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Marelli C, Fouilhoux A, Benoist J, De Lonlay P, Guffon‐Fouilhoux N, Brassier A, Cano A, Chabrol B, Pennisi A, Schiff M, Acquaviva C, Murphy E, Servais A, Lachmann R. Very long-term outcomes in 23 patients with cblA type methylmalonic acidemia. J Inherit Metab Dis 2022; 45:937-951. [PMID: 35618652 PMCID: PMC9540587 DOI: 10.1002/jimd.12525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVES To present the very long-term follow up of patients with cobalamin A (cblA) deficiency. METHODS A retrospective case series of adult (>16 years) patients with molecular or enzymatic diagnosis of cblA deficiency. RESULTS We included 23 patients (mean age: 27 ± 7.6 years; mean follow-up: 24.9 ± 7.6 years). Disease onset was mostly pediatric (78% < 1 year, median = 4 months) with acute neurologic deterioration (65%). Eight patients presented with chronic symptoms, and one had an adult-onset mild cblA deficiency. Most of the patients (61%) were initially classified as vitamin B12-unresponsive methylmalonic aciduria (MMA); in vitro B12 responsiveness was subsequently found in all the tested patients (n = 13). Initial management consisted of protein restriction (57%), B12 (17%), or both (26%). The main long-term problems were intellectual disability (39%) and renal failure (30%). However, 56.5% of the patients were living independently. Intellectual disability was equally distributed among the initial treatment groups, while renal failure (moderate and beginning at the age of 38 years) was present in only one out of seven patients initially treated with B12. CONCLUSIONS We provide a detailed picture of the long-term outcome of a series of adult cblA patients, mostly diagnosed before the enzymatic and molecular era. We confirm that about 35% of the patients do not present acutely, underlining the importance of measuring MMA in any case of unexplained chronic renal failure, intellectual disability, or growth delay. In addition, we describe a patient with a milder adult-onset form. Early B12 supplementation seems to protect from severe renal insufficiency.
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Affiliation(s)
- Cecilia Marelli
- Expert Centre for Neurogenetic Diseases and Adult Mitochondrial and Metabolic DiseasesUniversity Hospital of MontpellierMontpellierFrance
- MMDNUniversity of Montpellier, Ecole Pratique des Hautes Etudes, InsermMontpellierFrance
| | - Alain Fouilhoux
- Reference Center for Inborn Error of MetabolismHôpital Femme Mère Enfant, Hospices Civils de LyonBronFrance
| | - Jean‐Francois Benoist
- Inserm UMR_S1163Institut ImagineParisFrance
- Biochemistry DepartmentHôpital Necker Enfants Malades, Assistance Publique – Hôpitaux de ParisParisFrance
| | - Pascale De Lonlay
- Necker Hospital, Assistance Publique – Hôpitaux de Paris, Reference Center for Inborn Error of Metabolism and Filière G2M, Pediatrics DepartmentUniversity of ParisParisFrance
| | - Nathalie Guffon‐Fouilhoux
- Reference Center for Inborn Error of MetabolismHôpital Femme Mère Enfant, Hospices Civils de LyonBronFrance
| | - Anais Brassier
- Necker Hospital, Assistance Publique – Hôpitaux de Paris, Reference Center for Inborn Error of Metabolism and Filière G2M, Pediatrics DepartmentUniversity of ParisParisFrance
| | - Aline Cano
- Reference Center for Inherited Metabolic Disorders, Assistance Publique Hôpitaux de MarseilleCentre Hospitalier Universitaire de La Timone EnfantsMarseilleFrance
| | - Brigitte Chabrol
- Reference Center for Inherited Metabolic Disorders, Assistance Publique Hôpitaux de MarseilleCentre Hospitalier Universitaire de La Timone EnfantsMarseilleFrance
| | - Alessandra Pennisi
- Necker Hospital, Assistance Publique – Hôpitaux de Paris, Reference Center for Inborn Error of Metabolism and Filière G2M, Pediatrics DepartmentUniversity of ParisParisFrance
| | - Manuel Schiff
- Inserm UMR_S1163Institut ImagineParisFrance
- Necker Hospital, Assistance Publique – Hôpitaux de Paris, Reference Center for Inborn Error of Metabolism and Filière G2M, Pediatrics DepartmentUniversity of ParisParisFrance
| | - Cecile Acquaviva
- Center for Inherited Metabolic Disorders and Neonatal Screening, Est Biology and Pathology Department, Groupement Hospitalier Est (GHE)Hospices Civils de LyonBronFrance
| | - Elaine Murphy
- C. Dent Adult Metabolic UnitNational Hospital for Neurology and NeurosurgeryLondonUK
| | - Aude Servais
- Necker Hospital, Assistance Publique – Hôpitaux de Paris, Reference Center for Inborn Error of Metabolism and Filière G2M, Pediatrics DepartmentUniversity of ParisParisFrance
- Adult Nephrology and Transplantation DepartmentHôpital Necker Enfants Malades, APHPParisFrance
| | - Robin Lachmann
- C. Dent Adult Metabolic UnitNational Hospital for Neurology and NeurosurgeryLondonUK
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Impaired Function of a Rare Mutation in the MMUT Gene Causes Methylmalonic Acidemia in a Chinese Patient. Genet Res (Camb) 2022; 2022:5611697. [PMID: 35919035 PMCID: PMC9337929 DOI: 10.1155/2022/5611697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/17/2022] [Accepted: 06/14/2022] [Indexed: 11/18/2022] Open
Abstract
Methylmalonic acidemia (MMA) is an autosomal recessive metabolic disorder mainly caused by mutations in the methylmalonyl coenzyme A mutase (MCM) gene (MMUT) and leads to the reduced activity of MCM. In this study, a 3-year-old girl was diagnosed with carnitine deficiency secondary to methylmalonic acidemia by tandem mass spectrometry (MS/MS) and gas chromatography/mass spectrometry (GS/MS). Whole-exome sequencing (WES) was performed on the patient and identified two compound heterozygous mutations in MMUT: c.554C>T (p. S185F) and c.729–730insTT (p. D244Lfs
39). Bioinformatics analysis predicted that the rare missense mutation of c.554C>T would be damaging. Moreover, this rare mutation resulted in the reduced levels of MMUT mRNA and MMUT protein. Collectively, our findings provide a greater understanding of the effects of MMUT variants and will facilitate the diagnosis and treatment of patients with MMA.
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Hu S, Kong X. The genotype analysis and prenatal genetic diagnosis among 244 pedigrees with methylmalonic aciduria in China. Taiwan J Obstet Gynecol 2022; 61:290-298. [PMID: 35361390 DOI: 10.1016/j.tjog.2022.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES To investigate the phenotypes, biochemical features and genotypes for 244 pedigrees with methylmalonic aciduria (MMA) in China, and to perform the prenatal genetic diagnosis by chorionic villus for these pedigrees. MATERIALS AND METHODS Gene analyses were performed for 244 pedigrees. There are 130 pedigrees, chorionic villus sampling was performed on the pregnant women to conduct the prenatal diagnosis. RESULTS Among 244 patients, 168 (68.9%) cases were combined methylmalonic aciduria and homocystinuria, 76 (31.1%) cases were isolated methylmalonic aciduria. All the patients were diagnosed with MMA by their clinical manifestation, elevated blood propionylcarnitine, propionylcarnitine to acetylcarnitine ratio, and/or urine/blood methylmalonic acid with or without homocysteine. MMACHC, MMUT, SUCLG1 and LMBRD1 gene variants were found in 236 (96.7%) pedigrees included 6 probands with only one heterozygous variant out of 244 cases. For the 130 pedigrees who received a prenatal diagnosis, 22 fetuses were normal, 69 foetuses were carriers of heterozygous variants, and the remaining 39 foetuses harboured compound heterozygous variants or homozygous variants. The follow-up results were consistent with the prenatal diagnosis. CONCLUSION The present study indicates genetic heterogeneity in MMA patients. Genetic analysis is a convenient method for prenatal diagnosis that will aid in avoiding the delivery of MMA patients.
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Affiliation(s)
- Shuang Hu
- The First Affiliated Hospital of Zhengzhou University, Genetic and Prenatal Diagnosis Center, No.1 Jianshe East Road, Zhengzhou, Henan, CN 450052, China.
| | - Xiangdong Kong
- The First Affiliated Hospital of Zhengzhou University, Genetic and Prenatal Diagnosis Center, No.1 Jianshe East Road, Zhengzhou, Henan, CN 450052, China.
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4
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Niall P. Keegan,
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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5
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Şeker Yılmaz B, Kor D, Bulut FD, Kılavuz S, Ceylaner S, Önenli Mungan HN. Clinical and molecular findings in 37 Turkish patients with isolated methylmalonic acidemia. Turk J Med Sci 2021; 51:1220-1228. [PMID: 33453710 PMCID: PMC8283478 DOI: 10.3906/sag-2001-72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 01/16/2021] [Indexed: 11/03/2022] Open
Abstract
Background/aim Isolated methylmalonic acidemia (MMA) is caused by complete or partial deficiency of the enzyme methylmalonyl- CoA mutase (mut0 or mut– enzymatic subtype), a defect of its cofactor adenosyl-cobalamin (cblA, cblB, or cblD-MMA), or deficiency of the enzyme methylmalonyl-CoA epimerase. While onset of the disease ranges from the neonatal period to adulthood, most cases present with lethargy, vomiting and ketoacidosis in the early infancy. Major secondary complications are; growth failure, developmental delay, interstitial nephritis with progressive renal failure, basal ganglia injury and cardiomyopathy. We aimed to demonstrate clinical and molecular findings based on long-term follow up in our patient cohort. Materials and methods The study includes 37 Turkish patients with isolated MMA who were followed up for long term complications 1 to 14 years. All patients were followed up regularly with clinical, biochemical and dietary monitoring to determine long term complications. Next Generation Sequencing technique was used for mutation screening in five disease-causing genes including; MUT, MMAA, MMAB, MMADHC, MCEE genes. Mutation screening identified 30 different types of mutations. Results While 28 of these mutations were previously reported, one novel MMAA mutation p.H382Pfs*24 (c.1145delA) and one novel MUT mutation IVS3+1G>T(c.752+1G>T) has been reported. The most common clinical complications were growth retardation, renal involvement, mental motor retardation and developmental delay. Furthermore, one of our patients developed cardiomyopathy, another one died because of hepatic failure and one presented with lactic acidosis after linezolid exposure. Conclusion We have detected two novel mutations, including one splice-site mutation in the MUT gene and one frame shift mutation in the MMAA gene in 37 Turkish patients. We confirm the genotype-phenotype correlation in the study population according to the long-term complications.
