superfolder" mRNAs can be designed to improve both stability and expression that are further enhanced through pseudouridine nucleoside modification. Together, our study demonstrates simultaneous improvement of mRNA stability and protein expression and provides a computational-experimental platform for the enhancement of mRNA medicines.
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Affiliation(s)
- Kathrin Leppek
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Gun Woo Byeon
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University, California 94305, USA
| | | | - Craig H Kerr
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Adele F Xu
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Do Soon Kim
- Department of Biochemistry, Stanford University, California 94305, USA
| | - Ved V Topkar
- Program in Biophysics, Stanford University, Stanford, California 94305, USA
| | - Christian Choe
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Daphna Rothschild
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Gerald C Tiu
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | | | - Kotaro Fujii
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Eesha Sharma
- Department of Biochemistry, Stanford University, California 94305, USA
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University, California 94305, USA
| | | | - Jonathan Romano
- Eterna Massive Open Laboratory
- Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, New York, 14260, USA
| | - Bojan Tunguz
- Department of Biochemistry, Stanford University, California 94305, USA
| | | | - Maria Barna
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University, California 94305, USA
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6
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Hennessy EJ, FitzGerald GA. Battle for supremacy: nucleic acid interactions between viruses and cells. J Clin Invest 2021; 131:144227. [PMID: 33290272 PMCID: PMC7843224 DOI: 10.1172/jci144227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Since the COVID-19 pandemic swept across the globe, researchers have been trying to understand its origin, life cycle, and pathogenesis. There is a striking variability in the phenotypic response to infection with SARS-CoV-2 that may reflect differences in host genetics and/or immune response. It is known that the human epigenome is influenced by ethnicity, age, lifestyle, and environmental factors, including previous viral infections. This Review examines the influence of viruses on the host epigenome. We describe general lessons and methodologies that can be used to understand how the virus evades the host immune response. We consider how variation in the epigenome may contribute to heterogeneity in the response to SARS-CoV-2 and may identify a precision medicine approach to treatment.
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7
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Abstract
While host proteins incorporated into virions during viral budding from infected cell are known to play essential roles in multiple process of the life cycle of progeny virus, these characteristics have been largely neglected in studies on rabies virus (RABV). Here, we purified the RABV virions with good purity and integrity, and analyzed their proteome by nano LC–MS/MS, followed by the confirmation with immunoblot and immuno-electronic microscopy. In addition to the 5 viral proteins, 49 cellular proteins were reproducibly identified to be incorporated into matured RABV virions. Function annotation suggested that 24 of them were likely involved in virus replication. Furthermore, cryo-EM was employed to observe the purified RABV virions, generating high-resolution pictures of the bullet-shaped virion structure of RABV. This study has provided new insights into the host proteins composition in RABV virion and shed the light for further investigation on molecular mechanisms of RABV infection, as well as the discovery of new anti-RABV therapeutics.
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8
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Du S, Liu X, Cai Q. Viral-Mediated mRNA Degradation for Pathogenesis. Biomedicines 2018; 6:biomedicines6040111. [PMID: 30501096 PMCID: PMC6315618 DOI: 10.3390/biomedicines6040111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 11/21/2022] Open
Abstract
Cellular RNA decay machinery plays a vital role in regulating gene expression by altering the stability of mRNAs in response to external stresses, including viral infection. In the primary infection, viruses often conquer the host cell’s antiviral immune response by controlling the inherently cellular mRNA degradation machinery to facilitate viral gene expression and establish a successful infection. This review summarizes the current knowledge about the diverse strategies of viral-mediated regulatory RNA shutoff for pathogenesis, and particularly sheds a light on the mechanisms that viruses evolve to elude immune surveillance during infection.
