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Kron NS, Fieber LA, Baker L, Campbell C, Schmale MC. Host response to Aplysia Abyssovirus 1 in nervous system and gill. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 159:105211. [PMID: 38885747 PMCID: PMC11378725 DOI: 10.1016/j.dci.2024.105211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
The California sea hare (Aplysia californica) is a model for age associated cognitive decline. Recent researched identified a novel nidovirus, Aplysia Abyssovirus 1, with broad tropism enriched in the Aplysia nervous system. This virus is ubiquitous in wild and maricultured, young and old animals without obvious pathology. Here we re-evaluated gene expression data from several previous studies to investigate differential expression in the nervous system and gill in response to virus and aging as well as the mutational spectrum observed in the viral sequences obtained from these datasets. Viral load and age were highly correlated, indicating persistent infection. Upregulated genes in response to virus were enriched for immune genes and signatures of ER and proteostatic stress, while downregulated genes were enriched for mitochondrial metabolism. Differential expression with respect to age suggested increased iron accumulation and decreased glycolysis, fatty acid metabolism, and proteasome function. Interaction of gene expression trends associated with viral infection and aging suggest that viral infection likely plays a role in aging in the Aplysia nervous system. Mutation analysis of viral RNA identified signatures suggesting ADAR and AID/APOBEC like deaminase act as part of Aplysia anti-viral defense.
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Affiliation(s)
- Nicholas S Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA.
| | - Lynne A Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
| | - Lydia Baker
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
| | | | - Michael C Schmale
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
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Yang X, Xie L, Yin Y, Yang C, Xiao J, Wu H, Wang C, Tian Y, Feng H. Black carp A20 inhibits interferon signaling through de-ubiquitinating IKKβ. FISH & SHELLFISH IMMUNOLOGY 2024; 152:109781. [PMID: 39029718 DOI: 10.1016/j.fsi.2024.109781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/21/2024]
Abstract
IkappaB kinase beta (IKKβ) is a key member of IκB kinases and functions importantly in interferon (IFN) signaling. Phosphorylation and ubiquitination are involved in the activation of IKKβ. A20 is a de-ubiquitin enzyme and functions as a suppressor in inflammation signaling, which has been reported to be phosphorylated and activated by IKKβ. However, the role and relationship of IKKβ and A20 in teleost remains unclear. In this study, IKKβ (bcIKKβ) and A20 (bcA20) of black carp (Mylopharyngodon piceus) have been cloned and characterized. Overexpressed bcIKKβ in EPC cells showed strong anti-viral ability by activating both NF-κB and IFN signaling. EPC cells stable expressing bcIKKβ presented improved anti-viral activity as well. The interaction between bcA20 and bcIKKβ was identified, and overexpression of bcA20 was able to suppress bcIKKβ-mediated activation of NF-κB and IFN signaling. Meanwhile, knock-down of A20 increased host the antiviral ability of host cells. Importantly, it has been identified that bcA20 was able to remove K27-linked ubiquitination and decrease the phosphorylation of bcIKKβ. Thus, our data conclude that bcA20 suppresses the anti-viral activity of bcIKKβ and removes its K27-linked ubiquitination, which presents a new mechanism of IKKβ regulation.
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Affiliation(s)
- Xiao Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Lixia Xie
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yuqi Yin
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Can Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jun Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Hui Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Chanyuan Wang
- Department of Ophthalmology, Hunan Children's Hospital, Changsha, 410007, China
| | - Yu Tian
- Department of Ophthalmology, Hunan Children's Hospital, Changsha, 410007, China.
| | - Hao Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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3
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BenDavid E, Yang C, Zhou Y, Pfaller CK, Samuel CE, Ma D. Host WD repeat-containing protein 5 inhibits protein kinase R-mediated integrated stress response during measles virus infection. J Virol 2024:e0102024. [PMID: 39194235 DOI: 10.1128/jvi.01020-24] [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: 06/10/2024] [Accepted: 07/09/2024] [Indexed: 08/29/2024] Open
Abstract
Some negative-sense RNA viruses, including measles virus (MeV), share the characteristic that during their infection cycle, cytoplasmic inclusion bodies (IBs) are formed where components of the viral replication machinery are concentrated. As a foci of viral replication, how IBs act to enhance the efficiency of infection by affecting virus-host interactions remains an important topic of investigation. We previously established that upon MeV infection, the epigenetic host protein, WD repeat-containing protein 5 (WDR5), translocates to cytoplasmic viral IBs and facilitates MeV replication. We now show that WDR5 is recruited to IBs by forming a complex with IB-associated MeV phosphoprotein via a conserved binding motif located on the surface of WDR5. Furthermore, we provide evidence that WDR5 promotes viral replication by suppressing a major innate immune response pathway, the double-stranded RNA-mediated activation of protein kinase R and integrated stress response. IMPORTANCE MeV is a pathogen that remains a global concern, with an estimated 9 million measles cases and 128,000 measles deaths in 2022 according to the World Health Organization. A large population of the world still has inadequate access to the effective vaccine against the exceptionally transmissible MeV. Measles disease is characterized by a high morbidity in children and in immunocompromised individuals. An important area of research for negative-sense RNA viruses, including MeV, is the characterization of the complex interactome between virus and host occurring at cytoplasmic IBs where viral replication occurs. Despite the progress made in understanding IB structures, little is known regarding the virus-host interactions within IBs and the role of these interactions in promoting viral replication and antagonizing host innate immunity. Herein we provide evidence suggesting a model by which MeV IBs utilize the host protein WDR5 to suppress the protein kinase R-integrated stress response pathway.
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Affiliation(s)
- Ethan BenDavid
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Chuyuan Yang
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Yuqin Zhou
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Christian K Pfaller
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
| | - Dzwokai Ma
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
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Bortoletto E, Rosani U, Sakaguchi A, Yoon J, Nagasawa K, Venier P. Insights into ADAR gene complement, expression patterns, and RNA editing landscape in Chlamys farreri. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109743. [PMID: 38964433 DOI: 10.1016/j.fsi.2024.109743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Adenosine Deaminases Acting on RNA (ADARs) are evolutionarily conserved enzymes known to convert adenosine to inosine in double-stranded RNAs and participate in host-virus interactions. Conducting a meta-analysis of available transcriptome data, we identified and characterised eight ADAR transcripts in Chlamys farreri, a farmed marine scallop susceptible to Acute viral necrosis virus (AVNV) infections and mortality outbreaks. Accordingly, we identified six ADAR genes in the Zhikong scallop genome, revised previous gene annotations, and traced alternative splicing variants. In detail, each ADAR gene encodes a unique combination of functional domains, always including the Adenosine deaminase domain, RNA binding domains and, in one case, two copies of a Z-DNA binding domain. After phylogenetic analysis, five C. farreri ADARs clustered in the ADAR1 clade along with sequences from diverse animal phyla. Gene expression analysis indicated CF051320 as the most expressed ADAR, especially in the eye and male gonad. The other four ADAR1 genes and one ADAR2 gene exhibited variable expression levels, with CF105370 and CF051320 significantly increasing during early scallop development. ADAR-mediated single-base editing, evaluated across adult C. farreri tissues and developmental stages, was mainly detectable in intergenic regions (83 % and 85 %, respectively). Overall, the expression patterns of the six ADAR genes together with the editing and hyper-editing values computed on scallops RNA-seq samples support the adaptive value of ADAR1-mediated editing, particularly in the pre-settling larval stages.
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Affiliation(s)
| | - Umberto Rosani
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Akari Sakaguchi
- Laboratory of Aquaculture Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-8572, Japan
| | - Jeongwoong Yoon
- Laboratory of Aquaculture Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-8572, Japan
| | - Kazue Nagasawa
- Laboratory of Aquaculture Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-8572, Japan
| | - Paola Venier
- Department of Biology, University of Padova, 35121, Padova, Italy.
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He Q, Liu C, Liu Q, Wang L, Song L. CgADAR1 involved in regulating the synthesis of interferon-like protein in Crassostrea gigas. FISH & SHELLFISH IMMUNOLOGY 2024; 150:109620. [PMID: 38740229 DOI: 10.1016/j.fsi.2024.109620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/24/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
Adenosine deaminases acting on RNA 1 (ADAR1) is a dsRNA adenosine (A)-to-inosine (I) editing enzyme that regulates the innate immune response against virus invasion. In the present study, a novel CgADAR1 was identified from the oyster Crassostrea gigas. The open reading frame (ORF) of CgADAR1 was of 3444 bp encoding a peptide of 1147 amino acid residues with two Zα domains, one dsRNA binding motif (DSRM) and one RNA adenosine deaminase domain (ADEAMc). The mRNA transcripts of CgADAR1 were detected in all the examined tissues, with higher expression levels in mantle and gill, which were 7.11-fold and 4.90-fold (p < 0.05) of that in labial palp, respectively. The mRNA transcripts of CgADAR1 in haemocytes were significantly induced at 24 h and 36 h after Poly (A: U) stimulation, which were 6.03-fold (p < 0.01) and 1.37-fold (p < 0.001) of that in control group, respectively. At 48 h after Poly (A:U) stimulation, the mRNA expression of CgRIG-Ⅰ, CgIRF8 and CgIFNLP significantly increased, which were 4.36-fold (p < 0.001), 1.82-fold (p < 0.05) and 1.92-fold (p < 0.05) of that in control group. After CgADAR1 expression was inhibited by RNA interference (RNAi), the mRNA expression levels of CgMDA5, CgRIG-Ⅰ, CgTBK1, CgIRF8 and CgIFNLP were significantly increased, which were 11.88-fold, 11.51-fold, 2.22-fold, 2.85-fold and 2.52-fold of that in control group (p < 0.001), and the phosphorylation level of CgTBK1 was also significantly increased. These results suggested that CgADAR1 played a regulation role in the early stages of viral infection by inhibiting the synthesis of interferon-like protein.
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Affiliation(s)
- Qianqian He
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Chang Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
| | - Qian Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China.
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Pisetsky DS, Herbert A. The role of DNA in the pathogenesis of SLE: DNA as a molecular chameleon. Ann Rheum Dis 2024; 83:830-837. [PMID: 38749573 PMCID: PMC11168871 DOI: 10.1136/ard-2023-225266] [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: 11/10/2023] [Accepted: 04/11/2024] [Indexed: 06/14/2024]
Abstract
Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease characterised by antibodies to DNA (anti-DNA) and other nuclear macromolecules. Anti-DNA antibodies are markers for classification and disease activity and promote pathogenesis by forming immune complexes that deposit in the tissue or stimulate cytokine production. Studies on the antibody response to DNA have focused primarily on a conformation of DNA known as B-DNA, the classic right-handed double helix. Among other conformations of DNA, Z-DNA is a left-handed helix with a zig-zag backbone; hence, the term Z-DNA. Z-DNA formation is favoured by certain base sequences, with the energetically unfavourable flip from B-DNA to Z-DNA dependent on conditions. Z-DNA differs from B-DNA in its immunogenicity in animal models. Furthermore, anti-Z-DNA antibodies, but not anti-B-DNA antibodies, can be present in otherwise healthy individuals. In SLE, antibodies to Z-DNA can occur in association with antibodies to B-DNA as a cross-reactive response, rising and falling together. While formed transiently in chromosomal DNA, Z-DNA is stably present in bacterial biofilms; biofilms can provide protection against antibiotics and other challenges including elements of host defence. The high GC content of certain bacterial DNA also favours Z-DNA formation as do DNA-binding proteins of bacterial or host origin. Together, these findings suggest that sources of Z-DNA can enhance the immunogenicity of DNA and, in SLE, stimulate the production of cross-reactive antibodies that bind both B-DNA and Z-DNA. As such, DNA can act as a molecular chameleon that, when stabilised in the Z-DNA conformation, can drive autoimmunity.