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Affiliation(s)
- Berna Şeker Yılmaz
- Department of Pediatric Metabolism, University of Mersin, Faculty of Medicine, Mersin, Turkey,Genetics and Genomics Medicine Department, Institute of Child Health, University College London, London, UK
| | - Deniz Kor
- Department of Pediatric Metabolism, University Hospital Çukurova, Adana, Turkey
| | - Fatma Derya Bulut
- Department of Pediatric Metabolism, Adana City Research and Training Hospital, Adana, Turkey
| | - Sebile Kılavuz
- Department of Pediatric Metabolism, University Hospital Çukurova, Adana, Turkey
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Yang Y, Wang P, Jin B, Dong Z, Chen G, Liu D. Screening of Potential Key Transcripts Involved in Planarian Regeneration and Analysis of Its Regeneration Patterns by PacBio Long-Read Sequencing. Front Genet 2020; 11:580. [PMID: 32612637 PMCID: PMC7308552 DOI: 10.3389/fgene.2020.00580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/11/2020] [Indexed: 12/30/2022] Open
Abstract
Dugesia japonica is an excellent animal model for studying the regeneration mechanism due to its characteristics of rapid regeneration and easy breeding. PacBio sequencing was performed on the intact planarians (In) and regenerating planarians of 1 day (1d), 3 days (3d), and 5 days (5d) after amputation. The aim of this study is to deeply profile the transcriptome of D. japonica and to evaluate its regenerate changes. Using robust statistical analysis, we identified 5931, 5115, and 4669 transcripts differentially expressed between 1d and In, 3d and In, 5d and In, respectively. A total of 63 key transcripts were screened from these DETs. These key transcripts enhance the expression in different regenerate stages respectively to regulate specific processes including signal transduction, mitosis, protein synthesis, transport and degradation, apoptosis, neural development, and energy cycling. Finally, according to the biological processes involved in these potential key transcripts, we propose a hypothesis of head regeneration model about D. japonica. In addition, the weighted gene co-expression network analysis provides a new way to screen key transcripts from large amounts of data. Together, these analyses identify a number of potential key regulators controlling proliferation, differentiation, apoptosis, and signal transduction. What's more, this study provides a powerful data foundation for further research on planarians regeneration.
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Affiliation(s)
- Yibo Yang
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Peizheng Wang
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Baijie Jin
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Zimei Dong
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Guangwen Chen
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Dezeng Liu
- College of Life Science, Henan Normal University, Xinxiang, China
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7
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Kang L, Liu Y, Shen M, Liu Y, He R, Song J, Jin Y, Li M, Zhang Y, Dong H, Liu X, Yan H, Qin J, Zheng H, Chen Y, Li D, Wei H, Zhang H, Sun L, Zhu Z, Liang D, Yang Y. A study on a cohort of 301 Chinese patients with isolated methylmalonic acidemia. J Inherit Metab Dis 2020; 43:409-423. [PMID: 31622506 DOI: 10.1002/jimd.12183] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/28/2019] [Accepted: 10/16/2019] [Indexed: 01/03/2023]
Abstract
Methylmalonic acidemia (MMA) is the most common organic acidemia in China. This study aimed to characterise the genotypic and phenotypic variabilities, and the molecular epidemiology of Chinese patients with isolated MMA. Patients (n = 301) with isolated MMA were diagnosed by clinical examination, biochemical assays, and genetic analysis. Fifty-eight patients (19.3%) were detected by newborn screening and 243 patients (80.7%) were clinically diagnosed after onset. Clinical onset ranged from the age of 3 days to 23 years (mean age = 1.01 ± 0.15 years). Among 234 MMA patients whose detailed clinical data were available, 170 (72.6%) had early onset disease (before the age of 1 year), and 64 (27.4%) had late-onset disease. The 234 MMA patients manifested with neuropsychiatric impairment (65.4%), haematological abnormality (31.6%), renal damage (8.5%), and metabolic crises (67.1%). Haematological abnormality was significantly more common in early-onset patients than that in late-onset patients. The incidence of metabolic crises was significantly high (P < 0.001) in patients with mut type than those with other types of isolated MMA. Variations (n = 122) were identified in MMUT, MMAA, MMAB, MMADHC, SUCLG1, and SUCLA2, of which 45 were novel. c.729_730insTT was the most frequent MMUT mutation, with a significantly higher frequency in our patients than that in 151 reported European patients. The frequency of c.914T>C in MMUT in our cohort was also higher than that in 151 European patients. MMUT mutations c.729_730insTT and c.914T>C are specific for the Chinese population. Our study expanded the spectrum of phenotypes and genotypes in isolated MMA.
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Affiliation(s)
- Lulu Kang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yupeng Liu
- Department of Pediatrics, People's Hospital of Peking University, Beijing, China
| | - Ming Shen
- Translational Medicine Laboratory, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yi Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Ruxuan He
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jinqing Song
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Ying Jin
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Mengqiu Li
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yao Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Hui Dong
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xueqin Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Hui Yan
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jiong Qin
- Department of Pediatrics, People's Hospital of Peking University, Beijing, China
| | - Hong Zheng
- Department of Pediatrics, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Yongxing Chen
- Department of Endocrinology and Genetic, Henan Children's Hospital, Zhengzhou, China
| | - Dongxiao Li
- Department of Endocrinology and Genetic, Henan Children's Hospital, Zhengzhou, China
| | - Haiyan Wei
- Department of Endocrinology and Genetic, Henan Children's Hospital, Zhengzhou, China
| | - Huifeng Zhang
- Department of Pediatrics, Hebei Medical University Second Hospital, Shijiazhuang, China
| | - Liying Sun
- Center of Liver Transplantation, Beijing Friendship Hospital, Beijing, China
| | - Zhijun Zhu
- Center of Liver Transplantation, Beijing Friendship Hospital, Beijing, China
| | - Desheng Liang
- Center of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Yanling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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Iijima H, Ishige N, Kubota M. Clinical Application of Liquid Chromatography Tandem Mass Spectrometry Using Dried Blood Spot as a More Rapid Method for Determination of Methylmalonic Acid, Propionylcarnitine, and Total Homocysteine. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2020. [DOI: 10.1590/2326-4594-jiems-2019-0005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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9
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Rutten MGS, Rots MG, Oosterveer MH. Exploiting epigenetics for the treatment of inborn errors of metabolism. J Inherit Metab Dis 2020; 43:63-70. [PMID: 30916397 PMCID: PMC7041640 DOI: 10.1002/jimd.12093] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/25/2019] [Indexed: 12/16/2022]
Abstract
Gene therapy is currently considered as the optimal treatment for inborn errors of metabolism (IEMs), as it aims to permanently compensate for the primary genetic defect. However, emerging gene editing approaches such as CRISPR-Cas9, in which the DNA of the host organism is edited at a precise location, may have outperforming therapeutic potential. Gene editing strategies aim to correct the actual genetic mutation, while circumventing issues associated with conventional compensation gene therapy. Such strategies can also be repurposed to normalize gene expression changes that occur secondary to the genetic defect. Moreover, besides the genetic causes of IEMs, it is increasingly recognized that their clinical phenotypes are associated with epigenetic changes. Because epigenetic alterations are principally reversible, this may offer new opportunities for treatment of IEM patients. Here, we present an overview of the promises of epigenetics in eventually treating IEMs. We discuss the concepts of gene and epigenetic editing, and the advantages and disadvantages of current and upcoming gene-based therapies for treatment of IEMs.
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Affiliation(s)
- Martijn G. S. Rutten
- Department of PediatricsUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Marianne G. Rots
- Department of Pathology and Medical BiologyUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Maaike H. Oosterveer
- Department of PediatricsUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
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10
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Keyfi F, Abbaszadegan MR, Sankian M, Rolfs A, Orolicki S, Pournasrollah M, Alijanpour M, Varasteh A. Mutation analysis of genes related to methylmalonic acidemia: identification of eight novel mutations. Mol Biol Rep 2019; 46:271-285. [PMID: 30712249 DOI: 10.1007/s11033-018-4469-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 11/02/2018] [Indexed: 11/28/2022]
Abstract
Methylmalonic acidemia (MMA), an inherited metabolic disease, results from genetic defects in methylmalonyl-CoA mutase or any of the proteins involved in adenosylcobalamin synthesis. This enzyme is classified into several complementation groups and genotypic classes. In this work we explain the biochemical, structural and genetic analysis of 25 MMA patients, from Iran. The diagnosis was established by the measurement of propionylcarnitine in blood using tandem mass spectrometry and confirmed using a gas chromatography-flame ionization detector. Using clinical, biochemical, structural and molecular analyses we identified 15 mut MMA, three cblA, one cblB, and four cblC-deficient patients. Among mutations identified in the MUT gene (MUT) only one, the c.1874A>C (p.D625A) variant, is likely a mut- mutation. The remaining mutations are probably mut0. Here, we present the first molecular analysis of MMA in Iranian patients and have identified eight novel mutations. Four novel mutations (p.D625A, p.R326G, p.V157F, p.F379L) were seen exclusively in patients from northern Iran. One novel splice site mutation (c.2125-3C>G) in MUT and two novel mutation (p.N225M and p.A99P) in the MMAA gene were associated with patients from eastern Iran. The rs184829210 SNP was recognized only in patients with the novel c.958G>A (p.A320T) mutation. This study confirms pathogenesis of deficient enzyme activity in MUT, MMAA, MMAB, and MMACHC as previous observations. These results could act as a basis for the performance of pharmacological therapies for increasing the activity of proteins derived from these mutations.
