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Ma Q, Che L, Chen Y, Gu Z. Identification of five novel variants of ADAR1 in dyschromatosis symmetrica hereditaria by next-generation sequencing. Front Pediatr 2023; 11:1161502. [PMID: 37476031 PMCID: PMC10354868 DOI: 10.3389/fped.2023.1161502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/13/2023] [Indexed: 07/22/2023] Open
Abstract
Background Dyschromatosis symmetrica hereditaria (DSH) is a rare autosomal dominant inherited pigmentary dermatosis characterized by a mixture of hyperpigmented and hypopigmented freckles on the dorsal aspect of the distal extremities. To date, pathogenic mutations causing DSH have been identified in the adenosine deaminase acting on RNA1 gene (ADAR1), which is mapped to chromosome 1q21. Objective The present study aimed to investigate the underlying pathological mechanism in 14 patients with DSH from five unrelated Chinese families. Next-generation sequencing (NGS) and direct sequencing were performed on a proband with DSH to identify causative mutations. All coding, adjacent intronic, and 5'- and 3'-untranslated regions of ADAR1 were screened, and variants were identified. Result These mutations consisted of three missense mutations (NM_001025107: c.716G>A, NM_001111.5: c.3384G>C, and NM_001111.5: c.3385T>G), one nonsense mutation (NM_001111.5:c.511G>T), and one splice-site mutation (NM_001111.5: c.2080-1G>T) located in exon 2, exon 14, and the adjacent intronic region according to recommended Human Genome Variation Society (HGVS) nomenclature. Moreover, using polymerase chain reaction and Sanger sequencing, we identified five novel ADAR1 variants, which can be predicted to be pathogenic by in silico genome sequence analysis. Among the mutations, the missense mutations had no significant effect on the spatial structure of the protein, while the stop codon introduced by the nonsense mutation truncated the protein. Conclusion Our results highlighted that the advent of NGS has facilitated high-throughput screening for the identification of disease-causing mutations with high accuracy, stability, and specificity. Five novel genetic mutations were found in five unrelated families, thereby extending the pathogenic mutational spectrum of ADAR1 in DSH and providing new insights into this complex genetic disorder.
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Affiliation(s)
- Qian Ma
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Lingyi Che
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yibing Chen
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Zhuoyu Gu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
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Quin J, Sedmík J, Vukić D, Khan A, Keegan LP, O'Connell MA. ADAR RNA Modifications, the Epitranscriptome and Innate Immunity. Trends Biochem Sci 2021; 46:758-771. [PMID: 33736931 DOI: 10.1016/j.tibs.2021.02.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/28/2021] [Accepted: 02/18/2021] [Indexed: 12/22/2022]
Abstract
Modified bases act as marks on cellular RNAs so that they can be distinguished from foreign RNAs, reducing innate immune responses to endogenous RNA. In humans, mutations giving reduced levels of one base modification, adenosine-to-inosine deamination, cause a viral infection mimic syndrome, a congenital encephalitis with aberrant interferon induction. These Aicardi-Goutières syndrome 6 mutations affect adenosine deaminase acting on RNA 1 (ADAR1), which generates inosines in endogenous double-stranded (ds)RNA. The inosine base alters dsRNA structure to prevent aberrant activation of antiviral cytosolic helicase RIG-I-like receptors. We review how effects of inosines, ADARs, and other modified bases have been shown to be important in innate immunity and cancer.
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Affiliation(s)
- Jaclyn Quin
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Jiří Sedmík
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Dragana Vukić
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Anzer Khan
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Liam P Keegan
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic.
| | - Mary A O'Connell
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic.
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Zhang J, Yao Y, He H, Shen J. Clinical Interpretation of Sequence Variants. CURRENT PROTOCOLS IN HUMAN GENETICS 2020; 106:e98. [PMID: 32176464 PMCID: PMC7431429 DOI: 10.1002/cphg.98] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Clinical interpretation of DNA sequence variants is a critical step in reporting clinical genetic testing results. Application of next-generation sequencing technology in molecular genetic testing has facilitated diagnoses of genetic disorders in clinical practice. However, the large number of DNA sequence variants detected in clinical specimens, many of which have never been seen before, make clinical interpretation challenging. Recommendations by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) have been widely adopted by clinical laboratories around the world to guide clinical interpretation of sequence variants. The ClinGen Sequence Variant Interpretation Working Group and various disease-specific variant curation expert panels have also developed specifications for the ACMG/AMP recommendations. Despite these efforts to standardize variant interpretation in clinical practice, different laboratories may subjectively use professional judgment to determine which criteria are applicable when classifying a variant. In addition, clinicians and researchers who are not familiar with the variant interpretation process may have difficulty understanding clinical genetic reports and communicating the clinical significance of genetic testing results. Here we provide a step-by-step protocol for clinical interpretation of sequence variants, including practical examples. By following this protocol, clinical laboratory geneticists can interpret the clinical significance of sequence variants according to the ACMG/AMP recommendations and ClinGen framework. Furthermore, this article will help clinicians and researchers to understand variant classification in clinical genetic testing reports and evaluate the quality of the reports. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Interpreting the clinical significance of sequence variants Support Protocol: Reevaluating the clinical significance of sequence variants.