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Affiliation(s)
- David S Pisetsky
- Duke University Medical Center, Durham, North Carolina, USA
- Medical Research, Durham VA Health Care System, Durham, North Carolina, USA
| | - Alan Herbert
- InsideOutBio Inc, Charlestown, Massachusetts, USA
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Baquero-Pérez B, Bortoletto E, Rosani U, Delgado-Tejedor A, Medina R, Novoa EM, Venier P, Díez J. Elucidation of the Epitranscriptomic RNA Modification Landscape of Chikungunya Virus. Viruses 2024; 16:945. [PMID: 38932237 PMCID: PMC11209572 DOI: 10.3390/v16060945] [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: 05/02/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus to study the landscape of viral RNA modification in infected human cells. Among the 32 distinct RNA modifications analysed by mass spectrometry, inosine was found enriched in the genomic CHIKV RNA. However, orthogonal validation by Illumina RNA-seq analyses did not identify any inosine modification along the CHIKV RNA genome. Moreover, CHIKV infection did not alter the expression of ADAR1 isoforms, the enzymes that catalyse the adenosine to inosine conversion. Together, this study highlights the importance of a multidisciplinary approach to assess the presence of RNA modifications in viral RNA genomes.
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Affiliation(s)
- Belinda Baquero-Pérez
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Enrico Bortoletto
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; (E.B.); (U.R.)
| | - Umberto Rosani
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; (E.B.); (U.R.)
| | - Anna Delgado-Tejedor
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; (A.D.-T.); (R.M.); (E.M.N.)
| | - Rebeca Medina
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; (A.D.-T.); (R.M.); (E.M.N.)
| | - Eva Maria Novoa
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; (A.D.-T.); (R.M.); (E.M.N.)
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Paola Venier
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; (E.B.); (U.R.)
| | - Juana Díez
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
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Dorrity TJ, Shin H, Gertie JA, Chung H. The Sixth Sense: Self-nucleic acid sensing in the brain. Adv Immunol 2024; 161:53-83. [PMID: 38763702 PMCID: PMC11186578 DOI: 10.1016/bs.ai.2024.03.001] [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] [Indexed: 05/21/2024]
Abstract
Our innate immune system uses pattern recognition receptors (PRRs) as a first line of defense to detect microbial ligands and initiate an immune response. Viral nucleic acids are key ligands for the activation of many PRRs and the induction of downstream inflammatory and antiviral effects. Initially it was thought that endogenous (self) nucleic acids rarely activated these PRRs, however emerging evidence indicates that endogenous nucleic acids are able to activate host PRRs in homeostasis and disease. In fact, many regulatory mechanisms are in place to finely control and regulate sensing of self-nucleic acids by PRRs. Sensing of self-nucleic acids is particularly important in the brain, as perturbations to nucleic acid sensing commonly leads to neuropathology. This review will highlight the role of nucleic acid sensors in the brain, both in disease and homeostasis. We also indicate the source of endogenous stimulatory nucleic acids where known and summarize future directions for the study of this growing field.
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Key Words
- Brain
- DNA sensing PRRs: cGAS, AIM2, TLR9
- Neurodegeneration: Aicardi-Goutieres syndrome (AGS), Alzheimer's disease, Amyotrophic lateral sclerosis, Stroke, Traumatic brain injury
- Neurodevelopment
- Neuroinflammation
- Nuecleic acid immunity
- Pattern recognition receptors (PRRs)
- RNA sensing PRRs: MDA5, RIG-I, PKR, TLR3, TLR7/8
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Affiliation(s)
- Tyler J Dorrity
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, United States
| | - Heegwon Shin
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, United States
| | - Jake A Gertie
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, United States; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States; Medical Scientist Training Program, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Hachung Chung
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, United States.
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Ashley CN, Broni E, Miller WA. ADAR Family Proteins: A Structural Review. Curr Issues Mol Biol 2024; 46:3919-3945. [PMID: 38785511 PMCID: PMC11120146 DOI: 10.3390/cimb46050243] [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: 03/13/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
This review aims to highlight the structures of ADAR proteins that have been crucial in the discernment of their functions and are relevant to future therapeutic development. ADAR proteins can correct or diversify genetic information, underscoring their pivotal contribution to protein diversity and the sophistication of neuronal networks. ADAR proteins have numerous functions in RNA editing independent roles and through the mechanisms of A-I RNA editing that continue to be revealed. Provided is a detailed examination of the ADAR family members-ADAR1, ADAR2, and ADAR3-each characterized by distinct isoforms that offer both structural diversity and functional variability, significantly affecting RNA editing mechanisms and exhibiting tissue-specific regulatory patterns, highlighting their shared features, such as double-stranded RNA binding domains (dsRBD) and a catalytic deaminase domain (CDD). Moreover, it explores ADARs' extensive roles in immunity, RNA interference, and disease modulation, demonstrating their ambivalent nature in both the advancement and inhibition of diseases. Through this comprehensive analysis, the review seeks to underline the potential of targeting ADAR proteins in therapeutic strategies, urging continued investigation into their biological mechanisms and health implications.
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Affiliation(s)
- Carolyn N. Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA; (C.N.A.); (E.B.)
| | - Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA; (C.N.A.); (E.B.)
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA; (C.N.A.); (E.B.)
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
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Margvelani G, Welden JR, Maquera AA, Van Eyk JE, Murray C, Miranda Sardon SC, Stamm S. Influence of FTDP-17 mutants on circular tau RNAs. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167036. [PMID: 38286213 DOI: 10.1016/j.bbadis.2024.167036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/21/2023] [Accepted: 01/21/2024] [Indexed: 01/31/2024]
Abstract
At least 53 mutations in the microtubule associated protein tau gene (MAPT) have been identified that cause frontotemporal dementia. 47 of these mutations are localized between exons 7 and 13. They could thus affect the formation of circular RNAs (circRNAs) from the MAPT gene that occurs through backsplicing from exon 12 to either exon 10 or exon 7. We analyzed representative mutants and found that five FTDP-17 mutations increase the formation of 12➔7 circRNA and three different mutations increase the amount of 12➔10 circRNA. CircRNAs are translated after undergoing adenosine to inosine RNA editing, catalyzed by ADAR enzymes. We found that the interferon induced ADAR1-p150 isoform has the strongest effect on circTau RNA translation. ADAR1-p150 activity had a stronger effect on circTau RNA expression and strongly decreased 12➔7 circRNA, but unexpectedly increased 12➔10 circRNA. In both cases, ADAR-activity strongly promoted translation of circTau RNAs. Unexpectedly, we found that the 12➔7 circTau protein interacts with eukaryotic initiation factor 4B (eIF4B), which is reduced by four FTDP-17 mutations located in the second microtubule domain. These are the first studies of the effect of human mutations on circular RNA formation and translation. They show that point mutations influence circRNA expression levels, likely through changes in pre-mRNA structures. The effect of the mutations is surpassed by editing of the circular RNAs, leading to their translation. Thus, circular RNAs and their editing status should be considered when analyzing FTDP-17 mutations.
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Affiliation(s)
- Giorgi Margvelani
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Justin R Welden
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA; Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Andrea Arizaca Maquera
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | | | | | - Sandra C Miranda Sardon
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.
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de Reuver R, Maelfait J. Novel insights into double-stranded RNA-mediated immunopathology. Nat Rev Immunol 2024; 24:235-249. [PMID: 37752355 DOI: 10.1038/s41577-023-00940-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2023] [Indexed: 09/28/2023]
Abstract
Recent progress in human and mouse genetics has transformed our understanding of the molecular mechanisms by which recognition of self double-stranded RNA (self-dsRNA) causes immunopathology. Novel mouse models recapitulate loss-of-function mutations in the RNA editing enzyme ADAR1 that are found in patients with Aicardi-Goutières syndrome (AGS) - a monogenic inflammatory disease associated with increased levels of type I interferon. Extensive analyses of the genotype-phenotype relationships in these mice have now firmly established a causal relationship between increased intracellular concentrations of endogenous immunostimulatory dsRNA and type I interferon-driven immunopathology. Activation of the dsRNA-specific immune sensor MDA5 perpetuates the overproduction of type I interferons, and chronic engagement of the interferon-inducible innate immune receptors PKR and ZBP1 by dsRNA drives immunopathology by activating an integrated stress response or by inducing excessive cell death. Biochemical and genetic data support a role for the p150 isoform of ADAR1 in the cytosol in suppressing the spontaneous, pathological response to self-dsRNA.
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Affiliation(s)
- Richard de Reuver
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jonathan Maelfait
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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12
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Wang Z, Zhang D, Qiu X, Inuzuka H, Xiong Y, Liu J, Chen L, Chen H, Xie L, Kaniskan HÜ, Chen X, Jin J, Wei W. Structurally Specific Z-DNA Proteolysis Targeting Chimera Enables Targeted Degradation of Adenosine Deaminase Acting on RNA 1. J Am Chem Soc 2024; 146:7584-7593. [PMID: 38469801 PMCID: PMC10988290 DOI: 10.1021/jacs.3c13646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Given the prevalent advancements in DNA- and RNA-based PROTACs, there remains a significant need for the exploration and expansion of more specific DNA-based tools, thus broadening the scope and repertoire of DNA-based PROTACs. Unlike conventional A- or B-form DNA, Z-form DNA is a configuration that exclusively manifests itself under specific stress conditions and with specific target sequences, which can be recognized by specific reader proteins, such as ADAR1 or ZBP1, to exert downstream biological functions. The core of our innovation lies in the strategic engagement of Z-form DNA with ADAR1 and its degradation is achieved by leveraging a VHL ligand conjugated to Z-form DNA to recruit the E3 ligase. This ingenious construct engendered a series of Z-PROTACs, which we utilized to selectively degrade the Z-DNA-binding protein ADAR1, a molecule that is frequently overexpressed in cancer cells. This meticulously orchestrated approach triggers a cascade of PANoptotic events, notably encompassing apoptosis and necroptosis, by mitigating the blocking effect of ADAR1 on ZBP1, particularly in cancer cells compared with normal cells. Moreover, the Z-PROTAC design exhibits a pronounced predilection for ADAR1, as opposed to other Z-DNA readers, such as ZBP1. As such, Z-PROTAC likely elicits a positive immunological response, subsequently leading to a synergistic augmentation of cancer cell death. In summary, the Z-DNA-based PROTAC (Z-PROTAC) approach introduces a modality generated by the conformational change from B- to Z-form DNA, which harnesses the structural specificity intrinsic to potentiate a selective degradation strategy. This methodology is an inspiring conduit for the advancement of PROTAC-based therapeutic modalities, underscoring its potential for selectivity within the therapeutic landscape of PROTACs to target undruggable proteins.
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Affiliation(s)
- Zhen Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Dingpeng Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Xing Qiu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Li Chen
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - He Chen
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Ling Xie
- Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 United States
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xian Chen
- Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
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13
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Hong X, Wei Z, He L, Bu Q, Wu G, Chen G, He W, Deng Q, Huang S, Huang Y, Yu C, Luo X, Lin Y. High-throughput virtual screening to identify potential small molecule inhibitors of the Zα domain of the adenosine deaminases acting on RNA 1(ADAR1). Eur J Pharm Sci 2024; 193:106672. [PMID: 38103658 DOI: 10.1016/j.ejps.2023.106672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Changes in RNA editing are closely associated with diseases such as cancer, viral infections, and autoimmune disorders. Adenosine deaminase (ADAR1), which acts on RNA 1, plays a key role in adenosine to inosine editing and is a potential therapeutic target for these various diseases. The p150 subtype of ADAR1 is the only one that contains a Zα domain that binds to both Z-DNA and Z-RNA. The Zα domain modulates immune responses and may be suitable targets for antiviral therapy and cancer immunotherapy. In this study, we attempted to utilize molecular docking to identify potential inhibitors that bind to the ADAR1 Zα domain. The virtual docking method screened the potential activity of more than 100,000 compounds on the Zα domain of ADAR1 and filtered to obtain the highest scoring results.We identified 71 compounds promising to bind to ADAR1 and confirmed that two of them, lithospermic acid and Regaloside B, interacts with the ADAR1 Zα domain by surface plasmonic resonance technique. The molecular dynamics calculation of the complex of lithospermic acid and ADAR1 also showed that the binding effect of lithospermic acid to ADAR1 was stable.This study provides a new perspective for the search of ADAR1 inhibitors, and further studies on the anti-ADAR11 activity of these compounds have broad prospects.
