1
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Montano MM, Yeh I, Ketchart W. cGAS/STING-Independent Induction of Type I Interferon by Inhibitors of the Histone Methylase KDM5B. FASEB J 2025; 39:e70629. [PMID: 40353728 PMCID: PMC12068183 DOI: 10.1096/fj.202500628r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2025] [Revised: 04/16/2025] [Accepted: 05/05/2025] [Indexed: 05/14/2025]
Abstract
Studies support the role of hexamethylene bis-acetamide [HMBA] induced protein 1 (HEXIM1) as a tumor suppressor. We previously reported that the histone demethylase, KDM5B, inhibits the expression of HEXIM1, and KDM5B inhibitors (KDM5Bi) upregulate HEXIM1 expression. As a consequence, KDM5Bi inhibited cell proliferation, induced differentiation, potentiated sensitivity to cancer chemotherapy, and inhibited breast tumor metastasis. HEXIM1 is crucial for the regulation of triple-negative breast cancer (TNBC) phenotype by KDM5Bi. Type I Interferon (IFN-I) employs the immune system in the tumor microenvironment to restrict tumor growth. Moreover, therapeutic approaches (including mainstay chemotherapy) engage IFN-I signaling. We report herein that HEXIM1 and KDM5Bi induce IFN-I in TNBC. HEXIM1 and KDM5Bi downregulate the expression of polyribonucleotide nucleotidyltransferase 1 (PNPT1) resulting in the release of mitochondrial dsRNA (mt-dsRNA) into the cytoplasm. HEXIM1 also upregulates melanoma differentiation-associated protein 5 (MDA5), a cytoplasmic viral RNA receptor in the innate immune system. MDA5 is required for HEXIM1 and KDM5Bi to induce IFN-I and downstream signaling factors. We observed the augmentation of DNA damage response to Doxorubicin in the presence of KDM5Bi, and this action is a contributing factor in KDM5Bi-induced IFN-I. These actions of HEXIM1 and KDM5Bi occur independently of Cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (cGAS/STING), a major DNA sensing pathway and inducer of innate immunity. Via the upregulation of HEXIM1, KDM5Bi represent pharmacologically induced and tumor intrinsic IFN-I production that is cGAS/STING independent. This is critical because cGAS/STING induce an inflammatory response that promotes the survival of cancer cells, and STING is often impaired in malignant cancers.
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Affiliation(s)
- Monica M. Montano
- Department of PharmacologyCase Western Reserve University School of MedicineClevelandOhioUSA
| | - I‐Ju Yeh
- Department of PharmacologyCase Western Reserve University School of MedicineClevelandOhioUSA
- Stark Neuroscience Research InstituteIndiana University School of MedicineIndianapolisIndianaUSA
| | - Wannarasmi Ketchart
- Department of PharmacologyCase Western Reserve University School of MedicineClevelandOhioUSA
- Department of Pharmacology, Faculty of MedicineChulalongkorn UniversityBangkokThailand
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2
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Stopa V, Dafou D, Karagianni K, Nossent AY, Farrugia R, Devaux Y, Sopic M. Epitranscriptomics in atherosclerosis: Unraveling RNA modifications, editing and splicing and their implications in vascular disease. Vascul Pharmacol 2025; 159:107496. [PMID: 40239855 DOI: 10.1016/j.vph.2025.107496] [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: 01/31/2025] [Revised: 04/08/2025] [Accepted: 04/12/2025] [Indexed: 04/18/2025]
Abstract
Atherosclerosis remains a leading cause of morbidity and mortality worldwide, driven by complex molecular mechanisms involving gene regulation and post-transcriptional processes. Emerging evidence highlights the critical role of epitranscriptomics, the study of chemical modifications occurring on RNA molecules, in atherosclerosis development. Epitranscriptomics provides a new layer of regulation in vascular health, influencing cellular functions in endothelial cells, smooth muscle cells, and macrophages, thereby shedding light on the pathogenesis of atherosclerosis and presenting new opportunities for novel therapeutic targets. This review provides a comprehensive overview of the epitranscriptomic landscape, focusing on key RNA modifications such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), pseudouridine (Ψ), RNA editing mechanisms including A-to-I and C-to-U editing and RNA isoforms. The functional implications of these modifications in RNA stability, alternative splicing, and microRNA biology are discussed, with a focus on their roles in inflammatory signaling, lipid metabolism, and vascular cell adaptation within atherosclerotic plaques. We also highlight how these modifications influence the generation of RNA isoforms, potentially altering cellular phenotypes and contributing to disease progression. Despite the promise of epitranscriptomics, significant challenges remain, including the technical limitations in detecting RNA modifications in complex tissues and the need for deeper mechanistic insights into their causal roles in atherosclerotic pathogenesis. Integrating epitranscriptomics with other omics approaches, such as genomics, proteomics, and metabolomics, holds the potential to provide a more holistic understanding of the disease.
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Affiliation(s)
- Victoria Stopa
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Dimitra Dafou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Korina Karagianni
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - A Yaël Nossent
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Denmark
| | - Rosienne Farrugia
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg.
| | - Miron Sopic
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg; Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
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3
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Li JB, Walkley CR. Leveraging genetics to understand ADAR1-mediated RNA editing in health and disease. Nat Rev Genet 2025:10.1038/s41576-025-00830-5. [PMID: 40229561 DOI: 10.1038/s41576-025-00830-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2025] [Indexed: 04/16/2025]
Abstract
Endogenous, long double-stranded RNA (dsRNA) can resemble viral dsRNA and be recognized by cytosolic dsRNA sensors, triggering autoimmunity. Genetic studies of rare, inherited human diseases and experiments using mouse models have established the importance of adenosine-to-inosine RNA editing by the enzyme adenosine deaminase acting on RNA 1 (ADAR1) as a critical safeguard against autoinflammatory responses to cellular dsRNA. More recently, human genetic studies have revealed that dsRNA editing and sensing mechanisms are involved in common inflammatory diseases, emphasizing the broader role of dsRNA in modulating immune responses and disease pathogenesis. These findings have highlighted the therapeutic potential of targeting dsRNA editing and sensing, as exemplified by the emergence of ADAR1 inhibition in cancer therapy.
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Affiliation(s)
- Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, USA.
| | - Carl R Walkley
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia.
- Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia.
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4
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Deng X, Sun L, Zhang M, Basavaraj R, Wang J, Weng YL, Gao Y. Biochemical profiling and structural basis of ADAR1-mediated RNA editing. Mol Cell 2025; 85:1381-1394.e6. [PMID: 40101712 PMCID: PMC11972152 DOI: 10.1016/j.molcel.2025.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 12/27/2024] [Accepted: 02/19/2025] [Indexed: 03/20/2025]
Abstract
ADAR1 regulates RNA-induced immune responses by converting adenosine to inosine in double-stranded RNA. Mutations in ADAR1 are associated with human autoimmune disease, and targeting ADAR1 has been proposed for cancer immunotherapy. However, the molecular mechanisms underlying ADAR1-mediated editing remain unclear. Here, we provide detailed biochemical and structural characterizations of human ADAR1. Our biochemical profiling reveals that ADAR1 editing is both sequence and RNA-duplex-length dependent but can well tolerate mismatches near the editing site. High-resolution ADAR1-RNA complex structures, combined with mutagenesis, elucidate RNA binding, substrate selection, dimerization, and the essential role of RNA-binding domain 3. The ADAR1 structures also help explain the potential defects of disease-associated mutations, where biochemical and RNA sequencing analysis further indicate some of the mutations preferentially impact the editing of RNAs with short duplexes. These findings unveil the molecular basis of ADAR1 editing and provide insights into its immune-regulatory functions and therapeutic potential.
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Affiliation(s)
- Xiangyu Deng
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Lina Sun
- Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Min Zhang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rashmi Basavaraj
- Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Jin Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA; Center for NextGen Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi-Lan Weng
- Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, TX 77005, USA.
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5
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Jin YY, Guo Y, Xiong SW, Zhang N, Chen JH, Liu F. BALF editome profiling reveals A-to-I RNA editing associated with severity and complications of Mycoplasma pneumoniae pneumonia in children. mSphere 2025; 10:e0101224. [PMID: 39998235 PMCID: PMC11934315 DOI: 10.1128/msphere.01012-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Accepted: 01/09/2025] [Indexed: 02/26/2025] Open
Abstract
Mycoplasma pneumoniae is an important human respiratory pathogen that causes mild-to-moderate community-acquired M. pneumoniae pneumonia (MPP), particularly in children. RNA editing plays a vital role in pathogen infection and host immune response, but it remains largely unknown how it could be involved in the epigenetic regulation of host response to M. pneumoniae infection. In the present study, we performed an epitranscriptomic analysis of adenosine to inosine (A-to-I) editing in 39 bronchoalveolar lavage fluid (BALF) samples from the severe side (SS) and the opposite side (OS) of patients with MPP. Our editome profiling identified 87 differential RNA editing (DRE) events in 50 genes, especially missense editing events that recoded C-C motif chemokine receptor-like 2 (CCRL2, p.K147R) and cyclin I (CCNI, p.R75G). The expression of adenosine deaminase acting on RNA (ADAR) significantly increased on SS compared to OS and positively correlated with the average RNA editing level and individual DRE events. Meanwhile, functional enrichment analysis showed that DRE was observed in genes primarily associated with the negative regulation of innate immune response, type I interferon production, and cytokine production. Further comparison of SS between complicated MPP (CMPP) and non-complicated MPP (NCMPP) revealed RNA editing events associated with MPP complications, with a higher ADAR expression in CMPP than NCMPP. By identifying DRE events as biomarkers associated with MPP severity and complications, our editome profiling provides new insight into the potential role played by A-to-I RNA editing in modulating the host's immune system during M. pneumoniae infection.IMPORTANCEOur research investigates how Mycoplasma pneumoniae, a common respiratory pathogen, influences how our cells modify their genetic instructions. By studying RNA editing changes in bronchoalveolar lavage fluid from patients with M. pneumoniae pneumonia, we aim to investigate how M. pneumoniae infection alters epigenetics and contributes to the disease severity and complications. Understanding such epigenetic alterations not only sheds light on the mechanisms underlying M. pneumoniae infection but also holds potential implications for developing better diagnostic tools and therapies. Ultimately, this work may facilitate the design of more targeted treatments to alleviate the impact of respiratory infections caused by the pathogen. Our findings may also offer broader insights into how microbial infections reshape immune processes, highlighting the importance of RNA editing in host-pathogen interactions.
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Affiliation(s)
- Yun-Yun Jin
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- MOE Medical Basic Research Innovation Center for Gut Microbiota and Chronic Diseases, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Yun Guo
- Department of Respiratory Medicine & Clinical Allergy Center, Affiliated Children’s Hospital of Jiangnan University (Wuxi Children’s Hospital), Wuxi, Jiangsu, China
| | - Su-Wan Xiong
- Department of Respiratory Medicine & Clinical Allergy Center, Affiliated Children’s Hospital of Jiangnan University (Wuxi Children’s Hospital), Wuxi, Jiangsu, China
| | - Na Zhang
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- MOE Medical Basic Research Innovation Center for Gut Microbiota and Chronic Diseases, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Department of Ophthalmology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- MOE Medical Basic Research Innovation Center for Gut Microbiota and Chronic Diseases, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Feng Liu
- Department of Respiratory Medicine, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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6
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Isik CM, Bayyurt EBT, Sahin NO. The MNK-SYNGAP1 axis in specific learning disorder: gene expression pattern and new perspectives. Eur J Pediatr 2025; 184:260. [PMID: 40108041 PMCID: PMC11922980 DOI: 10.1007/s00431-025-06089-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Revised: 02/26/2025] [Accepted: 03/08/2025] [Indexed: 03/22/2025]
Abstract
Specific learning disorder (SLD) is a neurodevelopmental disorder that significantly affects children's academic performance. This study aimed to investigate the expression levels of the MAP Kinase Interacting Serine/Threonine Kinase 1-2 (MNK1, MNK2), Synaptic Ras GTPase Activating Protein 1 (SYNGAP1) genes, and the long non-coding RNA Synaptic Ras GTPase Activating Protein 1-Anti Sense1 (SYNGAP1-AS1), which are believed to play a key role in neurodevelopmental pathways, in children with SLD. Understanding the role of these genes in synaptic plasticity and cognitive function may provide insights into the molecular mechanisms underlying SLD. This study included 38 children diagnosed with SLD and 35 healthy controls aged 6 to 16. RNA was isolated from blood samples, and gene expression levels were measured using quantitative polymerase chain reaction (qPCR). The statistical analysis was conducted to compare the expression levels between the SLD and control groups and within SLD subgroups based on severity and sex. MNK1 and SYNGAP1 expression levels were significantly upregulated in the SLD group compared to the control group (8.33-fold and 16.52-fold increase, respectively; p < 0.001). lncSYNGAP1-AS1 showed a 26.58-fold increase, while MNK2 was downregulated by 2.2-fold, although these changes were not statistically significant. No significant differences were observed between sexes or between the severity subgroups of SLD. CONCLUSION he upregulation of MNK1 and SYNGAP1 in children with SLD suggests their involvement in the neurodevelopmental pathways associated with cognitive processes such as learning and memory. These findings provide a foundation for future research into the molecular basis and potential therapeutic targets of SLD. WHAT IS KNOWN • SYNGAP1 is a key regulator of synaptic plasticity and learning, primarily functioning through Ras signaling inhibition. Its deficiency impairs long-term potentiation (LTP) and is associated with neurodevelopmental disorders (NDDs) such as autism spectrum disorder (ASD) and intellectual disability. • The MAPK/ERK pathway plays a crucial role in learning and memory, and its dysregulation has been linked to several neurological conditions. MNK1/2 interacts with SYNGAP1 in synaptic signaling. WHAT IS NEW • This study is the first to demonstrate significant upregulation of SYNGAP1 and MKNK1 in children with SLD. • Understanding the role of the MKNK-SYNGAP1 axis may guide the development of targeted therapies aimed at enhancing synaptic plasticity to improve learning and memory outcomes in children with SLD.
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Affiliation(s)
- Cansu Mercan Isik
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey.
| | | | - Nil Ozbilum Sahin
- Department of Molecular Biology and Genetic, Faculty of Science, Cumhuriyet University, 58140, Sivas, Turkey
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7
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Chen Z, Behrendt R, Wild L, Schlee M, Bode C. Cytosolic nucleic acid sensing as driver of critical illness: mechanisms and advances in therapy. Signal Transduct Target Ther 2025; 10:90. [PMID: 40102400 PMCID: PMC11920230 DOI: 10.1038/s41392-025-02174-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 01/14/2025] [Accepted: 02/11/2025] [Indexed: 03/20/2025] Open
Abstract
Nucleic acids from both self- and non-self-sources act as vital danger signals that trigger immune responses. Critical illnesses such as acute respiratory distress syndrome, sepsis, trauma and ischemia lead to the aberrant cytosolic accumulation and massive release of nucleic acids that are detected by antiviral innate immune receptors in the endosome or cytosol. Activation of receptors for deoxyribonucleic acids and ribonucleic acids triggers inflammation, a major contributor to morbidity and mortality in critically ill patients. In the past decade, there has been growing recognition of the therapeutic potential of targeting nucleic acid sensing in critical care. This review summarizes current knowledge of nucleic acid sensing in acute respiratory distress syndrome, sepsis, trauma and ischemia. Given the extensive research on nucleic acid sensing in common pathological conditions like cancer, autoimmune disorders, metabolic disorders and aging, we provide a comprehensive summary of nucleic acid sensing beyond critical illness to offer insights that may inform its role in critical conditions. Additionally, we discuss potential therapeutic strategies that specifically target nucleic acid sensing. By examining nucleic acid sources, sensor activation and function, as well as the impact of regulating these pathways across various acute diseases, we highlight the driving role of nucleic acid sensing in critical illness.
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Affiliation(s)
- Zhaorong Chen
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Bonn, 53127, Bonn, Germany
| | - Rayk Behrendt
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127, Bonn, Germany
| | - Lennart Wild
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Bonn, 53127, Bonn, Germany
| | - Martin Schlee
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127, Bonn, Germany
| | - Christian Bode
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Bonn, 53127, Bonn, Germany.
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8
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Herbert A, Cherednichenko O, Lybrand TP, Egli M, Poptsova M. Zα and Zβ Localize ADAR1 to Flipons That Modulate Innate Immunity, Alternative Splicing, and Nonsynonymous RNA Editing. Int J Mol Sci 2025; 26:2422. [PMID: 40141064 PMCID: PMC11942513 DOI: 10.3390/ijms26062422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 02/27/2025] [Accepted: 03/04/2025] [Indexed: 03/28/2025] Open
Abstract
The double-stranded RNA editing enzyme ADAR1 connects two forms of genetic programming, one based on codons and the other on flipons. ADAR1 recodes codons in pre-mRNA by deaminating adenosine to form inosine, which is translated as guanosine. ADAR1 also plays essential roles in the immune defense against viruses and cancers by recognizing left-handed Z-DNA and Z-RNA (collectively called ZNA). Here, we review various aspects of ADAR1 biology, starting with codons and progressing to flipons. ADAR1 has two major isoforms, with the p110 protein lacking the p150 Zα domain that binds ZNAs with high affinity. The p150 isoform is induced by interferon and targets ALU inverted repeats, a class of endogenous retroelement that promotes their transcription and retrotransposition by incorporating Z-flipons that encode ZNAs and G-flipons that form G-quadruplexes (GQ). Both p150 and p110 include the Zβ domain that is related to Zα but does not bind ZNAs. Here we report strong evidence that Zβ binds the GQ that are formed co-transcriptionally by ALU repeats and within R-loops. By binding GQ, ADAR1 suppresses ALU-mediated alternative splicing, generates most of the reported nonsynonymous edits and promotes R-loop resolution. The recognition of the various alternative nucleic acid conformations by ADAR1 connects genetic programming by flipons with the encoding of information by codons. The findings suggest that incorporating G-flipons into editmers might improve the therapeutic editing efficacy of ADAR1.
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Affiliation(s)
- Alan Herbert
- Discovery, InsideOutBio, Charlestown, MA 02129, USA
| | - Oleksandr Cherednichenko
- International Laboratory of Bioinformatics, HSE University, 101000 Moscow, Russia; (O.C.); (M.P.)
| | - Terry P. Lybrand
- Department of Chemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232-0146, USA;
- Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, TN 37232-0146, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232-0146, USA;
| | - Maria Poptsova
- International Laboratory of Bioinformatics, HSE University, 101000 Moscow, Russia; (O.C.); (M.P.)
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9
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Sasaki N, Homme M, Murayama T, Osaki T, Tenma T, An T, Takegami Y, Tani T, Gedeon PC, Kobayashi Y, Cañadas I, Barbie DA, Yao R, Kitajima S. RNA sensing induced by chromosome missegregation augments anti-tumor immunity. Mol Cell 2025; 85:770-786.e7. [PMID: 39706184 PMCID: PMC11888943 DOI: 10.1016/j.molcel.2024.11.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 11/19/2024] [Accepted: 11/19/2024] [Indexed: 12/23/2024]
Abstract
Viral mimicry driven by endogenous double-stranded RNA (dsRNA) stimulates innate and adaptive immune responses. However, the mechanisms that regulate dsRNA-forming transcripts during cancer therapy remain unclear. Here, we demonstrate that dsRNA is significantly accumulated in cancer cells following pharmacologic induction of micronuclei, stimulating mitochondrial antiviral signaling (MAVS)-mediated dsRNA sensing in conjunction with the cyclic GMP-AMP synthase (cGAS)/stimulator of interferon genes (STING) pathway. Activation of cytosolic dsRNA sensing cooperates with double-stranded DNA (dsDNA) sensing to upregulate immune cell migration and antigen-presenting machinery. Tracing of dsRNA-sequences reveals that dsRNA-forming transcripts are predominantly generated from non-exonic regions, particularly in locations proximal to genes exhibiting high chromatin accessibility. Activation of this pathway by pulsed monopolar spindle 1 (MPS1) inhibitor treatment, which potently induces micronuclei formation, upregulates cytoplasmic dsRNA sensing and thus promotes anti-tumor immunity mediated by cytotoxic lymphocyte activation in vivo. Collectively, our findings uncover a mechanism in which dsRNA sensing cooperates with dsDNA sensing to boost immune responses, offering an approach to enhance the efficacy of cancer therapies targeting genomic instability.
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MESH Headings
- Humans
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/immunology
- RNA, Double-Stranded/metabolism
- Animals
- Nucleotidyltransferases/genetics
- Nucleotidyltransferases/metabolism
- Nucleotidyltransferases/immunology
- Cell Line, Tumor
- Mice
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Membrane Proteins/immunology
- Neoplasms/immunology
- Neoplasms/genetics
- Neoplasms/pathology
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Cycle Proteins/antagonists & inhibitors
- Mice, Inbred C57BL
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Adaptor Proteins, Signal Transducing/immunology
- Signal Transduction
- Micronuclei, Chromosome-Defective
- Immunity, Innate
- Lymphocyte Activation
- Genomic Instability
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Affiliation(s)
- Nobunari Sasaki
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan
| | - Mizuki Homme
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan
| | - Takahiko Murayama
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Tatsuya Osaki
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
| | - Toshiyuki Tenma
- Respiratory Center, Asahikawa Medical University Hospital, Asahikawa 078-8510, Japan
| | - Tadaichi An
- DNAFORM Precision Gene Technologies, Yokohama, Kanagawa 230-0051, Japan
| | - Yujiro Takegami
- DNAFORM Precision Gene Technologies, Yokohama, Kanagawa 230-0051, Japan
| | - Tetsuo Tani
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Patrick C Gedeon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yoshihisa Kobayashi
- Division of Molecular Pathology, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan
| | - Israel Cañadas
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan
| | - Shunsuke Kitajima
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan.
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10
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Tamizkar KH, Jantsch MF. RNA editing in disease: mechanisms and therapeutic potential. RNA (NEW YORK, N.Y.) 2025; 31:359-368. [PMID: 39746751 PMCID: PMC11874977 DOI: 10.1261/rna.080331.124] [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: 11/21/2024] [Accepted: 12/24/2024] [Indexed: 01/04/2025]
Abstract
Adenosine to inosine conversion by adenosine deaminases acting on RNA (ADARs) was first identified in the late 1980s of the previous century. As the conversion of adenosines to inosines can be easily detected by sequencing of cDNAs, where the presence of an inosine reads out as a guanosine, the analysis of this type of RNA editing has become widespread. Consequently, several pipelines for detecting inosines in transcriptomes have become available. Still, how to interpret the consequences and alterations of RNA-editing events in whole transciptome editomes is a matter of debate. In particular, the cause or consequence of altered editomes on disease development is poorly understood. Similarly, absolute frequencies of editing events in single molecules, their longitudinal distribution, and naturally occurring changes during development, in different tissues, or in response to physiological changes need to be explored. Lastly, while the use of site-directed RNA editing as a treatment of certain genetic diseases is rapidly evolving, the applicability of this technology still faces several technical obstacles. In this review, we describe the current state of knowledge on adenosine deamination-type RNA editing, its involvement in disease development, and its potential as a therapeutic. Lastly, we highlight open challenges and questions that need to be addressed.
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Affiliation(s)
- Kasra Honarmand Tamizkar
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
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11
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Kim HS, Eun JW, Jang SH, Kim JY, Jeong JY. The diverse landscape of RNA modifications in cancer development and progression. Genes Genomics 2025; 47:135-155. [PMID: 39643826 DOI: 10.1007/s13258-024-01601-y] [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: 10/25/2024] [Accepted: 11/22/2024] [Indexed: 12/09/2024]
Abstract
BACKGROUND RNA modifications, a central aspect of epitranscriptomics, add a regulatory layer to gene expression by modifying RNA function without altering nucleotide sequences. These modifications play vital roles across RNA species, influencing RNA stability, translation, and interaction dynamics, and are regulated by specific enzymes that add, remove, and interpret these chemical marks. OBJECTIVE This review examines the role of aberrant RNA modifications in cancer progression, exploring their potential as diagnostic and prognostic biomarkers and as therapeutic targets. We focus on how altered RNA modification patterns impact oncogenes, tumor suppressor genes, and overall tumor behavior. METHODS We performed an in-depth analysis of recent studies and advances in RNA modification research, highlighting key types and functions of RNA modifications and their roles in cancer biology. Studies involving preclinical models targeting RNA-modifying enzymes were reviewed to assess therapeutic efficacy and potential clinical applications. RESULTS Aberrant RNA modifications were found to significantly influence cancer initiation, growth, and metastasis. Dysregulation of RNA-modifying enzymes led to altered gene expression profiles in oncogenes and tumor suppressors, correlating with tumor aggressiveness, patient outcomes, and response to immunotherapy. Notably, inhibitors of these enzymes demonstrated potential in preclinical models by reducing tumor growth and enhancing the efficacy of existing cancer treatments. CONCLUSIONS RNA modifications present promising avenues for cancer diagnosis, prognosis, and therapy. Understanding the mechanisms of RNA modification dysregulation is essential for developing targeted treatments that improve patient outcomes. Further research will deepen insights into these pathways and support the clinical translation of RNA modification-targeted therapies.
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Affiliation(s)
- Hyung Seok Kim
- Department of Biochemistry, Kosin University College of Medicine, Seo-Gu, Busan, 49267, South Korea
| | - Jung Woo Eun
- Department of Gastroenterology, Ajou University School of Medicine, 164 Worldcup-Ro, Yeongtong-Gu, Suwon, 16499, South Korea
| | - Se Ha Jang
- Department of Gastroenterology, Ajou University School of Medicine, 164 Worldcup-Ro, Yeongtong-Gu, Suwon, 16499, South Korea
| | - Ji Yun Kim
- Department of Biochemistry, Kosin University College of Medicine, Seo-Gu, Busan, 49267, South Korea
| | - Jee-Yeong Jeong
- Department of Biochemistry, Kosin University College of Medicine, Seo-Gu, Busan, 49267, South Korea.
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12
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Miller CM, Morrison JH, Bankers L, Dran R, Kendrick JM, Briggs E, Ferguson VL, Poeschla EM. ADAR1 haploinsufficiency and sustained viral RdRp dsRNA synthesis synergize to dysregulate RNA editing and cause multi-system interferonopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.21.634124. [PMID: 39896491 PMCID: PMC11785089 DOI: 10.1101/2025.01.21.634124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
Sensing of viral double-stranded RNA by MDA5 triggers abundant but transient interferon-stimulated gene (ISGs) expression. If dsRNA synthesis is made persistent by transgenically expressing a picornaviral RNA-dependent RNA polymerase (RdRp) in mice, lifelong MDA5 activation and marked, global ISG upregulation result. This confers robust protection from viral diseases but in contrast to numerous other chronic MDA5 hyperactivation states, the mice suffer no autoimmune consequences. Here we find they further confound expectations by being resistant to a strong autoimmunity (lupus) provocation. However, knockout of one allele of Adar , which by itself is also well-tolerated, breaks the protective state and results in a severe disease that resembles interferonopathies caused by MDA5 gain-of-function mutations. In Adar +/- RdRp transgenic mice, A-to-I editing is both dysregulated and increased (numbers of genes and sites). This dsRNA-driven, MDA5-wild type model establishes that viral polymerase-sourced dsRNA can drive interferonopathy pathogenesis and illuminates the autoimmunity preventing role of ADAR1, while the ADAR1-intact viral RdRp model distinctively uncouples chronic MDA5 hyperactivity and autoinflammatory disease.
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13
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Akira A, Levanon E, Ben Aroya S. Leveraging Saccharomyces cerevisiae for ADAR research: From high-yield purification to high-throughput screening and therapeutic applications. Methods Enzymol 2025; 710:1-18. [PMID: 39870441 DOI: 10.1016/bs.mie.2024.11.026] [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] [Indexed: 01/29/2025]
Abstract
Saccharomyces cerevisiae, a model eukaryotic organism with a rich history in research and industry, has become a pivotal tool for studying Adenosine Deaminase Acting on RNA (ADAR) enzymes despite lacking these enzymes endogenously. This chapter reviews the diverse methodologies harnessed using yeast to elucidate ADAR structure and function, emphasizing its role in advancing our understanding of RNA editing. Initially, Saccharomyces cerevisiae was instrumental in the high-yield purification of ADARs, addressing challenges associated with enzyme stability and activity in other systems. The chapter highlights the successful application of yeast in high-throughput screening platforms that identify key structural motifs and substrate preferences of ADARs, showcasing its utility in revealing complex enzyme mechanics. Furthermore, we discuss the development of yeast-based systems to optimize guide RNA sequences for site-directed RNA editing (SDRE), demonstrating how these systems can be employed to refine therapeutic strategies targeting genetic mutations. Additionally, exogenous expression of ADARs from various species in yeast has shed light on enzyme potency and substrate recognition across different temperatures, offering insights into evolutionary adaptations. Overall, Saccharomyces cerevisiae has proven to be an invaluable asset in ADAR research, facilitating significant advances in our understanding of RNA editing mechanisms and therapeutic applications.
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Affiliation(s)
- Adi Akira
- Life Science, Bar Ilan University, Ramat Gan, Israel
| | - Erez Levanon
- Life Science, Bar Ilan University, Ramat Gan, Israel
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14
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Zhang Q, Walkley CR. Mouse models for understanding physiological functions of ADARs. Methods Enzymol 2025; 710:153-185. [PMID: 39870443 DOI: 10.1016/bs.mie.2024.11.024] [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] [Indexed: 01/29/2025]
Abstract
Adenosine-to-inosine (A-to-I) editing, is a highly prevalent posttranscriptional modification of RNA, mediated by the adenosine deaminases acting on RNA (ADAR) proteins. Mammalian transcriptomes contain tens of thousands to millions of A-to-I editing events. Mutations in ADAR can result in rare autoinflammatory disorders such as Aicardi-Goutières syndrome (AGS) through to irreversible conditions such as motor neuron disease, amyotrophic lateral sclerosis (ALS). Mouse models have played an important role in our current understanding of the physiology of ADAR proteins. With the advancement of genetic engineering technologies, a number of new mouse models have been recently generated, each providing additional insight into ADAR function. This review highlights both past and current mouse models, exploring the methodologies used in their generation, their respective discoveries, and the significance of these findings in relation to human ADAR physiology.
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Affiliation(s)
- Qinyi Zhang
- St.Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria, Australia; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Carl R Walkley
- St.Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria, Australia; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia.
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15
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Fishman A, Lamm AT. Obstacles in quantifying A-to-I RNA editing by Sanger sequencing. Methods Enzymol 2025; 710:285-302. [PMID: 39870450 DOI: 10.1016/bs.mie.2024.11.032] [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] [Indexed: 01/29/2025]
Abstract
Adenosine-to-Inosine (A-to-I) RNA editing is the most prevalent type of RNA editing, in which adenosine within a completely or largely double-stranded RNA (dsRNA) is converted to inosine by deamination. RNA editing was shown to be involved in many neurological diseases and cancer; therefore, detection of A-to-I RNA editing and quantitation of editing levels are necessary for both basic and clinical biomedical research. While high-throughput sequencing (HTS) is widely used for global detection of editing events, Sanger sequencing is the method of choice for precise characterization of editing site clusters (hyper-editing) and for comparing levels of editing at a particular site under different environmental conditions, developmental stages, genetic backgrounds, or disease states. To detect A-to-I editing events and quantify them using Sanger sequencing, RNA samples are reverse transcribed, cDNA is amplified using gene-specific primers, and then sequenced. The chromatogram outputs are then compared to the genomic DNA sequence. As editing occurs in the context of dsRNA, the reverse transcription step is performed at a temperature as high as 65 °C, using thermostable reverse transcriptase to open double-stranded structures. However, this measure alone is insufficient for transcripts possessing long stems comprised of hundreds of nucleotide pairs. Consequently, the editing levels detected by Sanger sequencing are significantly lower than those obtained by HTS, and the amplification yield is low. We suggest that the reverse transcription is biased towards unedited transcripts, and the severity of the bias is dependent on the transcript's secondary structure. Here, we show how this bias can be significantly reduced to allow reliable detection of editing levels and sufficient product yield.
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Affiliation(s)
- Alla Fishman
- Faculty of Biology, Technion - Israel Institute of Technology, Technion City, Haifa, Israel.
| | - Ayelet T Lamm
- Faculty of Biology, Technion - Israel Institute of Technology, Technion City, Haifa, Israel.
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16
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Rehwinkel J, Mehdipour P. ADAR1: from basic mechanisms to inhibitors. Trends Cell Biol 2025; 35:59-73. [PMID: 39030076 PMCID: PMC11718369 DOI: 10.1016/j.tcb.2024.06.006] [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: 02/13/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/21/2024]
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) converts adenosine to inosine in double-stranded RNA (dsRNA) molecules, a process known as A-to-I editing. ADAR1 deficiency in humans and mice results in profound inflammatory diseases characterised by the spontaneous induction of innate immunity. In cells lacking ADAR1, unedited RNAs activate RNA sensors. These include melanoma differentiation-associated gene 5 (MDA5) that induces the expression of cytokines, particularly type I interferons (IFNs), protein kinase R (PKR), oligoadenylate synthase (OAS), and Z-DNA/RNA binding protein 1 (ZBP1). Immunogenic RNAs 'defused' by ADAR1 may include transcripts from repetitive elements and other long duplex RNAs. Here, we review these recent fundamental discoveries and discuss implications for human diseases. Some tumours depend on ADAR1 to escape immune surveillance, opening the possibility of unleashing anticancer therapies with ADAR1 inhibitors.
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Affiliation(s)
- Jan Rehwinkel
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Parinaz Mehdipour
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK.
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17
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Cheng L, Liu Z, Shen C, Xiong Y, Shin SY, Hwang Y, Yang S, Chen Z, Zhang X. A Wonderful Journey: The Diverse Roles of Adenosine Deaminase Action on RNA 1 (ADAR1) in Central Nervous System Diseases. CNS Neurosci Ther 2025; 31:e70208. [PMID: 39753993 PMCID: PMC11702419 DOI: 10.1111/cns.70208] [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: 10/09/2024] [Revised: 12/03/2024] [Accepted: 12/20/2024] [Indexed: 01/14/2025] Open
Abstract
BACKGROUND Adenosine deaminase action on RNA 1 (ADAR1) can convert the adenosine in double-stranded RNA (dsRNA) molecules into inosine in a process known as A-to-I RNA editing. ADAR1 regulates gene expression output by interacting with RNA and other proteins; plays important roles in development, including growth; and is linked to innate immunity, tumors, and central nervous system (CNS) diseases. RESULTS In recent years, the role of ADAR1 in tumors has been widely discussed, but its role in CNS diseases has not been reviewed. It is worth noting that recent studies have shown ADAR1 has great potential in the treatment of neurodegenerative diseases, but the mechanisms are still unclear. Therefore, it is necessary to elaborate on the role of ADAR1 in CNS diseases. CONCLUSIONS Here, we focus on the effects and mechanisms of ADAR1 on CNS diseases such as Aicardi-AicardiGoutières syndrome, Alzheimer's disease, Parkinson's disease, glioblastoma, epilepsy, amyotrophic lateral sclerosis, and autism. We also evaluate the impact of ADAR1-based treatment strategies on these diseases, with a particular focus on the development and treatment strategies of new technologies such as microRNAs, nanotechnology, gene editing, and stem cell therapy. We hope to provide new directions and insights for the future development of ADAR1 gene editing technology in brain science and the treatment of CNS diseases.
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Affiliation(s)
- Lin Cheng
- Department of NeurologyAffiliated Hospital of Jiujiang UniversityJiujiangJiangxiChina
- Jiujiang Clinical Precision Medicine Research CenterJiujiangJiangxiChina
| | - Ziying Liu
- Jiujiang Clinical Precision Medicine Research CenterJiujiangJiangxiChina
- Department of PathologyAffiliated Hospital of Jiujiang UniversityJiujiangJiangxiChina
| | - Chunxiao Shen
- Jiujiang Clinical Precision Medicine Research CenterJiujiangJiangxiChina
- Department of PathologyAffiliated Hospital of Jiujiang UniversityJiujiangJiangxiChina
| | - Yinyi Xiong
- Department of RehabilitationAffiliated Hospital of Jiujiang UniversityJiujiangJiangxiChina
| | - Sang Yol Shin
- Department of Emergency Medical TechnologyWonkwang University College of MedicineIksanJeonbuk‐doRepublic of Korea
| | - Yong Hwang
- Department of Emergency MedicineWonkwang University College of MedicineIksanJeonbuk‐doRepublic of Korea
| | - Seung‐Bum Yang
- Department of ParamedicineWonkwang Health Science UniversityIksanJeonbuk‐doRepublic of Korea
| | - Zhiying Chen
- Department of NeurologyAffiliated Hospital of Jiujiang UniversityJiujiangJiangxiChina
- Jiujiang Clinical Precision Medicine Research CenterJiujiangJiangxiChina
| | - Xiaorong Zhang
- Jiujiang Clinical Precision Medicine Research CenterJiujiangJiangxiChina
- Department of PathologyAffiliated Hospital of Jiujiang UniversityJiujiangJiangxiChina
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18
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Zhang Y, Li L, Mendoza JJ, Wang D, Yan Q, Shi L, Gong Z, Zeng Z, Chen P, Xiong W. Advances in A-to-I RNA editing in cancer. Mol Cancer 2024; 23:280. [PMID: 39731127 DOI: 10.1186/s12943-024-02194-6] [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: 09/18/2024] [Accepted: 12/04/2024] [Indexed: 12/29/2024] Open
Abstract
RNA modifications are widespread throughout the mammalian transcriptome and play pivotal roles in regulating various cellular processes. These modifications are strongly linked to the development of many cancers. One of the most prevalent forms of RNA modifications in humans is adenosine-to-inosine (A-to-I) editing, catalyzed by the enzyme adenosine deaminase acting on RNA (ADAR) in double-stranded RNA (dsRNA). With advancements in RNA sequencing technologies, the role of A-to-I modification in cancer has garnered increasing attention. Research indicates that the levels and specific sites of A-to-I editing are significantly altered in many malignant tumors, correlating closely with tumor progression. This editing occurs in both coding and noncoding regions of RNA, influencing signaling pathways involved in cancer development. These modifications can either promote or suppress cancer progression through several mechanisms, including inducing non-synonymous amino acid mutations, altering the immunogenicity of dsRNAs, modulating mRNA interactions with microRNAs (miRNAs), and affecting the splicing of circular RNAs (circRNAs) as well as the function of long non-coding RNAs (lncRNAs). A comprehensive understanding of A-to-I RNA editing is crucial for advancing the diagnosis, treatment, and prognosis of human cancers. This review explores the regulatory mechanisms of A-to-I editing in cancers and examines their potential clinical applications. It also summarizes current research, identifies future directions, and highlights potential therapeutic implications.
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Affiliation(s)
- Yi Zhang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Lvyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Juana Jessica Mendoza
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Dan Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Qijia Yan
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Lei Shi
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China
- Furong Laboratory, Changsha, Hunan, 410078, China
| | - Pan Chen
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China.
- Furong Laboratory, Changsha, Hunan, 410078, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China.
- Furong Laboratory, Changsha, Hunan, 410078, China.
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19
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Li J, Zhu J, Yang H, Hou F. Sterile activation of RNA-sensing pathways in autoimmunity. J Mol Cell Biol 2024; 16:mjae029. [PMID: 39143032 PMCID: PMC11659683 DOI: 10.1093/jmcb/mjae029] [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: 01/26/2024] [Revised: 06/27/2024] [Accepted: 08/13/2024] [Indexed: 08/16/2024] Open
Abstract
RNA-sensing pathways play a pivotal role in host defense against pathogenic infections to maintain cellular homeostasis. However, in the absence of infection, certain endogenous RNAs can serve as the activators of RNA-sensing pathways as well. The inappropriate activation of RNA-sensing pathways by self-ligands leads to systemic inflammation and autoimmune diseases. In this review, we summarize current findings on the sterile activation of RNA sensors, as well as its implications in autoimmunity, inflammatory diseases, and therapeutics.
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Affiliation(s)
- Jiaxin Li
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Junyan Zhu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Yang
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Fajian Hou
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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20
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Luca D, Kato H. Mouse models of type I interferonopathies. Hum Mol Genet 2024:ddae187. [PMID: 39680957 DOI: 10.1093/hmg/ddae187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Accepted: 12/10/2024] [Indexed: 12/18/2024] Open
Abstract
Type I interferonopathies are severe monogenic diseases caused by mutations that result in chronically upregulated production of type I interferon. They present with a broad variety of symptoms, the mechanisms of which are being extensively studied. Mouse models of type I interferonopathies are an important resource for this purpose, and in this context, we review several key molecular and phenotypic findings that are advancing our understanding of the respective diseases. We focus on genotypes related to nucleic acid metabolism, sensing by cytosolic receptors and downstream signalling.
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Affiliation(s)
- Domnica Luca
- Institute of Cardiovascular Immunology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
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21
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Vukić D, Cherian A, Keskitalo S, Bong YT, Marônek M, Yadav L, Keegan LP, Varjosalo M, O'Connell MA. Distinct interactomes of ADAR1 nuclear and cytoplasmic protein isoforms and their responses to interferon induction. Nucleic Acids Res 2024; 52:14184-14204. [PMID: 39673305 DOI: 10.1093/nar/gkae1106] [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] [Received: 03/04/2024] [Revised: 09/29/2024] [Accepted: 11/04/2024] [Indexed: 12/16/2024] Open
Abstract
The RNA editing enzyme adenosine deaminase acting on RNA 1 (ADAR1) is essential for correct functioning of innate immune responses. The ADAR1p110 isoform is mainly nuclear and ADAR1p150, which is interferon (IFN) inducible, is predominately cytoplasmic. Using three different methods - co-immunoprecipitation (co-IP) of endogenous ADAR1, Strep-tag co-IP and BioID with individual ADAR1 isoforms - a comprehensive interactome was generated during both homeostasis and the IFN response. Both known and novel interactors as well as editing regulators were identified. Nuclear proteins were detected as stable interactors with both ADAR1 isoforms. In contrast, BioID identified distinct protein networks for each ADAR1 isoform, with nuclear components observed with ADAR1p110 and components of cytoplasmic cellular condensates with ADAR1p150. RNase A digestion distinguished between distal and proximal interactors, as did a double-stranded RNA (dsRNA)-binding mutant of ADAR1 which demonstrated the importance of dsRNA binding for ADAR1 interactions. IFN treatment did not affect the core ADAR1 interactomes but resulted in novel interactions, the majority of which are proximal interactions retained after RNase A treatment. Short treatment with high molecular weight poly(I:C) during the IFN response resulted in dsRNA-binding-dependent changes in the proximal protein network of ADAR1p110 and association of the ADAR1p150 proximal protein network with some components of antiviral stress granules.
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Affiliation(s)
- Dragana Vukić
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 62500, Czechia
- NationalCentre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 62500, Czechia
| | - Anna Cherian
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 62500, Czechia
- NationalCentre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 62500, Czechia
| | - Salla Keskitalo
- Institute of Biotechnology, HelsinkiInstitute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Yih Tyng Bong
- Institute of Biotechnology, HelsinkiInstitute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Martin Marônek
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 62500, Czechia
| | - Leena Yadav
- Institute of Biotechnology, HelsinkiInstitute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Liam P Keegan
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 62500, Czechia
| | - Markku Varjosalo
- Institute of Biotechnology, HelsinkiInstitute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Mary A O'Connell
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 62500, Czechia
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22
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Vesely C, Jantsch MF. Editing specificity of ADAR isoforms. Methods Enzymol 2024; 710:77-98. [PMID: 39870452 DOI: 10.1016/bs.mie.2024.11.021] [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] [Indexed: 01/29/2025]
Abstract
Adenosine to inosine deaminases acting on RNA (ADARs) enzymes are found in all metazoa. Their sequence and protein organization is conserved but also shows distinct differences. Moreover, the number of ADAR genes differs between organisms, ranging from one in flies to three in mammals. The distinct isoforms of ADARs and their specific roles determine the complexity of A-to-I RNA editing, its regulation and the versatility of these enzymes. Understanding the different isoform-specific functions and targets will provide a deeper understanding of the diverse biological processes influenced by ADARs, either through ADAR editing of dsRNAs or the interaction with RNAs and proteins. The detailed identification and assigning of isoform-specific targets is a crucial step towards our understanding of functional differences amongst ADAR isoforms and will help us to understand their individual implications for health and disease. This chapter delves into unique characteristics and functional implications of ADAR isoforms. We describe the ectopic overexpression in editing free cells and the use of RNA immunoprecipitation coupled with sequencing to determine isoform-specific interactions with RNAs and their editing sites. Additionally, we discuss new challenges in editing detection by different ADARs in the context of other modifications and provide ideas for potentially better methods to determine the "true editome".
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Affiliation(s)
- Cornelia Vesely
- Medical University of Vienna, Center of Anatomy and Cell Biology, Division of Cell and Developmental Biology, Schwarzspanier Strasse, Vienna, Austria.
| | - Michael F Jantsch
- Medical University of Vienna, Center of Anatomy and Cell Biology, Division of Cell and Developmental Biology, Schwarzspanier Strasse, Vienna, Austria.
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23
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Xu W, Sun Y, Breen P, Ruvkun G, Mao K. Caenorhabditis elegans inositol hexaphosphate pathways couple to RNA interference and pathogen defense. Proc Natl Acad Sci U S A 2024; 121:e2416982121. [PMID: 39602251 PMCID: PMC11626161 DOI: 10.1073/pnas.2416982121] [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: 08/22/2024] [Accepted: 11/05/2024] [Indexed: 11/29/2024] Open
Abstract
RNA interference (RNAi) is an evolutionarily conserved pathway that defends against viral infections in diverse organisms. Caenorhabditis elegans mutations that enhance RNAi have revealed pathways that may regulate antiviral defense. A genetic screen for C. elegans mutations that fail to up-regulate a defense response reporter transgene detected mutations that enhance RNAi to silence this reporter gene in the inositol polyphosphate multikinase impk-1, the synMuv B gene lin-15B, and the pathogen defense response gene pals-22. Using other assays for enhanced RNAi, we found that the impk-1 alleles and an ippk-1 gene inactivation of a later step in inositol hexaphosphate (IP6) synthesis, and the lin-15B and pals-22 alleles enhance RNAi. IP6 has been known for decades to bind and stabilize human adenosine deaminase that acts on RNA (ADAR) as well as the paralog tRNA editing ADAT. We show that the C. elegans IP6 pathway is also required for mRNA and tRNA editing. Thus, a deficiency in two axes of RNA editing enhances the already potent C. elegans RNAi antiviral defense, suggesting adenosine to inosine RNA editing may normally moderate this siRNA antiviral defense pathway. The C. elegans IP6-deficient mutants are synthetic lethal with a set of enhanced RNAi mutants that act in the polyploid hypodermis to regulate collagen secretion and signaling from that tissue, implicating IP6 signaling especially in this tissue. This enhanced antiviral RNAi response uses the C. elegans RIG-I-like receptor DRH-1 to activate the unfolded protein response (UPR). The production of primary siRNAs, rather than secondary siRNAs, contributes to this activation of the UPR through XBP-1 signaling. The gon-14 and pal-17 mutants that also emerged from this screen act in the mitochondrial defense pathway rather than by enhancing RNAi.
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Affiliation(s)
- Wenjing Xu
- Institute of Future Agriculture, Northwest Agriculture and Forestry University, Yangling, Shaanxi712100, China
| | - Yifan Sun
- Institute of Future Agriculture, Northwest Agriculture and Forestry University, Yangling, Shaanxi712100, China
| | - Peter Breen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Kai Mao
- Institute of Future Agriculture, Northwest Agriculture and Forestry University, Yangling, Shaanxi712100, China
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Genetics, Harvard Medical School, Boston, MA02115
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24
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Zerad L, Gacem N, Gayda F, Day L, Sinigaglia K, Richard L, Parisot M, Cagnard N, Mathis S, Bole-Feysot C, O’Connell MA, Pingault V, Dambroise E, Keegan LP, Vallat JM, Bondurand N. Overexpression of Egr1 Transcription Regulator Contributes to Schwann Cell Differentiation Defects in Neural Crest-Specific Adar1 Knockout Mice. Cells 2024; 13:1952. [PMID: 39682701 PMCID: PMC11639873 DOI: 10.3390/cells13231952] [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: 10/11/2024] [Revised: 11/05/2024] [Accepted: 11/15/2024] [Indexed: 12/18/2024] Open
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) is the principal enzyme for the adenosine-to-inosine RNA editing that prevents the aberrant activation of cytosolic nucleic acid sensors by endogenous double stranded RNAs and the activation of interferon-stimulated genes. In mice, the conditional neural crest deletion of Adar1 reduces the survival of melanocytes and alters the differentiation of Schwann cells that fail to myelinate nerve fibers in the peripheral nervous system. These myelination defects are partially rescued upon the concomitant removal of the Mda5 antiviral dsRNA sensor in vitro, suggesting implication of the Mda5/Mavs pathway and downstream effectors in the genesis of Adar1 mutant phenotypes. By analyzing RNA-Seq data from the sciatic nerves of mouse pups after conditional neural crest deletion of Adar1 (Adar1cKO), we here identified the transcription factors deregulated in Adar1cKO mutants compared to the controls. Through Adar1;Mavs and Adar1cKO;Egr1 double-mutant mouse rescue analyses, we then highlighted that the aberrant activation of the Mavs adapter protein and overexpression of the early growth response 1 (EGR1) transcription factor contribute to the Adar1 deletion associated defects in Schwann cell development in vivo. In silico and in vitro gene regulation studies additionally suggested that EGR1 might mediate this inhibitory effect through the aberrant regulation of EGR2-regulated myelin genes. We thus demonstrate the role of the Mda5/Mavs pathway, but also that of the Schwann cell transcription factors in Adar1-associated peripheral myelination defects.
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Affiliation(s)
- Lisa Zerad
- Laboratory of Embryology and Genetics of Human Malformations, Imagine Institute, INSERM UMR 1163, Université Paris Cité, 24 Boulevard du Montparnasse, 75015 Paris, France; (L.Z.); (N.G.); (F.G.); (L.D.); (V.P.)
| | - Nadjet Gacem
- Laboratory of Embryology and Genetics of Human Malformations, Imagine Institute, INSERM UMR 1163, Université Paris Cité, 24 Boulevard du Montparnasse, 75015 Paris, France; (L.Z.); (N.G.); (F.G.); (L.D.); (V.P.)
| | - Fanny Gayda
- Laboratory of Embryology and Genetics of Human Malformations, Imagine Institute, INSERM UMR 1163, Université Paris Cité, 24 Boulevard du Montparnasse, 75015 Paris, France; (L.Z.); (N.G.); (F.G.); (L.D.); (V.P.)
| | - Lucie Day
- Laboratory of Embryology and Genetics of Human Malformations, Imagine Institute, INSERM UMR 1163, Université Paris Cité, 24 Boulevard du Montparnasse, 75015 Paris, France; (L.Z.); (N.G.); (F.G.); (L.D.); (V.P.)
| | - Ketty Sinigaglia
- Central European Institute for Technology, Masaryk University (CEITEC MU), Kamenice 735/5, 625 00 Brno, Czech Republic; (K.S.); (M.A.O.); (L.P.K.)
| | - Laurence Richard
- Department of Neurology, Centre de Reference “Neuropathies Périphériques Rares”, CHU Limoges, 87000 Limoges, France; (L.R.); (J.M.V.)
| | - Melanie Parisot
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM U1163 et INSERM US24/CNRS UAR3633, Paris Descartes Sorbonne Paris Cite University, 75015 Paris, France; (M.P.); (C.B.-F.)
| | - Nicolas Cagnard
- Bioinformatics Platform, Imagine Institute, INSERM UMR 1163, 75015 Paris, France;
| | - Stephane Mathis
- Department of Neurology (Nerve-Muscle Unit) and ‘Grand Sud-Ouest’ National Reference Center for Neuromuscular Disorders, CHU Bordeaux, Pellegrin Hospital, 33000 Bordeaux, France;
| | - Christine Bole-Feysot
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM U1163 et INSERM US24/CNRS UAR3633, Paris Descartes Sorbonne Paris Cite University, 75015 Paris, France; (M.P.); (C.B.-F.)
| | - Mary A. O’Connell
- Central European Institute for Technology, Masaryk University (CEITEC MU), Kamenice 735/5, 625 00 Brno, Czech Republic; (K.S.); (M.A.O.); (L.P.K.)
| | - Veronique Pingault
- Laboratory of Embryology and Genetics of Human Malformations, Imagine Institute, INSERM UMR 1163, Université Paris Cité, 24 Boulevard du Montparnasse, 75015 Paris, France; (L.Z.); (N.G.); (F.G.); (L.D.); (V.P.)
| | - Emilie Dambroise
- Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, Imagine Institute, INSERM UMR 1163, Université Paris Cité, 24 Boulevard du Montparnasse, 75015 Paris, France;
| | - Liam P. Keegan
- Central European Institute for Technology, Masaryk University (CEITEC MU), Kamenice 735/5, 625 00 Brno, Czech Republic; (K.S.); (M.A.O.); (L.P.K.)
| | - Jean Michel Vallat
- Department of Neurology, Centre de Reference “Neuropathies Périphériques Rares”, CHU Limoges, 87000 Limoges, France; (L.R.); (J.M.V.)
| | - Nadege Bondurand
- Laboratory of Embryology and Genetics of Human Malformations, Imagine Institute, INSERM UMR 1163, Université Paris Cité, 24 Boulevard du Montparnasse, 75015 Paris, France; (L.Z.); (N.G.); (F.G.); (L.D.); (V.P.)
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25
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Heraud-Farlow JE, Taylor SR, Chalk AM, Escudero A, Hu SB, Goradia A, Sun T, Li Q, Nikolic I, Li JB, Fidalgo M, Guallar D, Simpson KJ, Walkley CR. GGNBP2 regulates MDA5 sensing triggered by self double-stranded RNA following loss of ADAR1 editing. Sci Immunol 2024; 9:eadk0412. [PMID: 39576872 DOI: 10.1126/sciimmunol.adk0412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 06/05/2024] [Accepted: 10/21/2024] [Indexed: 11/24/2024]
Abstract
Adenosine-to-inosine (A-to-I) editing of double-stranded RNA (dsRNA) by ADAR1 is an essential modifier of the immunogenicity of cellular dsRNA. The role of MDA5 in sensing unedited cellular dsRNA and the downstream activation of type I interferon (IFN) signaling are well established. However, we have an incomplete understanding of pathways that modify the response to unedited dsRNA. We performed a genome-wide CRISPR screen and showed that GGNBP2, CNOT10, and CNOT11 interact and regulate sensing of unedited cellular dsRNA. We found that GGNBP2 acts between dsRNA transcription and its cytoplasmic sensing by MDA5. GGNBP2 loss prevented induction of type I IFN and autoinflammation after the loss of ADAR1 editing activity by modifying the subcellular distribution of endogenous A-to-I editing substrates and reducing cytoplasmic dsRNA load. These findings reveal previously undescribed pathways to modify diseases associated with ADAR mutations and may be determinants of response or resistance to small-molecule ADAR1 inhibitors.
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Affiliation(s)
- Jacki E Heraud-Farlow
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Department of Medicine, St. Vincent's Hospital, Melbourne Medical School, University of Melbourne, Fitzroy, VIC 3065, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3168, Australia
| | - Scott R Taylor
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Alistair M Chalk
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Adriana Escudero
- Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC) - Health Research Institute (IDIS), Santiago de Compostela 15782, Spain
| | - Shi-Bin Hu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ankita Goradia
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Tao Sun
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Iva Nikolic
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology and Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Miguel Fidalgo
- Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC) - Health Research Institute (IDIS), Santiago de Compostela 15782, Spain
| | - Diana Guallar
- Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC) - Health Research Institute (IDIS), Santiago de Compostela 15782, Spain
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology and Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Department of Medicine, St. Vincent's Hospital, Melbourne Medical School, University of Melbourne, Fitzroy, VIC 3065, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3168, Australia
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26
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Mboukou A, Rajendra V, Messmer S, Mandl TC, Catala M, Tisné C, Jantsch MF, Barraud P. Dimerization of ADAR1 modulates site-specificity of RNA editing. Nat Commun 2024; 15:10051. [PMID: 39572551 PMCID: PMC11582362 DOI: 10.1038/s41467-024-53777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 10/15/2024] [Indexed: 11/24/2024] Open
Abstract
Adenosine-to-inosine editing is catalyzed by adenosine deaminases acting on RNA (ADARs) in double-stranded RNA (dsRNA) regions. Although three ADARs exist in mammals, ADAR1 is responsible for the vast majority of the editing events and acts on thousands of sites in the human transcriptome. ADAR1 has been proposed to form a stable homodimer and dimerization is suggested to be important for editing activity. In the absence of a structural basis for the dimerization of ADAR1, and without a way to prevent dimer formation, the effect of dimerization on enzyme activity or site specificity has remained elusive. Here, we report on the structural analysis of the third double-stranded RNA-binding domain of ADAR1 (dsRBD3), which reveals stable dimer formation through a large inter-domain interface. Exploiting these structural insights, we engineered an interface-mutant disrupting ADAR1-dsRBD3 dimerization. Notably, dimerization disruption did not abrogate ADAR1 editing activity but intricately affected editing efficiency at selected sites. This suggests a complex role for dimerization in the selection of editing sites by ADARs, and makes dimerization a potential target for modulating ADAR1 editing activity.
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Affiliation(s)
- Allegra Mboukou
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Vinod Rajendra
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Serafina Messmer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Therese C Mandl
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Marjorie Catala
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Carine Tisné
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Michael F Jantsch
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria.
| | - Pierre Barraud
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France.
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27
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Liang Z, Walkley CR, Heraud-Farlow JE. A-to-I RNA editing and hematopoiesis. Exp Hematol 2024; 139:104621. [PMID: 39187172 DOI: 10.1016/j.exphem.2024.104621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 08/28/2024]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing plays essential roles in modulating normal development and homeostasis. This process is catalyzed by adenosine deaminase acting on RNA (ADAR) family proteins. The most well-understood biological processes modulated by A-to-I editing are innate immunity and neurological development, attributed to ADAR1 and ADAR2, respectively. A-to-I editing by ADAR1 is also critical in regulating hematopoiesis. This review will focus on the role of A-to-I RNA editing and ADAR enzymes, particularly ADAR1, during normal hematopoiesis in humans and mice. Furthermore, we will discuss Adar1 mouse models that have been developed to understand the contribution of ADAR1 to hematopoiesis and its role in innate immune pathways.
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Affiliation(s)
- Zhen Liang
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria, Australia
| | - Carl R Walkley
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria, Australia.
| | - Jacki E Heraud-Farlow
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria, Australia.
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28
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Weldy CS, Li Q, Monteiro JP, Guo H, Galls D, Gu W, Cheng PP, Ramste M, Li D, Palmisano BT, Sharma D, Worssam MD, Zhao Q, Bhate A, Kundu RK, Nguyen T, Li JB, Quertermous T. Smooth muscle expression of RNA editing enzyme ADAR1 controls activation of RNA sensor MDA5 in atherosclerosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602569. [PMID: 39026721 PMCID: PMC11257488 DOI: 10.1101/2024.07.08.602569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Mapping the genomic architecture of complex disease has been predicated on the understanding that genetic variants influence disease risk through modifying gene expression. However, recent discoveries have revealed that a significant burden of disease heritability in common autoinflammatory disorders and coronary artery disease is mediated through genetic variation modifying post-transcriptional modification of RNA through adenosine-to-inosine (A-to-I) RNA editing. This common RNA modification is catalyzed by ADAR enzymes, where ADAR1 edits specific immunogenic double stranded RNA (dsRNA) to prevent activation of the double strand RNA (dsRNA) sensor MDA5 ( IFIH1 ) and stimulation of an interferon stimulated gene (ISG) response. Multiple lines of human genetic data indicate impaired RNA editing and increased dsRNA sensing by MDA5 to be an important mechanism of coronary artery disease (CAD) risk. Here, we provide a crucial link between observations in human genetics and mechanistic cell biology leading to progression of CAD. Through analysis of human atherosclerotic plaque, we implicate the vascular smooth muscle cell (SMC) to have a unique requirement for RNA editing, and that ISG induction occurs in SMC phenotypic modulation, implicating MDA5 activation. Through culture of human coronary artery SMCs, generation of a conditional SMC specific Adar1 deletion mouse model on a pro-atherosclerosis background with additional constitutive deletion of MDA5 ( Ifih1 ), and with incorporation of single cell RNA sequencing cellular profiling, we further show that Adar1 controls SMC phenotypic state by regulating Mda5 activation, is required to maintain vascular integrity, and controls progression of atherosclerosis and vascular calcification. Through this work, we describe a fundamental mechanism of CAD, where cell type and context specific RNA editing and sensing of dsRNA mediates disease progression, bridging our understanding of human genetics and disease causality. One Sentence Summary Smooth muscle expression of RNA editing enzyme ADAR1 regulates activation of double strand RNA sensor MDA5 in novel mechanism of atherosclerosis.
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29
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Young AA, Bohlin HE, Pierce JR, Cottrell KA. Suppression of double-stranded RNA sensing in cancer: molecular mechanisms and therapeutic potential. Biochem Soc Trans 2024; 52:2035-2045. [PMID: 39221819 PMCID: PMC11555700 DOI: 10.1042/bst20230727] [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: 06/26/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Immunotherapy has emerged as a therapeutic option for many cancers. For some tumors, immune checkpoint inhibitors show great efficacy in promoting anti-tumor immunity. However, not all tumors respond to immunotherapies. These tumors often exhibit reduced inflammation and are resistant to checkpoint inhibitors. Therapies that turn these 'cold' tumors 'hot' could improve the efficacy and applicability of checkpoint inhibitors, and in some cases may be sufficient on their own to promote anti-tumor immunity. One strategy to accomplish this goal is to activate innate immunity pathways within the tumor. Here we describe how this can be accomplished by activating double-stranded RNA (dsRNA) sensors. These sensors evolved to detect and respond to dsRNAs arising from viral infection but can also be activated by endogenous dsRNAs. A set of proteins, referred to as suppressors of dsRNA sensing, are responsible for preventing sensing 'self' dsRNA and activating innate immunity pathways. The mechanism of action of these suppressors falls into three categories: (1) Suppressors that affect mature RNAs through editing, degradation, restructuring, or binding. (2) Suppressors that affect RNA processing. (3) Suppressors that affect RNA expression. In this review we highlight suppressors that function through each mechanism, provide examples of the effects of disrupting those suppressors in cancer cell lines and tumors, and discuss the therapeutic potential of targeting these proteins and pathways.
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Affiliation(s)
- Addison A. Young
- Department of Biochemistry, Purdue University, West Lafayette, IN, U.S.A
| | - Holly E. Bohlin
- Department of Biochemistry, Purdue University, West Lafayette, IN, U.S.A
| | - Jackson R. Pierce
- Department of Biochemistry, Purdue University, West Lafayette, IN, U.S.A
| | - Kyle A. Cottrell
- Department of Biochemistry, Purdue University, West Lafayette, IN, U.S.A
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30
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Zhu Y, Zhang D, Wu L, Ouyang X, Zhu S, Wang X, Xiao Z, Tan Y, Li C. Two Novel and Two Recurrent Variants of the ADAR1 Gene in Three Chinese Families with Dyschromatosis Symmetrica Hereditaria. Clin Cosmet Investig Dermatol 2024; 17:2373-2379. [PMID: 39469661 PMCID: PMC11514803 DOI: 10.2147/ccid.s477138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 10/20/2024] [Indexed: 10/30/2024]
Abstract
Purpose Dyschromatosis symmetrica hereditaria (DSH) is a rare autosomal dominant inherited pigmentary dermatosis. The gene responsible for DSH has been identified as adenosine deaminase acting on RNA1 (ADAR1). This study aimed to identify the causative variants in the ADAR1 gene in three Chinese families with DSH. Patients and Methods Data and blood samples were collected from three Chinese families with DSH. Whole-exome and Sanger sequencing were performed to detect pathogenic gene mutation in the patients. Bioinformatics tools were used to predict the pathogenicity of the variants. Results Four heterozygous ADAR1 variants were identified, including two novel missense variants c.2369G>C (Arg790Pro), and 503C>T (Pro168Leu), and two previously reported variants: c.3232C>T(R1078C), and c.1472C>G (p.S491X). The novel c.503C>T variant was predicted as "deleterious" (score =-2.704) by PROVEAN, and "probably damaging" (score = 1) by PolyPhen2. The other novel variant c.2369G>C was also predicted as "deleterious" (score =-4.167) by PROVEAN, "probably damaging" (score = 1) by PolyPhen2, and "disease-causing" (p = 0.999) by Mutation Taster. Conclusion Two novel ADAR1 variants were found in Chinese patients with DSH. This research has expanded the ADAR1 gene database for DSH, enhancing our comprehension of the underlying mechanisms.
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Affiliation(s)
- Yunxia Zhu
- Department of Dermatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, People’s Republic of China
| | - Deng Zhang
- Department of Dermatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, People’s Republic of China
| | - Liang Wu
- Department of Dermatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, People’s Republic of China
| | - Xiaoliang Ouyang
- Department of Plastic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, People’s Republic of China
| | - Shengcai Zhu
- Department of Dermatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, People’s Republic of China
| | - Xiuping Wang
- Department of Dermatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, People’s Republic of China
| | - Zhen Xiao
- Department of Dermatology, Taiyuan Central Hospital, Taiyuan, Shanxi, People’s Republic of China
| | - Yanping Tan
- Department of Dermatology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi, People’s Republic of China
| | - Chunming Li
- Department of Dermatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, People’s Republic of China
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31
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Wang B, Le DS, Liu L, Zhang XX, Yang F, Lai GR, Zhang C, Zhao ML, Shen YP, Liao PS, Liu T, Liang YP. Targeting exosomal double-stranded RNA-TLR3 signaling pathway attenuates morphine tolerance and hyperalgesia. Cell Rep Med 2024; 5:101782. [PMID: 39413734 PMCID: PMC11513852 DOI: 10.1016/j.xcrm.2024.101782] [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: 03/11/2024] [Revised: 08/14/2024] [Accepted: 09/18/2024] [Indexed: 10/18/2024]
Abstract
Long-term morphine use leads to tolerance and hyperalgesia in patients with chronic pain, with neuroinflammation playing a key role, but its underlying mechanisms remain elusive. This study determines that repeated intrathecal morphine injections increase double-stranded RNA (dsRNA) production in spinal neurons, due to downregulated adenosine deaminase RNA specific 1 (ADAR1) expression. Lentivirus-induced ADAR1 elevation decreases the high levels of intracellular dsRNA and attenuates morphine tolerance and hyperalgesia. dsRNA is released into cerebrospinal fluid via exosomes (Exos) after repeated morphine injections and is taken up by microglia for TLR3-TRIF-IL-6 signaling activation. Blocking Exos release with GW4869 or inhibition of TLR3 signaling mitigates neuroinflammation, preventing the development of morphine tolerance and hyperalgesia. Intrathecal injection of TLR3 inhibitor alone shows analgesic effects in neuropathic pain, and co-administration with morphine amplifies the analgesic efficacy of morphine. These findings demonstrate that targeting dsRNA-TLR3 signaling to mitigate neuroinflammation could be a promising treatment for morphine tolerance.
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Affiliation(s)
- Bing Wang
- Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA; Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, Jiangsu, China
| | - Dong-Sheng Le
- Department of Pain Management, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Li Liu
- Department of Pain Management, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Xue-Xue Zhang
- Department of Pain Management, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Fan Yang
- Department of Pain Management, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Guo-Rong Lai
- Department of Pain Management, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Chao Zhang
- Department of Pain Management, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Mai-Lin Zhao
- Department of Pain Management, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Yun-Peng Shen
- Department of Anesthesiology, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Ping-Sheng Liao
- Department of Pain Management, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Tong Liu
- Institute of Pain Medicine and Special Environmental Medicine, Nantong University, Nantong, Jiangsu, China.
| | - Ying-Ping Liang
- Department of Pain Management, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China.
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Thomas R, Zaksauskaite R, Al-Kandari N, Hyde A, Abugable A, El-Khamisy S, van Eeden F. Second generation lethality in RNAseH2a knockout zebrafish. Nucleic Acids Res 2024; 52:11014-11028. [PMID: 39217460 PMCID: PMC11472149 DOI: 10.1093/nar/gkae725] [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] [Received: 12/20/2023] [Revised: 07/31/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024] Open
Abstract
Removal of ribonucleotides from DNA by RNaseH2 is essential for genome stability, and its impacted function causes the neurodegenerative disease, Aicardi Goutières Syndrome. We have created a zebrafish rnaseh2a mutant to model this process. Surprisingly, RNaseH2a knockouts show little phenotypic abnormality at adulthood in the first generation, unlike mouse knockout models, which are early embryonic lethal. However, the second generation offspring show reduced development, increased ribonucleotide incorporation and upregulation of key inflammatory markers, resulting in both maternal and paternal embryonic lethality. Thus, neither fathers or mothers can generate viable offspring even when crossed to wild-type partners. Despite their survival, rnaseh2a-/- adults show an accumulation of ribonucleotides in both the brain and testes that is not present in early development. Our data suggest that homozygotes possess RNaseH2 independent compensatory mechanisms that are inactive or overwhelmed by the inherited ribonucleotides in their offspring, or that zebrafish have a yet unknown tolerance mechanism. Additionally, we identify ribodysgenesis, the rapid removal of rNMPs and subsequently lethal fragmentation of DNA as responsible for maternal and paternal embryonic lethality.
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Affiliation(s)
- Ruth C Thomas
- Bateson Centre, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Ringaile Zaksauskaite
- Bateson Centre, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Norah Y Al-Kandari
- Bateson Centre, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Anne Cathrine Hyde
- Bateson Centre, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Arwa A Abugable
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Sherif F El-Khamisy
- Bateson Centre, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
- The Institute of Cancer Therapeutics, University of Bradford, BD7 1DP, UK
| | - Freek J van Eeden
- Bateson Centre, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
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33
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Hu Q, Chen Y, Zhou Q, Deng S, Hou W, Yi Y, Li C, Tang J. ADAR promotes USP38 auto-deubiquitylation and stabilization in an RNA editing-independent manner in esophageal squamous cell carcinoma. J Biol Chem 2024; 300:107789. [PMID: 39303916 PMCID: PMC11525134 DOI: 10.1016/j.jbc.2024.107789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 08/31/2024] [Accepted: 09/05/2024] [Indexed: 09/22/2024] Open
Abstract
Esophageal cancer is mainly divided into esophageal adenocarcinoma and esophageal squamous cell carcinoma (ESCC). China is one of the high-incidence areas of esophageal cancer, of which about 90% are ESCC. The deubiquitinase USP38 has been reported to play significant roles in several biological processes, including inflammatory responses, antiviral infection, cell proliferation, migration, invasion, DNA damage repair, and chemotherapy resistance. However, the role and mechanisms of USP38 in ESCC development remain still unclear. Furthermore, although many substrates of USP38 have been identified, few upstream regulatory factors of USP38 have been identified. In this study, we found that USP38 was significantly upregulated in esophageal cancer tissues. Knockdown of USP38 inhibited ESCC growth. USP38 stabilized itself through auto-deubiquitylation. In addition, we demonstrate that adenosine deaminase acting on RNA (ADAR) could enhance the stability of USP38 protein and facilitate USP38 auto-deubiquitylation by interacting with USP38 in an RNA editing-independent manner. ADAR inhibition of ESCC cell proliferation depended on USP38. In summary, these results highlight that the potential of targeting the ADAR-USP38 axis for ESCC treatment.
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Affiliation(s)
- Qingyong Hu
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China.
| | - Yahui Chen
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Qianru Zhou
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Shanshan Deng
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Wei Hou
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China; Department of Pathology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Yong Yi
- Center of Growth, Metabolism and Aging, Key Laboratory of Biological Resources and Ecological Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chenghua Li
- Center of Growth, Metabolism and Aging, Key Laboratory of Biological Resources and Ecological Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiancai Tang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China.
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Huang Y, Jiang W, Zhou R. DAMP sensing and sterile inflammation: intracellular, intercellular and inter-organ pathways. Nat Rev Immunol 2024; 24:703-719. [PMID: 38684933 DOI: 10.1038/s41577-024-01027-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2024] [Indexed: 05/02/2024]
Abstract
Damage-associated molecular patterns (DAMPs) are endogenous molecules that are released from host cells as a result of cell death or damage. The release of DAMPs in tissues is associated with loss of tissue homeostasis. Sensing of DAMPs by innate immune receptors triggers inflammation, which can be beneficial in initiating the processes that restore tissue homeostasis but can also drive inflammatory diseases. In recent years, the sensing of intracellular DAMPs has received extensive attention in the field of sterile inflammation. However, emerging studies have shown that DAMPs that originate from neighbouring cells, and even from distal tissues or organs, also mediate sterile inflammatory responses. This multi-level sensing of DAMPs is crucial for intercellular, trans-tissue and trans-organ communication. Here, we summarize how DAMP-sensing receptors detect DAMPs from intracellular, intercellular or distal tissue and organ sources to mediate sterile inflammation. We also discuss the possibility of targeting DAMPs or their corresponding receptors to treat inflammatory diseases.
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Affiliation(s)
- Yi Huang
- Key Laboratory of Immune Response and Immunotherapy, Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China
| | - Wei Jiang
- Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Rongbin Zhou
- Key Laboratory of Immune Response and Immunotherapy, Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China.
- Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
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35
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Nemec KM, Uy G, Chaluvadi VS, Purnell FS, Elfayoumi B, O'Brien CA, Aisenberg WH, Lombroso SI, Guo X, Blank N, Oon CH, Yaqoob F, Temsamrit B, Rawat P, Thaiss CA, Wang Q, Bennett ML, Bennett FC. Microglia replacement by ER-Hoxb8 conditionally immortalized macrophages provides insight into Aicardi-Goutières Syndrome neuropathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.613629. [PMID: 39345609 PMCID: PMC11430044 DOI: 10.1101/2024.09.18.613629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Microglia, the brain's resident macrophages, can be reconstituted by surrogate cells - a process termed "microglia replacement." To expand the microglia replacement toolkit, we here introduce estrogen-regulated (ER) homeobox B8 (Hoxb8) conditionally immortalized macrophages, a cell model for generation of immune cells from murine bone marrow, as a versatile model for microglia replacement. We find that ER-Hoxb8 macrophages are highly comparable to primary bone marrow-derived (BMD) macrophages in vitro, and, when transplanted into a microglia-free brain, engraft the parenchyma and differentiate into microglia-like cells. Furthermore, ER-Hoxb8 progenitors are readily transducible by virus and easily stored as stable, genetically manipulated cell lines. As a demonstration of this system's power for studying the effects of disease mutations on microglia in vivo, we created stable, Adar1-mutated ER-Hoxb8 lines using CRISPR-Cas9 to study the intrinsic contribution of macrophages to Aicardi-Goutières Syndrome (AGS), an inherited interferonopathy that primarily affects the brain and immune system. We find that Adar1 knockout elicited interferon secretion and impaired macrophage production in vitro, while preventing brain macrophage engraftment in vivo - phenotypes that can be rescued with concurrent mutation of Ifih1 (MDA5) in vitro, but not in vivo. Lastly, we extended these findings by generating ER-Hoxb8 progenitors from mice harboring a patient-specific Adar1 mutation (D1113H). We demonstrated the ability of microglia-specific D1113H mutation to drive interferon production in vivo, suggesting microglia drive AGS neuropathology. In sum, we introduce the ER-Hoxb8 approach to model microglia replacement and use it to clarify macrophage contributions to AGS.
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Affiliation(s)
- Kelsey M Nemec
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Genevieve Uy
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - V Sai Chaluvadi
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Freddy S Purnell
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Perelman School of Medicine. Philadelphia, PA, USA
| | - Bilal Elfayoumi
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carleigh A O'Brien
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - William H Aisenberg
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sonia I Lombroso
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Xinfeng Guo
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Niklas Blank
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Chet Huan Oon
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Fazeela Yaqoob
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian Temsamrit
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Priyanka Rawat
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christoph A Thaiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Qingde Wang
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mariko L Bennett
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - F Chris Bennett
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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36
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Fisher AJ, Beal PA. Structural perspectives on adenosine to inosine RNA editing by ADARs. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102284. [PMID: 39165563 PMCID: PMC11334849 DOI: 10.1016/j.omtn.2024.102284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Adenosine deaminases acting on RNA (ADARs) are enzymes that catalyze the hydrolytic deamination of adenosine to inosine. The editing feature of ADARs has garnered much attention as a therapeutic tool to repurpose ADARs to correct disease-causing mutations at the mRNA level in a technique called site-directed RNA editing (SDRE). Administering a short guide RNA oligonucleotide that hybridizes to a mutant sequence forms the requisite dsRNA substrate, directing ADARs to edit the desired adenosine. However, much is still unknown about ADARs' selectivity and sequence-specific effects on editing. Atomic-resolution structures can help provide additional insight to ADARs' selectivity and lead to novel guide RNA designs. Indeed, recent structures of ADAR domains have expanded our understanding on RNA binding and the base-flipping catalytic mechanism. These efforts have enabled the rational design of improved ADAR guide strands and advanced the therapeutic potential of the SDRE approach. While no full-length structure of any ADAR is known, this review presents an exposition of the structural basis for function of the different ADAR domains, focusing on human ADAR2. Key insights are extrapolated to human ADAR1, which is of substantial interest because of its widespread expression in most human tissues.
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Affiliation(s)
- Andrew J. Fisher
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
- Department of Molecular and Cellular Biology, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
| | - Peter A. Beal
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
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37
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Sinigaglia K, Cherian A, Du Q, Lacovich V, Vukić D, Melicherová J, Linhartova P, Zerad L, Stejskal S, Malik R, Prochazka J, Bondurand N, Sedláček R, O'Connell MA, Keegan LP. An ADAR1 dsRBD3-PKR kinase domain interaction on dsRNA inhibits PKR activation. Cell Rep 2024; 43:114618. [PMID: 39146181 DOI: 10.1016/j.celrep.2024.114618] [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: 12/04/2023] [Revised: 05/30/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024] Open
Abstract
Adar null mutant mouse embryos die with aberrant double-stranded RNA (dsRNA)-driven interferon induction, and Adar Mavs double mutants, in which interferon induction is prevented, die soon after birth. Protein kinase R (Pkr) is aberrantly activated in Adar Mavs mouse pup intestines before death, intestinal crypt cells die, and intestinal villi are lost. Adar Mavs Eifak2 (Pkr) triple mutant mice rescue all defects and have long-term survival. Adenosine deaminase acting on RNA 1 (ADAR1) and PKR co-immunoprecipitate from cells, suggesting PKR inhibition by direct interaction. AlphaFold studies on an inhibitory PKR dsRNA binding domain (dsRBD)-kinase domain interaction before dsRNA binding and on an inhibitory ADAR1 dsRBD3-PKR kinase domain interaction on dsRNA provide a testable model of the inhibition. Wild-type or editing-inactive human ADAR1 expressed in A549 cells inhibits activation of endogenous PKR. ADAR1 dsRNA binding is required for, but is not sufficient for, PKR inhibition. Mutating the ADAR1 dsRBD3-PKR contact prevents co-immunoprecipitation, ADAR1 inhibition of PKR activity, and co-localization of ADAR1 and PKR in cells.
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Affiliation(s)
- Ketty Sinigaglia
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Anna Cherian
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Qiupei Du
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Valentina Lacovich
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia
| | - Dragana Vukić
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Janka Melicherová
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Pavla Linhartova
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia
| | - Lisa Zerad
- Laboratory of Embryology and Genetics of Human Malformation, Imagine Institute, INSERM UMR 1163, Université de Paris Cité, 75015 Paris, France
| | - Stanislav Stejskal
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia
| | - Radek Malik
- Laboratory of Epigenetic Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czechia
| | - Jan Prochazka
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czechia
| | - Nadège Bondurand
- Laboratory of Embryology and Genetics of Human Malformation, Imagine Institute, INSERM UMR 1163, Université de Paris Cité, 75015 Paris, France
| | - Radislav Sedláček
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czechia
| | - Mary A O'Connell
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia.
| | - Liam P Keegan
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia.
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38
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Huang M, Mark A, Pham J, Vera K, Saravia-Butler AM, Beheshti A, Jiang Q, Fisch KM. RNA editing regulates host immune response and T cell homeostasis in SARS-CoV-2 infection. PLoS One 2024; 19:e0307450. [PMID: 39178184 PMCID: PMC11343423 DOI: 10.1371/journal.pone.0307450] [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] [Received: 02/15/2024] [Accepted: 07/04/2024] [Indexed: 08/25/2024] Open
Abstract
Adenosine to inosine (A-to-I) RNA editing by ADAR1 has been implicated in maintaining self-tolerance, preventing autoimmunity, and mediating antiviral immunity. Foreign viral double-stranded RNA triggers rapid interferon response and activates ADAR1 in the host immune system. Emerging data points to a role of ADAR1 A-to-I editing in the inflammatory response associated with severe COVID-19 disease. We identify A-to-I editing events within human whole transcriptome data from SARS-CoV-2 infected individuals, non-infected individuals, and individuals with other viral illnesses from nasopharyngeal swabs. High levels of RNA editing in host cells are associated with low SARS-CoV-2 viral load (p = 9.27 E-06), suggesting an inhibitory effect of ADAR1 on viral infection. Additionally, we find differentially expressed genes associated with RNA-modifications and interferon response. Single cell RNA-sequencing analysis of SARS-CoV-2 infected nasopharyngeal swabs reveals that cytotoxic CD8 T cells upregulate ADAR1 in COVID-19 positive samples (p = 0.0269). We further reveal ADAR1 expression increases with CD4 and CD8 T cell activation, and knockdown of ADAR1 leads to apoptosis and aberrant IL-2 secretion. Together, our data suggests A-to-I RNA editing is required to maintain healthy homeostasis of activated T cells to combat SARS-CoV-2 infection.
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Affiliation(s)
- Molly Huang
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Diego, La Jolla, California, United States of America
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | - Adam Mark
- Center for Computational Biology & Bioinformatics, University of California San Diego, La Jolla, California, United States of America
| | - Jessica Pham
- Division of Regenerative Medicine and Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Karina Vera
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Amanda M. Saravia-Butler
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, California, United States of America
| | - Afshin Beheshti
- Blue Marble Space Institute of Science, Seattle, Washington, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- COVID-19 International Research Team, Medford, Massachusetts, United States of America
| | - Qingfei Jiang
- Division of Regenerative Medicine and Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Kathleen M. Fisch
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Diego, La Jolla, California, United States of America
- Center for Computational Biology & Bioinformatics, University of California San Diego, La Jolla, California, United States of America
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39
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Gan WL, Ren X, Ng VHE, Ng L, Song Y, Tano V, Han J, An O, Xie J, Ng BYL, Tay DJT, Tang SJ, Shen H, Khare S, Chong KHC, Young DY, Wu B, DasGupta R, Chen L. Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver. Cell Rep 2024; 43:114400. [PMID: 38935501 DOI: 10.1016/j.celrep.2024.114400] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/23/2024] [Accepted: 06/11/2024] [Indexed: 06/29/2024] Open
Abstract
ADAR1-mediated RNA editing establishes immune tolerance to endogenous double-stranded RNA (dsRNA) by preventing its sensing, primarily by MDA5. Although deleting Ifih1 (encoding MDA5) rescues embryonic lethality in ADAR1-deficient mice, they still experience early postnatal death, and removing other MDA5 signaling proteins does not yield the same rescue. Here, we show that ablation of MDA5 in a liver-specific Adar knockout (KO) murine model fails to rescue hepatic abnormalities caused by ADAR1 loss. Ifih1;Adar double KO (dKO) hepatocytes accumulate endogenous dsRNAs, leading to aberrant transition to a highly inflammatory state and recruitment of macrophages into dKO livers. Mechanistically, progranulin (PGRN) appears to mediate ADAR1 deficiency-induced liver pathology, promoting interferon signaling and attracting epidermal growth factor receptor (EGFR)+ macrophages into dKO liver, exacerbating hepatic inflammation. Notably, the PGRN-EGFR crosstalk communication and consequent immune responses are significantly repressed in ADAR1high tumors, revealing that pre-neoplastic or neoplastic cells can exploit ADAR1-dependent immune tolerance to facilitate immune evasion.
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Affiliation(s)
- Wei Liang Gan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xi Ren
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Larry Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vincent Tano
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jian Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jinghe Xie
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, P.R. China
| | - Bryan Y L Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Daryl Jin Tai Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Haoqing Shen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shruti Khare
- Genome Institute of Singapore, Agency for Science Technology and Research, 60 Biopolis Street, Genome, #02-01, Singapore, Singapore
| | - Kelvin Han Chung Chong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Dan Yock Young
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Division of Gastroenterology and Hepatology, National University Health System, Singapore, Singapore
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Ramanuj DasGupta
- Genome Institute of Singapore, Agency for Science Technology and Research, 60 Biopolis Street, Genome, #02-01, Singapore, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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40
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Bernal YA, Durán E, Solar I, Sagredo EA, Armisén R. ADAR-Mediated A>I(G) RNA Editing in the Genotoxic Drug Response of Breast Cancer. Int J Mol Sci 2024; 25:7424. [PMID: 39000531 PMCID: PMC11242177 DOI: 10.3390/ijms25137424] [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: 05/04/2024] [Revised: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Epitranscriptomics is a field that delves into post-transcriptional changes. Among these modifications, the conversion of adenosine to inosine, traduced as guanosine (A>I(G)), is one of the known RNA-editing mechanisms, catalyzed by ADARs. This type of RNA editing is the most common type of editing in mammals and contributes to biological diversity. Disruption in the A>I(G) RNA-editing balance has been linked to diseases, including several types of cancer. Drug resistance in patients with cancer represents a significant public health concern, contributing to increased mortality rates resulting from therapy non-responsiveness and disease progression, representing the greatest challenge for researchers in this field. The A>I(G) RNA editing is involved in several mechanisms over the immunotherapy and genotoxic drug response and drug resistance. This review investigates the relationship between ADAR1 and specific A>I(G) RNA-edited sites, focusing particularly on breast cancer, and the impact of these sites on DNA damage repair and the immune response over anti-cancer therapy. We address the underlying mechanisms, bioinformatics, and in vitro strategies for the identification and validation of A>I(G) RNA-edited sites. We gathered databases related to A>I(G) RNA editing and cancer and discussed the potential clinical and research implications of understanding A>I(G) RNA-editing patterns. Understanding the intricate role of ADAR1-mediated A>I(G) RNA editing in breast cancer holds significant promise for the development of personalized treatment approaches tailored to individual patients' A>I(G) RNA-editing profiles.
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Affiliation(s)
- Yanara A Bernal
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | - Eduardo Durán
- Subdepartamento de Genómica y Genética Molecular, Sección Genética Humana, Instituto de Salud Pública de Chile, Avenida Marathon 1000, Ñuñoa, Santiago 7780050, Chile
| | - Isidora Solar
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | - Eduardo A Sagredo
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-171 77 Stockholm, Sweden
| | - Ricardo Armisén
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
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41
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Tang AD, Felton C, Hrabeta-Robinson E, Volden R, Vollmers C, Brooks AN. Detecting haplotype-specific transcript variation in long reads with FLAIR2. Genome Biol 2024; 25:173. [PMID: 38956576 PMCID: PMC11218413 DOI: 10.1186/s13059-024-03301-y] [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: 06/13/2023] [Accepted: 06/06/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND RNA-seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants (SNVs) in RNA have been demonstrated to alter transcript stability, localization, and function. In particular, the upregulation of ADAR, an enzyme that mediates adenosine-to-inosine editing, has been previously linked to an increase in the invasiveness of lung adenocarcinoma cells and associated with splicing regulation. Despite the functional importance of studying splicing and SNVs, the use of short-read RNA-seq has limited the community's ability to interrogate both forms of RNA variation simultaneously. RESULTS We employ long-read sequencing technology to obtain full-length transcript sequences, elucidating cis-effects of variants on splicing changes at a single molecule level. We develop a computational workflow that augments FLAIR, a tool that calls isoform models expressed in long-read data, to integrate RNA variant calls with the associated isoforms that bear them. We generate nanopore data with high sequence accuracy from H1975 lung adenocarcinoma cells with and without knockdown of ADAR. We apply our workflow to identify key inosine isoform associations to help clarify the prominence of ADAR in tumorigenesis. CONCLUSIONS Ultimately, we find that a long-read approach provides valuable insight toward characterizing the relationship between RNA variants and splicing patterns.
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Affiliation(s)
- Alison D Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Eva Hrabeta-Robinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Roger Volden
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA.
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42
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Rodriguez de Los Santos M, Kopell BH, Buxbaum Grice A, Ganesh G, Yang A, Amini P, Liharska LE, Vornholt E, Fullard JF, Dong P, Park E, Zipkowitz S, Kaji DA, Thompson RC, Liu D, Park YJ, Cheng E, Ziafat K, Moya E, Fennessy B, Wilkins L, Silk H, Linares LM, Sullivan B, Cohen V, Kota P, Feng C, Johnson JS, Rieder MK, Scarpa J, Nadkarni GN, Wang M, Zhang B, Sklar P, Beckmann ND, Schadt EE, Roussos P, Charney AW, Breen MS. Divergent landscapes of A-to-I editing in postmortem and living human brain. Nat Commun 2024; 15:5366. [PMID: 38926387 PMCID: PMC11208617 DOI: 10.1038/s41467-024-49268-z] [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: 12/13/2023] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) editing is a prevalent post-transcriptional RNA modification within the brain. Yet, most research has relied on postmortem samples, assuming it is an accurate representation of RNA biology in the living brain. We challenge this assumption by comparing A-to-I editing between postmortem and living prefrontal cortical tissues. Major differences were found, with over 70,000 A-to-I sites showing higher editing levels in postmortem tissues. Increased A-to-I editing in postmortem tissues is linked to higher ADAR and ADARB1 expression, is more pronounced in non-neuronal cells, and indicative of postmortem activation of inflammation and hypoxia. Higher A-to-I editing in living tissues marks sites that are evolutionarily preserved, synaptic, developmentally timed, and disrupted in neurological conditions. Common genetic variants were also found to differentially affect A-to-I editing levels in living versus postmortem tissues. Collectively, these discoveries offer more nuanced and accurate insights into the regulatory mechanisms of RNA editing in the human brain.
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Affiliation(s)
| | - Brian H Kopell
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Gauri Ganesh
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andy Yang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pardis Amini
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lora E Liharska
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Vornholt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John F Fullard
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pengfei Dong
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Park
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Zipkowitz
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Deepak A Kaji
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ryan C Thompson
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Donjing Liu
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - You Jeong Park
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimia Ziafat
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emily Moya
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brian Fennessy
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lillian Wilkins
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hannah Silk
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lisa M Linares
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brendan Sullivan
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Vanessa Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Prashant Kota
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Claudia Feng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | | | - Joseph Scarpa
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Minghui Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pamela Sklar
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Noam D Beckmann
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric E Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panos Roussos
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Michael S Breen
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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43
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Zhu ZJ, Teng M, Liu Y, Chen FJ, Yao Y, Li EZ, Luo J. Immune escape of avian oncogenic Marek's disease herpesvirus and antagonistic host immune responses. NPJ Vaccines 2024; 9:109. [PMID: 38879650 PMCID: PMC11180173 DOI: 10.1038/s41541-024-00905-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/07/2024] [Indexed: 06/19/2024] Open
Abstract
Marek's disease virus (MDV) is a highly pathogenic and oncogenic alpha herpesvirus that causes Marek's disease (MD), which is one of the most important immunosuppressive and rapid-onset neoplastic diseases in poultry. The onset of MD lymphomas and other clinical diseases can be efficiently prevented by vaccination; these vaccines are heralded as the first demonstration of a successful vaccination strategy against a cancer. However, the persistent evolution of epidemic MDV strains towards greater virulence has recently resulted in frequent outbreaks of MD in vaccinated chicken flocks worldwide. Herein, we provide an overall review focusing on the discovery and identification of the strategies by which MDV evades host immunity and attacks the immune system. We have also highlighted the decrease in the immune efficacy of current MD vaccines. The prospects, strategies and new techniques for the development of efficient MD vaccines, together with the possibilities of antiviral therapy in MD, are also discussed.
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Affiliation(s)
- Zhi-Jian Zhu
- College of Biological and Food Engineering & Affiliated Central Hospital, Huanghuai University, Zhumadian, 463000, People's Republic of China
- Institute for Animal Health & UK-China Center of Excellence for Research on Avian Disease, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Zhengzhou, 450002, People's Republic of China
| | - Man Teng
- Institute for Animal Health & UK-China Center of Excellence for Research on Avian Disease, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Zhengzhou, 450002, People's Republic of China
| | - Yu Liu
- College of Biological and Food Engineering & Affiliated Central Hospital, Huanghuai University, Zhumadian, 463000, People's Republic of China
| | - Fu-Jia Chen
- College of Biological and Food Engineering & Affiliated Central Hospital, Huanghuai University, Zhumadian, 463000, People's Republic of China
| | - Yongxiu Yao
- The Pirbright Institute & UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey, GU24 0NF, UK
| | - En-Zhong Li
- College of Biological and Food Engineering & Affiliated Central Hospital, Huanghuai University, Zhumadian, 463000, People's Republic of China.
| | - Jun Luo
- Institute for Animal Health & UK-China Center of Excellence for Research on Avian Disease, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China.
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China.
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Zhengzhou, 450002, People's Republic of China.
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471003, People's Republic of China.
- Longhu Laboratory, Zhengzhou, 450046, People's Republic of China.
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44
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Hu SB, Li JB. RNA editing and immune control: from mechanism to therapy. Curr Opin Genet Dev 2024; 86:102195. [PMID: 38643591 PMCID: PMC11162905 DOI: 10.1016/j.gde.2024.102195] [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: 01/18/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/23/2024]
Abstract
Adenosine-to-inosine RNA editing, catalyzed by the enzymes ADAR1 and ADAR2, stands as a pervasive RNA modification. A primary function of ADAR1-mediated RNA editing lies in labeling endogenous double-stranded RNAs (dsRNAs) as 'self', thereby averting their potential to activate innate immune responses. Recent findings have highlighted additional roles of ADAR1, independent of RNA editing, that are crucial for immune control. Here, we focus on recent progress in understanding ADAR1's RNA editing-dependent and -independent roles in immune control. We describe how ADAR1 regulates various dsRNA innate immune receptors through distinct mechanisms. Furthermore, we discuss the implications of ADAR1 and RNA editing in diseases, including autoimmune diseases and cancers.
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Affiliation(s)
- Shi-Bin Hu
- 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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45
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Huang E, Frydman C, Xiao X. Navigating the landscape of epitranscriptomics and host immunity. Genome Res 2024; 34:515-529. [PMID: 38702197 PMCID: PMC11146601 DOI: 10.1101/gr.278412.123] [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: 05/06/2024]
Abstract
RNA modifications, also termed epitranscriptomic marks, encompass chemical alterations to individual nucleotides, including processes such as methylation and editing. These marks contribute to a wide range of biological processes, many of which are related to host immune system defense. The functions of immune-related RNA modifications can be categorized into three main groups: regulation of immunogenic RNAs, control of genes involved in innate immune response, and facilitation of adaptive immunity. Here, we provide an overview of recent research findings that elucidate the contributions of RNA modifications to each of these processes. We also discuss relevant methods for genome-wide identification of RNA modifications and their immunogenic substrates. Finally, we highlight recent advances in cancer immunotherapies that aim to reduce cancer cell viability by targeting the enzymes responsible for RNA modifications. Our presentation of these dynamic research avenues sets the stage for future investigations in this field.
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Affiliation(s)
- Elaine Huang
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA
| | - Clara Frydman
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA;
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, California 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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46
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de los Santos MR, Kopell BH, Grice AB, Ganesh G, Yang A, Amini P, Liharska LE, Vornholt E, Fullard JF, Dong P, Park E, Zipkowitz S, Kaji DA, Thompson RC, Liu D, Park YJ, Cheng E, Ziafat K, Moya E, Fennessy B, Wilkins L, Silk H, Linares LM, Sullivan B, Cohen V, Kota P, Feng C, Johnson JS, Rieder MK, Scarpa J, Nadkarni GN, Wang M, Zhang B, Sklar P, Beckmann ND, Schadt EE, Roussos P, Charney AW, Breen MS. Divergent landscapes of A-to-I editing in postmortem and living human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.06.24306763. [PMID: 38765961 PMCID: PMC11100843 DOI: 10.1101/2024.05.06.24306763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Adenosine-to-inosine (A-to-I) editing is a prevalent post-transcriptional RNA modification within the brain. Yet, most research has relied on postmortem samples, assuming it is an accurate representation of RNA biology in the living brain. We challenge this assumption by comparing A-to-I editing between postmortem and living prefrontal cortical tissues. Major differences were found, with over 70,000 A-to-I sites showing higher editing levels in postmortem tissues. Increased A-to-I editing in postmortem tissues is linked to higher ADAR1 and ADARB1 expression, is more pronounced in non-neuronal cells, and indicative of postmortem activation of inflammation and hypoxia. Higher A-to-I editing in living tissues marks sites that are evolutionarily preserved, synaptic, developmentally timed, and disrupted in neurological conditions. Common genetic variants were also found to differentially affect A-to-I editing levels in living versus postmortem tissues. Collectively, these discoveries illuminate the nuanced functions and intricate regulatory mechanisms of RNA editing within the human brain.
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Affiliation(s)
| | - Brian H. Kopell
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Gauri Ganesh
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andy Yang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pardis Amini
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lora E. Liharska
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Vornholt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John F. Fullard
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pengfei Dong
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Park
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Zipkowitz
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Deepak A. Kaji
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ryan C. Thompson
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Donjing Liu
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - You Jeong Park
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimia Ziafat
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emily Moya
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brian Fennessy
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lillian Wilkins
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hannah Silk
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lisa M. Linares
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brendan Sullivan
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Vanessa Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Prashant Kota
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Claudia Feng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | | | - Joseph Scarpa
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Minghui Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pamela Sklar
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Noam D. Beckmann
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric E. Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panos Roussos
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Michael S. Breen
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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47
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Al Wardat S, Frassinelli L, Orecchini E, Rey F, Ciafrè SA, Galardi S, Garau J, Gagliardi S, Orcesi S, Tonduti D, Carelli S, Cereda C, Picardi E, Michienzi A. Characterization of the molecular dysfunctions occurring in Aicardi-Goutières syndrome patients with mutations in ADAR1. Genes Dis 2024; 11:101028. [PMID: 38292175 PMCID: PMC10827400 DOI: 10.1016/j.gendis.2023.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/09/2023] [Accepted: 05/25/2023] [Indexed: 02/01/2024] Open
Affiliation(s)
- Sofian Al Wardat
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy
| | - Loredana Frassinelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy
| | - Elisa Orecchini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy
| | - Federica Rey
- Pediatric Clinical Research Center “Romeo ed Enrica Invernizzi”, Department of Biomedical and Clinical Sciences, University of Milano, Milano 20157, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milano 20154, Italy
| | - Silvia Anna Ciafrè
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy
| | - Silvia Galardi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy
| | - Jessica Garau
- Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, Pavia 27100, Italy
| | - Stella Gagliardi
- Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, Pavia 27100, Italy
| | - Simona Orcesi
- Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, Pavia 27100, Italy
| | - Davide Tonduti
- Unit of Pediatric Neurology, C.O.A.L.A (Center for Diagnosis and Treatment of Leukodystrophies), Buzzi Children's Hospital, Milano 20154, Italy
| | - Stephana Carelli
- Pediatric Clinical Research Center “Romeo ed Enrica Invernizzi”, Department of Biomedical and Clinical Sciences, University of Milano, Milano 20157, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milano 20154, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milano 20154, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, Bari 70125, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), Bari 70126, Italy
- Biostructures and Biosystems National Institute (INBB), Rome 00136, Italy
| | - Alessandro Michienzi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy
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48
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Rey F, Esposito L, Maghraby E, Mauri A, Berardo C, Bonaventura E, Tonduti D, Carelli S, Cereda C. Role of epigenetics and alterations in RNA metabolism in leukodystrophies. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1854. [PMID: 38831585 DOI: 10.1002/wrna.1854] [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: 11/30/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 06/05/2024]
Abstract
Leukodystrophies are a class of rare heterogeneous disorders which affect the white matter of the brain, ultimately leading to a disruption in brain development and a damaging effect on cognitive, motor and social-communicative development. These disorders present a great clinical heterogeneity, along with a phenotypic overlap and this could be partially due to contributions from environmental stimuli. It is in this context that there is a great need to investigate what other factors may contribute to both disease insurgence and phenotypical heterogeneity, and novel evidence are raising the attention toward the study of epigenetics and transcription mechanisms that can influence the disease phenotype beyond genetics. Modulation in the epigenetics machinery including histone modifications, DNA methylation and non-coding RNAs dysregulation, could be crucial players in the development of these disorders, and moreover an aberrant RNA maturation process has been linked to leukodystrophies. Here, we provide an overview of these mechanisms hoping to supply a closer step toward the analysis of leukodystrophies not only as genetically determined but also with an added level of complexity where epigenetic dysregulation is of key relevance. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNA RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Federica Rey
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Letizia Esposito
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Erika Maghraby
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
- Department of Biology and Biotechnology "L. Spallanzani" (DBB), University of Pavia, Pavia, Italy
| | - Alessia Mauri
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Clarissa Berardo
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Eleonora Bonaventura
- Unit of Pediatric Neurology, COALA Center for Diagnosis and Treatment of Leukodystrophies, V. Buzzi Children's Hospital, Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Davide Tonduti
- Unit of Pediatric Neurology, COALA Center for Diagnosis and Treatment of Leukodystrophies, V. Buzzi Children's Hospital, Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Stephana Carelli
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
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Li Z, Liu S, Gao Z, Ji L, Jiao J, Zheng N, Li X, Wang G, Qin J, Wang Y. Dynamic Proteomic Changes in Tumor and Immune Organs Reveal Systemic Immune Response to Tumor Development. Mol Cell Proteomics 2024; 23:100756. [PMID: 38554776 PMCID: PMC11060955 DOI: 10.1016/j.mcpro.2024.100756] [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: 09/05/2023] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024] Open
Abstract
In orthotopic mouse tumor models, tumor progression is a complex process, involving interactions among tumor cells, host cell-derived stromal cells, and immune cells. Much attention has been focused on the tumor and its tumor microenvironment, while the host's macroenvironment including immune organs in response to tumorigenesis is poorly understood. Here, we report a temporal proteomic analysis on a subcutaneous tumor and three immune organs (LN, MLN, and spleen) collected on Days 0, 3, 7, 10, 14, and 21 after inoculation of mouse forestomach cancer cells in a syngeneic mouse model. Bioinformatics analysis identified key biological processes during distinct tumor development phases, including an initial acute immune response, the attack by the host immune system, followed by the adaptive immune activation, and the build-up of extracellular matrix. Proteomic changes in LN and spleen largely recapitulated the dynamics of the immune response in the tumor, consistent with an acute defense response on D3, adaptive immune response on D10, and immune evasion by D21. In contrast, the immune response in MLN showed a gradual and sustained activation, suggesting a delayed response from a distal immune organ. Combined analyses of tumors and host immune organs allowed the identification of potential therapeutic targets. A proof-of-concept experiment demonstrated that significant growth reduction can be achieved by dual inhibition of MEK and DDR2. Together, our temporal proteomic dataset of tumors and immune organs provides a useful resource for understanding the interaction between tumors and the immune system and has the potential for identifying new therapeutic targets for cancer treatment.
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Affiliation(s)
- Zhike Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Shuwen Liu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Zhouyong Gao
- Department of Thoracic Surgery, Baodi Clinical College, Tianjin Medical University, Tianjin, China; Department of Child Health Care, Kunshan Maternity and Child Health Care Institute, Kunshan, China
| | - Linlin Ji
- Department of Thoracic Surgery, Baodi Clinical College, Tianjin Medical University, Tianjin, China; Department of Thoracic Surgery, Weifang People's Hospital, Weifang, China
| | - Jiaqi Jiao
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Nairen Zheng
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xianju Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Guangshun Wang
- Department of Thoracic Surgery, Baodi Clinical College, Tianjin Medical University, Tianjin, China
| | - Jun Qin
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yi Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
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50
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Li B, Wang Z, Zhou H, Tan W, Zou J, Li Y, Yoshida S, Zhou Y. Bibliometric evaluation of global trends and characteristics of RNA methylation during angiogenesis. Heliyon 2024; 10:e29817. [PMID: 38681586 PMCID: PMC11046201 DOI: 10.1016/j.heliyon.2024.e29817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Background RNA methylation is involved in major life processes. Angiogenesis is a normal phenomenon that occurs constantly in the bodies of all mammals, once it is aberrant or something goes wrong, it may lead to pathological changes. The bibliometric analysis could produce a comprehensive overview of RNA methylation during angiogenesis. Methods The Web of Science Core Collection (WoSCC) database was used to screen publications about RNA methylation during angiogenesis from Jan 1, 2000 to Nov 24, 2022. Bibliometric and visualization analyses were conducted to understand publication trends by CiteSpace and VOSviewer. Results In total, 382 publications from 2000 to 2022 were included in the bibliometric and visualization analyses. On the whole, the number of publications had exponential growth. China was the country and Sun Yat-Sen University was the university associated with the largest number of publications, although publications from the United Kingdom and Soochow University were currently having the strongest impact. Cancer was the most studied topic in this field, and N6-methyladenosine is the most studied RNA methylation type. Conclusion There is a continuously increasing trend in publications related to RNA methylation and angiogenesis, which has attracted much attention, particularly since 2011. RNA methylation might be a promising target in the investigation of pathological angiogenesis and related disorders, which deserves further investigation.
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Affiliation(s)
- Bingyan Li
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
- National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Zicong Wang
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
- National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Haixiang Zhou
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
- National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Wei Tan
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
- National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Jingling Zou
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
- National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Yun Li
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
- National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Shigeo Yoshida
- Department of Ophthalmology, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Yedi Zhou
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
- National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
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