51
|
Meyer-Schuman R, Antonellis A. Emerging mechanisms of aminoacyl-tRNA synthetase mutations in recessive and dominant human disease. Hum Mol Genet 2017; 26:R114-R127. [PMID: 28633377 PMCID: PMC5886470 DOI: 10.1093/hmg/ddx231] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 12/29/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are responsible for charging amino acids to cognate tRNA molecules, which is the essential first step of protein translation. Interestingly, mutations in genes encoding ARS enzymes have been implicated in a broad spectrum of human inherited diseases. Bi-allelic mutations in ARSs typically cause severe, early-onset, recessive diseases that affect a wide range of tissues. The vast majority of these mutations show loss-of-function effects and impair protein translation. However, it is not clear how a subset cause tissue-specific phenotypes. In contrast, dominant ARS-mediated diseases specifically affect the peripheral nervous system-most commonly causing axonal peripheral neuropathy-and usually manifest later in life. These neuropathies are linked to heterozygosity for missense mutations in five ARS genes, which points to a shared mechanism of disease. However, it is not clear if a loss-of-function mechanism or a toxic gain-of-function mechanism is responsible for ARS-mediated neuropathy, or if a combination of these mechanisms operate on a mutation-specific basis. Here, we review our current understanding of recessive and dominant ARS-mediated disease. We also propose future directions for defining the molecular mechanisms of ARS mutations toward designing therapies for affected patient populations.
Collapse
Affiliation(s)
- Rebecca Meyer-Schuman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
52
|
Lin WX, Zheng QQ, Guo L, Cheng Y, Song YZ. [Clinical feature and molecular diagnostic analysis of the first non-caucasian child with infantile liver failure syndrome type 1]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2017; 19:913-920. [PMID: 28774368 PMCID: PMC7390053 DOI: 10.7499/j.issn.1008-8830.2017.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
Infantile liver failure syndrome type 1 (ILFS1) is a Mendelian disease due to biallelic mutations in the cytoplasmic leucyl-tRNA synthetase gene (LARS). This study aimed to report the clinical and molecular features of the first non-caucasian ILFS1 patient, providing reliable evidences for the definite diagnosis of ILFS1. The 2 years and 9 months old male patient was referred to the hospital with hepatosplenomegaly over 1 year. At age 17 months, he was found to have hepatosplenomegaly and anemia. Since then, he had been managed in different hospitals. The laboratory tests showed liver dysfunction, hypoproteinemia, coagulopathy and anemia, along with histologically-confirmed cirrhosis and fatty liver; however, the etiology remained undetermined. The subsequent SLC25A13 mutation analysis by means of prevalent mutation screening and Sanger sequencing only revealed a paternally-inherited mutation c.1658G>A, and no aberrant SLC25A13 transcripts could be detected from the maternal allele on cDNA cloning analysis, ruling out the possibility of citrin deficiency. Further target exome high-throughout sequencing of genes relevant to genetic liver diseases detected a paternal c.2133_2135del (p.L712del) and a maternal c.1183G>A (p.D395N) mutation in LARS gene. This finding was then confirmed by Sanger sequencing, and ILFS1 was thus definitely diagnosed. The child has been followed up till age 4 years, and his condition became stabilized.
Collapse
Affiliation(s)
- Wei-Xia Lin
- Department of Pediatrics, First Affiliated Hospital, Jinan University, Guangzhou 510630, China.
| | | | | | | | | |
Collapse
|
53
|
Li JQ, Qiu YL, Gong JY, Dou LM, Lu Y, Knisely AS, Zhang MH, Luan WS, Wang JS. Novel NBAS mutations and fever-related recurrent acute liver failure in Chinese children: a retrospective study. BMC Gastroenterol 2017. [PMID: 28629372 PMCID: PMC5477288 DOI: 10.1186/s12876-017-0636-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background Underlying causes in Chinese children with recurrent acute liver failure (RALF), including liver crises less than full acute liver failure, are incompletely understood. We sought to address this by searching for genes mutated in such children. Methods Five unrelated Chinese boys presenting between 2012 and 2015 with RALF of unexplained etiology were studied. Results of whole exome sequencing were screened for mutations in candidate genes. Mutations were verified in patients and their family members by Sanger sequencing. All 5 boys underwent liver biopsy. Results NBAS was the only candidate gene mutated in more than one patient (biallelic mutations, 3 of 5 patients; 5 separate mutations). All NBAS mutations were novel and predictedly pathogenic (frameshift insertion mutation c.6611_6612insCA, missense mutations c.2407G > A and c.3596G > A, nonsense mutation c.586C > T, and splicing-site mutation c.5389 + 1G > T). Of these mutations, 3 lay in distal (C-terminal) regions of NBAS, a novel distribution. Unlike the 2 patients without NBAS mutations, the 3 patients with confirmed NBAS mutations all suffered from a febrile illness before each episode of liver crisis (fever-related RALF), with markedly elevated alanine aminotransferase and aspartate aminotransferase activities 24-72 h after elevation of body temperature, succeeded by severe coagulopathy and mild to moderate jaundice. Conclusions As in other countries, so too in China; NBAS disease is a major cause of fever-related RALF in children. The mutation spectrum of NBAS in Chinese children seems different from that described in other populations. Electronic supplementary material The online version of this article (doi:10.1186/s12876-017-0636-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jia-Qi Li
- Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, 201508, China
| | - Yi-Ling Qiu
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Jing-Yu Gong
- Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, 201508, China
| | - Li-Min Dou
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Yi Lu
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - A S Knisely
- Institut für Pathologie, Medizinische Universität Graz, Auenbruggerplatz 25, A-8036, Graz, Austria
| | - Mei-Hong Zhang
- Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, 201508, China
| | - Wei-Sha Luan
- Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, 201508, China
| | - Jian-She Wang
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, 201102, China.