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Affiliation(s)
- Fatemeh Keyfi
- Department of Medical Laboratory Sciences, Varastegan Institute for Medical Sciences, Mashhad, Iran.,Division of Metabolic disorders, Pardis Clinical and Genetic Laboratory, Mashhad, Iran.,Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad R Abbaszadegan
- Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mojtaba Sankian
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arndt Rolfs
- Albrecht Kossel Institute for Neuroregeneration, University of Rostock, Rostock, Germany.,Chief Medical Director, Centogene AG, Rostock, Germany
| | | | - Mohammad Pournasrollah
- Non-contagious pediatric disease Research Center, Babol University of Medical Sciences, Babol, Iran
| | - Morteza Alijanpour
- Non-contagious pediatric disease Research Center, Babol University of Medical Sciences, Babol, Iran
| | - Abdolreza Varasteh
- Department of Medical Laboratory Sciences, Varastegan Institute for Medical Sciences, Mashhad, Iran. .,Division of Metabolic disorders, Pardis Clinical and Genetic Laboratory, Mashhad, Iran. .,Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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11
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Lin Y, Lin C, Lin W, Zheng Z, Han M, Fu Q. Mild clinical features of isolated methylmalonic acidemia associated with a novel variant in the MMAA gene in two Chinese siblings. BMC MEDICAL GENETICS 2018; 19:114. [PMID: 29996803 PMCID: PMC6042273 DOI: 10.1186/s12881-018-0635-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 06/26/2018] [Indexed: 11/25/2022]
Abstract
Background Methylmalonic acidemia (MMA) is an autosomal recessive inherited disorder caused by complete or partial deficiency of the enzyme methylmalonyl-CoA mutase (mut0 enzymatic subtype or mut– enzymatic subtype, respectively); a defect in the transport or synthesis of its cofactor, adenosyl-cobalamin (cblA, cblB, or cblD-MMA); or deficiency of the enzyme methylmalonyl-CoA epimerase. The cblA type of MMA is very rare in China. This study aimed to describe the biochemical, clinical, and genetic characteristics of two siblings in a Chinese family, suspected of having the cblA-type of MMA. Methods The Chinese family of Han ethnicity of two siblings with the cblA-type of MMA, was enrolled. Target-exome sequencing was performed for a panel of MMA-related genes to detect causative mutations. The influence of an identified missense variant on the protein’s structure and function was analysed using SIFT, PolyPhen-2, PROVEAN, and MutationTaster software. Moreover, homology modelling of the human wild-type and mutant proteins was performed using SWISSMODEL to evaluate the variant. Results The proband was identified via newborn screening (NBS); whereas, her elder brother, who had not undergone expanded NBS, was diagnosed later through genetic family screening. The younger sibling exhibited abnormal biochemical manifestations, and the clinical performance was relatively good after treatment, while the older brother had a mild biochemical and clinical phenotype, mainly featuring poor academic performance. A novel, homozygous missense c.365T>C variant in exon 2 of their MMAA genes was identified using next-generation sequencing and validated by Sanger sequencing. Several different types of bioinformatics software predicted that the novel variant c.365T>C (p.L122P) was deleterious. Furthermore, three-dimensional crystal structure analysis revealed that replacement of Leu122 with Pro122 led to the loss of two intramolecular hydrogen bonds between the residue at position 122 and Leu188 and Ala119, resulting in instability of the MMAA protein structure. Conclusions The two siblings suspected of having the cblA-type of MMA showed mild phenotypes during follow-up, and a novel, homozygous missense variant in their MMAA genes was identified. We believe that the clinical features of the two siblings were associated with the MMAA c.365T>C variant; however, further functional studies are warranted to confirm the variant’s pathogenicity. Electronic supplementary material The online version of this article (10.1186/s12881-018-0635-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yiming Lin
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Maternal and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Chunmei Lin
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Maternal and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Weihua Lin
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Maternal and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Zhenzhu Zheng
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Maternal and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Mingya Han
- Genuine Diagnostics Company Limited, 859 Shixiang West Road, Hangzhou, 310007, Zhejiang Province, China.
| | - Qingliu Fu
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Maternal and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China.
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12
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Zhao Z, Chu CC, Chang MY, Chang HT, Hsu YL. Management of adult-onset methylmalonic acidemia with hypotonia and acute respiratory failure: A case report. Medicine (Baltimore) 2018; 97:e11162. [PMID: 29924026 PMCID: PMC6024463 DOI: 10.1097/md.0000000000011162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
RATIONALE Methylmalonic acidemia (MMA) is an autosomal recessive disease of organic acidemia. PATIENT CONCERNS We report a 26-year-old male who presented with metabolic acidosis, acute renal failure required hemodialysis and acute respiratory failure required mechanical ventilation support. Progressive hypotonia of muscles made weaning from mechanical ventilator difficult. DIAGNOSES High level of serum methylmalonic acid and the mut genotype sequences confirmed the diagnosis of this adult-onset MMA. Two mut genotype sequences were found by analyzing all coding exons and exon-intron junctions. One genotype was well documented (Exon 6 Mutation, c. 1280G>A. p. G427D, heterozygous). The other mut genotype sequence had never been reported elsewhere (Intron 6 Novel, c. 1333-13_c. 1333-8delTTTTTC, heterozygous). INTERVENTIONS Diet modification, medication, regular hemodialysis and physical rehabilitation. Weaning strategy adjusted with help of electrical impedance tomography. OUTCOMES The muscle power of the patient gradually recovered. Extubation of the patient was successful and he was discharged without oxygen required. LESSONS This case gives us the lesson that MMA can be newly diagnosed in adult patient. A new mut genotype sequence was discovered. The use of electrical impedance tomography to select a suitable method for inspiratory muscle training was possible and useful.
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Affiliation(s)
- Zhanqi Zhao
- Department of Biomedical Engineering, Fourth Military Medical University, Xi’an, China
- Institute of Technical Medicine, Furtwangen University, Villingen-Schwenningen, Germany
| | | | | | - Hao-Tai Chang
- Division of Chest Medicine, Department of Internal Medicine, Far Eastern Memorial Hospital, Ban-Chiao District, New Taipei City, Taiwan
| | - Yeong-Long Hsu
- Division of Chest Medicine, Department of Internal Medicine, Far Eastern Memorial Hospital, Ban-Chiao District, New Taipei City, Taiwan
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13
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Tan Z, Jia X, Ma F, Feng Y, Lu H, Jin JO, Wu D, Yin L, Liu L, Zhang L. Increased MMAB level in mitochondria as a novel biomarker of hepatotoxicity induced by Efavirenz. PLoS One 2017; 12:e0188366. [PMID: 29190729 PMCID: PMC5708658 DOI: 10.1371/journal.pone.0188366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/06/2017] [Indexed: 12/02/2022] Open
Abstract
Background Efavirenz (EFV), a non-nucleoside reverse transcriptase inhibitor (NNRTI), has been widely used in the therapy of human immunodeficiency virus (HIV) infection. Some of its toxic effects on hepatic cells have been reported to display features of mitochondrial dysfunction through bioenergetic stress and autophagy, etc. However, alteration of protein levels, especially mitochondrial protein levels, in hepatic cells during treatment of EFV has not been fully investigated. Methods We built a cell model of EFV-induced liver toxicity through treating Huh-7 cells with different concentrations of EFV for different time followed by the analysis of cell viability using cell counting kit -8 (CCK8) and reactive oxygen species (ROS) using 2',7'-dichlorodihydrofluorescein diacetate (DCFH-DA) and MitoSox dye. Proteomic profiles in the mitochondria of Huh-7 cells stimulated by EFV were analyzed. Four differentially expressed proteins were quantified by real time RT-PCR. We also detected the expression of mitochondrial precursor Cob(I)yrinic acid a,c-diamide adenosyltransferase (MMAB) by immunohistochemistry analysis in clinical samples. The expression levels of MMAB and ROS were detected in EFV-treated Huh-7 cells with and without shRNA used to knock down MMAB, and in primary hepatocytes (PHC). The effects of other anti-HIV drugs (nevirapine (NVP) and tenofovirdisoproxil (TDF)), and hydrogen peroxide (H2O2) were also tested. Amino acid analysis and fatty aldehyde dehydrogenase (ALDH3A2) expression after MMAB expression knock-down with shRNA was used to investigate the metabolic effect of MMAB in Huh-7 cells. Results EFV treatment inhibited cell viability and increased ROS production with time- and concentration-dependence. Proteomic study was performed at 2 hours after EFV treatment. After treated Huh-7 cells with EFV (2.5mg/L or 10 mg/L) for 2 h, fifteen differentially expressed protein spots from purified mitochondrion that included four mitochondria proteins were detected in EFV-treated Huh-7 cells compared to controls. Consistent with protein expression levels, mRNA expression levels of mitochondrial protein MMAB were also increased by EFV treatment. In addition, the liver of EFV-treated HIV infected patients showed substantially higher levels of MMAB expression compared to the livers of untreated or protease inhibitor (PI)-treated HIV-infected patients. Furthermore, ROS were found to be decreased in Huh-7 cells treated with shMMAB compared with empty plasmid treated with EFV at the concentration of 2.5 or 10 mg/L. MMAB was increased in EFV-treated Huh-7 cells and primary hepatocytes. However, no change in MMAB expression was detected after treatment of Huh-7 cells and primary hepatocytes with anti-HIV drugs nevirapine (NVP) and tenofovirdisoproxil (TDF), or hydrogen peroxide (H2O2), although ROS was increased in these cells. Finally, knockdown of MMAB by shRNA induced increases in the β-Alanine (β-Ala) production levels and decrease in ALDH3A2 expression. Conclusions A mitochondrial proteomic study was performed to study the proteins related to EFV-inducted liver toxicity. MMAB might be a target and potential biomarker of hepatotoxicity in EFV-induced liver toxicity.
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Affiliation(s)
- Zhimi Tan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xiaofang Jia
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Fang Ma
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yanling Feng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hongzhou Lu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun-O Jin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Dage Wu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lin Yin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Li Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lijun Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- * E-mail:
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14
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Plessl T, Bürer C, Lutz S, Yue WW, Baumgartner MR, Froese DS. Protein destabilization and loss of protein‐protein interaction are fundamental mechanisms in
cblA
‐type methylmalonic aciduria. Hum Mutat 2017; 38:988-1001. [DOI: 10.1002/humu.23251] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/12/2017] [Accepted: 05/06/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Tanja Plessl
- Division of Metabolism and Children's Research CenterUniversity Children'sHospital Zurich Switzerland
- Zurich Center for Integrative Human PhysiologyUniversity of Zurich Switzerland
| | - Céline Bürer
- Division of Metabolism and Children's Research CenterUniversity Children'sHospital Zurich Switzerland
| | - Seraina Lutz
- Division of Metabolism and Children's Research CenterUniversity Children'sHospital Zurich Switzerland
| | - Wyatt W. Yue
- Structural Genomics ConsortiumNuffield Department of Clinical MedicineUniversity of Oxford Oxford United Kingdom
| | - Matthias R. Baumgartner
- Division of Metabolism and Children's Research CenterUniversity Children'sHospital Zurich Switzerland
- Zurich Center for Integrative Human PhysiologyUniversity of Zurich Switzerland
- radiz – Rare Disease Initiative ZurichClinical Research Priority Program for Rare DiseasesUniversity of ZurichZurich Switzerland
| | - D. Sean Froese
- Division of Metabolism and Children's Research CenterUniversity Children'sHospital Zurich Switzerland
- radiz – Rare Disease Initiative ZurichClinical Research Priority Program for Rare DiseasesUniversity of ZurichZurich Switzerland
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15
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Abstract
PURPOSE OF REVIEW Recent clinical studies and management guidelines for the treatment of the organic acidopathies methylmalonic acidemia (MMA) and propionic acidemia address the scope of interventions to maximize health and quality of life. Unfortunately, these disorders continue to cause significant morbidity and mortality due to acute and chronic systemic and end-organ injury. RECENT FINDINGS Dietary management with medical foods has been a mainstay of therapy for decades, yet well controlled patients can manifest growth, development, cardiac, ophthalmological, renal, and neurological complications. Patients with organic acidopathies suffer metabolic brain injury that targets specific regions of the basal ganglia in a distinctive pattern, and these injuries may occur even with optimal management during metabolic stress. Liver transplantation has improved quality of life and metabolic stability, yet transplantation in this population does not entirely prevent brain injury or the development of optic neuropathy and cardiac disease. SUMMARY Management guidelines should identify necessary screening for patients with methylmalonic acidemia and propionic acidemia, and improve anticipatory management of progressive end-organ disease. Liver transplantation improves overall metabolic control, but injury to nonregenerative tissues may not be mitigated. Continued use of medical foods in these patients requires prospective studies to demonstrate evidence of benefit in a controlled manner.
