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Liang Z, Walkley CR, Heraud-Farlow JE. A-to-I RNA Editing and Hematopoiesis. Exp Hematol 2024:104621. [PMID: 39187172 DOI: 10.1016/j.exphem.2024.104621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [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, 3065, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria, 3065, Australia; Present address: Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168 Australia; and Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168 Australia
| | - Carl R Walkley
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria, 3065, Australia; Centre for Innate Immunity and Infectious Diseases, 27-31 Wright St, Clayton 3168, VIC, Australia; Present address: Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168 Australia; and Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168 Australia.
| | - Jacki E Heraud-Farlow
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria, 3065, Australia; Centre for Innate Immunity and Infectious Diseases, 27-31 Wright St, Clayton 3168, VIC, Australia; Lead contact; Present address: Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168 Australia; and Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168 Australia.
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2
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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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3
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Deng Y, Zhou J, Li HB. The physiological and pathological roles of RNA modifications in T cells. Cell Chem Biol 2024:S2451-9456(24)00222-8. [PMID: 38986618 DOI: 10.1016/j.chembiol.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/20/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
RNA molecules undergo dynamic chemical modifications in response to various external or cellular stimuli. Some of those modifications have been demonstrated to post-transcriptionally modulate the RNA transcription, localization, stability, translation, and degradation, ultimately tuning the fate decisions and function of mammalian cells, particularly T cells. As a crucial part of adaptive immunity, T cells play fundamental roles in defending against infections and tumor cells. Recent findings have illuminated the importance of RNA modifications in modulating T cell survival, proliferation, differentiation, and functional activities. Therefore, understanding the epi-transcriptomic control of T cell biology enables a potential avenue for manipulating T cell immunity. This review aims to elucidate the physiological and pathological roles of internal RNA modifications in T cell development, differentiation, and functionality drawn from current literature, with the goal of inspiring new insights for future investigations and providing novel prospects for T cell-based immunotherapy.
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Affiliation(s)
- Yu Deng
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jing Zhou
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hua-Bing Li
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Geriatrics, Medical Center on Aging of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Chongqing International Institute for Immunology, Chongqing 401320, China.
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4
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Xing Y, Nakahama T, Wu Y, Inoue M, Kim JI, Todo H, Shibuya T, Kato Y, Kawahara Y. RNA editing of AZIN1 coding sites is catalyzed by ADAR1 p150 after splicing. J Biol Chem 2023; 299:104840. [PMID: 37209819 PMCID: PMC10404624 DOI: 10.1016/j.jbc.2023.104840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
Adenosine-to-inosine RNA editing is catalyzed by nuclear adenosine deaminase acting on RNA 1 (ADAR1) p110 and ADAR2, and cytoplasmic ADAR1 p150 in mammals, all of which recognize dsRNAs as targets. RNA editing occurs in some coding regions, which alters protein functions by exchanging amino acid sequences, and is therefore physiologically significant. In general, such coding sites are edited by ADAR1 p110 and ADAR2 before splicing, given that the corresponding exon forms a dsRNA structure with an adjacent intron. We previously found that RNA editing at two coding sites of antizyme inhibitor 1 (AZIN1) is sustained in Adar1 p110/Aadr2 double KO mice. However, the molecular mechanisms underlying RNA editing of AZIN1 remain unknown. Here, we showed that Azin1 editing levels were increased upon type I interferon treatment, which activated Adar1 p150 transcription, in mouse Raw 264.7 cells. Azin1 RNA editing was observed in mature mRNA but not precursor mRNA. Furthermore, we revealed that the two coding sites were editable only by ADAR1 p150 in both mouse Raw 264.7 and human embryonic kidney 293T cells. This unique editing was achieved by forming a dsRNA structure with a downstream exon after splicing, and the intervening intron suppressed RNA editing. Therefore, deletion of a nuclear export signal from ADAR1 p150, shifting its localization to the nucleus, decreased Azin1 editing levels. Finally, we demonstrated that Azin1 RNA editing was completely absent in Adar1 p150 KO mice. Thus, these findings indicate that RNA editing of AZIN1 coding sites is exceptionally catalyzed by ADAR1 p150 after splicing.