| |
Collapse
|
54
|
Musante L, Püttmann L, Kahrizi K, Garshasbi M, Hu H, Stehr H, Lipkowitz B, Otto S, Jensen LR, Tzschach A, Jamali P, Wienker T, Najmabadi H, Ropers HH, Kuss AW. Mutations of the aminoacyl-tRNA-synthetases SARS and WARS2 are implicated in the etiology of autosomal recessive intellectual disability. Hum Mutat 2017; 38:621-636. [PMID: 28236339 DOI: 10.1002/humu.23205] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 01/06/2017] [Accepted: 02/17/2017] [Indexed: 12/16/2022]
Abstract
Intellectual disability (ID) is the hallmark of an extremely heterogeneous group of disorders that comprises a wide variety of syndromic and non-syndromic phenotypes. Here, we report on mutations in two aminoacyl-tRNA synthetases that are associated with ID in two unrelated Iranian families. In the first family, we identified a homozygous missense mutation (c.514G>A, p.Asp172Asn) in the cytoplasmic seryl-tRNA synthetase (SARS) gene. The mutation affects the enzymatic core domain of the protein and impairs its enzymatic activity, probably leading to reduced cytoplasmic tRNASer concentrations. The mutant protein was predicted to be unstable, which could be substantiated by investigating ectopic mutant SARS in transfected HEK293T cells. In the second family, we found a compound heterozygous genotype of the mitochondrial tryptophanyl-tRNA synthetase (WARS2) gene, comprising a nonsense mutation (c.325delA, p.Ser109Alafs*15), which very likely entails nonsense-mediated mRNA decay and a missense mutation (c.37T>G, p.Trp13Gly). The latter affects the mitochondrial localization signal of WARS2, causing protein mislocalization. Including AIMP1, which we have recently implicated in the etiology of ID, three genes with a role in tRNA-aminoacylation are now associated with this condition. We therefore suggest that the functional integrity of tRNAs in general is an important factor in the development and maintenance of human cognitive functions.
Collapse
Affiliation(s)
- Luciana Musante
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lucia Püttmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Hao Hu
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Henning Stehr
- Stanford Cancer Institute, Stanford University, Stanford, California
| | | | - Sabine Otto
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars R Jensen
- Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | | | | | - Thomas Wienker
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Andreas W Kuss
- Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
55
|
Mutations in methionyl-tRNA synthetase gene in a Chinese family with interstitial lung and liver disease, postnatal growth failure and anemia. J Hum Genet 2017; 62:647-651. [PMID: 28148924 DOI: 10.1038/jhg.2017.10] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/31/2016] [Accepted: 01/03/2017] [Indexed: 12/25/2022]
Abstract
Methionyl-tRNA synthetase (MARS) catalyzes the ligation of methionine to tRNA. Heterozygous MARS mutations have been reported to cause Charcot-Marie-Tooth disease, axonal, type 2U (CMT2U). Homozygous or compound heterozygous mutations in MARS gene would cause interstitial lung and liver disease (ILLD), a severe disease onset in infancy or early childhood. Here we report a Chinese ILLD family with two affected boys diagnosed by exome sequencing. They carry novel compound heterozygous MARS mutations (p.Asp145Asn and p.Phe802Ser). Their phenotype is concordant with ILLD description. As ILLD patients were only reported by two studies, we summarized all the reported patients and characterized the principle clinical features as interstitial lung disease, developmental delay, postnatal growth failure, non-life-threatening liver dysfunction and anemia. Genotype-phenotype correlation analysis suggests most of the ILLD mutations locate in the catalytic domain of MARS. ILLD and CMT2U might have different disease mechanism.
Collapse
|
56
|
Racimo F, Marnetto D, Huerta-Sánchez E. Signatures of Archaic Adaptive Introgression in Present-Day Human Populations. Mol Biol Evol 2017; 34:296-317. [PMID: 27756828 PMCID: PMC5400396 DOI: 10.1093/molbev/msw216] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Comparisons of DNA from archaic and modern humans show that these groups interbred, and in some cases received an evolutionary advantage from doing so. This process-adaptive introgression-may lead to a faster rate of adaptation than is predicted from models with mutation and selection alone. Within the last couple of years, a series of studies have identified regions of the genome that are likely examples of adaptive introgression. In many cases, once a region was ascertained as being introgressed, commonly used statistics based on both haplotype as well as allele frequency information were employed to test for positive selection. Introgression by itself, however, changes both the haplotype structure and the distribution of allele frequencies, thus confounding traditional tests for detecting positive selection. Therefore, patterns generated by introgression alone may lead to false inferences of positive selection. Here we explore models involving both introgression and positive selection to investigate the behavior of various statistics under adaptive introgression. In particular, we find that the number and allelic frequencies of sites that are uniquely shared between archaic humans and specific present-day populations are particularly useful for detecting adaptive introgression. We then examine the 1000 Genomes dataset to characterize the landscape of uniquely shared archaic alleles in human populations. Finally, we identify regions that were likely subject to adaptive introgression and discuss some of the most promising candidate genes located in these regions.