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16
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Kumari C, Kapoor S, Varughese B, Pollipali SK, Ramji S. Mutation Analyses in Selected Exons of the MUT Gene in Indian Patients with Methylmalonic Acidemia. Indian J Clin Biochem 2016; 32:266-274. [PMID: 28811685 DOI: 10.1007/s12291-016-0600-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/29/2016] [Indexed: 01/27/2023]
Abstract
Deficiency or diminished activity of a cobalamin dependent enzyme methylmalonyl-CoA mutase causes inborn error of metabolism called methylmalonic acidemia (MMA). In this study we elucidated the spectrum of mutations in 21 Indian mut MMA patients by direct sequencing. Sequence analysis identified a total of 70 mutations in exon 2, 9, 11 and 12 of MUT gene. Out of which 26 mutations were predicted to be deleterious and rest were benign. The 23 novel mutations consist of four nonsense mutations (p.N6*, p.G539*, p.E609* and p.I671*), twelve missense mutations (p.K128I, p.N547T, p.D554Y, p.A558T, p.R559P, p.A631T, p.I647T, p.E656D, p.V657E, p.Q660H, p.K679N, and p.G696Y) and seven frame shift mutations (c.375_376insA, c.1642delA, c.1655delC, c.1825_1826insT, c.1957delGA, c.2014delA and c.2062_2063insGA). All of them are point mutations or micro rearrangements. Three of these mutations (p.K621N, p.G648D, p.G630E) have been previously reported; all of them are missense mutations. The mutations are distributed throughout the exon 2, 9, 11 and 12, 38.4 % mutation are located in exon 12.
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Affiliation(s)
- Chandrawati Kumari
- Pediatrics Genetic and Research Laboratory, Department of Pediatrics, Maulana Azad Medical College, New Medical Block, Opposite Old Casualty, Lok Nayak Hospital, New Delhi, 110002 India
| | - Seema Kapoor
- Pediatrics Genetic and Research Laboratory, Department of Pediatrics, Maulana Azad Medical College, New Medical Block, Opposite Old Casualty, Lok Nayak Hospital, New Delhi, 110002 India
| | - Bijo Varughese
- Pediatrics Genetic and Research Laboratory, Department of Pediatrics, Maulana Azad Medical College, New Medical Block, Opposite Old Casualty, Lok Nayak Hospital, New Delhi, 110002 India
| | - Sunil Kumar Pollipali
- Pediatrics Genetic and Research Laboratory, Department of Pediatrics, Maulana Azad Medical College, New Medical Block, Opposite Old Casualty, Lok Nayak Hospital, New Delhi, 110002 India
| | - Siddarth Ramji
- Department of Neonatology, Maulana Azad Medical College, New Delhi, 110002 India
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17
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Chu J, Pupavac M, Watkins D, Tian X, Feng Y, Chen S, Fenter R, Zhang VW, Wang J, Wong LJ, Rosenblatt DS. Next generation sequencing of patients with mut methylmalonic aciduria: Validation of somatic cell studies and identification of 16 novel mutations. Mol Genet Metab 2016; 118:264-71. [PMID: 27233228 DOI: 10.1016/j.ymgme.2016.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/18/2016] [Accepted: 05/18/2016] [Indexed: 12/13/2022]
Abstract
Mutations in the MUT gene, which encodes the mitochondrial enzyme methylmalonyl-CoA mutase, are responsible for the mut form of methylmalonic aciduria (MMA). In this study, a next generation sequencing (NGS) based gene panel was used to analyze 53 patients that had been diagnosed with mut MMA by somatic cell complementation analysis. A total of 54 different mutations in MUT were identified in 48 patients; 16 novel mutations were identified, including 1 initiation site mutation (c.2T>C [p.M1?]), 1 missense mutation (c.566A>T [p.N189I]), 2 nonsense mutations (c.129G>A [p.W43*] and c.1975C>T [p.Q659*]), 2 mutations affecting splice sites (c.753+3A>G and c.754-2A>G), 8 small insertions, deletions, and duplications (c.29dupT [p.L10Ffs*39], c.55dupG [p.V19Gfs*30], c.631_633delGAG [p.E211del], c.795_796insT [p.M266Yfs*7], c.1061delCinsGGA [p.S354Wfs*20], c.1065_1068dupATGG [p.S357Mfs*5], c.1181dupT [p.L394Ffs*30], c.1240delG [p.E414Kfs*17]), a large insertion (c.146_147ins279), and a large deletion involving exon 13. Phenotypic rescue and cDNA analysis were used to confirm that the c.146_147ins279 and c.631_633delGAG mutations were associated with the decreased methylmalonyl-CoA mutase function observed in the patient fibroblasts. In five patients, the NGS panel did not confirm the diagnosis made by complementation analysis. One of these patients was found to carry 2 novel mutations (c.433G > A [p.E145K] and c.511A>C [p.N171H]) in the SUCLG1 gene.
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Affiliation(s)
- Jordan Chu
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Mihaela Pupavac
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - David Watkins
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Xia Tian
- Department of Molecular Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Yanming Feng
- Department of Molecular Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Stella Chen
- Department of Molecular Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Remington Fenter
- Department of Molecular Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Victor W Zhang
- Department of Molecular Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Jing Wang
- Department of Molecular Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Lee-Jun Wong
- Department of Molecular Genetics, Baylor College of Medicine, Houston, TX, United States
| | - David S Rosenblatt
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
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18
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Keyfi F, Abbaszadegan MR, Rolfs A, Orolicki S, Moghaddassian M, Varasteh A. Identification of a novel deletion in the MMAA gene in two Iranian siblings with vitamin B12-responsive methylmalonic acidemia. Cell Mol Biol Lett 2016; 21:4. [PMID: 28536607 PMCID: PMC5415723 DOI: 10.1186/s11658-016-0005-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/23/2015] [Indexed: 11/25/2022] Open
Abstract
Background Adenosylcobalamin (vitamin B12) is a coenzyme required for the activity of methylmalonyl-CoA mutase. Defects in this enzyme are a cause of methylmalonic acidemia (MMA). Methylmalonic acidemia, cblA type, is an inborn error of vitamin B12 metabolism that occurs due to mutations in the MMAA gene. MMAA encodes the enzyme which is involved in translocation of cobalamin into the mitochondria. Methods One family with two MMA-affected children, one unaffected child, and their parents were studied. The two affected children were diagnosed by urine organic acid analysis using gas chromatography-mass spectrometry. MMAA was analyzed by PCR and sequencing of its coding region. Results A homozygous deletion in exon 4 of MMAA, c.674delA, was found in both affected children. This deletion causes a nucleotide frame shift resulting in a change from asparagine to methionine at amino acid 225 (p.N225M) and a truncated protein which loses the ArgK conserved domain site. mRNA expression analysis of MMAA confirmed these results. Conclusion We demonstrate that the deletion in exon 4 of the MMAA gene (c.674 delA) is a pathogenic allele via a nucleotide frame shift resulting in a stop codon and termination of protein synthesis 38 nucleotides (12 amino acids) downstream of the deletion.
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Affiliation(s)
- Fatemeh Keyfi
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Pardis Clinical and Genetic Laboratory, Mashhad, Iran
| | - Mohammad Reza Abbaszadegan
- Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Pardis Clinical and Genetic Laboratory, Mashhad, Iran
| | - Arndt Rolfs
- Director of the Albrecht Kossel Institute for Neuroregeneration, University of Rostock, Rostock, Germany.,Chief Medical Director, Centogene AG, Rostock, Germany
| | | | - Morteza Moghaddassian
- Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abdolreza Varasteh
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Pardis Clinical and Genetic Laboratory, Mashhad, Iran
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19
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Forny P, Schnellmann AS, Buerer C, Lutz S, Fowler B, Froese DS, Baumgartner MR. Molecular Genetic Characterization of 151Mut-Type Methylmalonic Aciduria Patients and Identification of 41 Novel Mutations inMUT. Hum Mutat 2016; 37:745-54. [DOI: 10.1002/humu.23013] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/05/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Patrick Forny
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
- radiz - Rare Disease Initiative Zurich; Clinical Research Priority Program for Rare Diseases; University of Zurich; Zurich Switzerland
- Zurich Center for Integrative Human Physiology; University of Zurich; Zurich Switzerland
| | - Anne-Sophie Schnellmann
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Celine Buerer
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Seraina Lutz
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Brian Fowler
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - D. Sean Froese
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
- radiz - Rare Disease Initiative Zurich; Clinical Research Priority Program for Rare Diseases; University of Zurich; Zurich Switzerland
| | - Matthias R. Baumgartner
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
- radiz - Rare Disease Initiative Zurich; Clinical Research Priority Program for Rare Diseases; University of Zurich; Zurich Switzerland
- Zurich Center for Integrative Human Physiology; University of Zurich; Zurich Switzerland
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20
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Stojiljkovic M, Klaassen K, Djordjevic M, Sarajlija A, Brasil S, Kecman B, Grkovic S, Kostic J, Rodriguez-Pombo P, Desviat LR, Pavlovic S, Perez B. Molecular and phenotypic characteristics of seven novel mutations causing branched-chain organic acidurias. Clin Genet 2016; 90:252-7. [PMID: 26830710 DOI: 10.1111/cge.12751] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 01/12/2023]
Abstract
Specific mitochondrial enzymatic deficiencies in the catabolism of branched-chain amino acids cause methylmalonic aciduria (MMA), propionic acidemia (PA) and maple syrup urine disease (MSUD). Disease-causing mutations were identified in nine unrelated branched-chain organic acidurias (BCOA) patients. We detected eight previously described mutations: p.Asn219Tyr, p.Arg369His p.Val553Glyfs*17 in MUT, p.Thr198Serfs*6 in MMAA, p.Ile144_Leu181del in PCCB, p.Gly288Valfs*11, p.Tyr438Asn in BCKDHA and p.Ala137Val in BCKDHB gene. Interestingly, we identified seven novel genetic variants: p.Leu549Pro, p.Glu564*, p.Leu641Pro in MUT, p.Tyr206Cys in PCCB, p.His194Arg, p.Val298Met in BCKDHA and p.Glu286_Met290del in BCKDHB gene. In silico and/or eukaryotic expression studies confirmed pathogenic effect of all novel genetic variants. Aberrant enzymes p.Leu549Pro MUT, p.Leu641Pro MUT and p.Tyr206Cys PCCB did not show residual activity in activity assays. In addition, activity of MUT enzymes was not rescued in the presence of vitamin B12 precursor in vitro which was in accordance with non-responsiveness or partial responsiveness of patients to vitamin B12 therapy. Our study brings the first molecular genetic data and detailed phenotypic characteristics for MMA, PA and MSUD patients for Serbia and the whole South-Eastern European region. Therefore, our study contributes to the better understanding of molecular landscape of BCOA in Europe and to general knowledge on genotype-phenotype correlation for these rare diseases.
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Affiliation(s)
- M Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - K Klaassen
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - M Djordjevic
- Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", School of Medicine, University of Belgrade, Belgrade, Serbia
| | - A Sarajlija
- Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", School of Medicine, University of Belgrade, Belgrade, Serbia
| | - S Brasil
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biologia Molecular, Universidad Autonoma de Madrid, CBMSO, UAM, CIBERER, Madrid, Spain
| | - B Kecman
- Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", School of Medicine, University of Belgrade, Belgrade, Serbia
| | - S Grkovic
- Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", School of Medicine, University of Belgrade, Belgrade, Serbia
| | - J Kostic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - P Rodriguez-Pombo
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biologia Molecular, Universidad Autonoma de Madrid, CBMSO, UAM, CIBERER, Madrid, Spain
| | - L R Desviat
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biologia Molecular, Universidad Autonoma de Madrid, CBMSO, UAM, CIBERER, Madrid, Spain
| | - S Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - B Perez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biologia Molecular, Universidad Autonoma de Madrid, CBMSO, UAM, CIBERER, Madrid, Spain
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21
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Abstract
Defects in the human gene encoding methylmalonyl-CoA mutase enzyme (MCM) give rise to a rare autosomal recessive inherited disorder of propionate metabolism termed mut methylmalonic acidemia (MMA). Patients with mut MMA have been divided into two subgroups: mut0 with complete loss of MCM activity and mut- with residual activity in the presence of adenosylcobalamin (AdoCbl). The disease typically presents in the first weeks or months of life and is clinically characterized by recurrent vomiting, metabolic acidosis, hyperammonemia, lethargy, poor feeding, failure to thrive and neurological deficit. To better elucidate the spectrum of mutations causing mut MMA in Saudi patients, we screened a cohort of 60 Saudi patients affected by either forms of the disease for mutations in the MUT gene. A total of 13 different mutations, including seven previously reported missense changes and six novel mutations, were detected in a homozygous state except for two compound heterozygous cases. The six novel mutations identified herein consist of three nonsense, two missense and one frameshift, distributed throughout the whole protein. This study describes for the first time the clinical and mutational spectrum of mut MMA in Saudi Arabian patients.
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Clinical features and MUT gene mutation spectrum in Chinese patients with isolated methylmalonic acidemia: identification of ten novel allelic variants. World J Pediatr 2015; 11:358-65. [PMID: 26454439 DOI: 10.1007/s12519-015-0043-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 07/14/2015] [Indexed: 01/07/2023]
Abstract
BACKGROUND This study aims to study MUT gene mutation spectrum in Chinese patients with isolated methylmalonic academia (MMA) and their clinical features for the potential genotype-phenotype correlation. METHODS Forty-three patients were diagnosed with isolated MMA by elevated blood propionylcarnitine, propionylcarnitine to acetylcarnitine ratio, and urine methylmalonate without hyperhomocysteinemia. The MUT gene was amplified by polymerase chain reaction and directly sequenced. Those patients with at least one variant allele were included. The novel missense mutations were assessed by bioinformatic analysis and screened against alleles sequenced from 50 control participants. RESULTS Among the 43 patients, 38 had typical clinical presentations, and the majority (30/38) experienced earlyonset MMA. Eight patients died and seven were lost to follow-up. Twenty patients had poor outcomes and eight showed normal development. The 43 identified MUT gene mutations had at least one variant allele, whereas 35 had two mutant alleles. Of the 33 mutations reported before, eight recurrent mutations were identified in 32 patients, and c.729_730insTT (p.D244Lfs*39) was the most common (12/78) in the mutant alleles. Of the 10 novel mutations, six were missense mutations and four were premature termination codon mutations. The six novel missense mutations seemed to be pathogenic. CONCLUSIONS A total of 10 novel MUT mutations were detected in the Chinese population. c.729_730insTT (p.D244Lfs*39) was the most frequent mutation. A genotype-phenotype correlation could not be found, but the genotypic characterization indicated the need of genetic counseling for MMA patients and early prenatal diagnoses for high-risk families.
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Molecular, biochemical, and structural analysis of a novel mutation in patients with methylmalonyl-CoA mutase deficiency. Gene 2015; 576:208-13. [PMID: 26449400 DOI: 10.1016/j.gene.2015.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 09/26/2015] [Accepted: 10/01/2015] [Indexed: 11/20/2022]
Abstract
BACKGROUND Methylmalonic aciduria (MMA) is an inborn error of metabolism resulting from genetic defects in methylmalonyl-CoA mutase (MCM). This enzyme is encoded by the MUT gene and is required for the degradation of odd-chain fatty acids, the amino acids valine, isoleucine, methionine, and threonine, and cholesterol. METHOD Three unrelated affected patients with isolated MMA and their parents were studied. The MUT gene was analyzed by PCR and sequencing of its entire coding region and the highly conserved exon-intron splice junctions. The homology modeling of the novel mutation found in the MUT gene was performed using the online Swiss-Prot server for automated modeling and then analyzed with special bioinformatics software to better study the structural effects caused by the mutation. RESULT We found one homozygous nucleotide change in intron 12 of the MUT gene (c.2125-3 C>G). The variant is located near the highly conserved acceptor splice site of intron 12. A region at the C-terminus of the protein from ASP709 to GLN748 has been deleted by the alteration of c.2125-3 C>G in intron 12 of the MUT gene. Further studies of the novel mutation in the MUT gene by means of homology modeling revealed abnormalities in the protein's structure, which causes the protein to act malfunctioning and also the mRNA expression analysis of MUT gene confirmed these results. CONCLUSION We report this novel mutation, including its clinical and biochemical features and genetic defects, in the MUT gene of three patients affected with isolated MMA. Structural analyses of the mutated protein identified changes in the energy and stereochemical features of the protein that unfortunately altered the protein's functionalities. Therefore, we demonstrate that a novel splice site mutation in intron 12 of the MUT gene is a potential highly pathogenic allele via inhibition of alternative splicing.
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Sawangareetrakul P, Ketudat Cairns JR, Vatanavicharn N, Liammongkolkul S, Wasant P, Svasti J, Champattanachai V. Analysis of Novel Mutations and Methylmalonyl-CoA Mutase Levels in Thai Patients with Isolated Methylmalonic Acidemia. Biochem Genet 2015; 53:310-8. [DOI: 10.1007/s10528-015-9694-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/05/2015] [Indexed: 11/30/2022]
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Ghoraba DA, Mohammed MM, Zaki OK. Mutation analysis of methylmalonyl CoA mutase gene exon 2 in Egyptian families: Identification of 25 novel allelic variants. Meta Gene 2015; 3:71-88. [PMID: 25750861 PMCID: PMC4349194 DOI: 10.1016/j.mgene.2014.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 01/22/2014] [Accepted: 02/03/2014] [Indexed: 11/30/2022] Open
Abstract
Methylmalonic aciduria (MMA) is an autosomal recessive disorder of methylmalonate and cobalamin (cbl; vitamin B12) metabolism. It is an inborn error of organic acid metabolism which commonly results from a defect in the gene encoding the methylmalonyl-CoA mutase (MCM) apoenzyme. Here we report the results of mutation study of exon 2 of the methylmalonyl CoA mutase (MUT) gene, coding MCM residues from 1 to 128, in ten unrelated Egyptian families affected with methylmalonic aciduria. Patients were presented with a wide-anion gap metabolic acidosis. The diagnosis has established by the measurement of C3 (propionylcarnitine) and C3:C2 (propionylcarnitine/acetylcarnitine) in blood by using liquid chromatography–tandem mass spectrometry (LC/MS–MS) and was confirmed by the detection of an abnormally elevated level of methylmalonic acid in urine by using gas chromatography–mass spectrometry (GC/MS) and isocratic cation exchange high-performance liquid-chromatography (HPLC). Direct sequencing of gDNA of the MUT gene exon 2 has revealed a total of 26 allelic variants: ten of which were intronic, eight were located upstream to the exon 2 coding region, four were novel modifications predicted to affect the splicing region, three were novel mutations within the coding region: c.15G > A (p.K5K), c.165C > A (p.N55K) and c.7del (p.R3EfsX14), as well as the previously reported mutation c.323G > A (p.R108H).
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Affiliation(s)
- Dina A Ghoraba
- Medical Genetics Unit, Children's Hospital, Faculty of Medicine and University Hospitals, Cairo, Egypt
| | - Magdy M Mohammed
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Osama K Zaki
- Medical Genetics Unit, Children's Hospital, Faculty of Medicine and University Hospitals, Cairo, Egypt
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Baumgartner MR, Hörster F, Dionisi-Vici C, Haliloglu G, Karall D, Chapman KA, Huemer M, Hochuli M, Assoun M, Ballhausen D, Burlina A, Fowler B, Grünert SC, Grünewald S, Honzik T, Merinero B, Pérez-Cerdá C, Scholl-Bürgi S, Skovby F, Wijburg F, MacDonald A, Martinelli D, Sass JO, Valayannopoulos V, Chakrapani A. Proposed guidelines for the diagnosis and management of methylmalonic and propionic acidemia. Orphanet J Rare Dis 2014; 9:130. [PMID: 25205257 PMCID: PMC4180313 DOI: 10.1186/s13023-014-0130-8] [Citation(s) in RCA: 392] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 08/05/2014] [Indexed: 12/15/2022] Open
Abstract
Methylmalonic and propionic acidemia (MMA/PA) are inborn errors of metabolism characterized by accumulation of propionic acid and/or methylmalonic acid due to deficiency of methylmalonyl-CoA mutase (MUT) or propionyl-CoA carboxylase (PCC). MMA has an estimated incidence of ~ 1: 50,000 and PA of ~ 1:100’000 -150,000. Patients present either shortly after birth with acute deterioration, metabolic acidosis and hyperammonemia or later at any age with a more heterogeneous clinical picture, leading to early death or to severe neurological handicap in many survivors. Mental outcome tends to be worse in PA and late complications include chronic kidney disease almost exclusively in MMA and cardiomyopathy mainly in PA. Except for vitamin B12 responsive forms of MMA the outcome remains poor despite the existence of apparently effective therapy with a low protein diet and carnitine. This may be related to under recognition and delayed diagnosis due to nonspecific clinical presentation and insufficient awareness of health care professionals because of disease rarity. These guidelines aim to provide a trans-European consensus to guide practitioners, set standards of care and to help to raise awareness. To achieve these goals, the guidelines were developed using the SIGN methodology by having professionals on MMA/PA across twelve European countries and the U.S. gather all the existing evidence, score it according to the SIGN evidence level system and make a series of conclusive statements supported by an associated level of evidence. Although the degree of evidence rarely exceeds level C (evidence from non-analytical studies like case reports and series), the guideline should provide a firm and critical basis to guide practice on both acute and chronic presentations, and to address diagnosis, management, monitoring, outcomes, and psychosocial and ethical issues. Furthermore, these guidelines highlight gaps in knowledge that must be filled by future research. We consider that these guidelines will help to harmonize practice, set common standards and spread good practices, with a positive impact on the outcomes of MMA/PA patients.