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Affiliation(s)
- Xiaoshan Hong
- Department of gynecology, Guangdong Women and Children Medical Hospital, Guangzhou 511400, China
| | - Zhifu Wei
- Department of gynecology, The Affiliated Shunde Hospital of Jinan University, Foshan 528300, China
| | - Lulu He
- Department of gynecology, Guangdong Women and Children Medical Hospital, Guangzhou 511400, China
| | - Qiaowen Bu
- Department of gynecology, Guangdong Women and Children Medical Hospital, Guangzhou 511400, China
| | - Guosong Wu
- Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou 510006, China
| | - Guanqiao Chen
- Department of gynecology, Guangdong Women and Children Medical Hospital, Guangzhou 511400, China
| | - Wanshan He
- Department of gynecology, Guangdong Women and Children Medical Hospital, Guangzhou 511400, China
| | - Qiuhua Deng
- Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou 510006, China
| | - Shiqi Huang
- Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou 510006, China
| | - Yongmei Huang
- Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou 510006, China.
| | - Cai Yu
- College of Pharmacy, Jinan University, Guangzhou 511436, China.
| | - Xiping Luo
- Department of gynecology, Guangdong Women and Children Medical Hospital, Guangzhou 511400, China.
| | - Yu Lin
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510006, China; Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou 510006, China.
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14
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Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
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Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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15
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Nassour J, Przetocka S, Karlseder J. Telomeres as hotspots for innate immunity and inflammation. DNA Repair (Amst) 2024; 133:103591. [PMID: 37951043 PMCID: PMC10842095 DOI: 10.1016/j.dnarep.2023.103591] [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: 07/24/2023] [Revised: 10/05/2023] [Accepted: 10/24/2023] [Indexed: 11/13/2023]
Abstract
Aging is marked by the gradual accumulation of deleterious changes that disrupt organ function, creating an altered physiological state that is permissive for the onset of prevalent human diseases. While the exact mechanisms governing aging remain a subject of ongoing research, there are several cellular and molecular hallmarks that contribute to this biological process. This review focuses on two factors, namely telomere dysfunction and inflammation, which have emerged as crucial contributors to the aging process. We aim to discuss the mechanistic connections between these two distinct hallmarks and provide compelling evidence highlighting the loss of telomere protection as a driver of pro-inflammatory states associated with aging. By reevaluating the interplay between telomeres, innate immunity, and inflammation, we present novel perspectives on the etiology of aging and its associated diseases.
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Affiliation(s)
- Joe Nassour
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, 12801 E. 17th Ave, Aurora, CO 80045, USA; The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Sara Przetocka
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Jan Karlseder
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA.
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16
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Wang L, Zhu Y, Zhang L, Guo L, Wang X, Pan Z, Jiang X, Wu F, He G. Mechanisms of PANoptosis and relevant small-molecule compounds for fighting diseases. Cell Death Dis 2023; 14:851. [PMID: 38129399 PMCID: PMC10739961 DOI: 10.1038/s41419-023-06370-2] [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: 07/04/2023] [Revised: 11/10/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Pyroptosis, apoptosis, and necroptosis are mainly programmed cell death (PCD) pathways for host defense and homeostasis. PANoptosis is a newly distinct inflammatory PCD pathway that is uniquely regulated by multifaceted PANoptosome complexes and highlights significant crosstalk and coordination among pyroptosis (P), apoptosis (A), and/or necroptosis(N). Although some studies have focused on the possible role of PANpoptosis in diseases, the pathogenesis of PANoptosis is complex and underestimated. Furthermore, the progress of PANoptosis and related agonists or inhibitors in disorders has not yet been thoroughly discussed. In this perspective, we provide perspectives on PANoptosome and PANoptosis in the context of diverse pathological conditions and human diseases. The treatment targeting on PANoptosis is also summarized. In conclusion, PANoptosis is involved in plenty of disorders including but not limited to microbial infections, cancers, acute lung injury/acute respiratory distress syndrome (ALI/ARDS), ischemia-reperfusion, and organic failure. PANoptosis seems to be a double-edged sword in diverse conditions, as PANoptosis induces a negative impact on treatment and prognosis in disorders like COVID-19 and ALI/ARDS, while PANoptosis provides host protection from HSV1 or Francisella novicida infection, and kills cancer cells and suppresses tumor growth in colorectal cancer, adrenocortical carcinoma, and other cancers. Compounds and endogenous molecules focused on PANoptosis are promising therapeutic strategies, which can act on PANoptosomes-associated members to regulate PANoptosis. More researches on PANoptosis are needed to better understand the pathology of human conditions and develop better treatment.
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Affiliation(s)
- Lian Wang
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Yanghui Zhu
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Lu Zhang
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Linghong Guo
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Xiaoyun Wang
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Zhaoping Pan
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Xian Jiang
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China.
| | - Fengbo Wu
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China.
| | - Gu He
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China.
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.
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17
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Zambrano-Mila MS, Witzenberger M, Rosenwasser Z, Uzonyi A, Nir R, Ben-Aroya S, Levanon EY, Schwartz S. Dissecting the basis for differential substrate specificity of ADAR1 and ADAR2. Nat Commun 2023; 14:8212. [PMID: 38081817 PMCID: PMC10713624 DOI: 10.1038/s41467-023-43633-0] [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: 02/08/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Millions of adenosines are deaminated throughout the transcriptome by ADAR1 and/or ADAR2 at varying levels, raising the question of what are the determinants guiding substrate specificity and how these differ between the two enzymes. We monitor how secondary structure modulates ADAR2 vs ADAR1 substrate selectivity, on the basis of systematic probing of thousands of synthetic sequences transfected into cell lines expressing exclusively ADAR1 or ADAR2. Both enzymes induce symmetric, strand-specific editing, yet with distinct offsets with respect to structural disruptions: -26 nt for ADAR2 and -35 nt for ADAR1. We unravel the basis for these differences in offsets through mutants, domain-swaps, and ADAR homologs, and find it to be encoded by the differential RNA binding domain (RBD) architecture. Finally, we demonstrate that this offset-enhanced editing can allow an improved design of ADAR2-recruiting therapeutics, with proof-of-concept experiments demonstrating increased on-target and potentially decreased off-target editing.
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Affiliation(s)
- Marlon S Zambrano-Mila
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Monika Witzenberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Zohar Rosenwasser
- Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Anna Uzonyi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Shay Ben-Aroya
- Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Erez Y Levanon
- Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel.
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18
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Song J, Liu Y, Yin Y, Wang H, Zhang X, Li Y, Zhao X, Zhang G, Meng X, Jin Y, Lu D, Yin Y. PTIR1 acts as an isoform of DDX58 and promotes tumor immune resistance through activation of UCHL5. Cell Rep 2023; 42:113388. [PMID: 37934668 DOI: 10.1016/j.celrep.2023.113388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 09/22/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023] Open
Abstract
Cancer evades host immune surveillance by virtue of poor immunogenicity. Here, we report an immune suppressor, designated as PTIR1, that acts as a promotor of tumor immune resistance. PTIR1 is selectively induced in human cancers via alternative splicing of DDX58 (RIG-I), and its induction is closely related to poor outcome in patients with cancer. Through blocking the recruitment of leukocytes, PTIR1 facilitates cancer immune escape and tumor-intrinsic resistance to immunotherapeutic treatments. Unlike RIG-I, PTIR1 is capable of binding to the C terminus of UCHL5 and activates its ubiquitinating function, which in turn inhibits immunoproteasome activity and limits neoantigen processing and presentation, consequently blocking T cell recognition and attack against cancer. Moreover, we find that the adenosine deaminase ADAR1 induces A-to-I RNA editing on DDX58 transcript, thus triggering PTIR1 production. Collectively, our data uncover the immunosuppressive role of PTIR1 in tumorigenesis and propose that ADAR1-PTIR1-UCHL5 signaling is a potential cancer immunotherapeutic target.
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Affiliation(s)
- Jia Song
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Yang Liu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Yue Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Hui Wang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Xin Zhang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Yang Li
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Xuyang Zhao
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Guangze Zhang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Xiangyan Meng
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Yan Jin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Dan Lu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China.
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China; Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen 518036, P.R. China.
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19
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Wales-McGrath B, Mercer H, Piontkivska H. Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections. BMC Genomics 2023; 24:685. [PMID: 37968596 PMCID: PMC10652522 DOI: 10.1186/s12864-023-09778-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND RNA editing is a process that increases transcriptome diversity, often through Adenosine Deaminases Acting on RNA (ADARs) that catalyze the deamination of adenosine to inosine. ADAR editing plays an important role in regulating brain function and immune activation, and is dynamically regulated during brain development. Additionally, the ADAR1 p150 isoform is induced by interferons in viral infection and plays a role in antiviral immune response. However, the question of how virus-induced ADAR expression affects host transcriptome editing remains largely unanswered. This question is particularly relevant in the context of congenital infections, given the dynamic regulation of ADAR editing during brain development, the importance of this editing for brain function, and subsequent neurological symptoms of such infections, including microcephaly, sensory issues, and other neurodevelopmental abnormalities. Here, we begin to address this question, examining ADAR expression in publicly available datasets of congenital infections of human cytomegalovirus (HCMV) microarray expression data, as well as mouse cytomegalovirus (MCMV) and mouse/ human induced pluripotent neuroprogenitor stem cell (hiNPC) Zika virus (ZIKV) RNA-seq data. RESULTS We found that in all three datasets, ADAR1 was overexpressed in infected samples compared to uninfected samples. In the RNA-seq datasets, editing rates were also analyzed. In all mouse infections cases, the number of editing sites was significantly increased in infected samples, albeit this was not the case for hiNPC ZIKV samples. Mouse ZIKV samples showed altered editing of well-established protein-recoding sites such as Gria3, Grik5, and Nova1, as well as editing sites that may impact miRNA binding. CONCLUSIONS Our findings provide evidence for changes in ADAR expression and subsequent dysregulation of ADAR editing of host transcriptomes in congenital infections. These changes in editing patterns of key neural genes have potential significance in the development of neurological symptoms, thus contributing to neurodevelopmental abnormalities. Further experiments should be performed to explore the full range of editing changes that occur in different congenital infections, and to confirm the specific functional consequences of these editing changes.
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Affiliation(s)
- Benjamin Wales-McGrath
- University of Pennsylvania, Perelman School of Medicine, Department of Genetics, Philadelphia, PA, USA
- Children's Hospital of Philadelphia, Division of Cancer Pathobiology, Philadelphia, PA, USA
| | - Heather Mercer
- Department of Biological and Environmental Sciences, University of Mount Union, Alliance, OH, USA
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH, USA.
- School of Biomedical Sciences, Kent State University, Kent, OH, USA.
- Brain Health Research Institute, Kent State University, Kent, OH, USA.
- Healthy Communities Research Institute, Kent State University, Kent, OH, USA.
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20
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Kong LZ, Kim SM, Wang C, Lee SY, Oh SC, Lee S, Jo S, Kim TD. Understanding nucleic acid sensing and its therapeutic applications. Exp Mol Med 2023; 55:2320-2331. [PMID: 37945923 PMCID: PMC10689850 DOI: 10.1038/s12276-023-01118-6] [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: 06/29/2023] [Revised: 08/16/2023] [Accepted: 08/20/2023] [Indexed: 11/12/2023] Open
Abstract
Nucleic acid sensing is involved in viral infections, immune response-related diseases, and therapeutics. Based on the composition of nucleic acids, nucleic acid sensors are defined as DNA or RNA sensors. Pathogen-associated nucleic acids are recognized by membrane-bound and intracellular receptors, known as pattern recognition receptors (PRRs), which induce innate immune-mediated antiviral responses. PRR activation is tightly regulated to eliminate infections and prevent abnormal or excessive immune responses. Nucleic acid sensing is an essential mechanism in tumor immunotherapy and gene therapies that target cancer and infectious diseases through genetically engineered immune cells or therapeutic nucleic acids. Nucleic acid sensing supports immune cells in priming desirable immune responses during tumor treatment. Recent studies have shown that nucleic acid sensing affects the efficiency of gene therapy by inhibiting translation. Suppression of innate immunity induced by nucleic acid sensing through small-molecule inhibitors, virus-derived proteins, and chemical modifications offers a potential therapeutic strategy. Herein, we review the mechanisms and regulation of nucleic acid sensing, specifically covering recent advances. Furthermore, we summarize and discuss recent research progress regarding the different effects of nucleic acid sensing on therapeutic efficacy. This study provides insights for the application of nucleic acid sensing in therapy.
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Affiliation(s)
- Ling-Zu Kong
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Seok-Min Kim
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Chunli Wang
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Soo Yun Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Se-Chan Oh
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Sunyoung Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Life Sciences, Korea University, Seoul, 02841, Korea
| | - Seona Jo
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Tae-Don Kim
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Korea.
- Biomedical Mathematics Group, Institute for Basic Science (IBS), Daejeon, Republic of Korea.
- Department of Biopharmaceutical Convergence, School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea.
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21
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Shibata C, Otsuka M, Shimizu T, Seimiya T, Kishikawa T, Aoki T, Fujishiro M. Extracellular vesicle‑mediated RNA editing may underlie the heterogeneity and spread of hepatocellular carcinoma in human tissue and in vitro. Oncol Rep 2023; 50:194. [PMID: 37732519 PMCID: PMC10539718 DOI: 10.3892/or.2023.8631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/01/2023] [Indexed: 09/22/2023] Open
Abstract
Extracellular vesicles (EVs) produced by various cells, including tumor cells, carry biomolecules to neighboring cells. In hepatocellular carcinoma (HCC), adenosine to inosine RNA editing of antizyme inhibitor 1 (AZIN1), specifically regulated by adenosine deaminase acting on RNA‑1 (ADAR1), promotes carcinogenesis. The present study examined if EVs and ADAR1 in the EVs released from HCC cells are transferred to neighboring cells in co‑culture systems and reporter assay. Distribution of the ADAR1 expression in human tissues were examined by immunohistochemistry. EVs released from HCC cells containing ADAR1 were delivered to neighboring HCC cells and non‑cancerous hepatocytes. The increased ADAR1 protein levels resulted in serine to glycine substitution at residue 367 of AZIN1, which augmented transformation potential and increased aggressive behavior of cancer cells. In clinically resected samples, ADAR1 distribution was highly heterogeneous within the tumor specimen and denser in non‑cancerous tissue surrounding the HCC tissue. These observations suggested that ADAR1 protein may be delivered from HCC cells to neighboring cells via EVs and that EV‑mediated RNA editing may serve a pivotal role in determining HCC heterogeneity and spread.
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Affiliation(s)
- Chikako Shibata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
- Research Fellow of Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Motoyuki Otsuka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Density and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Takayuki Shimizu
- Department of Hepatobiliary and Pancreatic Surgery, Dokkyo Medical University, Tochigi 321-0293, Japan
| | - Takahiro Seimiya
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Takahiro Kishikawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Taku Aoki
- Department of Hepatobiliary and Pancreatic Surgery, Dokkyo Medical University, Tochigi 321-0293, Japan
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
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22
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McEntee CM, Cavalier AN, LaRocca TJ. ADAR1 suppression causes interferon signaling and transposable element transcript accumulation in human astrocytes. Front Mol Neurosci 2023; 16:1263369. [PMID: 38035265 PMCID: PMC10685929 DOI: 10.3389/fnmol.2023.1263369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/25/2023] [Indexed: 12/02/2023] Open
Abstract
Neuroinflammation is a central mechanism of brain aging and Alzheimer's disease (AD), but the exact causes of age- and AD-related neuroinflammation are incompletely understood. One potential modulator of neuroinflammation is the enzyme adenosine deaminase acting on RNA 1 (ADAR1), which regulates the accumulation of endogenous double-stranded RNA (dsRNA), a pro-inflammatory/innate immune activator. However, the role of ADAR1 and its transcriptomic targets in astrocytes, key mediators of neuroinflammation, have not been comprehensively investigated. Here, we knock down ADAR1 in primary human astrocytes via siRNA transfection and use transcriptomics (RNA-seq) to show that this results in: (1) increased expression of type I interferon and pro-inflammatory signaling pathways and (2) an accumulation of transposable element (TE) transcripts with the potential to form dsRNA. We also show that our findings may be clinically relevant, as ADAR1 gene expression declines with brain aging and AD in humans, and this is associated with a similar increase in TE transcripts. Together, our results suggest an important role for ADAR1 in preventing pro-inflammatory activation of astrocytes in response to endogenous dsRNA with aging and AD.
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Affiliation(s)
- Cali M. McEntee
- Department of Health and Exercise Science, Colorado State University, Fort Collins, CO, United States
- Center for Healthy Aging, Colorado State University, Fort Collins, CO, United States
| | - Alyssa N. Cavalier
- Department of Health and Exercise Science, Colorado State University, Fort Collins, CO, United States
- Center for Healthy Aging, Colorado State University, Fort Collins, CO, United States
| | - Thomas J. LaRocca
- Department of Health and Exercise Science, Colorado State University, Fort Collins, CO, United States
- Center for Healthy Aging, Colorado State University, Fort Collins, CO, United States
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23
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Zhu L, Li B, Li R, Hu L, Zhang Y, Zhang Z, Jiang S, Zhang X. METTL3 suppresses pancreatic ductal adenocarcinoma progression through activating endogenous dsRNA-induced anti-tumor immunity. Cell Oncol (Dordr) 2023; 46:1529-1541. [PMID: 37178367 DOI: 10.1007/s13402-023-00829-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2023] [Indexed: 05/15/2023] Open
Abstract
PURPOSE Although immunotherapy improves clinical outcomes in several types of malignancies, as an immunologically 'cold' tumor, pancreatic ductal adenocarcinoma (PDAC) is arrantly resistant to immunotherapy. However, the role of N6-methyladenosine (m6A) modification in the immune microenvironment of PDAC is still poorly understood. METHODS The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets were used to identify differentially expressed m6A related enzymes. The biological role and mechanism of METTL3 in PDAC growth and metastasis were determined in vitro and in vivo. RNA-sequencing and bioinformatics analysis were used to identify signaling pathways involved in METTL3. Western blot, m6A dot blot assays, co-immunoprecipitation, immunofluorescence, and flow cytometry were used to explore the molecular mechanism. RESULTS Here, we demonstrate that METTL3, the key regulator of m6A modification, is downregulated in PDAC, and negatively correlates with PDAC malignant features. Elevated METTL3 suppresses PDAC growth and overcomes resistance to immune checkpoint blockade. Mechanistically, METTL3 promotes the accumulation of endogenous double-stranded RNA (dsRNA) through protecting m6A-transcripts from further Adenosine-to-inosine (A-to-I) editing. The dsRNA stress activates RIG-I-like receptors (RLRs) to enhance anti-tumor immunity, finally suppressing PDAC progression. CONCLUSION Our findings indicate that tumor cell-intrinsic m6A modification participates in the regulation of tumor immune landscape. Adjusting the m6A level may be an effective strategy to overcome the resistance to immunotherapy and increase responsiveness to immunotherapy in PDAC.
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Affiliation(s)
- Lili Zhu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Immune Therapy Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Botai Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Immune Therapy Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rongkun Li
- Institute of Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lipeng Hu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanli Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhigang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuheng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Xueli Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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24
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Ivanišević V, Žilić L, Čunko M, Fadiga H, Munitić I, Jurak I. RNA Editing-Dependent and -Independent Roles of Adenosine Deaminases Acting on RNA Proteins in Herpesvirus Infection-Hints on Another Layer of Complexity. Viruses 2023; 15:2007. [PMID: 37896783 PMCID: PMC10611208 DOI: 10.3390/v15102007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
The Adenosine Deaminases Acting on RNA (ADAR) catalyze the posttranscriptional deamination of adenosine residues to inosine in double-stranded RNAs (dsRNAs, A-to-I editing), preventing the overactivation of dsRNA sensor molecules and interferons. RNA editing is the cornerstone of innate immunity that distinguishes between self and non-self (virus), and it is essential for normal regulation of cellular homeostasis. Although much is already known about the role of ADAR proteins in RNA virus infection, the role of ADAR proteins in herpesvirus infection remains largely unexplored. In this review, we provide several lines of evidence from studies of different herpesviruses for another level of complexity in regulating the already intricate biphasic life cycle of herpesviruses.
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Affiliation(s)
| | | | | | | | | | - Igor Jurak
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia (L.Ž.)
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25
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Du JQ, Zhang F, Wang CQ, Zhu JF, Xu LX, Yang YH, Han MF, Hu Y. Effects of peripheral blood neutrophil/lymphocyte ratio levels and their changes on the prognosis of patients with early cervical cancer. Front Oncol 2023; 13:1139809. [PMID: 37829340 PMCID: PMC10565220 DOI: 10.3389/fonc.2023.1139809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/13/2023] [Indexed: 10/14/2023] Open
Abstract
Although some studies have reported on the levels and clinical significance of peripheral blood neutrophil/lymphocyte ratio (NLR) in cervical cancer, the role of NLR levels and their changes preoperatively and postoperatively in early cervical cancer remain unclear. Our analyses explored the preoperative and postoperative NLR in 203 patients with stage I-IIA cervical cancer and evaluated the relationship between NLR changes, clinicopathological characteristics, and patient prognosis. The cut-off preoperative and postoperative NLR values were determined using receiver operating characteristic curve analysis. Preoperative NLR correlated with age, menopausal status, tumor size, and vascular infiltration, whereas postoperative NLR correlated with tumor differentiation. Patients with cervical cancer with a high preoperative NLR had significantly shorter overall survival (OS) and progression-free survival (PFS) than other patients, whereas PFS was significantly lower in the high postoperative NLR group. When comparing postoperative and preoperative NLR values, we observed a significantly higher rate of increase in postmenopausal patients and those without vascular infiltration than that among premenopausal patients and those with vascular infiltration. However, no clear difference in prognosis was observed between the groups with increased and decreased NLR. Therefore, a high peripheral blood NLR may predict a poor prognosis in patients with early cervical cancer. The effect of NLR changes on the prognosis of patients with cervical cancer requires further verification in multicenter studies.
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Affiliation(s)
- Jun-Qiang Du
- Department of Gynecology, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Fan Zhang
- Department of Gynecology, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Chao-Qun Wang
- Department of Pathology, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Ju-Fan Zhu
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Li-Xia Xu
- Department of Gynecology, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Yi-Heng Yang
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Meng-Fei Han
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yan Hu
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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26
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Margvelani G, Welden JR, Maquera AA, Van Eyk JE, Murray C, Miranda Sardon SC, Stamm S. Influence of FTDP-17 mutants on circular Tau RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.08.556913. [PMID: 37786725 PMCID: PMC10541600 DOI: 10.1101/2023.09.08.556913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
At least 53 mutations in the microtubule associated protein tau gene (MAPT) have been identified that cause frontotemporal dementia. 47 of these mutations are localized between exons 7 and 13. They could thus affect the formation of circular RNAs (circRNAs) from the MAPT gene that occur through backsplicing from exon 12 to either exon 10 or exon 7. We analyzed representative mutants and found that five FTDP-17 mutations increase the formation of 12➔7 circRNA and three different mutations increase the amount of 12➔10 circRNA. CircRNAs are translated after undergoing adenosine to inosine RNA editing, catalyzed by ADAR enzymes. We found that the interferon induced ADAR1-p150 isoform has the strongest effect on circTau RNA translation. ADAR1-p150 activity had a stronger effect on circTau RNA expression and strongly decreased 12➔7 circRNA, but unexpectedly increased 12➔10 circRNA. In both cases, ADAR-activity strongly promoted translation of circTau RNAs. Unexpectedly, we found that the 12➔7 circTau protein interacts with eukaryotic initiation factor 4B (eIF4B), which is reduced by four FTDP-17 mutations located in the second microtubule domain. These are the first studies of the effect of human mutations on circular RNA formation and translation. They show that point mutations influence circRNA expression levels, likely through changes in the secondary pre-mRNA structures. The effect of the mutations is surpassed by editing of the circular RNAs, leading to their translation. Thus, circular RNAs and their editing status should be considered when analyzing FTDP-17 mutations. Highlights 47/53 known FTDP-17 mutations are located in regions that could influence generation of circular RNAs from the MAPT geneCircular Tau RNAs are translated after adenosine to inosine RNA editing, most effectively caused by ADAR1-p150FTDP-17 mutations influence both circTau RNA and circTau protein expression levelsCircTau protein expression levels do not correlate with circTau RNA expression levelsCircTau proteins bind to eukaryotic initiation factor 4B, which is antagonized by FTDP-17 mutations in exon 10. Graphic Abstract
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27
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Datta R, Adamska JZ, Bhate A, Li JB. A-to-I RNA editing by ADAR and its therapeutic applications: From viral infections to cancer immunotherapy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1817. [PMID: 37718249 PMCID: PMC10947335 DOI: 10.1002/wrna.1817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
ADAR deaminases catalyze adenosine-to-inosine (A-to-I) editing on double-stranded RNA (dsRNA) substrates that regulate an umbrella of biological processes. One of the two catalytically active ADAR enzymes, ADAR1, plays a major role in innate immune responses by suppression of RNA sensing pathways which are orchestrated through the ADAR1-dsRNA-MDA5 axis. Unedited immunogenic dsRNA substrates are potent ligands for the cellular sensor MDA5. Upon activation, MDA5 leads to the induction of interferons and expression of hundreds of interferon-stimulated genes with potent antiviral activity. In this way, ADAR1 acts as a gatekeeper of the RNA sensing pathway by striking a fine balance between innate antiviral responses and prevention of autoimmunity. Reduced editing of immunogenic dsRNA by ADAR1 is strongly linked to the development of common autoimmune and inflammatory diseases. In viral infections, ADAR1 exhibits both antiviral and proviral effects. This is modulated by both editing-dependent and editing-independent functions, such as PKR antagonism. Several A-to-I RNA editing events have been identified in viruses, including in the insidious viral pathogen, SARS-CoV-2 which regulates viral fitness and infectivity, and could play a role in shaping viral evolution. Furthermore, ADAR1 is an attractive target for immuno-oncology therapy. Overexpression of ADAR1 and increased dsRNA editing have been observed in several human cancers. Silencing ADAR1, especially in cancers that are refractory to immune checkpoint inhibitors, is a promising therapeutic strategy for cancer immunotherapy in conjunction with epigenetic therapy. The mechanistic understanding of dsRNA editing by ADAR1 and dsRNA sensing by MDA5 and PKR holds great potential for therapeutic applications. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Rohini Datta
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julia Z Adamska
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Amruta Bhate
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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28
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Liang Z, Goradia A, Walkley CR, Heraud-Farlow JE. Generation of a new Adar1p150 -/- mouse demonstrates isoform-specific roles in embryonic development and adult homeostasis. RNA (NEW YORK, N.Y.) 2023; 29:1325-1338. [PMID: 37290963 PMCID: PMC10573302 DOI: 10.1261/rna.079509.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/09/2023] [Indexed: 06/10/2023]
Abstract
The RNA editing enzyme adenosine deaminase acting on RNA 1 (ADAR1) is an essential regulator of the innate immune response to both cellular and viral double-stranded RNA (dsRNA). Adenosine-to-inosine (A-to-I) editing by ADAR1 modifies the sequence and structure of endogenous dsRNA and masks it from the cytoplasmic dsRNA sensor melanoma differentiation-associated protein 5 (MDA5), preventing innate immune activation. Loss-of-function mutations in ADAR are associated with rare autoinflammatory disorders including Aicardi-Goutières syndrome (AGS), defined by a constitutive systemic up-regulation of type I interferon (IFN). The murine Adar gene encodes two protein isoforms with distinct functions: ADAR1p110 is constitutively expressed and localizes to the nucleus, whereas ADAR1p150 is primarily cytoplasmic and is inducible by IFN. Recent studies have demonstrated the critical requirement for ADAR1p150 to suppress innate immune activation by self dsRNAs. However, detailed in vivo characterization of the role of ADAR1p150 during development and in adult mice is lacking. We identified a new ADAR1p150-specific knockout mouse mutant based on a single nucleotide deletion that resulted in the loss of the ADAR1p150 protein without affecting ADAR1p110 expression. The Adar1p150 -/- died embryonically at E11.5-E12.5 accompanied by cell death in the fetal liver and an activated IFN response. Somatic loss of ADAR1p150 in adults was lethal and caused rapid hematopoietic failure, demonstrating an ongoing requirement for ADAR1p150 in vivo. The generation and characterization of this mouse model demonstrates the essential role of ADAR1p150 in vivo and provides a new tool for dissecting the functional differences between ADAR1 isoforms and their physiological contributions.
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Affiliation(s)
- Zhen Liang
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Ankita Goradia
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Jacki E Heraud-Farlow
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
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29
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Garland KM, Kwiatkowski AJ, Tossberg JT, Crooke PS, Aune TM, Wilson JT. Nanoparticle Delivery of Immunostimulatory Alu RNA for Cancer Immunotherapy. CANCER RESEARCH COMMUNICATIONS 2023; 3:1800-1809. [PMID: 37691856 PMCID: PMC10487107 DOI: 10.1158/2767-9764.crc-22-0354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 06/28/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
It was recently found that patients with relapsing remitting multiple sclerosis exhibit widespread loss of adenosine-to-inosine (A-to-I) RNA editing, which contributes to the accumulation of immunostimulatory double-stranded Alu RNA in circulating leukocytes and an attendant increase in levels of proinflammatory cytokines (e.g., type I IFNs). A specific Alu RNA (i.e., AluJb RNA) was implicated in activating multiple RNA-sensing pathways and found to be a potent innate immune agonist. Here, we have performed a bioinformatic analysis of A-to-I RNA editing in human melanoma samples and determined that pre-therapy levels of A-to-I RNA editing negatively correlate with survival times, suggesting that an accumulation of endogenous double-stranded Alu RNA might contribute to cancer patient survival. Furthermore, we demonstrated that immunostimulatory Alu RNA can be leveraged pharmacologically for cancer immunotherapy. AluJb RNA was in vitro transcribed and then formulated with endosome-destabilizing polymer nanoparticles to improve intracellular delivery of the RNA and enable activation of RNA-sensing pathways. AluJb RNA/polymer complexes (i.e., Alu-NPs) were engineered to form colloidally stable nanoparticles that exhibited immunostimulatory activity in vitro and in vivo. Finally, the therapeutic potential of Alu-NPs for the treatment of cancer was demonstrated by attenuated tumor growth and prolonged survival in the B16.F10 murine melanoma tumor model. Thus, these data collectively implicate intratumoral Alu RNA as a potentiator of antitumor innate immunity and identify AluJb RNA as a novel nucleic acid immunotherapeutic for cancer. Significance Loss of A-to-I editing leads to accumulation of unedited Alu RNAs that activate innate immunity via RNA-sensing pattern recognition receptors. When packaged into endosome-releasing polymer nanoparticles, AluJB RNA becomes highly immunostimulatory and can be used pharmacologically to inhibit tumor growth in mouse melanoma models. These findings identify Alu RNAs as a new class of nucleic acid innate immune agonists for cancer immunotherapy.
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Affiliation(s)
- Kyle M. Garland
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee
| | - Alexander J. Kwiatkowski
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee
| | - John T. Tossberg
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Philip S. Crooke
- Department of Mathematics, Vanderbilt University, Nashville, Tennessee
| | - Thomas M. Aune
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John T. Wilson
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee
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30
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Chen J, Jin J, Jiang J, Wang Y. Adenosine deaminase acting on RNA 1 (ADAR1) as crucial regulators in cardiovascular diseases: structures, pathogenesis, and potential therapeutic approach. Front Pharmacol 2023; 14:1194884. [PMID: 37663249 PMCID: PMC10469703 DOI: 10.3389/fphar.2023.1194884] [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: 03/27/2023] [Accepted: 07/11/2023] [Indexed: 09/05/2023] Open
Abstract
Cardiovascular diseases (CVDs) are a group of diseases that have a major impact on global health and are the leading cause of death. A large number of chemical base modifications in ribonucleic acid (RNA) are associated with cardiovascular diseases. A variety of ribonucleic acid modifications exist in cells, among which adenosine deaminase-dependent modification is one of the most common ribonucleic acid modifications. Adenosine deaminase acting on ribonucleic acid 1 (Adenosine deaminase acting on RNA 1) is a widely expressed double-stranded ribonucleic acid adenosine deaminase that forms inosine (A-to-I) by catalyzing the deamination of adenosine at specific sites of the target ribonucleic acid. In this review, we provide a comprehensive overview of the structure of Adenosine deaminase acting on RNA 1 and summarize the regulatory mechanisms of ADAR1-mediated ribonucleic acid editing in cardiovascular diseases, indicating Adenosine deaminase acting on RNA 1 as a promising therapeutic target in cardiovascular diseases.
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Affiliation(s)
- Jieying Chen
- Department of Cardiology ofThe Second Affiliated Hospital, School of Medicine Zhejiang University, Hangzhou, China
| | - Junyan Jin
- Department of Cardiology ofThe Second Affiliated Hospital, School of Medicine Zhejiang University, Hangzhou, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China
| | - Jun Jiang
- Department of Cardiology ofThe Second Affiliated Hospital, School of Medicine Zhejiang University, Hangzhou, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China
| | - Yaping Wang
- Department of Cardiology ofThe Second Affiliated Hospital, School of Medicine Zhejiang University, Hangzhou, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China
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31
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DeAntoneo C, Herbert A, Balachandran S. Z-form nucleic acid-binding protein 1 (ZBP1) as a sensor of viral and cellular Z-RNAs: walking the razor's edge. Curr Opin Immunol 2023; 83:102347. [PMID: 37276820 PMCID: PMC10526625 DOI: 10.1016/j.coi.2023.102347] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023]
Abstract
Z-form nucleic acid-binding protein 1 (ZBP1) detects viral Z-form RNAs (Z-RNAs), activates receptor-interacting protein kinase 3, and triggers cell death during both RNA and DNA virus infections. Such cell death promotes virus clearance by eliminating infected cells and galvanizing antiviral immunity, and is thus often targeted for evasion by virus-encoded suppressors. Recent evidence demonstrates that ZBP1 can also be activated by cellular Z-RNAs transcribed from endogenous retroelements within mammalian genomes. These cellular Z-RNAs, if not edited and neutralized by adenosine deaminase RNA-specific 1, trigger ZBP1-dependent cell death and inflammation, which may drive disease in Aicardi-Goutière's syndrome and related interferonopathies. Thus, while well-controlled activation of ZBP1 by viral Z-RNAs during infections is beneficial, the same pathway can have harmful consequences when inappropriately triggered by cellular Z-RNAs in other disease settings.
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Affiliation(s)
- Carly DeAntoneo
- Drexel University College of Medicine, 2900 W. Queen Lane, Philadelphia, PA 19129, USA; Center for Immunology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Alan Herbert
- InsideOutBio, 42 8th Street, Charlestown, MA, USA
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32
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Samuel CE. Interferon at the crossroads of SARS-CoV-2 infection and COVID-19 disease. J Biol Chem 2023; 299:104960. [PMID: 37364688 PMCID: PMC10290182 DOI: 10.1016/j.jbc.2023.104960] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023] Open
Abstract
A novel coronavirus now known as SARS-CoV-2 emerged in late 2019, possibly following a zoonotic crossover from a coronavirus present in bats. This virus was identified as the pathogen responsible for the severe respiratory disease, coronavirus disease-19 (COVID-19), which as of May 2023, has killed an estimated 6.9 million people globally according to the World Health Organization. The interferon (IFN) response, a cornerstone of antiviral innate immunity, plays a key role in determining the outcome of infection by SARS-CoV-2. This review considers evidence that SARS-CoV-2 infection leads to IFN production; that virus replication is sensitive to IFN antiviral action; molecular mechanisms by which the SARS-CoV-2 virus antagonizes IFN action; and how genetic variability of SARS-CoV-2 and the human host affects the IFN response at the level of IFN production or action or both. Taken together, the current understanding suggests that deficiency of an effective IFN response is an important determinant underlying some cases of critical COVID-19 disease and that IFNλ and IFNα/β have potential as therapeutics for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA.
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33
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Lv T, Jiang S, Wang X, Hou Y. Profiling A-to-I RNA editing during mouse somatic reprogramming at the single-cell level. Heliyon 2023; 9:e18133. [PMID: 37519753 PMCID: PMC10375800 DOI: 10.1016/j.heliyon.2023.e18133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023] Open
Abstract
Mouse somatic cells can be reprogrammed into induced pluripotent stem cells through a highly heterogeneous process regulated by numerous biological factors, including adenosine-to-inosine (A-to-I) RNA editing. In this study, we analyzed A-to-I RNA editing sites using a single-cell RNA sequencing (scRNA-seq) dataset with high-depth and full-length coverage. Our method revealed that A-to-I RNA editing frequency varied widely at the single-cell level and underwent dynamic changes. We also found that A-to-I RNA editing level was correlated with the expression of the RNA editing enzyme ADAR1. The analysis combined with gene ontology (GO) enrichment revealed that ADAR1-dependent A-to-I editing may downregulate the expression levels of Igtp, Irgm2, Mndal, Ifi202b, and Tapbp in the early stage, to inhibit the pathways of cellular response to interferon-beta and regulation of protein complex stability to promote mesenchymal-epithelial transition (MET). Notably, we identified a negative correlation between A-to-I RNA editing frequency and the expression of certain genes, such as Nras, Ube2l6, Zfp987, and Adsl.
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Affiliation(s)
- Tianhang Lv
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Siyuan Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Yong Hou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
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34
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Xing Y, Nakahama T, Wu Y, Inoue M, Kim JI, Todo H, Shibuya T, Kato Y, Kawahara Y. RNA editing of AZIN1 coding sites is catalyzed by ADAR1 p150 after splicing. J Biol Chem 2023; 299:104840. [PMID: 37209819 PMCID: PMC10404624 DOI: 10.1016/j.jbc.2023.104840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
Adenosine-to-inosine RNA editing is catalyzed by nuclear adenosine deaminase acting on RNA 1 (ADAR1) p110 and ADAR2, and cytoplasmic ADAR1 p150 in mammals, all of which recognize dsRNAs as targets. RNA editing occurs in some coding regions, which alters protein functions by exchanging amino acid sequences, and is therefore physiologically significant. In general, such coding sites are edited by ADAR1 p110 and ADAR2 before splicing, given that the corresponding exon forms a dsRNA structure with an adjacent intron. We previously found that RNA editing at two coding sites of antizyme inhibitor 1 (AZIN1) is sustained in Adar1 p110/Aadr2 double KO mice. However, the molecular mechanisms underlying RNA editing of AZIN1 remain unknown. Here, we showed that Azin1 editing levels were increased upon type I interferon treatment, which activated Adar1 p150 transcription, in mouse Raw 264.7 cells. Azin1 RNA editing was observed in mature mRNA but not precursor mRNA. Furthermore, we revealed that the two coding sites were editable only by ADAR1 p150 in both mouse Raw 264.7 and human embryonic kidney 293T cells. This unique editing was achieved by forming a dsRNA structure with a downstream exon after splicing, and the intervening intron suppressed RNA editing. Therefore, deletion of a nuclear export signal from ADAR1 p150, shifting its localization to the nucleus, decreased Azin1 editing levels. Finally, we demonstrated that Azin1 RNA editing was completely absent in Adar1 p150 KO mice. Thus, these findings indicate that RNA editing of AZIN1 coding sites is exceptionally catalyzed by ADAR1 p150 after splicing.
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Affiliation(s)
- Yanfang Xing
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Taisuke Nakahama
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Integrated Frontier Research for Medical Science Division and RNA Frontier Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan.
| | - Yuke Wu
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Maal Inoue
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Jung In Kim
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hiroyuki Todo
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Toshiharu Shibuya
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yuki Kato
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Integrated Frontier Research for Medical Science Division and RNA Frontier Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Integrated Frontier Research for Medical Science Division and RNA Frontier Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan; Genome Editing Research and Development Center, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
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35
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Chiavetta RF, Titoli S, Barra V, Cancemi P, Melfi R, Di Leonardo A. Site-Specific RNA Editing of Stop Mutations in the CFTR mRNA of Human Bronchial Cultured Cells. Int J Mol Sci 2023; 24:10940. [PMID: 37446121 DOI: 10.3390/ijms241310940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
It is reported that about 10% of cystic fibrosis (CF) patients worldwide have nonsense (stop) mutations in the CFTR gene, which cause the premature termination of CFTR protein synthesis, leading to a truncated and non-functional protein. To address this issue, we investigated the possibility of rescuing the CFTR nonsense mutation (UGA) by sequence-specific RNA editing in CFTR mutant CFF-16HBEge, W1282X, and G542X human bronchial cells. We used two different base editor tools that take advantage of ADAR enzymes (adenosine deaminase acting on RNA) to edit adenosine to inosine (A-to-I) within the mRNA: the REPAIRv2 (RNA Editing for Programmable A to I Replacement, version 2) and the minixABE (A to I Base Editor). Immunofluorescence experiments show that both approaches were able to recover the CFTR protein in the CFTR mutant cells. In addition, RT-qPCR confirmed the rescue of the CFTR full transcript. These findings suggest that site-specific RNA editing may efficiently correct the UGA premature stop codon in the CFTR transcript in CFF-16HBEge, W1282X, and G542X cells. Thus, this approach, which is safer than acting directly on the mutated DNA, opens up new therapeutic possibilities for CF patients with nonsense mutations.
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Affiliation(s)
- Roberta F Chiavetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Simona Titoli
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Viviana Barra
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Patrizia Cancemi
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
- Centro di Oncobiologia Sperimentale (C.O.B.S.), Viale Delle Scienze, 90128 Palermo, Italy
| | - Raffaella Melfi
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Aldo Di Leonardo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
- Centro di Oncobiologia Sperimentale (C.O.B.S.), Viale Delle Scienze, 90128 Palermo, Italy
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36
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Di Fusco D, Segreto MT, Iannucci A, Maresca C, Franzè E, Di Maggio G, Di Grazia A, Boccanera S, Laudisi F, Marafini I, Paoluzi OA, Michenzi A, Monteleone G, Monteleone I. An essential role of adenosine deaminase acting on RNA 1 in coeliac disease mucosa. Front Immunol 2023; 14:1175348. [PMID: 37223095 PMCID: PMC10200931 DOI: 10.3389/fimmu.2023.1175348] [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: 02/27/2023] [Accepted: 04/25/2023] [Indexed: 05/25/2023] Open
Abstract
Background and aim Type I interferons (IFNs) are highly expressed in the gut mucosa of celiac disease (CD) gut mucosa and stimulates immune response prompted by gluten ingestion, but the processes that maintain the production of these inflammatory molecules are not well understood. Adenosine deaminase acting on RNA 1 (ADAR1), an RNA-editing enzyme, plays a crucial role in inhibiting self or viral RNAs from activating auto-immune mediated responses, most notably within the type-I IFN production pathway. The aim of this study was to assess whether ADAR1 could contribute to the induction and/or progression of gut inflammation in patients with celiac disease. Material and methods ADAR1 expression was assessed by Real time PCR and Western blotting in duodenal biopsy taken from inactive and active celiac disease (CD) patients and normal controls (CTR). To analyze the role of ADAR1 in inflamed CD mucosa, lamina propria mononuclear cells (LPMC) were isolated from inactive CD and ADAR1 was silenced in with a specific antisense oligonucleotide (AS) and then incubated with a synthetic analogue of viral dsRNA (poly I:C). IFN-inducing pathways (IRF3, IRF7) in these cells were evaluated with Western blotting and inflammatory cytokines were evaluated with flow cytometry. Lastly, the role of ADAR1 was investigated in a mouse model of poly I:C-driven small intestine atrophy. Results Reduced ADAR1 expression was seen in duodenal biopsies compared to inactive CD and normal controls. Ex vivo organ cultures of duodenal mucosal biopsies, taken from inactive CD patients, stimulated with a peptic-tryptic digest of gliadin displayed a decreased expression of ADAR1. ADAR1 silencing in LPMC stimulated with a synthetic analogue of viral dsRNA strongly boosted the activation of IRF3 and IRF7 and the production of type-I IFN, TNF-α and IFN-γ. Administration of ADAR1 antisense but not sense oligonucleotide to mice with poly I:C-induced intestinal atrophy, significantly increased gut damage and inflammatory cytokines production. Conclusions These data show that ADAR1 is an important regulator of intestinal immune homeostasis and demonstrate that defective ADAR1 expression could provide to amplifying pathogenic responses in CD intestinal mucosa.
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Affiliation(s)
- Davide Di Fusco
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | | | - Andrea Iannucci
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Rome, Italy
| | - Claudia Maresca
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Eleonora Franzè
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Giulia Di Maggio
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Antonio Di Grazia
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Siro Boccanera
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Federica Laudisi
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Irene Marafini
- Unità Operativa Complessa (UOC) Gastroenterologia, Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Omero Alessandro Paoluzi
- Unità Operativa Complessa (UOC) Gastroenterologia, Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Alessandro Michenzi
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Rome, Italy
| | - Giovanni Monteleone
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
- Unità Operativa Complessa (UOC) Gastroenterologia, Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Ivan Monteleone
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Rome, Italy
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37
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Uhl S, Jang C, Frere JJ, Jordan TX, Simon AE, tenOever BR. ADAR1 Biology Can Hinder Effective Antiviral RNA Interference. J Virol 2023; 97:e0024523. [PMID: 37017521 PMCID: PMC10134826 DOI: 10.1128/jvi.00245-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/10/2023] [Indexed: 04/06/2023] Open
Abstract
Viruses constantly evolve and adapt to the antiviral defenses of their hosts. The biology of viral circumvention of these selective pressures can often be attributed to the acquisition of novel antagonistic gene products or by rapid genome change that prevents host recognition. To study viral evasion of RNA interference (RNAi)-based defenses, we established a robust antiviral system in mammalian cells using recombinant Sendai virus designed to be targeted by endogenous host microRNAs (miRNAs) with perfect complementarity. Using this system, we previously demonstrated the intrinsic ability of positive-strand RNA viruses to escape this selective pressure via homologous recombination, which was not observed in negative-strand RNA viruses. Here, we show that given extensive time, escape of miRNA-targeted Sendai virus was enabled by host adenosine deaminase acting on RNA 1 (ADAR1). Independent of the viral transcript targeted, ADAR1 editing resulted in disruption of the miRNA-silencing motif, suggesting an intolerance for extensive RNA-RNA interactions necessary for antiviral RNAi. This was further supported in Nicotiana benthamiana, where exogenous expression of ADAR1 interfered with endogenous RNAi. Together, these results suggest that ADAR1 diminishes the effectiveness of RNAi and may explain why it is absent in species that utilize this antiviral defense system. IMPORTANCE All life at the cellular level has the capacity to induce an antiviral response. Here, we examine the result of imposing the antiviral response of one branch of life onto another and find evidence for conflict. To determine the consequences of eliciting an RNAi-like defense in mammals, we applied this pressure to a recombinant Sendai virus in cell culture. We find that ADAR1, a host gene involved in regulation of the mammalian response to virus, prevented RNAi-mediated silencing and subsequently allowed for viral replication. In addition, the expression of ADAR1 in Nicotiana benthamiana, which lacks ADARs and has an endogenous RNAi system, suppresses gene silencing. These data indicate that ADAR1 is disruptive to RNAi biology and provide insight into the evolutionary relationship between ADARs and antiviral defenses in eukaryotic life.
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Affiliation(s)
- Skyler Uhl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology | Medicine, New York University, New York, New York, USA
| | - Chanyong Jang
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, Maryland, USA
| | - Justin J. Frere
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology | Medicine, New York University, New York, New York, USA
| | - Tristan X. Jordan
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Anne E. Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, Maryland, USA
| | - Benjamin R. tenOever
- Department of Microbiology | Medicine, New York University, New York, New York, USA
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38
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Tassinari V, La Rosa P, Guida E, Colopi A, Caratelli S, De Paolis F, Gallo A, Cenciarelli C, Sconocchia G, Dolci S, Cesarini V. Contribution of A-to-I RNA editing, M6A RNA Methylation, and Alternative Splicing to physiological brain aging and neurodegenerative diseases. Mech Ageing Dev 2023; 212:111807. [PMID: 37023929 DOI: 10.1016/j.mad.2023.111807] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Aging is a physiological and progressive phenomenon in all organisms' life cycle, characterized by the accumulation of degenerative processes triggered by several alterations within molecular pathways. These changes compromise cell fate, resulting in the loss of functions in tissues throughout the body, including the brain. Physiological brain aging has been linked to structural and functional alterations, as well as to an increased risk of neurodegenerative diseases. Post-transcriptional RNA modifications modulate mRNA coding properties, stability, translatability, expanding the coding capacity of the genome, and are involved in all cellular processes. Among mRNA post-transcriptional modifications, the A-to-I RNA editing, m6A RNA Methylation and Alternative Splicing play a critical role in all the phases of a neuronal cell life cycle and alterations in their mechanisms of action significantly contribute to aging and neurodegeneration. Here we review our current understanding of the contribution of A-to-I RNA editing, m6A RNA Methylation, and Alternative Splicing to physiological brain aging process and neurodegenerative diseases.
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Affiliation(s)
- Valentina Tassinari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy; Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, Rome, Italy; European Center for Brain Research, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Eugenia Guida
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Ambra Colopi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Sara Caratelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Francesca De Paolis
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Angela Gallo
- RNA Editing Lab., Oncohaematology Department, Cellular and Gene Therapy Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carlo Cenciarelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Giuseppe Sconocchia
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Susanna Dolci
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Valeriana Cesarini
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy.
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39
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Ke PY. Crosstalk between Autophagy and RLR Signaling. Cells 2023; 12:cells12060956. [PMID: 36980296 PMCID: PMC10047499 DOI: 10.3390/cells12060956] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Autophagy plays a homeostatic role in regulating cellular metabolism by degrading unwanted intracellular materials and acts as a host defense mechanism by eliminating infecting pathogens, such as viruses. Upon viral infection, host cells often activate retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) signaling to induce the transcription of type I interferons, thus establishing the first line of the innate antiviral response. In recent years, numerous studies have shown that virus-mediated autophagy activation may benefit viral replication through different actions on host cellular processes, including the modulation of RLR-mediated innate immunity. Here, an overview of the functional molecules and regulatory mechanism of the RLR antiviral immune response as well as autophagy is presented. Moreover, a summary of the current knowledge on the biological role of autophagy in regulating RLR antiviral signaling is provided. The molecular mechanisms underlying the crosstalk between autophagy and RLR innate immunity are also discussed.
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Affiliation(s)
- Po-Yuan Ke
- Department of Biochemistry & Molecular Biology, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
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40
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Nakahama T, Kawahara Y. The RNA-editing enzyme ADAR1: a regulatory hub that tunes multiple dsRNA-sensing pathways. Int Immunol 2023; 35:123-133. [PMID: 36469491 DOI: 10.1093/intimm/dxac056] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA-editing enzyme that catalyzes adenosine-to-inosine conversions in double-stranded RNAs (dsRNAs). In mammals, ADAR1 is composed of two isoforms: a nuclear short p110 isoform and a cytoplasmic long p150 isoform. Whereas both isoforms contain right-handed dsRNA-binding and deaminase domains, ADAR1 p150 harbors a Zα domain that binds to left-handed dsRNAs, termed Z-RNAs. Myeloma differentiation-associated gene 5 (MDA5) sensing of endogenous dsRNAs as non-self leads to the induction of type I interferon (IFN)-stimulated genes, but recent studies revealed that ADAR1 p150-mediated RNA editing, but not ADAR1 p110, prevents this MDA5-mediated sensing. ADAR1 p150-specific RNA-editing sites are present and at least a Zα domain-Z-RNA interaction is required for this specificity. Mutations in the ADAR1 gene cause Aicardi-Goutières syndrome (AGS), an infant encephalopathy with type I IFN overproduction. Insertion of a point mutation in the Zα domain of the Adar1 gene induces AGS-like encephalopathy in mice, which is rescued by concurrent deletion of MDA5. This finding indicates that impaired ADAR1 p150-mediated RNA-editing is a mechanism underlying AGS caused by an ADAR1 mutation. ADAR1 p150 also prevents ZBP1 sensing of endogenous Z-RNA, which leads to programmed cell death, via the Zα domain and its RNA-editing activity. Furthermore, ADAR1 prevents protein kinase R (PKR) sensing of endogenous right-handed dsRNAs, which leads to translational shutdown and growth arrest. Thus, ADAR1 acts as a regulatory hub that blocks sensing of endogenous dsRNAs as non-self by multiple sensor proteins, both in RNA editing-dependent and -independent manners, and is a potential therapeutic target for diseases, especially cancer.
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Affiliation(s)
- Taisuke Nakahama
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.,Integrated Frontier Research for Medical Science Division and RNA Frontier Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565-0871, Japan.,Division of Microbiology and Immunology, Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka 565-0871, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.,Integrated Frontier Research for Medical Science Division and RNA Frontier Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565-0871, Japan.,Division of Microbiology and Immunology, Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka 565-0871, Japan
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41
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Rajendren S, Ye X, Dunker W, Richardson A, Karijolich J. The cellular and KSHV A-to-I RNA editome in primary effusion lymphoma and its role in the viral lifecycle. Nat Commun 2023; 14:1367. [PMID: 36914661 PMCID: PMC10011561 DOI: 10.1038/s41467-023-37105-8] [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: 09/23/2022] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
Adenosine-to-inosine RNA editing is a major contributor to transcriptome diversity in animals with far-reaching biological consequences. Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of several human malignancies including primary effusion lymphoma (PEL). The extent of RNA editing within the KSHV transcriptome is unclear as is its contribution to the viral lifecycle. Here, we leverage a combination of biochemical and genomic approaches to determine the RNA editing landscape in host- and KSHV transcriptomes during both latent and lytic replication in PEL. Analysis of RNA editomes reveals it is dynamic, with increased editing upon reactivation and the potential to deregulate pathways critical for latency and tumorigenesis. In addition, we identify conserved RNA editing events within a viral microRNA and discover their role in miRNA biogenesis as well as viral infection. Together, these results describe the editome of PEL cells as well as a critical role for A-to-I editing in the KSHV lifecycle.
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Affiliation(s)
- Suba Rajendren
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232-2363, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, 37232-2363, USA
- Vanderbilt Center for Immunobiology, Nashville, TN, 37232-2363, USA
| | - Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232-2363, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, 37232-2363, USA
- Vanderbilt Center for Immunobiology, Nashville, TN, 37232-2363, USA
| | - William Dunker
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232-2363, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, 37232-2363, USA
- Vanderbilt Center for Immunobiology, Nashville, TN, 37232-2363, USA
| | - Antiana Richardson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232-2363, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, 37232-2363, USA
- Vanderbilt Center for Immunobiology, Nashville, TN, 37232-2363, USA
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232-2363, USA.
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, 37232-2363, USA.
- Vanderbilt Center for Immunobiology, Nashville, TN, 37232-2363, USA.
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-2363, USA.
- Vanderbilt-Ingram Cancer Center, Nashville, TN, 37232-2363, USA.
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42
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Zhao Y, Zheng X, Li M, Zhao J, Wang X, Zhu H. ADAR1 improved Treg cell function through the miR-21b/Foxp3 axis and inhibits the progression of acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation. Int Immunopharmacol 2023; 115:109620. [PMID: 36577155 DOI: 10.1016/j.intimp.2022.109620] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 12/04/2022] [Accepted: 12/17/2022] [Indexed: 12/27/2022]
Abstract
Th17/Treg equilibrium towards the pro-inflammatory Th17 side contributes greatly to the rejection during allogeneic hematopoietic stem cell transplantation (allo-HSCT). Forkhead box P3 (Foxp3) is important in the pathogenic conversion between Th17 and Treg cells. However, how Foxp3 expression was regulated is largely unknown. Here, we investigated the role of RNA-editing enzyme ADAR1 in Foxp3-mediated Th17/Treg imbalance and progression of acute graft-versus-host disease (aGVHD), a most serious complication in patients received allo-HSCT. Th1, Th17 and Treg cells were respectively isolated from peripheral blood CD4 + T cells of allo-HSCT patients, and we found that proportions of Th1 and Th17 were markedly increased, while Treg proportion was significantly decreased in aGVHD patients post transplantation compared with non-aGVHD patients, accompanied by decreased ADAR1 and increased miR-21b levels. RNA-immunoprecipitation (RIP) combined with gain- and loss-of-function experiments demonstrated that ADAR1 improved Treg cell functions and negatively regulated the production of miR-21b, a Foxp3-targeting miRNA. Inhibition of miR-21b improved Treg functions, and Foxp3 knockdown could eliminate the effect of miR-21b inhibition or ADAR1 overexpression on Treg function. Finally, an aGVHD mouse model was established and Ad-O/E-ADAR1 was injected into aGVHD mice to verify the effect of ADAR1 on aGVHD progression in vivo. The results showed that ADAR1 overexpression decreased Th17 proportion and increased Treg proportion in aGVHD mice and obviously improved tissue necrosis and reticular structure of aGVHD liver and lung in vivo. Collectively, ADAR1 suppresses miR-21b production and improves Foxp3-mediated Treg cell function to inhibit the progression of aGVHD after allo-HSCT.
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Affiliation(s)
- Yanru Zhao
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Xiaoyan Zheng
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Miaojing Li
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Jing Zhao
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Xiaoning Wang
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Huachao Zhu
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China.
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43
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Welden JR, Margvelani G, Arizaca Maquera KA, Gudlavalleti B, Miranda Sardón S, Campos A, Robil N, Lee D, Hernandez A, Wang WX, Di J, de la Grange P, Nelson P, Stamm S. RNA editing of microtubule-associated protein tau circular RNAs promotes their translation and tau tangle formation. Nucleic Acids Res 2022; 50:12979-12996. [PMID: 36533443 PMCID: PMC9825173 DOI: 10.1093/nar/gkac1129] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/06/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022] Open
Abstract
Aggregation of the microtubule-associated protein tau characterizes tauopathies, including Alzheimer's disease and frontotemporal lobar degeneration (FTLD-Tau). Gene expression regulation of tau is complex and incompletely understood. Here we report that the human tau gene (MAPT) generates two circular RNAs (circRNAs) through backsplicing of exon 12 to either exon 7 (12→7 circRNA) or exon 10 (12→10 circRNA). Both circRNAs lack stop codons. The 12→7 circRNA contains one start codon and is translated in a rolling circle, generating a protein consisting of multimers of the microtubule-binding repeats R1-R4. For the 12→10 circRNA, a start codon can be introduced by two FTLD-Tau mutations, generating a protein consisting of multimers of the microtubule-binding repeats R2-R4, suggesting that mutations causing FTLD may act in part through tau circRNAs. Adenosine to inosine RNA editing dramatically increases translation of circRNAs and, in the 12→10 circRNA, RNA editing generates a translational start codon by changing AUA to AUI. Circular tau proteins self-aggregate and promote aggregation of linear tau proteins. Our data indicate that adenosine to inosine RNA editing initiates translation of human circular tau RNAs, which may contribute to tauopathies.
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Affiliation(s)
| | - Giorgi Margvelani
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | | | - Bhavani Gudlavalleti
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Sandra C Miranda Sardón
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Alexandre Rosa Campos
- Sanford Burnham Prebys Medical Discovery Institute Proteomics Core, La Jolla, CA, USA
| | | | - Daniel C Lee
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA,Alzheimer's Disease Research Center Neuroscience, University of Kentucky, Lexington, KY, USA
| | | | - Wang-Xia Wang
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA,Alzheimer's Disease Research Center and Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | - Jing Di
- Alzheimer's Disease Research Center and Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | | | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA,Alzheimer's Disease Research Center and Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
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44
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Samuel CE. Interferonopathy Resulting from Dysregulation of Interferon Production. J Interferon Cytokine Res 2022; 42:655-657. [PMID: 35793522 DOI: 10.1089/jir.2022.0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
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45
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BenDavid E, Pfaller CK, Pan Y, Samuel CE, Ma D. Host 5'-3' Exoribonuclease XRN1 Acts as a Proviral Factor for Measles Virus Replication by Downregulating the dsRNA-Activated Kinase PKR. J Virol 2022; 96:e0131922. [PMID: 36300942 PMCID: PMC9683022 DOI: 10.1128/jvi.01319-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/22/2022] [Indexed: 11/20/2022] Open
Abstract
Many negative-sense RNA viruses, including measles virus (MeV), are thought to carry out much of their viral replication in cytoplasmic membraneless foci known as inclusion bodies (IBs). The mechanisms by which IBs facilitate efficient viral replication remain largely unknown but may involve an intricate network of regulation at the host-virus interface. Viruses are able to modulate such interactions by a variety of strategies including adaptation of their genomes and "hijacking" of host proteins. The latter possibility broadens the molecular reservoir available for a virus to enhance its replication and/or antagonize host antiviral responses. Here, we show that the cellular 5'-3' exoribonuclease, XRN1, is a host protein hijacked by MeV. We found that upon MeV infection, XRN1 is translocated to cytoplasmic IBs where it acts in a proviral manner by preventing the accumulation of double-stranded RNA (dsRNA) within the IBs. This leads to the suppression of the dsRNA-induced innate immune responses mediated via the protein kinase R (PKR)-integrated stress response (ISR) pathway. IMPORTANCE Measles virus remains a major global health threat due to its high transmissibility and significant morbidity in children and immunocompromised individuals. Although there is an effective vaccine against MeV, a large population in the world remains without access to the vaccine, contributing to more than 7,000,000 measles cases and 60,000 measles deaths in 2020 (CDC). For negative-sense RNA viruses including MeV, one active research area is the exploration of virus-host interactions occurring at cytoplasmic IBs where viral replication takes place. In this study we present evidence suggesting a model in which MeV IBs antagonize host innate immunity by recruiting XRN1 to reduce dsRNA accumulation and subsequent PKR kinase activation/ISR induction. In the absence of XRN1, the increased dsRNA level acts as a potent activator of the antiviral PKR/ISR pathway leading to suppression of global cap-dependent mRNA translation and inhibition of viral replication.
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Affiliation(s)
- Ethan BenDavid
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
| | | | - Yue Pan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Charles E. Samuel
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
| | - Dzwokai Ma
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
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46
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RNA Editing Alterations Define Disease Manifestations in the Progression of Experimental Autoimmune Encephalomyelitis (EAE). Cells 2022; 11:cells11223582. [PMID: 36429012 PMCID: PMC9688714 DOI: 10.3390/cells11223582] [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: 09/09/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
RNA editing is an epitranscriptomic modification, leading to targeted changes in RNA transcripts. It is mediated by the action of ADAR (adenosine deaminases acting on double-stranded (ds) RNA and APOBEC (apolipoprotein B mRNA editing enzyme catalytic polypeptide-like) deaminases and appears to play a major role in the pathogenesis of many diseases. Here, we assessed its role in experimental autoimmune encephalomyelitis (EAE), a widely used non-clinical model of autoimmune inflammatory diseases of the central nervous system (CNS), which resembles many aspects of human multiple sclerosis (MS). We have analyzed in silico data from microglia isolated at different timepoints through disease progression to identify the global editing events and validated the selected targets in murine tissue samples. To further evaluate the functional role of RNA editing, we induced EAE in transgenic animals lacking expression of APOBEC-1. We found that RNA-editing events, mediated by the APOBEC and ADAR deaminases, are significantly reduced throughout the course of disease, possibly affecting the protein expression necessary for normal neurological function. Moreover, the severity of the EAE model was significantly higher in APOBEC-1 knock-out mice, compared to wild-type controls. Our results implicate regulatory epitranscriptomic mechanisms in EAE pathogenesis that could be extrapolated to MS and other neurodegenerative disorders (NDs) with common clinical and molecular features.
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47
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Zhang Q, Xiu B, Zhang L, Chen M, Chi W, Li L, Guo R, Xue J, Yang B, Huang X, Shao ZM, Huang S, Chi Y, Wu J. Immunosuppressive lncRNA LINC00624 promotes tumor progression and therapy resistance through ADAR1 stabilization. J Immunother Cancer 2022; 10:jitc-2022-004666. [PMID: 36252997 PMCID: PMC9577936 DOI: 10.1136/jitc-2022-004666] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Despite the success of HER2-targeted therapy in achieving prolonged survival in approximately 50% of treated individuals, treatment resistance is still an important challenge for HER2+ breast cancer (BC) patients. The influence of both adaptive and innate immune responses on the therapeutic outcomes of HER2+BC patients has been extensively demonstrated. METHODS Long non-coding RNAs expressed in non-pathological complete response (pCR) HER2 positive BC were screened and validated by RNA-seq. Survival analysis were made by Kaplan-Meier method. Cell death assay and proliferation assay were performed to confirm the phenotype of LINC00624. RT-qPCR and western blot were used to assay the IFN response. Xenograft mouse model were used for in vivo confirmation of anti-neu treatment resistance. RNA pull-down and immunoblot were used to confirm the interaction of ADAR1 and LINC00624. ADAR1 recombinant protein were purified from baculovirus expression system. B16-OVA cells were used to study antigen presentation both in vitro and in vivo. Flow cytometry was used to determine the tumor infiltrated immune cells of xenograft model. Antisense oligonucleotides (ASOs) were used for in vivo treatment. RESULTS In this study, we found that LINC00624 blocked the antitumor effect of HER2- targeted therapy both in vitro and in vivo by inhibiting type I interferon (IFN) pathway activation. The double-stranded RNA-like structure of LINC00624 can bind and be edited by the adenosine (A) to inosine (I) RNA-editing enzyme adenosine deaminase RNA specific 1 (ADAR1), and this editing has been shown to release the growth inhibition and attenuate the innate immune response caused by the IFN response. Notably, LINC00624 promoted the stabilization of ADAR1 by inhibiting its ubiquitination-induced degradation triggered by β-TrCP. In contrast, LINC00624 inhibited major histocompatibility complex (MHC) class I antigen presentation and limited CD8+T cell infiltration in the cancer microenvironment, resulting in immune checkpoint blockade inhibition and anti-HER2 treatment resistance mediated through ADAR1. CONCLUSIONS In summary, these results suggest that LINC00624 is a cancer immunosuppressive lncRNA and targeting LINC00624 through ASOs in tumors expressing high levels of LINC00624 has great therapeutic potential in future clinical applications.
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Affiliation(s)
- Qi Zhang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bingqiu Xiu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liyi Zhang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ming Chen
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weiru Chi
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lun Li
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Rong Guo
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Jingyan Xue
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Benlong Yang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaoyan Huang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shenglin Huang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China,Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yayun Chi
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiong Wu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China,Collaborative Innovation Center for Cancer Medicine, Shanghai Medical College, Fudan University, Shanghai, China
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48
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Hao Y, Yang B, Yang J, Shi X, Yang X, Zhang D, Zhao D, Yan W, Chen L, Zheng H, Zhang K, Liu X. ZBP1: A Powerful Innate Immune Sensor and Double-Edged Sword in Host Immunity. Int J Mol Sci 2022; 23:ijms231810224. [PMID: 36142136 PMCID: PMC9499459 DOI: 10.3390/ijms231810224] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Z-conformation nucleic acid binding protein 1 (ZBP1), a powerful innate immune sensor, has been identified as the important signaling initiation factor in innate immune response and the multiple inflammatory cell death known as PANoptosis. The initiation of ZBP1 signaling requires recognition of left-handed double-helix Z-nucleic acid (includes Z-DNA and Z-RNA) and subsequent signaling transduction depends on the interaction between ZBP1 and its adapter proteins, such as TANK-binding kinase 1 (TBK1), interferon regulatory factor 3 (IRF3), receptor-interacting serine/threonine-protein kinase 1 (RIPK1), and RIPK3. ZBP1 activated innate immunity, including type-I interferon (IFN-I) response and NF-κB signaling, constitutes an important line of defense against pathogenic infection. In addition, ZBP1-mediated PANoptosis is a double-edged sword in anti-infection, auto-inflammatory diseases, and tumor immunity. ZBP1-mediated PANoptosis is beneficial for eliminating infected cells and tumor cells, but abnormal or excessive PANoptosis can lead to a strong inflammatory response that is harmful to the host. Thus, pathogens and host have each developed multiplex tactics targeting ZBP1 signaling to maintain strong virulence or immune homeostasis. In this paper, we reviewed the mechanisms of ZBP1 signaling, the effects of ZBP1 signaling on host immunity and pathogen infection, and various antagonistic strategies of host and pathogen against ZBP1. We also discuss existent gaps regarding ZBP1 signaling and forecast potential directions for future research.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Haixue Zheng
- Correspondence: (H.Z.); (K.Z.); Tel.: +86-15214078335 (K.Z.)
| | - Keshan Zhang
- Correspondence: (H.Z.); (K.Z.); Tel.: +86-15214078335 (K.Z.)
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49
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Delli Ponti R, Broglia L, Vandelli A, Armaos A, Torrent Burgas M, Sanchez de Groot N, Tartaglia GG. A high-throughput approach to predict A-to-I effects on RNA structure indicates a change of double-stranded content in non-coding RNAs. IUBMB Life 2022; 75:411-426. [PMID: 36057100 DOI: 10.1002/iub.2673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/21/2022] [Indexed: 11/09/2022]
Abstract
RNA molecules undergo a number of chemical modifications whose effects can alter their structure and molecular interactions. Previous studies have shown that RNA editing can impact the formation of ribonucleoprotein complexes and influence the assembly of membrane-less organelles such as stress-granules. For instance, N6-methyladenosine (m6A) enhances SG formation and N1-methyladenosine (m1A) prevents their transition to solid-like aggregates. Yet, very little is known about adenosine to inosine (A-to-I) modification that is very abundant in human cells and not only impacts mRNAs but also non-coding RNAs. Here, we built the CROSSalive predictor of A-to-I effects on RNA structure based on high-throughput in-cell experiments. Our method shows an accuracy of 90% in predicting the single and double-stranded content of transcripts and identifies a general enrichment of double-stranded regions caused by A-to-I in long intergenic non-coding RNAs (lincRNAs). For the individual cases of NEAT1, NORAD and XIST, we investigated the relationship between A-to-I editing and interactions with RNA-binding proteins using available CLIP data and catRAPID predictions. We found that A-to-I editing is linked to alteration of interaction sites with proteins involved in phase-separation, which suggests that RNP assembly can be influenced by A-to-I. CROSSalive is available at http://service.tartaglialab.com/new_submission/crossalive. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Riccardo Delli Ponti
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore
| | - Laura Broglia
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Genoa, Italy
| | - Andrea Vandelli
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Alexandros Armaos
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Genoa, Italy
| | - Marc Torrent Burgas
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Natalia Sanchez de Groot
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Genoa, Italy.,Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome, Italy
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50
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Double-stranded RNA induction asa potential dynamic biomarkerfor DNA-demethylating agents. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:370-383. [PMID: 36035755 PMCID: PMC9385881 DOI: 10.1016/j.omtn.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 07/15/2022] [Indexed: 11/22/2022]
Abstract
Hypomethylating agents (HMAs), such as azacitidine and decitabine, induce cancer cell death by demethylating DNAs to promote the expression of tumor-suppressor genes. HMAs also reactivate the transcription of endogenous double-stranded RNAs (dsRNAs) that trigger the innate immune response and subsequent apoptosis via viral mimicry. However, the expression patterns of endogenous dsRNAs and their relevance in the efficacy of HMAs remain largely uninvestigated. Here, we employ amidine-conjugated spiropyran (Am-SP) to examine the dynamic expression pattern of total dsRNAs regulated by HMAs. By analyzing the bone-marrow aspirates of myelodysplastic syndrome or acute myeloid leukemia patients who received the HMAs, we find a dramatic increase in total dsRNA levels upon treatment only in patients who later benefited from the therapy. We further apply our approach in solid tumor cell lines and show that the degree of dsRNA induction correlates with the effectiveness of decitabine in most cases. Notably, when dsRNA induction is accompanied by increased expression of nc886 RNA, decitabine becomes ineffective. Collectively, our study establishes the potential application of monitoring the total dsRNA levels by a small molecule as an analytical method and a dynamic marker to predict the clinical outcome of the HMA therapy.
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