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Affiliation(s)
- Yanfang Xing
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Taisuke Nakahama
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Integrated Frontier Research for Medical Science Division and RNA Frontier Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan.
| | - Yuke Wu
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Maal Inoue
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Jung In Kim
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hiroyuki Todo
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Toshiharu Shibuya
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yuki Kato
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Integrated Frontier Research for Medical Science Division and RNA Frontier Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Integrated Frontier Research for Medical Science Division and RNA Frontier Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan; Genome Editing Research and Development Center, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
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5
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Rivera M, Zhang H, Pham J, Isquith J, Zhou QJ, Sasik R, Mark A, Ma W, Holm F, Fisch KM, Kuo DJ, Jamieson C, Jiang Q. Malignant A-to-I RNA editing by ADAR1 drives T-cell acute lymphoblastic leukemia relapse via attenuating dsRNA sensing. RESEARCH SQUARE 2023:rs.3.rs-2444524. [PMID: 37398458 PMCID: PMC10312963 DOI: 10.21203/rs.3.rs-2444524/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Leukemia initiating cells (LICs) are regarded as the origin of leukemia relapse and therapeutic resistance. Identifying direct stemness determinants that fuel LIC self-renewal is critical for developing targeted approaches to eliminate LICs and prevent relapse. Here, we show that the RNA editing enzyme ADAR1 is a crucial stemness factor that promotes LIC self-renewal by attenuating aberrant double-stranded RNA (dsRNA) sensing. Elevated adenosine-to-inosine (A-to-I) editing is a common attribute of relapsed T-ALL regardless of molecular subtypes. Consequently, knockdown of ADAR1 severely inhibits LIC self-renewal capacity and prolongs survival in T-ALL PDX models. Mechanistically, ADAR1 directs hyper-editing of immunogenic dsRNA and retains unedited nuclear dsRNA to avoid detection by the innate immune sensor MDA5. Moreover, we uncovered that the cell intrinsic level of MDA5 dictates the dependency on ADAR1-MDA5 axis in T-ALL. Collectively, our results show that ADAR1 functions as a self-renewal factor that limits the sensing of endogenous dsRNA. Thus, targeting ADAR1 presents a safe and effective therapeutic strategy for eliminating T-ALL LICs.
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Affiliation(s)
- Maria Rivera
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| | - Haoran Zhang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| | - Jessica Pham
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jane Isquith
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qingchen Jenny Zhou
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| | - Roman Sasik
- Center for Computational Biology & Bioinformatics (CCBB), University of California, San Diego, La Jolla, 92093-0681
| | - Adam Mark
- Center for Computational Biology & Bioinformatics (CCBB), University of California, San Diego, La Jolla, 92093-0681
| | - Wenxue Ma
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Frida Holm
- Department of Women’s and Children’s Health, Division of Pediatric Oncology and Surgery, Karolinska Institutet, Sweden
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics (CCBB), University of California, San Diego, La Jolla, 92093-0681
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Diego, La Jolla, CA
| | - Dennis John Kuo
- Moores Cancer Center, La Jolla, CA 92037, USA
- Division of Pediatric Hematology-Oncology, Rady Children’s Hospital San Diego, University of California, San Diego, CA
| | - Catriona Jamieson
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| | - Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
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6
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Lu D, Lu J, Liu Q, Zhang Q. Emerging role of the RNA-editing enzyme ADAR1 in stem cell fate and function. Biomark Res 2023; 11:61. [PMID: 37280687 DOI: 10.1186/s40364-023-00503-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/13/2023] [Indexed: 06/08/2023] Open
Abstract
Stem cells are critical for organism development and the maintenance of tissue homeostasis. Recent studies focusing on RNA editing have indicated how this mark controls stem cell fate and function in both normal and malignant states. RNA editing is mainly mediated by adenosine deaminase acting on RNA 1 (ADAR1). The RNA editing enzyme ADAR1 converts adenosine in a double-stranded RNA (dsRNA) substrate into inosine. ADAR1 is a multifunctional protein that regulate physiological processes including embryonic development, cell differentiation, and immune regulation, and even apply to the development of gene editing technologies. In this review, we summarize the structure and function of ADAR1 with a focus on how it can mediate distinct functions in stem cell self-renewal and differentiation. Targeting ADAR1 has emerged as a potential novel therapeutic strategy in both normal and dysregulated stem cell contexts.