Collapse
Affiliation(s)
- Fernando Racimo
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Davide Marnetto
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | | |
Collapse
|
57
|
Hasosah MY, Iskandarani AI, Shawli AI, Alsahafi AF, Sukkar GA, Qurashi MA. Neuroblastoma amplified sequence gene mutation: A rare cause of recurrent liver failure in children. Saudi J Gastroenterol 2017; 23:206-208. [PMID: 28611345 PMCID: PMC5470381 DOI: 10.4103/1319-3767.207714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Neuroblastoma amplified sequence (NBAS) gene mutation or infantile liver failure syndrome type 2 (ILFS type 2) is an extremely rare disease characterized by episodic liver failure precipitated by intercurrent febrile illness, and liver function recovering completely. Here, we report a 4-year-old girl with recurrent hepatitis. A diagnosis of ILFS type 2 was made based on NBAS mutation gene found by whole-exome sequencing. Our case provides a new insight toward considering NBAS mutation as a part of the differential diagnoses of any infant presenting with recurrent liver failure or hepatitis. We recommend sequencing NBAS in cases of recurrent hepatitis in infancy of unknown cause, especially in individuals with fever-associated hepatic dysfunction.
Collapse
Affiliation(s)
- Mohammed Y. Hasosah
- Department of Pediatric Gastroenterology, King Saud Bin Abdulaziz University for Health Sciences, National Guard Hospital, Jeddah, Saudi Arabia,Address for correspondence: Dr. Mohammed Y. Hasosah, Department of Pediatric Gastroenterology, King Saud Bin Abdulaziz University for Health Sciences, King Abdul-Aziz Medical City, King Abdullah International Medical Research Center (KAIMRC) National Guard Hospital, Jeddah - 21482, Saudi Arabia. E-mail:
| | - Alaa I. Iskandarani
- Department of Pediatric Gastroenterology, King Saud Bin Abdulaziz University for Health Sciences, National Guard Hospital, Jeddah, Saudi Arabia
| | - Ayman I. Shawli
- Department of Genetics, King Saud Bin Abdulaziz University for Health Sciences, National Guard Hospital, Jeddah, Saudi Arabia
| | - Ashraf F. Alsahafi
- Department of Pediatric Gastroenterology, King Saud Bin Abdulaziz University for Health Sciences, National Guard Hospital, Jeddah, Saudi Arabia
| | - Ghassan A. Sukkar
- Department of Pediatric Gastroenterology, King Saud Bin Abdulaziz University for Health Sciences, National Guard Hospital, Jeddah, Saudi Arabia
| | - Mansour A. Qurashi
- Department of Neonate, King Saud Bin Abdulaziz University for Health Sciences, National Guard Hospital, Jeddah, Saudi Arabia
| |
Collapse
|
58
|
Oprescu SN, Griffin LB, Beg AA, Antonellis A. Predicting the pathogenicity of aminoacyl-tRNA synthetase mutations. Methods 2016; 113:139-151. [PMID: 27876679 DOI: 10.1016/j.ymeth.2016.11.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/12/2016] [Accepted: 11/18/2016] [Indexed: 10/24/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed, essential enzymes responsible for charging tRNA with cognate amino acids-the first step in protein synthesis. ARSs are required for protein translation in the cytoplasm and mitochondria of all cells. Surprisingly, mutations in 28 of the 37 nuclear-encoded human ARS genes have been linked to a variety of recessive and dominant tissue-specific disorders. Current data indicate that impaired enzyme function is a robust predictor of the pathogenicity of ARS mutations. However, experimental model systems that distinguish between pathogenic and non-pathogenic ARS variants are required for implicating newly identified ARS mutations in disease. Here, we outline strategies to assist in predicting the pathogenicity of ARS variants and urge cautious evaluation of genetic and functional data prior to linking an ARS mutation to a human disease phenotype.
Collapse
Affiliation(s)
- Stephanie N Oprescu
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Laurie B Griffin
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, United States; Medical Scientist Training Program, and University of Michigan Medical School, Ann Arbor, MI, United States
| | - Asim A Beg
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States; Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, United States.
