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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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Alotaibi RN, Howe BJ, Moreno Uribe LM, Sanchez C, Deleyiannis FW, Padilla C, Poletta FA, Orioli IM, Buxó CJ, Wehby GL, Vieira AR, Murray J, Valencia-Ramírez C, Restrepo Muñeton CP, Long RE, Shaffer JR, Reis SE, Weinberg SM, Neiswanger K, McNeil DW, Marazita ML. Genetic Analyses of Enamel Hypoplasia in Multiethnic Cohorts. Hum Hered 2022; 87:000522642. [PMID: 35172313 PMCID: PMC9378791 DOI: 10.1159/000522642] [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: 09/01/2021] [Accepted: 02/09/2022] [Indexed: 11/19/2022] Open
Abstract
Enamel hypoplasia causes reduction in the thickness of affected enamel and is one of the most common dental anomalies. This defect is caused by environmental and/or genetic factors that interfere with tooth formation, emphasizing the importance of investigating enamel hypoplasia on an epidemiological and genetic level. A genome-wide association of enamel hypoplasia was performed in multiple cohorts, overall comprising 7,159 individuals ranging in age from 7-82 years. Mixed-models were used to test for genetic association while simultaneously accounting for relatedness and genetic population structure. Meta-analysis was then performed. More than 5 million single-nucleotide polymorphisms were tested in individual cohorts. Analyses of the individual cohorts and meta-analysis identified association signals close to genome-wide significance (P < 510-8), and many suggestive association signals (510-8 < P < 510-6) near genes with plausible roles in tooth/enamel development. The strongest association signal (P = 1.5710-9) was observed near BMP2K in one of the individual cohorts. Additional suggestive signals were observed near genes with plausible roles in tooth development in the meta-analysis, such as SLC4A4 which can influence enamel hypoplasia. Additional human genetic studies are needed to replicate these results and functional studies in model systems are needed to validate our findings.
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Affiliation(s)
- Rasha N. Alotaibi
- Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brian J. Howe
- Department of Family Dentistry, College of Dentistry, University of Iowa, Iowa City, Iowa, USA
| | - Lina M. Moreno Uribe
- The Iowa Institute for Oral Health Research, College of Dentistry, University of Iowa, Iowa City, Iowa, USA
- Department of Orthodontics, School of Dentistry, University of Iowa, Iowa City, Iowa, USA
| | - Carla Sanchez
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Carmencita Padilla
- Department of Pediatrics, College of Medicine, University of the Philippines, Manila, Philippines
| | - Fernando A. Poletta
- ECLAMC/INAGEMP CEMIC, Dirección de Investigación A. Galván, Buenos Aires, Argentina
| | - Ieda M. Orioli
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carmen J. Buxó
- School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - George L. Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, Iowa, USA
| | - Alexandre R. Vieira
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jeffrey Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | | | | | - Ross E. Long
- Lancaster Cleft Palate Clinic, Lancaster, Pennsylvania, USA
| | - John R. Shaffer
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Steven E. Reis
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Seth M. Weinberg
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Katherine Neiswanger
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel W. McNeil
- Department of Psychology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, West Virginia, USA
- Department of Dental Practice and Rural Health, School of Dentistry, West Virginia University, Morgantown, West Virginia, USA
| | - Mary L. Marazita
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Kobayashi T, Kono M, Suganuma M, Akita H, Takai A, Tsutsui K, Inasaka Y, Takeichi T, Muro Y, Akiyama M. Analysis of genotype/phenotype correlations in Japanese patients with dyschromatosis symmetrica hereditaria. NAGOYA JOURNAL OF MEDICAL SCIENCE 2018; 80:267-277. [PMID: 29915444 PMCID: PMC5995736 DOI: 10.18999/nagjms.80.2.267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dyschromatosis symmetrica hereditaria (DSH) is one of the genetic pigmentation disorders and shows characteristic mixture of hyper- and hypo-pigmented small macules on the extremities. Heterozygous mutations in the adenosine deaminase acting on RNA1 gene (ADAR1) cause DSH. In the present study, we report five cases of DSH and identify a distinct known mutation in each patient. Furthermore, we review previously described cases with the five ADAR1 mutations found in the present study. We reviewed clinical and molecular findings in the present and previously reported cases and found an identical mutation can result in various phenotypic severities, even in one family. We found novel phenotype-genotype correlations between the presence/absence of facial lesions and the ADAR1 mutation c.3286C>T. The absence of freckle-like macules in the face was found to be more commonly associated with the mutation c.3286C>T than with the other 4 ADAR1 mutations (odds ratio = 0.056 [95% CI: 0.007–0.47, p < 0.005]). We objectively evaluated the severity of skin manifestations in the extremities using our definition of severity levels for such manifestations. This is the first semi-quantitative evaluation of skin manifestations in DSH. Using our definition, we found that patients with facial lesions with or without hypopigmented macules tend to show more severe symptoms on the extremities than patients without facials lesions show. Furthermore, no significant difference in the severity of the skin lesions was observed between the upper and the lower extremities, suggesting that sun exposure does not affect significantly the pathogenesis of DSH skin lesions.