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Affiliation(s)
- Di Lu
- The Biotherapy Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Jianxi Lu
- The Biotherapy Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Qiuli Liu
- The Biotherapy Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Qi Zhang
- The Biotherapy Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
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7
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Rupani DN, Thege FI, Chandra V, Rajaei H, Cowan RW, Wörmann SM, Le Roux O, Malaney P, Manning SL, Hashem J, Bailey-Lundberg J, Rhim AD, McAllister F. Adar1 deletion causes degeneration of the exocrine pancreas via Mavs-dependent interferon signaling. Development 2023; 150:dev201097. [PMID: 36458554 PMCID: PMC10110501 DOI: 10.1242/dev.201097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022]
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA-binding protein that deaminates adenosine (A) to inosine (I). A-to-I editing alters post-transcriptional RNA processing, making ADAR1 a crucial regulator of gene expression. Consequently, Adar1 has been implicated in organogenesis. To determine the role of Adar1 in pancreatic development and homeostasis, we conditionally deleted Adar1 from the murine pancreas (Ptf1aCre/+; Adar1Fl/Fl). The resulting mice had stunted growth, likely due to malabsorption associated with exocrine pancreatic insufficiency. Analyses of pancreata revealed ductal cell expansion, heightened interferon-stimulated gene expression and an increased influx of immune cells. Concurrent deletion of Adar1 and Mavs, a signaling protein implicated in the innate immune pathway, rescued the degenerative phenotype and resulted in normal pancreatic development. Taken together, our work suggests that the primary function of Adar1 in the pancreas is to prevent aberrant activation of the Mavs-mediated innate immune pathway, thereby maintaining pancreatic homeostasis.
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Affiliation(s)
- Dhwani N. Rupani
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fredrik I. Thege
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vidhi Chandra
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hajar Rajaei
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert W. Cowan
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sonja M. Wörmann
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Olivereen Le Roux
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Prerna Malaney
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sara L. Manning
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jack Hashem
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer Bailey-Lundberg
- Department of Anesthesiology, Center for Perioperative Medicine, McGovern Medical School, The University of Texas Health Sciences Center, Houston, TX 77030, USA
- Center for Interventional Gastroenterology at UTHealth (iGUT), McGovern Medical School, Houston, TX 77030, USA
| | - Andrew D. Rhim
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Florencia McAllister
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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8
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Li Y, Ruan GX, Chen W, Huang H, Zhang R, Wang J, Li Y, Xu S, Ou X. RNA-Editing Enzyme ADAR1 p150 Isoform Is Critical for Germinal Center B Cell Response. THE JOURNAL OF IMMUNOLOGY 2022; 209:1071-1082. [DOI: 10.4049/jimmunol.2200149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/11/2022] [Indexed: 01/04/2023]
Abstract
Abstract
Adenosine deaminase acting on RNA (ADAR)1 is the principal enzyme for adenosine-to-inosine editing, an RNA modification–avoiding cytosolic nucleic acid sensor’s activation triggered by endogenous dsRNAs. Two ADAR1 isoforms exist in mammals, a longer IFN-inducible and mainly cytoplasm-localized p150 isoform and a shorter constitutively expressed and primarily nucleus-localized p110 isoform. Studies of ADAR1 mutant mice have demonstrated that ADAR1 is essential for multiple physiological processes, including embryonic development, innate immune response, and B and T lymphocyte development. However, it remained unknown whether ADAR1 plays a role in the humoral immune response. In this study, we conditionally delete Adar1 in activated B cells and show that ADAR1-deficient mice have a defective T cell–dependent Ab response and diminished germinal center (GC) B cells. Using various double mutant mice concurrently deficient in ADAR1 and different downstream dsRNA sensors, we demonstrate that ADAR1 regulates the GC response by preventing hyperactivation of the melanoma differentiation-associated protein 5 (MDA5) but not the protein kinase R or RNase L pathway. We also show that p150 is exclusively responsible for ADAR1’s function in the GC response, and the p110 isoform cannot substitute for the p150’s role, even when p110 is constitutively expressed in the cytoplasm. We further demonstrated that the dsRNA-binding but not the RNA-editing activity is required for ADAR1’s function in the GC response. Thus, our data suggest that the ADAR1 p150 isoform plays a crucial role in regulating the GC B cell response.