| |
Collapse
|
59
|
Martínez-Montes AM, Fernández A, Pérez-Montarelo D, Alves E, Benítez RM, Nuñez Y, Óvilo C, Ibañez-Escriche N, Folch JM, Fernández AI. Using RNA-Seq SNP data to reveal potential causal mutations related to pig production traits and RNA editing. Anim Genet 2016; 48:151-165. [PMID: 27642173 DOI: 10.1111/age.12507] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2016] [Indexed: 01/13/2023]
Abstract
RNA-Seq technology is widely used in quantitative gene expression studies and identification of non-annotated transcripts. However this technology also can be used for polymorphism detection and RNA editing in transcribed regions in an efficient and cost-effective way. This study used SNP data from an RNA-Seq assay to identify genes and mutations underlying production trait variations in an experimental pig population. The hypothalamic and hepatic transcriptomes of nine extreme animals for growth and fatness from an (Iberian × Landrace) × Landrace backcross were analyzed by RNA-Seq methodology, and SNP calling was conducted. More than 125 000 single nucleotide variants (SNVs) were identified in each tissue, and 78% were considered to be potential SNPs, those SNVs segregating in the context of this study. Potential informative SNPs were detected by considering those showing a homozygous or heterozygous genotype in one extreme group and the alternative genotype in the other group. In this way, 4396 and 1862 informative SNPs were detected in hypothalamus and liver respectively. Out of the 32 SNPs selected for validation, 25 (80%) were confirmed as actual SNPs. Association analyses for growth, fatness and premium cut yields with 19 selected SNPs were carried out, and four potential causal genes (RETSAT, COPA, RNMT and PALMD) were identified. Interestingly, new RNA editing modifications were detected and validated for the NR3C1:g.102797 (ss1985401074) and ACSM2B:g.13374 (ss1985401075) positions and for the COG3:g3.4525 (ss1985401087) modification previously identified across vertebrates, which could lead to phenotypic variation and should be further investigated.
Collapse
Affiliation(s)
- A M Martínez-Montes
- Mejora Genética Animal, Instituto Nacional de Tecnología Agraria y Alimentaria, Ctra. de la Coruña km. 7.5, 28040, Madrid, Spain
| | - A Fernández
- Mejora Genética Animal, Instituto Nacional de Tecnología Agraria y Alimentaria, Ctra. de la Coruña km. 7.5, 28040, Madrid, Spain
| | - D Pérez-Montarelo
- Mejora Genética Animal, Instituto Nacional de Tecnología Agraria y Alimentaria, Ctra. de la Coruña km. 7.5, 28040, Madrid, Spain
| | - E Alves
- Mejora Genética Animal, Instituto Nacional de Tecnología Agraria y Alimentaria, Ctra. de la Coruña km. 7.5, 28040, Madrid, Spain
| | - R M Benítez
- Mejora Genética Animal, Instituto Nacional de Tecnología Agraria y Alimentaria, Ctra. de la Coruña km. 7.5, 28040, Madrid, Spain
| | - Y Nuñez
- Mejora Genética Animal, Instituto Nacional de Tecnología Agraria y Alimentaria, Ctra. de la Coruña km. 7.5, 28040, Madrid, Spain
| | - C Óvilo
- Mejora Genética Animal, Instituto Nacional de Tecnología Agraria y Alimentaria, Ctra. de la Coruña km. 7.5, 28040, Madrid, Spain
| | - N Ibañez-Escriche
- Genètica i Millora Animal, Institut de Recerca i Tecnologies Agroalimentàries, 25198, Lleida, Spain
| | - J M Folch
- Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Campus UAB, 08193, Bellaterra, Spain.,Ciència Animal i dels Aliments, Universitat Autonoma de Barcelona, 08193, Bellaterra, Spain
| | - A I Fernández
- Mejora Genética Animal, Instituto Nacional de Tecnología Agraria y Alimentaria, Ctra. de la Coruña km. 7.5, 28040, Madrid, Spain
| |
Collapse
|
60
|
Nowaczyk MJM, Huang L, Tarnopolsky M, Schwartzentruber J, Majewski J, Bulman DE, Hartley T, Boycott KM. A novel multisystem disease associated with recessive mutations in the tyrosyl-tRNA synthetase (YARS) gene. Am J Med Genet A 2016; 173:126-134. [PMID: 27633801 DOI: 10.1002/ajmg.a.37973] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/15/2016] [Indexed: 01/14/2023]
Abstract
Aminoacyl-tRNA synthetases (ARSs) are a group of ubiquitously expressed enzymes that are best known for their function in the first step of protein translation but have been increasingly associated with secondary functions including transcription and translation control and extracellular signaling. Mutations in numerous ARSs have been linked to a growing number of both autosomal dominant and autosomal recessive human diseases. The tyrosyl-tRNA synthetase (YARS) links the amino acid tyrosine to its cognate tRNA. We report two siblings who presented with failure to thrive (FTT), hypertriglyceridemia, developmental delay, liver dysfunction, lung cysts, and abnormal subcortical white matter. Using exome sequencing the siblings were found to harbor bi-allelic pathogenic-appearing variants within the YARS gene (NM_003680.3):c.638C>T p.(Pro213Leu) and c.1573G>A p.(Gly525Arg). These YARS variants occur in the catalytic domain and the C-terminal domain, respectively. Mutations in YARS have been previously associated with an autosomal dominant form of Charcot-Marie-Tooth (CMT); our findings suggest the disease spectrum associated with YARS dysregulation is broader than peripheral neuropathy. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Małgorzata J M Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Lijia Huang
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Mark Tarnopolsky
- Department of Paediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | - Jacek Majewski
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Dennis E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| |
Collapse
|
61
|
Kopajtich R, Murayama K, Janecke AR, Haack TB, Breuer M, Knisely AS, Harting I, Ohashi T, Okazaki Y, Watanabe D, Tokuzawa Y, Kotzaeridou U, Kölker S, Sauer S, Carl M, Straub S, Entenmann A, Gizewski E, Feichtinger RG, Mayr JA, Lackner K, Strom TM, Meitinger T, Müller T, Ohtake A, Hoffmann GF, Prokisch H, Staufner C. Biallelic IARS Mutations Cause Growth Retardation with Prenatal Onset, Intellectual Disability, Muscular Hypotonia, and Infantile Hepatopathy. Am J Hum Genet 2016; 99:414-22. [PMID: 27426735 DOI: 10.1016/j.ajhg.2016.05.027] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/25/2016] [Indexed: 12/29/2022] Open
Abstract
tRNA synthetase deficiencies are a growing group of genetic diseases associated with tissue-specific, mostly neurological, phenotypes. In cattle, cytosolic isoleucyl-tRNA synthetase (IARS) missense mutations cause hereditary weak calf syndrome. Exome sequencing in three unrelated individuals with severe prenatal-onset growth retardation, intellectual disability, and muscular hypotonia revealed biallelic mutations in IARS. Studies in yeast confirmed the pathogenicity of identified mutations. Two of the individuals had infantile hepatopathy with fibrosis and steatosis, leading in one to liver failure in the course of infections. Zinc deficiency was present in all affected individuals and supplementation with zinc showed a beneficial effect on growth in one.