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Affiliation(s)
- Shujuan Du
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Xiaoqing Liu
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Qiliang Cai
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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9
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Reardon TR, Murray AJ, Turi GF, Wirblich C, Croce KR, Schnell MJ, Jessell TM, Losonczy A. Rabies Virus CVS-N2c(ΔG) Strain Enhances Retrograde Synaptic Transfer and Neuronal Viability. Neuron 2016; 89:711-24. [PMID: 26804990 DOI: 10.1016/j.neuron.2016.01.004] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/22/2015] [Accepted: 12/24/2015] [Indexed: 12/20/2022]
Abstract
Virally based transsynaptic tracing technologies are powerful experimental tools for neuronal circuit mapping. The glycoprotein-deletion variant of the SAD-B19 vaccine strain rabies virus (RABV) has been the reagent of choice in monosynaptic tracing, since it permits the mapping of synaptic inputs to genetically marked neurons. Since its introduction, new helper viruses and reagents that facilitate complementation have enhanced the efficiency of SAD-B19(ΔG) transsynaptic transfer, but there has been little focus on improvements to the core RABV strain. Here we generate a new deletion mutant strain, CVS-N2c(ΔG), and examine its neuronal toxicity and efficiency in directing retrograde transsynaptic transfer. We find that by comparison with SAD-B19(ΔG), the CVS-N2c(ΔG) strain exhibits a reduction in neuronal toxicity and a marked enhancement in transsynaptic neuronal transfer. We conclude that the CVS-N2c(ΔG) strain provides a more effective means of mapping neuronal circuitry and of monitoring and manipulating neuronal activity in vivo in the mammalian CNS.
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Affiliation(s)
- Thomas R Reardon
- Departments of Neuroscience and Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Andrew J Murray
- Departments of Neuroscience and Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA.
| | - Gergely F Turi
- Department of Neuroscience, Columbia University, New York, NY 10032, USA
| | - Christoph Wirblich
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Katherine R Croce
- Departments of Neuroscience and Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Matthias J Schnell
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Thomas M Jessell
- Departments of Neuroscience and Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10032, USA.
| | - Attila Losonczy
- Department of Neuroscience, Columbia University, New York, NY 10032, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10032, USA
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10
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Genome-wide gene-gene interaction analysis for next-generation sequencing. Eur J Hum Genet 2015; 24:421-8. [PMID: 26173972 DOI: 10.1038/ejhg.2015.147] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 04/21/2015] [Accepted: 05/26/2015] [Indexed: 01/13/2023] Open
Abstract
The critical barrier in interaction analysis for next-generation sequencing (NGS) data is that the traditional pairwise interaction analysis that is suitable for common variants is difficult to apply to rare variants because of their prohibitive computational time, large number of tests and low power. The great challenges for successful detection of interactions with NGS data are (1) the demands in the paradigm of changes in interaction analysis; (2) severe multiple testing; and (3) heavy computations. To meet these challenges, we shift the paradigm of interaction analysis between two SNPs to interaction analysis between two genomic regions. In other words, we take a gene as a unit of analysis and use functional data analysis techniques as dimensional reduction tools to develop a novel statistic to collectively test interaction between all possible pairs of SNPs within two genome regions. By intensive simulations, we demonstrate that the functional logistic regression for interaction analysis has the correct type 1 error rates and higher power to detect interaction than the currently used methods. The proposed method was applied to a coronary artery disease dataset from the Wellcome Trust Case Control Consortium (WTCCC) study and the Framingham Heart Study (FHS) dataset, and the early-onset myocardial infarction (EOMI) exome sequence datasets with European origin from the NHLBI's Exome Sequencing Project. We discovered that 6 of 27 pairs of significantly interacted genes in the FHS were replicated in the independent WTCCC study and 24 pairs of significantly interacted genes after applying Bonferroni correction in the EOMI study.