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Affiliation(s)
- Junyu Zhang
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yanyi Yao
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Haixian He
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, China
| | - Jun Shen
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
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Wang P, Yu S, Liu J, Zhang D, Kang X. Seven novel mutations of ADAR in multi-ethnic pedigrees with dyschromatosis symmetrica hereditaria in China. Mol Genet Genomic Med 2019; 7:e00905. [PMID: 31423758 PMCID: PMC6785447 DOI: 10.1002/mgg3.905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/31/2019] [Accepted: 07/08/2019] [Indexed: 12/24/2022] Open
Abstract
Background Dyschromatosis symmetrica hereditaria (DSH;OMIM: #127400) is a rare autosomal dominant skin disease of hyperpigmented and hypopigmented macules on the dorsal aspects of the feet and hands. The adenosine deaminase RNA‐Specific (ADAR;OMIM: *146920) gene was identified as causing DSH. Although more than 200 mutations are reported, no research has included the pedigrees of ethnic minorities in China. To investigate clinical features and genetic factors among multi‐ethnic families, seven multi‐ethnic pedigrees with DSH were collected for analysis of hereditary characteristics and ADAR mutations. Methods All 15 exons and exon–intron sequences of the ADAR gene were amplified and Sanger sequenced from 25 patients and 36 normal controls from seven multi‐ethnic DSH families with 100 healthy normal controls. Seven mutations were analyzed by Polyphen 2, SIFT and Provean. All mutations in ADAR with DSH were reviewed and genetic and clinical features were summarized for analysis. The ADEAMc domain may be a hot spot of ADAR mutations among patients with DSH. Results Seven novel mutations were identified in seven multi‐ethnic pedigrees: c.497delA(p.Arg105fs), c.3352C>T(p.Gln1058*) and c.3722delT(p.Ser1181fs) were found in three Uygur families with DSH; c.1330A>G(p.Val332Met) and c.2702A>T(p.His841Leu) were found in two Kazakh pedigrees and c.1176G>A(p.Lys326Glu) and c.2861G>A(p.Arg892His) in two Hui pedigrees. We summarized 203 different mutations of ADAR from people with DSH. Conclusions Seven novel mutations were identified in seven multi‐ethnic families with DSH. Our study expands the genetic spectrum of ADAR mutations in DSH.
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Affiliation(s)
- Peng Wang
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Shirong Yu
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Jianyong Liu
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Dezhi Zhang
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Xiaojing Kang
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
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Mendelian disease caused by variants affecting recognition of Z-DNA and Z-RNA by the Zα domain of the double-stranded RNA editing enzyme ADAR. Eur J Hum Genet 2019; 28:114-117. [PMID: 31320745 DOI: 10.1038/s41431-019-0458-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/02/2019] [Accepted: 06/11/2019] [Indexed: 11/09/2022] Open
Abstract
Variants in the human double-stranded RNA editing enzyme ADAR produce three well-characterized rare Mendelian Diseases: Dyschromatosis Symmetrica Hereditaria (OMIM: 127400), Aicardi-Goutières syndrome (OMIM: 615010) and Bilateral Striatal Necrosis/Dystonia. ADAR encodes p150 and p110 protein isoforms. p150 incorporates the Zα domain that binds left-handed Z-DNA and Z-RNA with high affinity through contact of highly conserved residues with the DNA and RNA double helix. In certain individuals, frameshift variants on one parental chromosome in the second exon of ADAR produce haploinsufficiency of p150 while maintaining normal expression of p110. In other individuals, loss of p150 expression from one chromosome allows mapping of Zα p150 variants from the other parental chromosome directly to phenotype. The analysis reveals that loss of function Zα variants cause dysregulation of innate interferon responses to double-stranded RNA. This approach confirms a biological role for the left-handed conformation in human disease, further validating the power of Mendelian genetics to deliver unambiguous answers to difficult questions. The findings reveal that the human genome encodes genetic information using both shape and sequence.