Collapse
Affiliation(s)
- Robert Kopajtich
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba 266-0007, Japan; Chiba Cancer Center Research Institute, Chiba 260-8717, Japan
| | - Andreas R Janecke
- Department of Pediatrics I, Medical University of Innsbruck, 6020 Innsbruck, Austria; Division of Human Genetics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Tobias B Haack
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Maximilian Breuer
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - A S Knisely
- Institute of Liver Studies, King's College Hospital, London SE5 9RS, UK; Institute of Pathology, Medical University of Graz, 8036 Graz, Austria
| | - Inga Harting
- Department of Neuroradiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Toya Ohashi
- Department of Pediatrics, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Yasushi Okazaki
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan
| | - Daisaku Watanabe
- Department of Large Animal Clinics, School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan
| | - Yoshimi Tokuzawa
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan
| | - Urania Kotzaeridou
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Stefan Kölker
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Sven Sauer
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Matthias Carl
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Simon Straub
- Department of Pediatrics I, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Andreas Entenmann
- Department of Pediatrics I, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Elke Gizewski
- Department of Neuroradiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - René G Feichtinger
- Department of Paediatrics, Paracelsus Medical University, SALK Salzburg, 5020 Salzburg, Austria
| | - Johannes A Mayr
- Department of Paediatrics, Paracelsus Medical University, SALK Salzburg, 5020 Salzburg, Austria
| | - Karoline Lackner
- Institute of Pathology, Medical University of Graz, 8036 Graz, Austria
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Thomas Müller
- Department of Pediatrics I, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Akira Ohtake
- Department of Pediatrics, Faculty of Medicine, Saitama Medical University, Moroyama, Saitama 350-0495, Japan
| | - Georg F Hoffmann
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Christian Staufner
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany.
| |
Collapse
|
62
|
Bais P, Beebe K, Morelli KH, Currie ME, Norberg SN, Evsikov AV, Miers KE, Seburn KL, Guergueltcheva V, Kremensky I, Jordanova A, Bult CJ, Burgess RW. Metabolite profile of a mouse model of Charcot-Marie-Tooth type 2D neuropathy: implications for disease mechanisms and interventions. Biol Open 2016; 5:908-20. [PMID: 27288508 PMCID: PMC4958279 DOI: 10.1242/bio.019273] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Charcot–Marie–Tooth disease encompasses a genetically heterogeneous class of heritable polyneuropathies that result in axonal degeneration in the peripheral nervous system. Charcot–Marie–Tooth type 2D neuropathy (CMT2D) is caused by dominant mutations in glycyl tRNA synthetase (GARS). Mutations in the mouse Gars gene result in a genetically and phenotypically valid animal model of CMT2D. How mutations in GARS lead to peripheral neuropathy remains controversial. To identify putative disease mechanisms, we compared metabolites isolated from the spinal cord of Gars mutant mice and their littermate controls. A profile of altered metabolites that distinguish the affected and unaffected tissue was determined. Ascorbic acid was decreased fourfold in the spinal cord of CMT2D mice, but was not altered in serum. Carnitine and its derivatives were also significantly reduced in spinal cord tissue of mutant mice, whereas glycine was elevated. Dietary supplementation with acetyl-L-carnitine improved gross motor performance of CMT2D mice, but neither acetyl-L-carnitine nor glycine supplementation altered the parameters directly assessing neuropathy. Other metabolite changes suggestive of liver and kidney dysfunction in the CMT2D mice were validated using clinical blood chemistry. These effects were not secondary to the neuromuscular phenotype, as determined by comparison with another, genetically unrelated mouse strain with similar neuromuscular dysfunction. However, these changes do not seem to be causative or consistent metabolites of CMT2D, because they were not observed in a second mouse Gars allele or in serum samples from CMT2D patients. Therefore, the metabolite ‘fingerprint’ we have identified for CMT2D improves our understanding of cellular biochemical changes associated with GARS mutations, but identification of efficacious treatment strategies and elucidation of the disease mechanism will require additional studies. Summary: A metabolomics analysis of a mouse model of Charcot–Marie–Tooth type 2D neuropathy revealed a clear distinction between mutant and control samples, and the therapeutic potential of a subset of these changes was explored.