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Affiliation(s)
- Tomoko Kobayashi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Michihiro Kono
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mutsumi Suganuma
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hirotaka Akita
- Department of Dermatology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Ayaka Takai
- Department of Dermatology, National Defense Medical College, Tokorozawa, Japan
| | - Kiyohiro Tsutsui
- Division of Dermatology, Ishikawa Prefectural Central Hospital, Kanazawa, Japan
| | - Yu Inasaka
- Division of Dermatology, Aichi Koseiren Konan Kosei Hospital, Konan, Japan
| | - Takuya Takeichi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinao Muro
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masashi Akiyama
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Forni D, Mozzi A, Pontremoli C, Vertemara J, Pozzoli U, Biasin M, Bresolin N, Clerici M, Cagliani R, Sironi M. Diverse selective regimes shape genetic diversity at ADAR genes and at their coding targets. RNA Biol 2015; 12:149-61. [PMID: 25826567 DOI: 10.1080/15476286.2015.1017215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
A-to-I RNA editing operated by ADAR enzymes is extremely common in mammals. Several editing events in coding regions have pivotal physiological roles and affect protein sequence (recoding events) or function. We analyzed the evolutionary history of the 3 ADAR family genes and of their coding targets. Evolutionary analysis indicated that ADAR evolved adaptively in primates, with the strongest selection in the unique N-terminal domain of the interferon-inducible isoform. Positively selected residues in the human lineage were also detected in the ADAR deaminase domain and in the RNA binding domains of ADARB1 and ADARB2. During the recent history of human populations distinct variants in the 3 genes increased in frequency as a result of local selective pressures. Most selected variants are located within regulatory regions and some are in linkage disequilibrium with eQTLs in monocytes. Finally, analysis of conservation scores of coding editing sites indicated that editing events are counter-selected within regions that are poorly tolerant to change. Nevertheless, a minority of recoding events occurs at highly conserved positions and possibly represents the functional fraction. These events are enriched in pathways related to HIV-1 infection and to epidermis/hair development. Thus, both ADAR genes and their targets evolved under variable selective regimes, including purifying and positive selection. Pressures related to immune response likely represented major drivers of evolution for ADAR genes. As for their coding targets, we suggest that most editing events are slightly deleterious, although a minority may be beneficial and contribute to antiviral response and skin homeostasis.
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Key Words
- 1000G,1000 Genomes Pilot Project
- A to I, adenosine to inosine
- A-to-I editing
- ADAR
- ADAR editing sites
- AGS, Aicardi-Goutières Syndrome
- BEB, Bayes Empirical Bayes
- BS-REL, branch site-random effects likelihood
- CEU, Europeans
- CHBJPT, Chinese plus Japanese
- DAF, derived allele frequency
- DIND, Derived Intra-allelic Nucleotide Diversity
- DSH, dyschromatosis symmetrica hereditaria
- FDR, false discovery rate
- GARD, Genetic Algorithm Recombination Detection
- GERP Genomic Evolutionary Rate Profiling
- IFN, Interferon
- LD, linkage disequilibrium
- LRT, likelihood ratio test
- MAF, minor allele frequency
- MEME, Mixed Effects Model of Evolution
- RBD, dsRNA binding domain
- SLAC, single-likelihood ancestor counting
- YRI, Yoruba
- eQTL, Expression quantitative trait loci
- evolutionary analysis
- iHS, Integrated Haplotype Score
- positive selection
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Affiliation(s)
- Diego Forni
- a Bioinformatics ; Scientific Institute IRCCS E. MEDEA ; Bosisio Parini , Italy
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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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