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Affiliation(s)
- Yuxing Li
- *Harbin Institute of Technology, Harbin, China
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Gui-Xin Ruan
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenjing Chen
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Hengjun Huang
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Rui Zhang
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jing Wang
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yan Li
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Shengli Xu
- ‡Singapore Immunology Network, Agency for Science, Technology and Research, Singapore; and
- §Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Xijun Ou
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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9
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de Reuver R, Verdonck S, Dierick E, Nemegeer J, Hessmann E, Ahmad S, Jans M, Blancke G, Van Nieuwerburgh F, Botzki A, Vereecke L, van Loo G, Declercq W, Hur S, Vandenabeele P, Maelfait J. ADAR1 prevents autoinflammation by suppressing spontaneous ZBP1 activation. Nature 2022; 607:784-789. [PMID: 35859175 DOI: 10.1038/s41586-022-04974-w] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 06/13/2022] [Indexed: 12/20/2022]
Abstract
The RNA-editing enzyme adenosine deaminase acting on RNA 1 (ADAR1) limits the accumulation of endogenous immunostimulatory double-stranded RNA (dsRNA)1. In humans, reduced ADAR1 activity causes the severe inflammatory disease Aicardi-Goutières syndrome (AGS)2. In mice, complete loss of ADAR1 activity is embryonically lethal3-6, and mutations similar to those found in patients with AGS cause autoinflammation7-12. Mechanistically, adenosine-to-inosine (A-to-I) base modification of endogenous dsRNA by ADAR1 prevents chronic overactivation of the dsRNA sensors MDA5 and PKR3,7-10,13,14. Here we show that ADAR1 also inhibits the spontaneous activation of the left-handed Z-nucleic acid sensor ZBP1. Activation of ZBP1 elicits caspase-8-dependent apoptosis and MLKL-mediated necroptosis of ADAR1-deficient cells. ZBP1 contributes to the embryonic lethality of Adar-knockout mice, and it drives early mortality and intestinal cell death in mice deficient in the expression of both ADAR and MAVS. The Z-nucleic-acid-binding Zα domain of ADAR1 is necessary to prevent ZBP1-mediated intestinal cell death and skin inflammation. The Zα domain of ADAR1 promotes A-to-I editing of endogenous Alu elements to prevent dsRNA formation through the pairing of inverted Alu repeats, which can otherwise induce ZBP1 activation. This shows that recognition of Alu duplex RNA by ZBP1 may contribute to the pathological features of AGS that result from the loss of ADAR1 function.
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Affiliation(s)
- Richard de Reuver
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Simon Verdonck
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Evelien Dierick
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Josephine Nemegeer
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Eline Hessmann
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Sadeem Ahmad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Maude Jans
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Gillian Blancke
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- NXTGNT, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.,Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | | | - Lars Vereecke
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Geert van Loo
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Wim Declercq
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Peter Vandenabeele
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jonathan Maelfait
- VIB-UGent Center for Inflammation Research, Ghent, Belgium. .,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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10
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Krueger A, Łyszkiewicz M, Heissmeyer V. Post-transcriptional control of T-cell development in the thymus. Immunol Lett 2022; 247:1-12. [DOI: 10.1016/j.imlet.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/18/2022] [Accepted: 04/26/2022] [Indexed: 11/05/2022]
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11
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Tassinari V, Cerboni C, Soriani A. Self or Non-Self? It Is also a Matter of RNA Recognition and Editing by ADAR1. BIOLOGY 2022; 11:biology11040568. [PMID: 35453767 PMCID: PMC9024829 DOI: 10.3390/biology11040568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 01/19/2023]
Abstract
Simple Summary A fundamental feature of innate immune cells is to detect the presence of non-self, such as potentially harmful nucleic acids, by germline-encoded specialized receptors called pattern recognition receptors (PRRs). ADAR1 is one key enzyme avoiding aberrant type I interferon (IFN-I) production and immune cell activation by the conversion of adenosine to inosine (A-to-I) in double-stranded RNA (dsRNA) structures that arise in self mRNA containing specific repetitive elements. This review intends to give an up-to-date and detailed overview of the ADAR1-mediated ability to modulate the immune response in autoimmune diseases and cancer progression. Abstract A-to-I editing is a post-transcriptional mechanism affecting coding and non-coding dsRNAs, catalyzed by the adenosine deaminases acting on the RNA (ADAR) family of enzymes. A-to-I modifications of endogenous dsRNA (mainly derived from Alu repetitive elements) prevent their recognition by cellular dsRNA sensors, thus avoiding the induction of antiviral signaling and uncontrolled IFN-I production. This process, mediated by ADAR1 activity, ensures the activation of an innate immune response against foreign (non-self) but not self nucleic acids. As a consequence, ADAR1 mutations or its de-regulated activity promote the development of autoimmune diseases and strongly impact cell growth, also leading to cancer. Moreover, the excessive inflammation promoted by Adar1 ablation also impacts T and B cell maturation, as well as the development of dendritic cell subsets, revealing a new role of ADAR1 in the homeostasis of the immune system.
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12
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Song B, Shiromoto Y, Minakuchi M, Nishikura K. The role of RNA editing enzyme ADAR1 in human disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1665. [PMID: 34105255 PMCID: PMC8651834 DOI: 10.1002/wrna.1665] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/02/2021] [Accepted: 04/22/2021] [Indexed: 12/19/2022]
Abstract
Adenosine deaminase acting on RNA (ADAR) catalyzes the posttranscriptional conversion of adenosine to inosine in double-stranded RNA (dsRNA), which can lead to the creation of missense mutations in coding sequences. Recent studies show that editing-dependent functions of ADAR1 protect dsRNA from dsRNA-sensing molecules and inhibit innate immunity and the interferon-mediated response. Deficiency in these ADAR1 functions underlie the pathogenesis of autoinflammatory diseases such as the type I interferonopathies Aicardi-Goutieres syndrome and dyschromatosis symmetrica hereditaria. ADAR1-mediated editing of endogenous coding and noncoding RNA as well as ADAR1 editing-independent interactions with DICER can also have oncogenic or tumor suppressive effects that affect tumor proliferation, invasion, and response to immunotherapy. The combination of proviral and antiviral roles played by ADAR1 in repressing the interferon response and editing viral RNAs alters viral morphogenesis and cell susceptibility to infection. This review analyzes the structure and function of ADAR1 with a focus on its position in human disease pathways and the mechanisms of its disease-associated effects. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Brian Song
- Department of Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Yusuke Shiromoto
- Department of Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Moeko Minakuchi
- Department of Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Kazuko Nishikura
- Department of Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, USA
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13
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Inoue M, Nakahama T, Yamasaki R, Shibuya T, Kim JI, Todo H, Xing Y, Kato Y, Morii E, Kawahara Y. An Aicardi-Goutières Syndrome-Causative Point Mutation in Adar1 Gene Invokes Multiorgan Inflammation and Late-Onset Encephalopathy in Mice. THE JOURNAL OF IMMUNOLOGY 2021; 207:3016-3027. [PMID: 34772697 DOI: 10.4049/jimmunol.2100526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/13/2021] [Indexed: 12/23/2022]
Abstract
Aicardi-Goutières syndrome (AGS) is a congenital inflammatory disorder accompanied by overactivated type I IFN signaling and encephalopathy with leukodystrophy and intracranial calcification. To date, none of the mouse models carrying an AGS-causative mutation has mimicked such brain pathology. Here, we established a mutant mouse model carrying a K948N point mutation, corresponding to an AGS-causative K999N mutation, located in a deaminase domain of the Adar1 gene that encodes an RNA editing enzyme. Adar1K948N/K948N mice displayed postnatal growth retardation. Hyperplasia of splenic white pulps with germinal centers and hepatic focal inflammation were observed from 2 mo of age. Inflammation developed in the lungs and heart with lymphocyte infiltration in an age-dependent manner. Furthermore, white matter abnormalities with astrocytosis and microgliosis were detected at 1 y of age. The increased expression of IFN-stimulated genes was detected in multiple organs, including the brain, from birth. In addition, single-nucleus RNA sequencing revealed that this elevated expression of IFN-stimulated genes was commonly observed in all neuronal subtypes, including neurons, oligodendrocytes, and astrocytes. We further showed that a K948N point mutation reduced the RNA editing activity of ADAR1 in vivo. The pathological abnormalities found in Adar1K948N/K948N mice were ameliorated by either the concurrent deletion of MDA5, a cytosolic sensor of unedited transcripts, or the sole expression of active ADAR1 p150, an isoform of ADAR1. Collectively, such data suggest that although the degree is mild, Adar1K948N/K948N mice mimic multiple AGS phenotypes, including encephalopathy, which is caused by reduced RNA editing activity of the ADAR1 p150 isoform.
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Affiliation(s)
- Maal Inoue
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Taisuke Nakahama
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Ryuichiro Yamasaki
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Toshiharu Shibuya
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Jung In Kim
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hiroyuki Todo
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yanfang Xing
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuki Kato
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Eiichi Morii
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan; and
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan; .,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan.,Genome Editing Research and Development Center, Graduate School of Medicine, Osaka University, Osaka, Japan
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14
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Mutations in the adenosine deaminase ADAR1 that prevent endogenous Z-RNA binding induce Aicardi-Goutières-syndrome-like encephalopathy. Immunity 2021; 54:1976-1988.e7. [PMID: 34525338 DOI: 10.1016/j.immuni.2021.08.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/27/2021] [Accepted: 08/18/2021] [Indexed: 11/22/2022]
Abstract
Mutations in the adenosine-to-inosine RNA-editing enzyme ADAR1 p150, including point mutations in the Z-RNA recognition domain Zα, are associated with Aicardi-Goutières syndrome (AGS). Here, we examined the in vivo relevance of ADAR1 binding of Z-RNA. Mutation of W197 in Zα, which abolished Z-RNA binding, reduced RNA editing. Adar1W197A/W197A mice displayed severe growth retardation after birth, broad expression of interferon-stimulated genes (ISGs), and abnormal development of multiple organs. Notably, malformation of the brain was accompanied by white matter vacuolation and gliosis, reminiscent of AGS-associated encephalopathy. Concurrent deletion of the double-stranded RNA sensor MDA5 ameliorated these abnormalities. ADAR1 (W197A) expression increased in a feedback manner downstream of type I interferons, resulting in increased RNA editing at a subset of, but not all, ADAR1 target sites. This increased expression did not ameliorate inflammation in Adar1W197A/W197A mice. Thus, editing of select endogenous RNAs by ADAR1 is essential for preventing inappropriate MDA5-mediated inflammation, with relevance to the pathogenesis of AGS.
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15
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Kim JI, Nakahama T, Yamasaki R, Costa Cruz PH, Vongpipatana T, Inoue M, Kanou N, Xing Y, Todo H, Shibuya T, Kato Y, Kawahara Y. RNA editing at a limited number of sites is sufficient to prevent MDA5 activation in the mouse brain. PLoS Genet 2021; 17:e1009516. [PMID: 33983932 PMCID: PMC8118328 DOI: 10.1371/journal.pgen.1009516] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/28/2021] [Indexed: 12/22/2022] Open
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1), an enzyme responsible for adenosine-to-inosine RNA editing, is composed of two isoforms: nuclear p110 and cytoplasmic p150. Deletion of Adar1 or Adar1 p150 genes in mice results in embryonic lethality with overexpression of interferon-stimulating genes (ISGs), caused by the aberrant recognition of unedited endogenous transcripts by melanoma differentiation-associated protein 5 (MDA5). However, among numerous RNA editing sites, how many RNA sites require editing, especially by ADAR1 p150, to avoid MDA5 activation and whether ADAR1 p110 contributes to this function remains elusive. In particular, ADAR1 p110 is abundant in the mouse brain where a subtle amount of ADAR1 p150 is expressed, whereas ADAR1 mutations cause Aicardi-Goutières syndrome, in which the brain is one of the most affected organs accompanied by the elevated expression of ISGs. Therefore, understanding RNA editing-mediated prevention of MDA5 activation in the brain is especially important. Here, we established Adar1 p110-specific knockout mice, in which the upregulated expression of ISGs was not observed. This result suggests that ADAR1 p150-mediated RNA editing is enough to suppress MDA5 activation. Therefore, we further created Adar1 p110/Adar2 double knockout mice to identify ADAR1 p150-mediated editing sites. This analysis demonstrated that although the elevated expression of ISGs was not observed, only less than 2% of editing sites were preserved in the brains of Adar1 p110/Adar2 double knockout mice. Of note, we found that some sites were highly edited, which was comparable to those found in wild-type mice, indicating the presence of ADAR1 p150-specific sites. These data suggest that RNA editing at a very limited sites, which is mediated by a subtle amount of ADAR1 p150, is sufficient to prevents MDA5 activation, at least in the mouse brain.
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Affiliation(s)
- Jung In Kim
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Taisuke Nakahama
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Ryuichiro Yamasaki
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Pedro Henrique Costa Cruz
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Tuangtong Vongpipatana
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Maal Inoue
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Nao Kanou
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Yanfang Xing
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hiroyuki Todo
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Toshiharu Shibuya
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Yuki Kato
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan
- Genome Editing Research and Development Center, Graduate School of Medicine, Osaka University, Suita, Japan
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16
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Wang H, Chen S, Wei J, Song G, Zhao Y. A-to-I RNA Editing in Cancer: From Evaluating the Editing Level to Exploring the Editing Effects. Front Oncol 2021; 10:632187. [PMID: 33643923 PMCID: PMC7905090 DOI: 10.3389/fonc.2020.632187] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 12/21/2020] [Indexed: 12/21/2022] Open
Abstract
As an important regulatory mechanism at the posttranscriptional level in metazoans, adenosine deaminase acting on RNA (ADAR)-induced A-to-I RNA editing modification of double-stranded RNA has been widely detected and reported. Editing may lead to non-synonymous amino acid mutations, RNA secondary structure alterations, pre-mRNA processing changes, and microRNA-mRNA redirection, thereby affecting multiple cellular processes and functions. In recent years, researchers have successfully developed several bioinformatics software tools and pipelines to identify RNA editing sites. However, there are still no widely accepted editing site standards due to the variety of parallel optimization and RNA high-seq protocols and programs. It is also challenging to identify RNA editing by normal protocols in tumor samples due to the high DNA mutation rate. Numerous RNA editing sites have been reported to be located in non-coding regions and can affect the biosynthesis of ncRNAs, including miRNAs and circular RNAs. Predicting the function of RNA editing sites located in non-coding regions and ncRNAs is significantly difficult. In this review, we aim to provide a better understanding of bioinformatics strategies for human cancer A-to-I RNA editing identification and briefly discuss recent advances in related areas, such as the oncogenic and tumor suppressive effects of RNA editing.
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Affiliation(s)
- Heming Wang
- Clinical Medical College, Changchun University of Chinese Medicine, Changchun, China
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China
- Shanghai Institute of Liver Diseases, Shanghai, China
| | - Sinuo Chen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China
- Shanghai Institute of Liver Diseases, Shanghai, China
| | - Jiayi Wei
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China
- Shanghai Institute of Liver Diseases, Shanghai, China
| | - Guangqi Song
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China
- Shanghai Institute of Liver Diseases, Shanghai, China
| | - Yicheng Zhao
- Clinical Medical College, Changchun University of Chinese Medicine, Changchun, China
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17
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Heraud-Farlow JE, Walkley CR. What do editors do? Understanding the physiological functions of A-to-I RNA editing by adenosine deaminase acting on RNAs. Open Biol 2020; 10:200085. [PMID: 32603639 PMCID: PMC7574547 DOI: 10.1098/rsob.200085] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) editing is a post-transcriptional modification of RNA which changes its sequence, coding potential and secondary structure. Catalysed by the adenosine deaminase acting on RNA (ADAR) proteins, ADAR1 and ADAR2, A-to-I editing occurs at approximately 50 000-150 000 sites in mice and into the millions of sites in humans. The vast majority of A-to-I editing occurs in repetitive elements, accounting for the discrepancy in total numbers of sites between species. The species-conserved primary role of editing by ADAR1 in mammals is to suppress innate immune activation by unedited cell-derived endogenous RNA. In the absence of editing, inverted paired sequences, such as Alu elements, are thought to form stable double-stranded RNA (dsRNA) structures which trigger activation of dsRNA sensors, such as MDA5. A small subset of editing sites are within coding sequences and are evolutionarily conserved across metazoans. Editing by ADAR2 has been demonstrated to be physiologically important for recoding of neurotransmitter receptors in the brain. Furthermore, changes in RNA editing are associated with various pathological states, from the severe autoimmune disease Aicardi-Goutières syndrome, to various neurodevelopmental and psychiatric conditions and cancer. However, does detection of an editing site imply functional importance? Genetic studies in humans and genetically modified mouse models together with evolutionary genomics have begun to clarify the roles of A-to-I editing in vivo. Furthermore, recent developments suggest there may be the potential for distinct functions of editing during pathological conditions such as cancer.
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Affiliation(s)
- Jacki E Heraud-Farlow
- Cancer and RNA Laboratory, 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
| | - Carl R Walkley
- Cancer and RNA Laboratory, 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.,Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC 3000, Australia
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