Collapse
Affiliation(s)
- Preeti Bais
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA
| | | | - Kathryn H Morelli
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA Graduate School of Biomedical Science and Engineering, University of Maine, Orono, 04469 ME, USA
| | | | | | - Alexei V Evsikov
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA Department of Molecular Medicine, USF Health, University of South Florida, Tampa, 33620 FL, USA
| | | | | | | | - Ivo Kremensky
- National Genetics Laboratory, Department of Obstetrics and Gynecology, University Hospital of Obstetrics and Gynecology, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Albena Jordanova
- Molecular Neurogenomics Group, VIB Department of Molecular Genetics, University of Antwerp, 2610 Antwerpen, Belgium Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Carol J Bult
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA
| | - Robert W Burgess
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA Graduate School of Biomedical Science and Engineering, University of Maine, Orono, 04469 ME, USA
| |
Collapse
|
63
|
Wedatilake Y, Niazi R, Fassone E, Powell CA, Pearce S, Plagnol V, Saldanha JW, Kleta R, Chong WK, Footitt E, Mills PB, Taanman JW, Minczuk M, Clayton PT, Rahman S. TRNT1 deficiency: clinical, biochemical and molecular genetic features. Orphanet J Rare Dis 2016; 11:90. [PMID: 27370603 PMCID: PMC4930608 DOI: 10.1186/s13023-016-0477-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/24/2016] [Indexed: 11/10/2022] Open
Abstract
Background TRNT1 (CCA-adding transfer RNA nucleotidyl transferase) enzyme deficiency is a new metabolic disease caused by defective post-transcriptional modification of mitochondrial and cytosolic transfer RNAs (tRNAs). Results We investigated four patients from two families with infantile-onset cyclical, aseptic febrile episodes with vomiting and diarrhoea, global electrolyte imbalance during these episodes, sideroblastic anaemia, B lymphocyte immunodeficiency, retinitis pigmentosa, hepatosplenomegaly, exocrine pancreatic insufficiency and renal tubulopathy. Other clinical features found in children include sensorineural deafness, cerebellar atrophy, brittle hair, partial villous atrophy and nephrocalcinosis. Whole exome sequencing and bioinformatic filtering were utilised to identify recessive compound heterozygous TRNT1 mutations (missense mutation c.668T>C, p.Ile223Thr and a novel splice mutation c.342+5G>T) segregating with disease in the first family. The second family was found to have a homozygous TRNT1 mutation (c.569G>T), p.Arg190Ile, (previously published). We found normal mitochondrial translation products using passage matched controls and functional perturbation of 3’ CCA addition to mitochondrial tRNAs (tRNACys, tRNALeuUUR and tRNAHis) in fibroblasts from two patients, demonstrating a pathomechanism affecting the CCA addition to mt-tRNAs. Acute management of these patients included transfusion for anaemia, fluid and electrolyte replacement and immunoglobulin therapy. We also describe three-year follow-up findings after treatment by bone marrow transplantation in one patient, with resolution of fever and reversal of the abnormal metabolic profile. Conclusions Our report highlights that TRNT1 mutations cause a spectrum of disease ranging from a childhood-onset complex disease with manifestations in most organs to an adult-onset isolated retinitis pigmentosa presentation. Systematic review of all TRNT1 cases and mutations reported to date revealed a distinctive phenotypic spectrum and metabolic and other investigative findings, which will facilitate rapid clinical recognition of future cases.
Collapse
Affiliation(s)
- Yehani Wedatilake
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Rojeen Niazi
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Elisa Fassone
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | | | | | | | - José W Saldanha
- Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, London, UK
| | - Robert Kleta
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK.,UCL Genetics Institute, London, UK.,Division of Medicine, UCL, London, UK
| | - W Kling Chong
- Radiology Department, Great Ormond Street Hospital, London, UK
| | - Emma Footitt
- Metabolic medicine department, Great Ormond Street Hospital, London, UK
| | - Philippa B Mills
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Jan-Willem Taanman
- Department of Clinical Neurosciences, UCL Institute of Neurology, London, UK
| | | | - Peter T Clayton
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Shamima Rahman
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK. .,Mitochondrial Research Group, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, 30, Guilford Street, London, WC1N 1EH, UK.
| |
Collapse
|
64
|
Storkebaum E. Peripheral neuropathy via mutant tRNA synthetases: Inhibition of protein translation provides a possible explanation. Bioessays 2016; 38:818-29. [PMID: 27352040 PMCID: PMC5094542 DOI: 10.1002/bies.201600052] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent evidence indicates that inhibition of protein translation may be a common pathogenic mechanism for peripheral neuropathy associated with mutant tRNA synthetases (aaRSs). aaRSs are enzymes that ligate amino acids to their cognate tRNA, thus catalyzing the first step of translation. Dominant mutations in five distinct aaRSs cause Charcot‐Marie‐Tooth (CMT) peripheral neuropathy, characterized by length‐dependent degeneration of peripheral motor and sensory axons. Surprisingly, loss of aminoacylation activity is not required for mutant aaRSs to cause CMT. Rather, at least for some mutations, a toxic‐gain‐of‐function mechanism underlies CMT‐aaRS. Interestingly, several mutations in two distinct aaRSs were recently shown to inhibit global protein translation in Drosophila models of CMT‐aaRS, by a mechanism independent of aminoacylation, suggesting inhibition of translation as a common pathogenic mechanism. Future research aimed at elucidating the molecular mechanisms underlying the translation defect induced by CMT‐mutant aaRSs should provide novel insight into the molecular pathogenesis of these incurable diseases.
