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Zhang Y, Zhang LS, Dai Q, Chen P, Lu M, Kairis EL, Murugaiah V, Xu J, Shukla RK, Liang X, Zou Z, Cormet-Boyaka E, Qiu J, Peeples ME, Sharma A, He C, Li J. 5-methylcytosine (m 5C) RNA modification controls the innate immune response to virus infection by regulating type I interferons. Proc Natl Acad Sci U S A 2022; 119:e2123338119. [PMID: 36240321 PMCID: PMC9586267 DOI: 10.1073/pnas.2123338119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 08/23/2022] [Indexed: 11/18/2022] Open
Abstract
5-methylcytosine (m5C) is one of the most prevalent modifications of RNA, playing important roles in RNA metabolism, nuclear export, and translation. However, the potential role of RNA m5C methylation in innate immunity remains elusive. Here, we show that depletion of NSUN2, an m5C methyltransferase, significantly inhibits the replication and gene expression of a wide range of RNA and DNA viruses. Notably, we found that this antiviral effect is largely driven by an enhanced type I interferon (IFN) response. The antiviral signaling pathway is dependent on the cytosolic RNA sensor RIG-I but not MDA5. Transcriptome-wide mapping of m5C following NSUN2 depletion in human A549 cells revealed a marked reduction in the m5C methylation of several abundant noncoding RNAs (ncRNAs). However, m5C methylation of viral RNA was not noticeably altered by NSUN2 depletion. In NSUN2-depleted cells, the host RNA polymerase (Pol) III transcribed ncRNAs, in particular RPPH1 and 7SL RNAs, were substantially up-regulated, leading to an increase of unshielded 7SL RNA in cytoplasm, which served as a direct ligand for the RIG-I-mediated IFN response. In NSUN2-depleted cells, inhibition of Pol III transcription or silencing of RPPH1 and 7SL RNA dampened IFN signaling, partially rescuing viral replication and gene expression. Finally, depletion of NSUN2 in an ex vivo human lung model and a mouse model inhibits viral replication and reduces pathogenesis, which is accompanied by enhanced type I IFN responses. Collectively, our data demonstrate that RNA m5C methylation controls antiviral innate immunity through modulating the m5C methylome of ncRNAs and their expression.
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Affiliation(s)
- Yuexiu Zhang
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Li-Sheng Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
- The Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
- The Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
| | - Phylip Chen
- Center for Vaccines and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43205
| | - Mijia Lu
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Elizabeth L. Kairis
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Valarmathy Murugaiah
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Jiayu Xu
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Rajni Kant Shukla
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Xueya Liang
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Zhongyu Zou
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
- The Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
| | - Estelle Cormet-Boyaka
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Mark E. Peeples
- Center for Vaccines and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43205
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43205
| | - Amit Sharma
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
- The Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637
| | - Jianrong Li
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
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Wellmerling J, Rayner RE, Chang SW, Kairis EL, Kim SH, Sharma A, Boyaka PN, Cormet-Boyaka E. Targeting the EGFR-ERK axis using the compatible solute ectoine to stabilize CFTR mutant F508del. FASEB J 2022; 36:e22270. [PMID: 35412656 PMCID: PMC9009300 DOI: 10.1096/fj.202100458rrr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 03/01/2022] [Accepted: 03/09/2022] [Indexed: 11/11/2022]
Abstract
Mutations in the CFTR gene lead to cystic fibrosis, a genetic disease associated with chronic infection and inflammation and ultimately respiratory failure. The most common CF-causing mutation is F508del and CFTR modulators (correctors and potentiators) are being developed to rescue its trafficking and activity defects. However, there are currently no modulators that stabilize the rescued membrane F508del-CFTR which is endocytosed and quickly degraded resulting in a shorter half-life than wild-type (WT). We previously reported that the extracellular signal-regulated kinase (ERK) MAPK pathway is involved in CFTR degradation upon cigarette smoke exposure. Interestingly, we found that ERK phosphorylation was increased in CF human bronchial epithelial (HBE) cells (CF-HBE41o- and primary CF-HBE) compared to non-CF controls, and this was likely due to signaling by the epidermal growth factor receptor (EGFR). EGFR can be activated by several ligands, and we provide evidence that amphiregulin (AREG) is important for activating this signaling axis in CF. The natural osmolyte ectoine stabilizes membrane macromolecules. We show that ectoine decreases ERK phosphorylation, increases the half-life of rescued CFTR, and increases CFTR-mediated chloride transport in combination with the CFTR corrector VX-661. Additionally, ectoine reduces production of AREG and interleukin-8 by CF primary bronchial epithelial cells. In conclusion, EGFR-ERK signaling negatively regulates CFTR and is hyperactive in CF, and targeting this axis with ectoine may prove beneficial for CF patients.
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Affiliation(s)
- Jack Wellmerling
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Rachael E Rayner
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Sheng-Wei Chang
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Elizabeth L Kairis
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Sun Hee Kim
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Amit Sharma
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Prosper N Boyaka
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Estelle Cormet-Boyaka
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
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Xue M, Zhang Y, Wang H, Kairis EL, Lu M, Ahmad S, Attia Z, Harder O, Zhang Z, Wei J, Chen P, Gao Y, Peeples ME, Sharma A, Boyaka P, He C, Hur S, Niewiesk S, Li J. Viral RNA N6-methyladenosine modification modulates both innate and adaptive immune responses of human respiratory syncytial virus. PLoS Pathog 2021; 17:e1010142. [PMID: 34929018 PMCID: PMC8759664 DOI: 10.1371/journal.ppat.1010142] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/14/2022] [Accepted: 11/19/2021] [Indexed: 12/29/2022] Open
Abstract
Human respiratory syncytial virus (RSV) is the leading cause of respiratory tract infections in humans. A well-known challenge in the development of a live attenuated RSV vaccine is that interferon (IFN)-mediated antiviral responses are strongly suppressed by RSV nonstructural proteins which, in turn, dampens the subsequent adaptive immune responses. Here, we discovered a novel strategy to enhance innate and adaptive immunity to RSV infection. Specifically, we found that recombinant RSVs deficient in viral RNA N6-methyladenosine (m6A) and RSV grown in m6A methyltransferase (METTL3)-knockdown cells induce higher expression of RIG-I, bind more efficiently to RIG-I, and enhance RIG-I ubiquitination and IRF3 phosphorylation compared to wild-type virion RNA, leading to enhanced type I IFN production. Importantly, these m6A-deficient RSV mutants also induce a stronger IFN response in vivo, are significantly attenuated, induce higher neutralizing antibody and T cell immune responses in mice and provide complete protection against RSV challenge in cotton rats. Collectively, our results demonstrate that inhibition of RSV RNA m6A methylation enhances innate immune responses which in turn promote adaptive immunity.
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Affiliation(s)
- Miaoge Xue
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Yuexiu Zhang
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Haitao Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Elizabeth L. Kairis
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Mijia Lu
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Sadeem Ahmad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Zayed Attia
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Olivia Harder
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Zijie Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jiangbo Wei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, United States of America
| | - Phylip Chen
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Youling Gao
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Mark E. Peeples
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Amit Sharma
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Prosper Boyaka
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Chuan He
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois, United States of America
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Stefan Niewiesk
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Jianrong Li
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
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