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Herbert A. ADAR and Immune Silencing in Cancer. Trends Cancer 2019; 5:272-282. [DOI: 10.1016/j.trecan.2019.03.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 01/03/2023]
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Napier BA, Brubaker SW, Sweeney TE, Monette P, Rothmeier GH, Gertsvolf NA, Puschnik A, Carette JE, Khatri P, Monack DM. Complement pathway amplifies caspase-11-dependent cell death and endotoxin-induced sepsis severity. J Exp Med 2016; 213:2365-2382. [PMID: 27697835 PMCID: PMC5068231 DOI: 10.1084/jem.20160027] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 08/25/2016] [Indexed: 01/18/2023] Open
Abstract
Cell death and release of proinflammatory mediators contribute to mortality during sepsis. Specifically, caspase-11-dependent cell death contributes to pathology and decreases in survival time in sepsis models. Priming of the host cell, through TLR4 and interferon receptors, induces caspase-11 expression, and cytosolic LPS directly stimulates caspase-11 activation, promoting the release of proinflammatory cytokines through pyroptosis and caspase-1 activation. Using a CRISPR-Cas9-mediated genome-wide screen, we identified novel mediators of caspase-11-dependent cell death. We found a complement-related peptidase, carboxypeptidase B1 (Cpb1), to be required for caspase-11 gene expression and subsequent caspase-11-dependent cell death. Cpb1 modifies a cleavage product of C3, which binds to and activates C3aR, and then modulates innate immune signaling. We find the Cpb1-C3-C3aR pathway induces caspase-11 expression through amplification of MAPK activity downstream of TLR4 and Ifnar activation, and mediates severity of LPS-induced sepsis (endotoxemia) and disease outcome in mice. We show C3aR is required for up-regulation of caspase-11 orthologues, caspase-4 and -5, in primary human macrophages during inflammation and that c3aR1 and caspase-5 transcripts are highly expressed in patients with severe sepsis; thus, suggesting that these pathways are important in human sepsis. Our results highlight a novel role for complement and the Cpb1-C3-C3aR pathway in proinflammatory signaling, caspase-11 cell death, and sepsis severity.
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Affiliation(s)
- Brooke A Napier
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Sky W Brubaker
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Timothy E Sweeney
- Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305
| | - Patrick Monette
- Department of Biology, Middlebury College, Middlebury, VT 05753
| | | | - Nina A Gertsvolf
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Andreas Puschnik
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Purvesh Khatri
- Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305
| | - Denise M Monack
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
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STAT2-dependent induction of RNA adenosine deaminase ADAR1 by type I interferon differs between mouse and human cells in the requirement for STAT1. Virology 2015; 485:363-70. [PMID: 26335850 DOI: 10.1016/j.virol.2015.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/01/2015] [Accepted: 08/04/2015] [Indexed: 12/24/2022]
Abstract
Expression of adenosine deaminase acting on RNA1 (ADAR1) is driven by alternative promoters. Promoter PA, activated by interferon (IFN), produces transcripts that encode the inducible p150 ADAR1 protein, whereas PB specifies the constitutively expressed p110 protein. We show using Stat1(-/-), Stat2(-/-) and IRF9(-/-) MEFs that induction of ADAR1 p150 occurs by STAT2- and IRF9-dependent signaling that is enhanced by, but not obligatorily dependent upon, STAT1. Chromatin immunoprecipitation analysis demonstrated STAT2 at the PA promoter in IFN-treated Stat1(-/-) cells, whereas IFN-treated wild-type cells showed both STAT1 and STAT2 bound at PA. By contrast, with human 2fTGH cells and mutants U3A or U6A, ADAR1 induction by IFN was dependent upon both STAT1 and STAT2. These results suggest that transcriptional activation of Adar1 by IFN occurs in the absence of STAT1 by a non-canonical STAT2-dependent pathway in mouse but not human cells.
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Liu Q, Wang Z, Wu Y, Cao L, Tang Q, Xing X, Ma H, Zhang S, Luo Y. Five novel mutations in the ADAR1 gene associated with dyschromatosis symmetrica hereditaria. BMC MEDICAL GENETICS 2014; 15:69. [PMID: 24950769 PMCID: PMC4105233 DOI: 10.1186/1471-2350-15-69] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/02/2014] [Indexed: 12/20/2022]
Abstract
Background Dyschromatosis symmetrica hereditaria (DSH) is an autosomal dominantly inherited skin disease associated with mutations of ADAR1, the gene that encodes a double-stranded RNA-specific adenosine deaminase. The purpose of this study was to investigate the potential mutations in ADAR1 in seven Chinese families with DSH. Methods All the coding exons including adjacent intronic as well as 5′ and 3′ untranslated region (UTR) of ADAR1 were screened by direct sequencing. Moreover, quantitative reverse-transcription polymerase chain (qRT-PCR) and Western blot were applied to determine the pathogenic effects associated with the mutations. Results Molecular genetic investigations detected five novel mutations (c.556C > T, c.3001C > T, c.1936_1937insTG, c.1065_1068delGACA and c.1601G > A resulting in p.Gln186X, p.Arg1001Cys, p.Phe646LeufsX16, p.Asp357ArgfsX47 and p.Gly471AspfsX30 protein changes, respectively) as well as two previously reported (c.2744C > T and c.3463C > T causing p.Ser915Phe and p.Arg1155Trp protein changes, respectively). Among them, we found that the substitution c.1601G > A at the last nucleotide of exon 2 compromised the recognition of the splice donor site of intron 2, inducing an aberrant transcript with 190-bp deletion in exon 2 and causing an approximately 50% reduction of ADAR1 mRNA level in affected individual. In addition, consistent with the predicted results, the expression patterns of other novel mutations were detected by Western blot. Conclusion We identified five novel and two recurrent mutations of the ADAR1 gene in seven Chinese families with DSH and investigated potential effects of the novel mutations in this study. Our study expands the database on mutations of ADAR1 and for the first time, demonstrates the importance of exonic nucleotides at exon-intron junctions for ADAR1 splicing.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yang Luo
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110001, China.
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