Collapse
Affiliation(s)
- Erik Storkebaum
- Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Faculty of Medicine, University of Münster, Münster, Germany
| |
Collapse
|
65
|
Lane M, Boczonadi V, Bachtari S, Gomez-Duran A, Langer T, Griffiths A, Kleinle S, Dineiger C, Abicht A, Holinski-Feder E, Schara U, Gerner P, Horvath R. Mitochondrial dysfunction in liver failure requiring transplantation. J Inherit Metab Dis 2016; 39:427-436. [PMID: 27053192 PMCID: PMC4851707 DOI: 10.1007/s10545-016-9927-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/10/2016] [Accepted: 03/10/2016] [Indexed: 01/14/2023]
Abstract
Liver failure is a heterogeneous condition which may be fatal and the primary cause is frequently unknown. We investigated mitochondrial oxidative phosphorylation in patients undergoing liver transplantation. We studied 45 patients who had liver transplantation due to a variety of clinical presentations. Blue native polyacrylamide gel electrophoresis with immunodetection of respiratory chain complexes I-V, biochemical activity of respiratory chain complexes II and IV and quantification of mitochondrial DNA (mtDNA) copy number were investigated in liver tissue collected from the explanted liver during transplantation. Abnormal mitochondrial function was frequently present in this cohort: ten of 40 patients (25 %) had a defect of one or more respiratory chain enzyme complexes on blue native gels, 20 patients (44 %) had low activity of complex II and/or IV and ten (22 %) had a reduced mtDNA copy number. Combined respiratory chain deficiency and reduced numbers of mitochondria were detected in all three patients with acute liver failure. Low complex IV activity in biliary atresia and complex II defects in cirrhosis were common findings. All six patients diagnosed with liver tumours showed variable alterations in mitochondrial function, probably due to the heterogeneity of the presenting tumour. In conclusion, mitochondrial dysfunction is common in severe liver failure in non-mitochondrial conditions. Therefore, in contrast to the common practice detection of respiratory chain abnormalities in liver should not restrict the inclusion of patients for liver transplantation. Furthermore, improving mitochondrial function may be targeted as part of a complex therapy approach in different forms of liver diseases.
Collapse
Affiliation(s)
- Maria Lane
- Institute of Genetic Medicine, John Walton Muscular Dystrophy Research Centre and Wellcome Trust Centre for Mitochondrial Research, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Veronika Boczonadi
- Institute of Genetic Medicine, John Walton Muscular Dystrophy Research Centre and Wellcome Trust Centre for Mitochondrial Research, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Sahar Bachtari
- Department of Paediatric Gastroenterology, University of Duisburg-Essen, Essen, Germany
| | - Aurora Gomez-Duran
- Institute of Genetic Medicine, John Walton Muscular Dystrophy Research Centre and Wellcome Trust Centre for Mitochondrial Research, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Thorsten Langer
- Department for Neuropediatrics and Muscular Diseases, Center for Pediatrics and Adolescent Medicine University Medical Center Freiburg, Freiburg, Germany
| | - Alexandra Griffiths
- Institute of Genetic Medicine, John Walton Muscular Dystrophy Research Centre and Wellcome Trust Centre for Mitochondrial Research, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | | | | | | | | | - Ulrike Schara
- Department of Paediatric Neurology, University of Duisburg-Essen, Essen, Germany
| | - Patrick Gerner
- Department of Paediatric Gastroenterology, University of Duisburg-Essen, Essen, Germany
- Paediatric Gastroenterology/Hepatology, University of Freiburg, Freiburg, Germany
| | - Rita Horvath
- Institute of Genetic Medicine, John Walton Muscular Dystrophy Research Centre and Wellcome Trust Centre for Mitochondrial Research, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK.
| |
Collapse
|
66
|
Fang P, Guo M. Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification. Life (Basel) 2015; 5:1703-25. [PMID: 26670257 PMCID: PMC4695845 DOI: 10.3390/life5041703] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/30/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, aaRSs in higher species have evolved important non-translational functions. These translational and non-translational functions of aaRS are attractive for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The interplay between amino acids, tRNA, ATP, EF-Tu and non-canonical binding partners, had shaped each family with distinct pattern of key sites for regulation, with characters varying among species across the path of evolution. These sporadic variations in the aaRSs offer great opportunity to target these essential enzymes for therapy. Up to this day, growing numbers of aaRS inhibitors have been discovered and developed. Here, we summarize the latest developments and structural studies of aaRS inhibitors, and classify them with distinct binding modes into five categories.