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Nizon M, Ottolenghi C, Valayannopoulos V, Arnoux JB, Barbier V, Habarou F, Desguerre I, Boddaert N, Bonnefont JP, Acquaviva C, Benoist JF, Rabier D, Touati G, de Lonlay P. Long-term neurological outcome of a cohort of 80 patients with classical organic acidurias. Orphanet J Rare Dis 2013; 8:148. [PMID: 24059531 PMCID: PMC4016503 DOI: 10.1186/1750-1172-8-148] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 09/10/2013] [Indexed: 01/05/2023] Open
Abstract
Background Classical organic acidurias including methylmalonic aciduria (MMA), propionic aciduria (PA) and isovaleric aciduria (IVA) are severe inborn errors of the catabolism of branched-chain amino acids and odd-numbered chain fatty acids, presenting with severe complications. Methods This study investigated the long-term outcome of 80 patients with classical organic aciduria (38 with MMA, 24 with PA and 18 with IVA) by integrating clinical, radiological, biochemical and genetic data. Results Patients were followed-up for a mean of 14 years [age 3.3-46.3 years]. PA included a greater number of patients with abnormal neurological examination (37% in PA, 24% in MMA and 0% in IVA), lower psychometric scores (abnormal evaluation at age 3 years in 61% of patients with PA versus 26% in MMA and 18% in IVA) and more frequent basal ganglia lesions (56% of patients versus 36% in MMA and 17% in IVA). All patients with IVA presented a normal neurological examination and only 1/3 presented cognitive troubles. Prognosis for MMA was intermediate. Biochemical metabolite analysis excluding acute decompensations revealed significant progressive increases of glycine, alanine and glutamine particularly in PA and possibly in MMA but no correlation with neurological outcome. A significant increase of plasma methylmalonic acid was found in MMA patients with intellectual deficiency (mean level of 199 μmol/L versus 70 μmol/L, p < 0.05), with an estimated significant probability of severe outcome for average levels between birth and age 6 years above 167 μmol/L. Urinary 3-hydroxypropionate (3-HP) levels were significantly higher in PA patients with intellectual deficiency (mean level of 68.9 μmol/mmol of creatinine versus 34.6 μmol/mmol of creatinine, p < 0.01), with an estimated significant probability of severe outcome for average levels between birth and age 6 years above 55 μmol/mmol. As for molecular analysis, prognosis of MMA patients with mutations involving the MMAA gene was better compared to patients with mutations involving the MUT gene. Conclusion Propionic aciduria had the most severe neurological prognosis. Our radiological and biochemical data are consistent with a mitochondrial toxicity mechanism. Follow-up plasma MMA and urinary 3-HP levels may have prognostic significance calling for greater efforts to optimize long-term management in these patients.
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Affiliation(s)
- Mathilde Nizon
- Centre de Référence des Maladies Héréditaires du Métabolisme, Hôpital Necker-Enfants Malades, APHP, Université Paris Descartes, Institut Imagine, Paris, France.
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Xu S, Bhajoo SH, Jiang W. Genetic diagnosis of one family with incomplete clinical data. J Pediatr Endocrinol Metab 2013; 26:903-8. [PMID: 23729607 DOI: 10.1515/jpem-2013-0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/22/2013] [Indexed: 11/15/2022]
Abstract
A 6-day-old female patient suddenly died of congestive heart failure, hepatomegaly and hypoglycemic encephalopathy. Tandem mass spectrometry (MS) analysis revealed a possibility of carnitine deficiency. However, many of the clinical symptoms had not yet occurred at that time, and the clinical data was incomplete. We aim to derive a systematic procedure of identifying pathogenic mutations for similar patients. Physicians could save patients' lives with effective treatment at a much earlier stage. Direct sequencing of the exons and exon-intron boundaries of GAA, SLC25A5, CPT1, CPT2, SLC25A20 and MUT genes were performed on the parents of the patient. DNA from the blood spots of the patient was analyzed for the MUT gene. The results revealed that the patient was a compound heterozygote with MUT. c. 729_730insTT and c. 1677-1G>A. cDNA sequence demonstrated MUT c. 1677-1G>A resulting in the deletion of eight nucleotides and the introduction of 13 novel amino acids before premature termination.
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29
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FunSAV: predicting the functional effect of single amino acid variants using a two-stage random forest model. PLoS One 2012; 7:e43847. [PMID: 22937107 PMCID: PMC3427247 DOI: 10.1371/journal.pone.0043847] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 07/26/2012] [Indexed: 11/26/2022] Open
Abstract
Single amino acid variants (SAVs) are the most abundant form of known genetic variations associated with human disease. Successful prediction of the functional impact of SAVs from sequences can thus lead to an improved understanding of the underlying mechanisms of why a SAV may be associated with certain disease. In this work, we constructed a high-quality structural dataset that contained 679 high-quality protein structures with 2,048 SAVs by collecting the human genetic variant data from multiple resources and dividing them into two categories, i.e., disease-associated and neutral variants. We built a two-stage random forest (RF) model, termed as FunSAV, to predict the functional effect of SAVs by combining sequence, structure and residue-contact network features with other additional features that were not explored in previous studies. Importantly, a two-step feature selection procedure was proposed to select the most important and informative features that contribute to the prediction of disease association of SAVs. In cross-validation experiments on the benchmark dataset, FunSAV achieved a good prediction performance with the area under the curve (AUC) of 0.882, which is competitive with and in some cases better than other existing tools including SIFT, SNAP, Polyphen2, PANTHER, nsSNPAnalyzer and PhD-SNP. The sourcecodes of FunSAV and the datasets can be downloaded at http://sunflower.kuicr.kyoto-u.ac.jp/sjn/FunSAV.
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Yi Q, Lv J, Tian F, Wei H, Ning Q, Luo X. Clinical characteristics and gene mutation analysis of methylmalonic aciduria. ACTA ACUST UNITED AC 2011; 31:384-389. [DOI: 10.1007/s11596-011-0386-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Indexed: 10/18/2022]
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31
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Jorge-Finnigan A, Aguado C, Sánchez-Alcudia R, Abia D, Richard E, Merinero B, Gámez A, Banerjee R, Desviat LR, Ugarte M, Pérez B. Functional and structural analysis of five mutations identified in methylmalonic aciduria cblB type. Hum Mutat 2010; 31:1033-42. [PMID: 20556797 DOI: 10.1002/humu.21307] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
ATP:cob(I)alamin adenosyltransferase (ATR, E.C.2.5.1.17) converts reduced cob(I)alamin to the adenosylcobalamin cofactor. Mutations in the MMAB gene encoding ATR are responsible for the cblB type methylmalonic aciduria. Here we report the functional analysis of five cblB mutations to determine the underlying molecular basis of the dysfunction. The transcriptional profile along with minigenes analysis revealed that c.584G>A, c.349-1G>C, and c.290G>A affect the splicing process. Wild-type ATR and the p.I96T (c.287T>C) and p.R191W (c.571C>T) mutant proteins were expressed in a prokaryote and a eukaryotic expression systems. The p.I96T protein was enzymatically active with a K(M) for ATP and K(D) for cob(I)alamin similar to wild-type enzyme, but exhibited a 40% reduction in specific activity. Both p.I96T and p.R191W mutant proteins are less stable than the wild-type protein, with increased stability when expressed under permissive folding conditions. Analysis of the oligomeric state of both mutants showed a structural defect for p.I96T and also a significant impact on the amount of recovered mutant protein that was more pronounced for p.R191W that, along with the structural analysis, suggest they might be misfolded. These results could serve as a basis for the implementation of pharmacological therapies aimed at increasing the residual activity of this type of mutations.
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Affiliation(s)
- Ana Jorge-Finnigan
- Centro de Diagnéstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain/Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
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Abstract
Vitamin B12 (cobalamin, Cbl) is an essential nutrient in human metabolism. Genetic diseases of vitamin B12 utilisation constitute an important fraction of inherited newborn disease. Functionally, B12 is the cofactor for methionine synthase and methylmalonyl CoA mutase. To function as a cofactor, B12 must be metabolised through a complex pathway that modifies its structure and takes it through subcellular compartments of the cell. Through the study of inherited disorders of vitamin B12 utilisation, the genes for eight complementation groups have been identified, leading to the determination of the general structure of vitamin B12 processing and providing methods for carrier testing, prenatal diagnosis and approaches to treatment.
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33
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Pérez B, Angaroni C, Sánchez-Alcudia R, Merinero B, Pérez-Cerdá C, Specola N, Rodríguez-Pombo P, Wajner M, de Kremer RD, Cornejo V, Desviat LR, Ugarte M. The molecular landscape of propionic acidemia and methylmalonic aciduria in Latin America. J Inherit Metab Dis 2010; 33:S307-14. [PMID: 20549364 DOI: 10.1007/s10545-010-9116-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 04/09/2010] [Accepted: 04/19/2010] [Indexed: 12/30/2022]
Abstract
In this work, we review the clinical and genetic data in 14 Latin American propionic acidemia (PA) and 15 methylmalonic aciduria (MMAuria) patients. In the PA patients, we have identified four different changes in the PCCA gene, including one novel one (c.414+5G>A) affecting the splicing process. The PCCB mutational spectrum included two prevalent changes accounting for close to 60% of the mutant alleles studied and one novel change (c.494G>C) which by functional analysis is clearly pathogenic. We have also identified the deep intronic change c.654+462A>G, and the results of the antisense treatment in the patient's cell line confirmed the functional recovery of PCC activity. All PA patients bearing out-of-frame mutations presented the disease earlier while patients bearing in hemizygous fashion p.E168K and p.R165W presented the disease later. Regarding the MMAuria patients, we have found three novel mutations in the MUT gene (c.1068G>A, c.1587_1594del8 and c.593delA) and one in the MMAB gene (c.349-1 G>C). Two patients with MMAuria with homocystinuria cblC type are carriers of the frequent c.271dupA mutation. All mut(0), cblB and cblC patients presented the symptoms early and in general had more neurological complications, while cblA and mut(-) patients exhibited a late-onset presentation, and in general the long-term outcome was better. The results presented in this work emphasize the importance of the genetic analysis of the patients not only for diagnostic purposes but also to research into novel therapies based on the genotype.
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Affiliation(s)
- Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
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Pérez B, Rincón A, Jorge-Finnigan A, Richard E, Merinero B, Ugarte M, Desviat LR. Pseudoexon exclusion by antisense therapy in methylmalonic aciduria (MMAuria). Hum Mutat 2010; 30:1676-82. [PMID: 19862841 DOI: 10.1002/humu.21118] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Development of pseudoexon exclusion therapies by antisense modification of pre-mRNA splicing represents a type of personalized genetic medicine. Here we present the cellular antisense therapy and the cell-based splicing assays to investigate the effect of two novel deep intronic changes c.1957-898A>G and c.1957-920C>A identified in the methylmalonyl-coenzyme A (CoA) mutase (MUT) gene. The results show that the nucleotide change c.1957-898A>G is a pathological mutation activating pseudoexon insertion and that antisense morpholino oligonucleotide (AMO) treatment in patient fibroblasts leads to recovery of MUT activity to levels 25 to 100% of control range. On the contrary, the change c.1957-920C>A, identified in two fibroblasts cell lines in cis with c.1885A>G (p.R629G) or c.458T>A (p.D153V), appears to be a rare variant of uncertain clinical significance. The functional analysis of c.1885A>G and c.458T>A indicate that they are the disease-causing mutations in these two patients. The results presented here highlight the necessity of scanning the described intronic region for mutations in MUT-affected patients, followed by functional analyses to demonstrate the pathogenicity of the identified changes, and extend previous work of the applicability of the antisense approach in methylmalonic aciduria (MMAuria) for a novel intronic mutation.
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Affiliation(s)
- B Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa Universidad Autónoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain
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Dhir A, Buratti E. Alternative splicing: role of pseudoexons in human disease and potential therapeutic strategies. FEBS J 2010; 277:841-55. [PMID: 20082636 DOI: 10.1111/j.1742-4658.2009.07520.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
What makes a nucleotide sequence an exon (or an intron) is a question that still lacks a satisfactory answer. Indeed, most eukaryotic genes are full of sequences that look like perfect exons, but which are nonetheless ignored by the splicing machinery (hence the name 'pseudoexons'). The existence of these pseudoexons has been known since the earliest days of splicing research, but until recently the tendency has been to view them as an interesting, but rather rare, curiosity. In recent years, however, the importance of pseudoexons in regulating splicing processes has been steadily revalued. Even more importantly, clinically oriented screening studies that search for splicing mutations are beginning to uncover a situation where aberrant pseudoexon inclusion as a cause of human disease is more frequent than previously thought. Here we aim to provide a review of the mechanisms that lead to pseudoexon activation in human genes and how the various cis- and trans-acting cellular factors regulate their inclusion. Moreover, we list the potential therapeutic approaches that are being tested with the aim of inhibiting their inclusion in the final mRNA molecules.
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Affiliation(s)
- Ashish Dhir
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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Vorechovsky I. Transposable elements in disease-associated cryptic exons. Hum Genet 2009; 127:135-54. [PMID: 19823873 DOI: 10.1007/s00439-009-0752-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 09/27/2009] [Indexed: 11/28/2022]
Abstract
Transposable elements (TEs) make up a half of the human genome, but the extent of their contribution to cryptic exon activation that results in genetic disease is unknown. Here, a comprehensive survey of 78 mutation-induced cryptic exons previously identified in 51 disease genes revealed the presence of TEs in 40 cases (51%). Most TE-containing exons were derived from short interspersed nuclear elements (SINEs), with Alus and mammalian interspersed repeats (MIRs) covering >18 and >16% of the exonized sequences, respectively. The majority of SINE-derived cryptic exons had splice sites at the same positions of the Alu/MIR consensus as existing SINE exons and their inclusion in the mRNA was facilitated by phylogenetically conserved changes that improved both traditional and auxiliary splicing signals, thus marking intronic TEs amenable for pathogenic exonization. The overrepresentation of MIRs among TE exons is likely to result from their high average exon inclusion levels, which reflect their strong splice sites, a lack of splicing silencers and a high density of enhancers, particularly (G)AA(G) motifs. These elements were markedly depleted in antisense Alu exons, had the most prominent position on the exon-intron gradient scale and are proposed to promote exon definition through enhanced tertiary RNA interactions involving unpaired (di)adenosines. The identification of common mechanisms by which the most dynamic parts of the genome contribute both to new exon creation and genetic disease will facilitate detection of intronic mutations and the development of computational tools that predict TE hot-spots of cryptic exon activation.
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Affiliation(s)
- Igor Vorechovsky
- Division of Human Genetics, University of Southampton School of Medicine, MP808, Tremona Road, Southampton SO16 6YD, UK.
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Honjo RS, Casella EB, Vieira MA, Bertola DR, Albano LMJ, Oliveira LA, Nomachi S, Hanai J, Benoist JF, Ellard S, Young E, Kim CA. Spondylocostal dysostosis associated with methylmalonic aciduria. Genet Test Mol Biomarkers 2009; 13:181-3. [PMID: 19371216 DOI: 10.1089/gtmb.2008.0069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Spondylocostal dysostosis (SCD) is a genetic disorder characterized by vertebral segmentation and formation defects associated with changes of the ribs. Autosomal dominant and recessive modes of inheritance have been reported. Methylmalonic aciduria (MMA) is an inborn error of propionate or cobalamin metabolism. It is an autosomal recessive disorder and one of the most frequent forms of branched-chain organic acidurias. Here we report on a case of a Brazilian boy with both diseases. As we know, it is the first case in the literature with the occurrence of both SCD and MMA--the first a skeletal disease and the latter an inborn error of metabolism.
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Affiliation(s)
- Rachel S Honjo
- Instituto da Criança, University of São Paulo, São Paulo, Brazil.
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Merinero B, Pérez B, Pérez-Cerdá C, Rincón A, Desviat LR, Martínez MA, Sala PR, García MJ, Aldamiz-Echevarría L, Campos J, Cornejo V, Del Toro M, Mahfoud A, Martínez-Pardo M, Parini R, Pedrón C, Peña-Quintana L, Pérez M, Pourfarzam M, Ugarte M. Methylmalonic acidaemia: examination of genotype and biochemical data in 32 patients belonging to mut, cblA or cblB complementation group. J Inherit Metab Dis 2008; 31:55-66. [PMID: 17957493 DOI: 10.1007/s10545-007-0667-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 08/07/2007] [Accepted: 09/13/2007] [Indexed: 11/25/2022]
Abstract
Methylmalonic acidaemia (MMA) is a genetic disorder caused by defects in methylmalonyl-CoA mutase or in any of the different proteins involved in the synthesis of adenosylcobalamin. The aim of this work was to examine the biochemical and clinical phenotype of 32 MMA patients according to their genotype, and to study the mutant mRNA stability by real-time PCR analysis. Using cellular and biochemical methods, we classified our patient cohort as having the MMA forms mut (n = 19), cblA (n = 9) and cblB (n = 4). All the mut (0) and some of the cblB patients had the most severe clinical and biochemical manifestations, displaying non-inducible propionate incorporation in the presence of hydroxocobalamin (OHCbl) in vitro and high plasma odd-numbered long-chain fatty acid (OLCFA) concentrations under dietary therapy. In contrast, mut (-) and cblA patients exhibited a milder phenotype with propionate incorporation enhanced by OHCbl and normal OLCFA levels under dietary therapy. No missense mutations identified in the MUT gene, including mut (0) and mut (-) changes, affected mRNA stability. A new sequence variation (c.562G>C) in the MMAA gene was identified. Most of the cblA patients carried premature termination codons (PTC) in both alleles. Interestingly, the transcripts containing the PTC mutations were insensitive to nonsense-mediated decay (NMD).
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Affiliation(s)
- B Merinero
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Facultad de Ciencias, Universidad Autónoma, CIBER de Enfermedades Raras, Madrid, Spain
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Rincón A, Aguado C, Desviat LR, Sánchez-Alcudia R, Ugarte M, Pérez B. Propionic and methylmalonic acidemia: antisense therapeutics for intronic variations causing aberrantly spliced messenger RNA. Am J Hum Genet 2007; 81:1262-70. [PMID: 17966092 PMCID: PMC2276355 DOI: 10.1086/522376] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 08/09/2007] [Indexed: 11/03/2022] Open
Abstract
We describe the use of antisense morpholino oligonucleotides (AMOs) to restore normal splicing caused by intronic molecular defects identified in methylmalonic acidemia (MMA) and propionic acidemia (PA). The three new point mutations described in deep intronic regions increase the splicing scores of pseudoexons or generate consensus binding motifs for splicing factors, such as SRp40, which favor the intronic inclusions in MUT (r.1957ins76), PCCA (r.1284ins84), or PCCB (r.654ins72) messenger RNAs (mRNAs). Experimental confirmation that these changes are pathogenic and cause the activation of the pseudoexons was obtained by use of minigenes. AMOs were targeted to the 5? or 3? cryptic splice sites to block access of the splicing machinery to the pseudoexonic regions in the pre-mRNA. Using this antisense therapeutics, we have obtained correctly spliced mRNA that was effectively translated, and propionyl coenzyme A (CoA) carboxylase (PCC) or methylmalonylCoA mutase (MCM) activities were rescued in patients' fibroblasts. The effect of AMOs was sequence and dose dependent. In the affected patient with MUT mutation, close to 100% of MCM activity, measured by incorporation of (14)C-propionate, was obtained after 48 h, and correctly spliced MUT mRNA was still detected 15 d after treatment. In the PCCA-mutated and PCCB-mutated cell lines, 100% of PCC activity was measured after 72 h of AMO delivery, and the presence of biotinylated PCCA protein was detected by western blot in treated PCCA-deficient cells. Our results demonstrate that the aberrant inclusions of the intronic sequences are disease-causing mutations in these patients. These findings provide a new therapeutic strategy in these genetic disorders, potentially applicable to a large number of cases with deep intronic changes that, at the moment, remain undetected by standard mutation-detection techniques.
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Affiliation(s)
- A Rincón
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universitad Autónoma de Madrid, Universidad Autónoma, Madrid, Spain
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Chandler RJ, Sloan J, Fu H, Tsai M, Stabler S, Allen R, Kaestner KH, Kazazian HH, Venditti CP. Metabolic phenotype of methylmalonic acidemia in mice and humans: the role of skeletal muscle. BMC MEDICAL GENETICS 2007; 8:64. [PMID: 17937813 PMCID: PMC2140053 DOI: 10.1186/1471-2350-8-64] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Accepted: 10/15/2007] [Indexed: 12/12/2022]
Abstract
Background Mutations in methylmalonyl-CoA mutase cause methylmalonic acidemia, a common organic aciduria. Current treatment regimens rely on dietary management and, in severely affected patients, liver or combined liver-kidney transplantation. For undetermined reasons, transplantation does not correct the biochemical phenotype. Methods To study the metabolic disturbances seen in this disorder, we have created a murine model with a null allele at the methylmalonyl-CoA mutase locus and correlated the results observed in the knock-out mice to patient data. To gain insight into the origin and magnitude of methylmalonic acid (MMA) production in humans with methylmalonyl-CoA mutase deficiency, we evaluated two methylmalonic acidemia patients who had received different variants of combined liver-kidney transplants, one with a complete liver replacement-kidney transplant and the other with an auxiliary liver graft-kidney transplant, and compared their metabolite production to four untransplanted patients with intact renal function. Results Enzymatic, Western and Northern analyses demonstrated that the targeted allele was null and correctable by lentiviral complementation. Metabolite studies defined the magnitude and tempo of plasma MMA concentrations in the mice. Before a fatal metabolic crisis developed in the first 24–48 hours, the methylmalonic acid content per gram wet-weight was massively elevated in the skeletal muscle as well as the kidneys, liver and brain. Near the end of life, extreme elevations in tissue MMA were present primarily in the liver. The transplant patients studied when well and on dietary therapy, displayed massive elevations of MMA in the plasma and urine, comparable to the levels seen in the untransplanted patients with similar enzymatic phenotypes and dietary regimens. Conclusion The combined observations from the murine metabolite studies and patient investigations indicate that during homeostasis, a large portion of circulating MMA has an extra-heptorenal origin and likely derives from the skeletal muscle. Our studies suggest that modulating skeletal muscle metabolism may represent a strategy to increase metabolic capacity in methylmalonic acidemia as well as other organic acidurias. This mouse model will be useful for further investigations exploring disease mechanisms and therapeutic interventions in methylmalonic acidemia, a devastating disorder of intermediary metabolism.
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Affiliation(s)
- Randy J Chandler
- Genetic Diseases Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Keeratichamroen S, Cairns JRK, Sawangareetrakul P, Liammongkolkul S, Champattanachai V, Srisomsap C, Kamolsilp M, Wasant P, Svasti J. Novel Mutations Found in Two Genes of Thai Patients with Isolated Methylmalonic Acidemia. Biochem Genet 2007; 45:421-30. [PMID: 17410422 DOI: 10.1007/s10528-007-9085-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Accepted: 01/09/2007] [Indexed: 12/01/2022]
Abstract
Molecular genetic analysis of three patients diagnosed with isolated methylmalonic acidemia (MMA) revealed that one was mut (0) MMA, with a mutation in the MUT gene encoding the L: -methylmalonyl-CoA mutase (MCM), and two were cblB MMA, with mutations in the MMAB gene required for synthesizing the deoxyadenosylcobalamin cofactor of MCM. The mut (0) patient was homozygous for a novel nonsense mutation in MUT, p.R31X (c.167C --> T), and heterozygous for three previously described polymorphisms, p.K212K (c.712A --> G), p.H532R (c.1671A --> G), and p.V671I (c.2087G --> A). The new MMAB mutation, p.E152X (c.454G --> T), was found to be homozygous in one cblB patient and heterozygous in the other patient, who also had four intron polymorphisms in this gene.
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Affiliation(s)
- Siriporn Keeratichamroen
- Laboratory of Biochemistry, Chulabhorn Research Institute, Vibhavadee Rangsit Road, Bangkok, 10210, Thailand
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Richard E, Alvarez-Barrientos A, Pérez B, Desviat LR, Ugarte M. Methylmalonic acidaemia leads to increased production of reactive oxygen species and induction of apoptosis through the mitochondrial/caspase pathway. J Pathol 2007; 213:453-61. [DOI: 10.1002/path.2248] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Worgan LC, Niles K, Tirone JC, Hofmann A, Verner A, Sammak A, Kucic T, Lepage P, Rosenblatt DS. Spectrum of mutations in mut methylmalonic acidemia and identification of a common Hispanic mutation and haplotype. Hum Mutat 2006; 27:31-43. [PMID: 16281286 DOI: 10.1002/humu.20258] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Cobalamin nonresponsive methylmalonic acidemia (MMA, mut complementation class) results from mutations in the nuclear gene MUT, which codes for the mitochondrial enzyme methylmalonyl CoA mutase (MCM). To better elucidate the spectrum of mutations that cause MMA, the MUT gene was sequenced in 160 patients with mut MMA. Sequence analysis identified mutations in 96% of disease alleles. Mutations were found in all coding exons, but predominantly in exons 2, 3, 6, and 11. A total of 116 different mutations, 68 of which were novel, were identified. Of the 116 different mutations, 53% were missense mutations, 22% were deletions, duplications or insertions, 16% were nonsense mutations, and 9% were splice-site mutations. Sixty-one of the mutations have only been identified in one family. A novel mutation in exon 2, c.322C>T (p.R108C), was identified in 16 of 27 Hispanic patients. SNP genotyping data demonstrated that Hispanic patients with this mutation share a common haplotype. Three other mutations were seen exclusively in Hispanic patients: c.280G>A (p.G94R), c.1022dupA, and c.970G>A (p.A324T). Seven mutations were seen almost exclusively in black patients, including the previously reported c.2150G>T (p.G717V) mutation, which was identified in 12 of 29 black patients. Two mutations were seen only in Asian patients. Some frequently identified mutations were not population-specific and were identified in patients of various ethnic backgrounds. Some of these mutations were found in mutation clusters in exons 2, 3, 6, and 11, suggesting a recurrent mutation.
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Affiliation(s)
- Lisa C Worgan
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
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Sakamoto O, Ohura T, Matsubara Y, Takayanagi M, Tsuchiya S. Mutation and haplotype analyses of the MUT gene in Japanese patients with methylmalonic acidemia. J Hum Genet 2006; 52:48-55. [PMID: 17075691 DOI: 10.1007/s10038-006-0077-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2006] [Accepted: 09/26/2006] [Indexed: 11/26/2022]
Abstract
Methylmalonic acidemia (MMA) is caused by a deficiency in the activity of L: -methylmalonyl-CoA mutase (MCM), a vitamin B12 (or cobalamin, Cbl)-dependent enzyme. Apoenzyme-deficient MMA (mut MMA) results from mutations in the nuclear gene MUT. Most of the MUT mutations are thought to be private or restricted to only a few pedigrees. Our group elucidated the spectrum of mutations of Japanese mut MMA patients by performing mutation and haplotype analyses in 29 patients with mut MMA. A sequence analysis identified mutations in 95% (55/58) of the disease alleles. Five mutations were relatively frequent (p.E117X, c.385 + 5G > A, p.R369H, p.L494X, and p.R727X) and four were novel (p.M1V, c.753_753 + 5delGGTATA, c.1560G > C, and c.2098_2099delAT). Haplotype analysis suggested that all of the frequent mutations, with the exception of p.R369H, were spread by the founder effect. Among 46 Japanese patients investigated in the present and previous studies, 76% (70/92) of the mutations were located in exons 2, 6, 8, and 13. This finding - that a limited number of mutations account for most of the mutations in Japanese mut MMA patients - is in contrast with results of a previous study in Caucasian patients.
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Affiliation(s)
- Osamu Sakamoto
- Department of Pediatrics, Tohoku University School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Toshihiro Ohura
- Department of Pediatrics, Tohoku University School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan.
| | - Yoichi Matsubara
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
| | | | - Shigeru Tsuchiya
- Department of Pediatrics, Tohoku University School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
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Richard E, Monteoliva L, Juarez S, Pérez B, Desviat LR, Ugarte M, Albar JP. Quantitative analysis of mitochondrial protein expression in methylmalonic acidemia by two-dimensional difference gel electrophoresis. J Proteome Res 2006; 5:1602-10. [PMID: 16823967 DOI: 10.1021/pr050481r] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isolated methylmalonic acidemia (MMA) is a rare metabolic disease due to the deficient activity of L-methylmalonyl-CoA mutase (MCM). This mitochondrial enzyme converts L-methylmalonyl-CoA to succinyl-CoA using adenosylcobalamin (Adocbl) as cofactor. Isolated MMA is subdivided into five forms: mut MMA associated with MCM deficiency, three different defects related to mitochondrial Adocbl formation (cblA, cblB, and cblH), and cblD variant 2. We performed proteomic analysis on mitochondria from an individual with cblH/cblD disorder using 2-D DIGE to identify differentially expressed proteins in this disease. Comparative analysis of control/patient mitochondrial proteome allowed us to identify differential expression of 10 proteins. The most notable groups included proteins involved in apoptosis (cytochrome c), oxidative stress (manganese superoxide dismutase) and cell metabolism (succinyl-CoA ligase (GDP forming) and mitochondrial glycerophosphate dehydrogenase). Immunoblot analysis further validated 2-D DIGE results of two of these proteins in multiple MMA patients, suggesting that the differences in expression are a general effect in this disorder. It is feasible that the differential proteins identified in this study have a biological significance and might be related to the pathophysiology of MMA.
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Affiliation(s)
- Eva Richard
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Universidad Autónoma de Madrid, Madrid, Spain.
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Cavicchi C, Donati MA, Funghini S, la Marca G, Malvagia S, Ciani F, Poggi GM, Pasquini E, Zammarchi E, Morrone A. Genetic and biochemical approach to early prenatal diagnosis in a family with mut methylmalonic aciduria. Clin Genet 2006; 69:72-6. [PMID: 16451139 DOI: 10.1111/j.1399-0004.2005.00547.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetic and biochemical prenatal diagnosis was performed at 11 weeks of gestation in a family with a proband affected by mut methylmalonic aciduria (MMA) and homozygotes for the MUT gene c.643G>A (p.Gly215Ser) mutation. Both chorionic villus and amniotic fluid samples were used. The presence of high levels of methylmalonic acid and propionylcarnitine determined by gas chromatography/mass spectrometry and LC/MS/MS analysis, respectively, and the identification of the p.Gly215Ser at a homozygous level in foetal DNA allowed a certain, rapid and early diagnosis. To our knowledge, this is the first mut MMA prenatal diagnosis carried out by genetic and biochemical approach.
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Affiliation(s)
- C Cavicchi
- Metabolic and Muscular Unit, Department of Paediatrics, University of Florence, Meyer Children's Hospital, Florence, Italy
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Lerner-Ellis JP, Gradinger AB, Watkins D, Tirone JC, Villeneuve A, Dobson CM, Montpetit A, Lepage P, Gravel RA, Rosenblatt DS. Mutation and biochemical analysis of patients belonging to the cblB complementation class of vitamin B12-dependent methylmalonic aciduria. Mol Genet Metab 2006; 87:219-25. [PMID: 16410054 DOI: 10.1016/j.ymgme.2005.11.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2005] [Revised: 11/16/2005] [Accepted: 11/18/2005] [Indexed: 10/25/2022]
Abstract
Methylmalonic aciduria, cblB type (OMIM 251110) is an inborn error of vitamin B(12) metabolism that occurs due to mutations in the MMAB gene. MMAB encodes the enzyme ATP:cobalamin adenosyltransferase, which catalyzes the synthesis of the coenzyme adenosylcobalamin required for the activity of the mitochondrial enzyme methylmalonyl CoA mutase (MCM). MCM catalyzes the isomerization of methylmalonyl CoA to succinyl CoA. Deficient MCM activity results in methylmalonic aciduria and a susceptibility to life-threatening acidotic crises. The MMAB gene was sequenced from genomic DNA from a panel of 35 cblB patients, including five patients previously investigated. Nineteen MMAB mutations were identified, including 13 previously unknown mutations. These included 11 missense mutations, two duplications, one deletion, four splice-site mutations, and one nonsense mutation. None of these mutations was identified in 100 control alleles. Most of the missense mutations (9/11) were clustered in exon 7; many of these affected amino acid residues that are part of the probable active site of the enzyme. One previously described mutation, c.556C >T (p.R186W), was particularly common, accounting for 33% of pathogenic alleles. It was seen almost exclusively in patients of European background and was typically associated with presentation in the first year of life.
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