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11
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Glycoprotein from street rabies virus BD06 induces early and robust immune responses when expressed from a non-replicative adenovirus recombinant. Arch Virol 2015; 160:2315-23. [DOI: 10.1007/s00705-015-2512-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/23/2015] [Indexed: 12/25/2022]
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12
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Kipkorir T, Colangelo CM, Manuelidis L. Proteomic analysis of host brain components that bind to infectious particles in Creutzfeldt-Jakob disease. Proteomics 2015; 15:2983-98. [PMID: 25930988 DOI: 10.1002/pmic.201500059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/26/2015] [Accepted: 04/29/2015] [Indexed: 11/07/2022]
Abstract
Transmissible encephalopathies (TSEs), such as Creutzfeldt-Jakob disease (CJD) and scrapie, are caused by infectious agents that provoke strain-specific patterns of disease. Misfolded host prion protein (PrP-res amyloid) is believed to be the causal infectious agent. However, particles that are stripped of PrP retain both high infectivity and viral proteins not detectable in uninfected mouse controls. We here detail host proteins bound with FU-CJD agent infectious brain particles by proteomic analysis. More than 98 proteins were differentially regulated, and 56 FU-CJD exclusive proteins were revealed after PrP, GFAP, C1q, ApoE, and other late pathologic response proteins were removed. Stripped FU-CJD particles revealed HSC70 (144× the uninfected control), cyclophilin B, an FU-CJD exclusive protein required by many viruses, and early endosome-membrane pathways known to facilitate viral processing, replication, and spread. Synaptosomal elements including synapsin-2 (at 33×) and AP180 (a major FU-CJD exclusive protein) paralleled the known ultrastructural location of 25 nm virus-like TSE particles and infectivity in synapses. Proteins without apparent viral or neurodegenerative links (copine-3), and others involved in viral-induced protein misfolding and aggregation, were also identified. Human sCJD brain particles contained 146 exclusive proteins, and heat shock, synaptic, and viral pathways were again prominent, in addition to Alzheimer, Parkinson, and Huntington aggregation proteins. Host proteins that bind TSE infectious particles can prevent host immune recognition and contribute to prolonged cross-species transmissions (the species barrier). Our infectious particle strategy, which reduces background sequences by >99%, emphasizes host targets for new therapeutic initiatives. Such therapies can simultaneously subvert common pathways of neurodegeneration.
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13
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Zhang J, Ye C, Ruan X, Zan J, Xu Y, Liao M, Zhou J. The chaperonin CCTα is required for efficient transcription and replication of rabies virus. Microbiol Immunol 2015; 58:590-9. [PMID: 25082455 DOI: 10.1111/1348-0421.12186] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 07/08/2014] [Accepted: 07/24/2014] [Indexed: 12/25/2022]
Abstract
Negri bodies (NBs) are formed in the cytoplasm of rabies virus (RABV)-infected cells and are accompanied by a number of host factors to NBs, in which replication and transcription occur. Here, it was found that chaperonin containing TCP-1 subunit alpha (CCTα) relocalizes to NBs in RABV-infected cells, and that cotransfection of nucleo- and phospho-proteins of RABV is sufficient to recruit CCTα to the NBs' structure. Inhibition of CCTα expression by specific short hairpin RNA knockdown inhibited the replication and transcription of RABV. Therefore, this study showed that the host factor CCTα is associated with RABV infection and is very likely required for efficient virus transcription and replication.
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Affiliation(s)
- Jinyang Zhang
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, 310058; State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University, Hangzhou, 310003; Research Center of Molecular Medicine of Yunnan Province, Kunming University of Science and Technology, Kunming, 650500, China
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14
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García K, Ramírez-Araya S, Díaz Á, Reyes-Cerpa S, Espejo RT, Higuera G, Romero J. Inactivated E. coli transformed with plasmids that produce dsRNA against infectious salmon anemia virus hemagglutinin show antiviral activity when added to infected ASK cells. Front Microbiol 2015; 6:300. [PMID: 25932022 PMCID: PMC4399331 DOI: 10.3389/fmicb.2015.00300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/26/2015] [Indexed: 12/12/2022] Open
Abstract
Infectious salmon anemia virus (ISAV) has caused great losses to the Chilean salmon industry, and the success of prevention and treatment strategies is uncertain. The use of RNA interference (RNAi) is a promising approach because during the replication cycle, the ISAV genome must be transcribed to mRNA in the cytoplasm. We explored the capacity of E. coli transformed with plasmids that produce double-stranded RNA (dsRNA) to induce antiviral activity when added to infected ASK cells. We transformed the non-pathogenic Escherichia coli HT115 (DE3) with plasmids that expressed highly conserved regions of the ISAV genes encoding the nucleoprotein (NP), fusion (F), hemagglutinin (HE), and matrix (M) proteins as dsRNA, which is the precursor of the RNAi mechanism. The inactivated transformed bacteria carrying dsRNA were tested for their capacity to silence the target ISAV genes, and the dsRNA that were able to inhibit gene expression were subsequently tested for their ability to attenuate the cytopathic effect (CPE) and reduce the viral load. Of the four target genes tested, inactivated E. coli transformed with plasmids producing dsRNA targeting HE showed antiviral activity when added to infected ASK cells.