Collapse
Affiliation(s)
- Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
| |
Collapse
|
67
|
Schmidt WM, Rutledge SL, Schüle R, Mayerhofer B, Züchner S, Boltshauser E, Bittner RE. Disruptive SCYL1 Mutations Underlie a Syndrome Characterized by Recurrent Episodes of Liver Failure, Peripheral Neuropathy, Cerebellar Atrophy, and Ataxia. Am J Hum Genet 2015; 97:855-61. [PMID: 26581903 DOI: 10.1016/j.ajhg.2015.10.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/16/2015] [Indexed: 12/15/2022] Open
Abstract
Hereditary ataxias comprise a group of genetically heterogeneous disorders characterized by clinically variable cerebellar dysfunction and accompanied by involvement of other organ systems. The molecular underpinnings for many of these diseases are widely unknown. Previously, we discovered the disruption of Scyl1 as the molecular basis of the mouse mutant mdf, which is affected by neurogenic muscular atrophy, progressive gait ataxia with tremor, cerebellar vermis atrophy, and optic-nerve thinning. Here, we report on three human individuals, from two unrelated families, who presented with recurrent episodes of acute liver failure in early infancy and are affected by cerebellar vermis atrophy, ataxia, and peripheral neuropathy. By whole-exome sequencing, compound-heterozygous mutations within SCYL1 were identified in all affected individuals. We further show that in SCYL1-deficient human fibroblasts, the Golgi apparatus is massively enlarged, which is in line with the concept that SCYL1 regulates Golgi integrity. Thus, our findings define SCYL1 mutations as the genetic cause of a human hepatocerebellar neuropathy syndrome.
Collapse
Affiliation(s)
- Wolfgang M Schmidt
- Neuromuscular Research Department, Center of Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - S Lane Rutledge
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany; German Research Center for Neurodegenerative Diseases, University of Tübingen, 72076 Tübingen, Germany; Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Benjamin Mayerhofer
- Neuromuscular Research Department, Center of Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Stephan Züchner
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Eugen Boltshauser
- Division of Pediatric Neurology, University Children's Hospital, 8032 Zurich, Switzerland
| | - Reginald E Bittner
- Neuromuscular Research Department, Center of Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria.
| |
Collapse
|
68
|
Casey JP, Slattery S, Cotter M, Monavari AA, Knerr I, Hughes J, Treacy EP, Devaney D, McDermott M, Laffan E, Wong D, Lynch SA, Bourke B, Crushell E. Clinical and genetic characterisation of infantile liver failure syndrome type 1, due to recessive mutations in LARS. J Inherit Metab Dis 2015; 38:1085-92. [PMID: 25917789 DOI: 10.1007/s10545-015-9849-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/31/2015] [Accepted: 04/02/2015] [Indexed: 11/30/2022]
Abstract
BACKGROUND Recessive LARS mutations were recently reported to cause a novel syndrome, infantile liver failure syndrome type 1 (ILFS1), in six Irish Travellers. We have since identified four additional patients, including one of Ashkenazi origin, representing the largest ILFS1 cohort to date. Our study aims to define the ILFS1 clinical phenotype to help guide diagnosis and patient management. METHODS We clinically evaluated and reviewed the medical records of ten ILFS1 patients. Clinical features, histopathology and natural histories were compared and patient management strategies reviewed. RESULTS Early failure to thrive, recurrent liver dysfunction, anemia, hypoalbuminemia and seizures were present in all patients. Most patients (90 %) had developmental delay. Encephalopathic episodes triggered by febrile illness have occurred in 80 % and were fatal in two children. Two patients are currently >28 years old and clinically well. Leucine supplementation had no appreciable impact on patient well-being. However, we suggest that the traditional management of reducing/stopping protein intake in patients with metabolic hepatopathies may not be appropriate for ILFS1. We currently recommend ensuring sufficient natural protein intake when unwell. CONCLUSIONS We report the first non-Irish ILFS1 patient, suggesting ILFS1 may be more extensive than anticipated. Low birth weight, early failure to thrive, anemia and hypoalbuminemia are amongst the first presenting features, with liver dysfunction before age 1. Episodic hepatic dysfunction is typically triggered by febrile illness, and becomes less severe with increasing age. While difficult to anticipate, two patients are currently >28 years old, suggesting that survival beyond childhood may be associated with a favourable long-term prognosis.
Collapse
Affiliation(s)
- Jillian P Casey
- Genetics Department, Temple Street Children's University Hospital, Dublin 1, Ireland
- UCD Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Suzanne Slattery
- National Centre for Inherited Metabolic Disorders, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Melanie Cotter
- Department of Haematology, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - A A Monavari
- National Centre for Inherited Metabolic Disorders, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Ina Knerr
- National Centre for Inherited Metabolic Disorders, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Joanne Hughes
- National Centre for Inherited Metabolic Disorders, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Eileen P Treacy
- National Centre for Inherited Metabolic Disorders, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Deirdre Devaney
- Histopathology Department, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Michael McDermott
- Pathology Department, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland
| | - Eoghan Laffan
- Department of Radiology, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Derek Wong
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Sally Ann Lynch
- Genetics Department, Temple Street Children's University Hospital, Dublin 1, Ireland
- UCD Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland
| | - Billy Bourke
- Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland
| | - Ellen Crushell
- UCD Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland.
- National Centre for Inherited Metabolic Disorders, Temple Street Children's University Hospital, