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Holm LL, Doktor TK, Hansen MB, Petersen USS, Andresen BS. Vulnerable exons, like ACADM exon 5, are highly dependent on maintaining a correct balance between splicing enhancers and silencers. Hum Mutat 2021; 43:253-265. [PMID: 34923709 DOI: 10.1002/humu.24321] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/08/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022]
Abstract
It is now widely accepted that aberrant splicing of constitutive exons is often caused by mutations affecting cis-acting splicing regulatory elements, but there is a misconception that all exons have an equal dependency on splicing regulatory elements and thus a similar susceptibility to aberrant splicing. We investigated exonic mutations in ACADM exon 5 to experimentally examine their effect on splicing and found that 7 out of 11 tested mutations affected exon inclusion, demonstrating that this constitutive exon is particularly vulnerable to exonic splicing mutations. Employing ACADM exon 5 and 6 as models, we demonstrate that the balance between splicing enhancers and silencers, flanking intron length, and flanking splice site strength are important factors that determine exon definition and splicing efficiency of the exon in question. Our study shows that two constitutive exons in ACADM have different inherent vulnerabilities to exonic splicing mutations. This suggests that in silico prediction of potential pathogenic effects on splicing from exonic mutations may be improved by also considering the inherent vulnerability of the exon. Moreover, we show that single nucleotide polymorphism that affect either of two different exonic splicing silencers, located far apart in exon 5, all protect against both immediately flanking and more distant exonic splicing mutations.
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Affiliation(s)
- Lise L Holm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Michael B Hansen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Ulrika S S Petersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
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Tajima G, Hara K, Tsumura M, Kagawa R, Okada S, Sakura N, Hata I, Shigematsu Y, Kobayashi M. Screening of MCAD deficiency in Japan: 16years' experience of enzymatic and genetic evaluation. Mol Genet Metab 2016; 119:322-328. [PMID: 27856190 DOI: 10.1016/j.ymgme.2016.10.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 10/18/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is a representative disorder of fatty acid oxidation and is one of the most prevalent inborn errors of metabolism among Caucasian populations. In Japan, however, it was as late as 2000 when the first patient was found, and enzymatic and genetic evaluation of MCAD deficiency began. METHODS We measured octanoyl-CoA dehydrogenase activity in lymphocytes of symptomatic children and newborn screening (NBS)-positive subjects who showed elevated levels of C8-acylcarnitine in blood. The results were further confirmed by direct sequencing of the ACADM gene. RESULTS The disease was diagnosed in 9 out of 18 symptomatic children. The affected patients showed residual activities from 0% to 3% of the normal average value, except for one patient with 10% activity. Concerning 50 NBS-positive subjects, 18 with enzymatic activities around 10% or lower and 14 with activities ranging from 13% to 30% were judged to be affected patients, and biallelic variants were detected in most of the cases tested. Newborns with higher enzymatic activities were estimated to be heterozygous carriers or healthy subjects, though biallelic variants were detected in 5 of them. Genetic analysis detected 22 kinds of variant alleles. The most prevalent was c.449_452delCTGA (p.T150Rfs), which was followed by c.50G>A (p.R17H), c.1085G>A (p.G362E), c.157C>T (p.R53C), and c.843A>T (p.R281S); these five variants accounted for approximately 60% of all the alleles examined. CONCLUSION Our study has revealed the unique genetic backgrounds of MCAD deficiency among Japanese, based on the largest series of non-Caucasian cases. A continuous spectrum of severity was also observed in our series of NBS-positive cases, suggesting that it is essential for every nation and ethnic group to accumulate its own information on gene variants, together with their enzymatic evaluation, in order to establish an efficient NBS system for MCAD deficiency.
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Affiliation(s)
- Go Tajima
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan; Division of Neonatal Screening, Research Institute, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan.
| | - Keiichi Hara
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan; Department of Pediatrics, National Hospital Organization Kure Medical Center, 3-1 Aoyama-cho, Kure 737-0023, Japan.
| | - Miyuki Tsumura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan.
| | - Reiko Kagawa
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan.
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan.
| | - Nobuo Sakura
- Nursing House for Severe Motor and Intellectual Severities, Suzugamine, 104-27 Minaga, Itsukaichi-cho, Saeki-ku, Hiroshima 731-5122, Japan.
| | - Ikue Hata
- Department of Pediatrics, School of Medical Sciences, University of Fukui, 23 Shimogogetsu, Matsuoka, Eiheiji-cho, Fukui 910-1193, Japan.
| | - Yosuke Shigematsu
- Department of Pediatrics, School of Medical Sciences, University of Fukui, 23 Shimogogetsu, Matsuoka, Eiheiji-cho, Fukui 910-1193, Japan.
| | - Masao Kobayashi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan.
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Medium-chain acyl-CoA deficiency: outlines from newborn screening, in silico predictions, and molecular studies. ScientificWorldJournal 2013; 2013:625824. [PMID: 24294134 PMCID: PMC3833120 DOI: 10.1155/2013/625824] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 09/12/2013] [Indexed: 12/30/2022] Open
Abstract
Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is a disorder of fatty acid oxidation characterized by hypoglycemic crisis under fasting or during stress conditions, leading to lethargy, seizures, brain damage, or even death. Biochemical acylcarnitines data obtained through newborn screening by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were confirmed by molecular analysis of the medium-chain acyl-CoA dehydrogenase (ACADM) gene. Out of 324.000 newborns screened, we identified 14 MCADD patients, in whom, by molecular analysis, we found a new nonsense c.823G>T (p.Gly275∗) and two new missense mutations: c.253G>C (p.Gly85Arg) and c.356T>A (p.Val119Asp). Bioinformatics predictions based on both phylogenetic conservation and functional/structural software were used to characterize the new identified variants. Our findings confirm the rising incidence of MCADD whose existence is increasingly recognized due to the efficacy of an expanded newborn screening panel by LC-MS/MS making possible early specific therapies that can prevent possible crises in at-risk infants. We noticed that the “common” p.Lys329Glu mutation only accounted for 32% of the defective alleles, while, in clinically diagnosed patients, this mutation accounted for 90% of defective alleles. Unclassified variants (UVs or VUSs) are especially critical when considering screening programs. The functional and pathogenic characterization of genetic variants presented here is required to predict their medical consequences in newborns.
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