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Affiliation(s)
- Katherine García
- Laboratorio de Biotecnología, Unidad de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Sebastián Ramírez-Araya
- Laboratorio de Biotecnología, Unidad de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Álvaro Díaz
- Laboratorio de Biotecnología, Unidad de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Sebastián Reyes-Cerpa
- Facultad de Química y Biología, Centro de Biotecnología Acuícola, Universidad de Santiago de Chile Santiago, Chile
| | - Romilio T Espejo
- Laboratorio de Biotecnología, Unidad de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile ; Centro Nacional de Genómica y Bioinformática (Omics Solutions) Santiago, Chile
| | - Gastón Higuera
- Laboratorio de Biotecnología, Unidad de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Jaime Romero
- Laboratorio de Biotecnología, Unidad de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
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15
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Wallis D, Loesch K, Galaviz S, Sun Q, DeJesus M, Ioerger T, Sacchettini JC. High-Throughput Differentiation and Screening of a Library of Mutant Stem Cell Clones Defines New Host-Based Genes Involved in Rabies Virus Infection. Stem Cells 2015; 33:2509-22. [PMID: 25752821 DOI: 10.1002/stem.1983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/02/2015] [Indexed: 12/25/2022]
Abstract
We used a genomic library of mutant murine embryonic stem cells (ESCs) and report the methodology required to simultaneously culture, differentiate, and screen more than 3,200 heterozygous mutant clones to identify host-based genes involved in both sensitivity and resistance to rabies virus infection. Established neuronal differentiation protocols were miniaturized such that many clones could be handled simultaneously, and molecular markers were used to show that the resultant cultures were pan-neuronal. Next, we used a green fluorescent protein (GFP) labeled rabies virus to develop, validate, and implement one of the first host-based, high-content, high-throughput screens for rabies virus. Undifferentiated cell and neuron cultures were infected with GFP-rabies and live imaging was used to evaluate GFP intensity at time points corresponding to initial infection/uptake and early and late replication. Furthermore, supernatants were used to evaluate viral shedding potential. After repeated testing, 63 genes involved in either sensitivity or resistance to rabies infection were identified. To further explore hits, we used a completely independent system (siRNA) to show that reduction in target gene expression leads to the observed phenotype. We validated the immune modulatory gene Unc13d and the dynein adapter gene Bbs4 by treating wild-type ESCs and primary neurons with siRNA; treated cultures were resistant to rabies infection/replication. Overall, the potential of such in vitro functional genomics screens in stem cells adds additional value to other libraries of stem cells. This technique is applicable to any bacterial or virus interactome and any cell or tissue types that can be differentiated from ESCs.
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Affiliation(s)
- Deeann Wallis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Kimberly Loesch
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Stacy Galaviz
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Qingan Sun
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Michael DeJesus
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, USA
| | - Thomas Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, USA
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
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16
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Rasekhian M, Roohvand F, Teimoori-Toolabi L, Amini S, Azadmanesh K. Application of the 3'-noncoding region of poliovirus RNA for cell-based regulation of mRNA stability: implication for biotechnological applications. Biotechnol Appl Biochem 2014; 61:699-706. [PMID: 24612228 DOI: 10.1002/bab.1218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 02/12/2014] [Indexed: 11/08/2022]
Abstract
Enrichment of production yield of therapeutic proteins in mammalian cell cultures by modulation of the mRNA stability of the target protein to increase its in vivo half-life is a new strategy in biotechnological applications. The present article describes one of the most novel approaches to modulate mRNA stability by application of 3'-noncoding region (3'NCR) from RNA viral genome in the expression constructs. Our data indicated that although utilizing the 3'NCR sequence form poliovirus (PV-3'NCR) downstream of the target gene might generally stabilize the secondary structure of RNA, it influenced the mRNA stability (and thereby the amount of protein production) in a cell type and time-dependent manner, thus indicating a central role of mRNA-stabilizing binding sites/cellular factors in this process. Our data might be of interest to the biotechnology community to improve recombinant protein production in mammalian cell cultures and RNA-based therapy/vaccination approaches.
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Affiliation(s)
- Mahsa Rasekhian
- Virology Department, Pasteur Institute of Iran, Tehran, Iran
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17
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Affiliation(s)
- Stephanie L. Moon
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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18
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Narayanan K, Makino S. Interplay between viruses and host mRNA degradation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:732-41. [PMID: 23274304 PMCID: PMC3632658 DOI: 10.1016/j.bbagrm.2012.12.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/13/2012] [Accepted: 12/16/2012] [Indexed: 12/17/2022]
Abstract
Messenger RNA degradation is a fundamental cellular process that plays a critical role in regulating gene expression by controlling both the quality and the abundance of mRNAs in cells. Naturally, viruses must successfully interface with the robust cellular RNA degradation machinery to achieve an optimal balance between viral and cellular gene expression and establish a productive infection in the host. In the past several years, studies have discovered many elegant strategies that viruses have evolved to circumvent the cellular RNA degradation machinery, ranging from disarming the RNA decay pathways and co-opting the factors governing cellular mRNA stability to promoting host mRNA degradation that facilitates selective viral gene expression and alters the dynamics of host–pathogen interaction. This review summarizes the current knowledge of the multifaceted interaction between viruses and cellular mRNA degradation machinery to provide an insight into the regulatory mechanisms that influence gene expression in viral infections. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Affiliation(s)
- Krishna Narayanan
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA.
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19
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Moon SL, Anderson JR, Kumagai Y, Wilusz CJ, Akira S, Khromykh AA, Wilusz J. A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability. RNA (NEW YORK, N.Y.) 2012; 18:2029-40. [PMID: 23006624 PMCID: PMC3479393 DOI: 10.1261/rna.034330.112] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/17/2012] [Indexed: 05/25/2023]
Abstract
All arthropod-borne flaviviruses generate a short noncoding RNA (sfRNA) from the viral 3' untranslated region during infection due to stalling of the cellular 5'-to-3' exonuclease XRN1. We show here that formation of sfRNA also inhibits XRN1 activity. Cells infected with Dengue or Kunjin viruses accumulate uncapped mRNAs, decay intermediates normally targeted by XRN1. XRN1 repression also resulted in the increased overall stability of cellular mRNAs in flavivirus-infected cells. Importantly, a mutant Kunjin virus that cannot form sfRNA but replicates to normal levels failed to affect host mRNA stability or XRN1 activity. Expression of sfRNA in the absence of viral infection demonstrated that sfRNA formation was directly responsible for the stabilization of cellular mRNAs. Finally, numerous cellular mRNAs were differentially expressed in an sfRNA-dependent fashion in a Kunjin virus infection. We conclude that flaviviruses incapacitate XRN1 during infection and dysregulate host mRNA stability as a result of sfRNA formation.
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Affiliation(s)
- Stephanie L. Moon
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - John R. Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Yutaro Kumagai
- Laboratory of Host Defense, Immunology Frontier Research Center, Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Carol J. Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Shizuo Akira
- Laboratory of Host Defense, Immunology Frontier Research Center, Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Alexander A. Khromykh
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
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20
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Moon SL, Barnhart MD, Wilusz J. Inhibition and avoidance of mRNA degradation by RNA viruses. Curr Opin Microbiol 2012; 15:500-5. [PMID: 22626865 DOI: 10.1016/j.mib.2012.04.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 04/27/2012] [Indexed: 11/27/2022]
Abstract
The cellular mRNA decay machinery plays a major role in regulating the quality and quantity of gene expression in cells. This machinery involves multiple enzymes and pathways that converge to promote the exonucleolytic decay of mRNAs. The transcripts made by RNA viruses are susceptible to degradation by this machinery and, in fact, can be actively targeted. Thus, to maintain gene expression and replication, RNA viruses have evolved a number of strategies to avoid and/or inactivate aspects of the cellular mRNA decay machinery. Recent work uncovering the mechanisms used by RNA viruses to maintain the stability of their transcripts is described below.
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Affiliation(s)
- Stephanie L Moon
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, United States
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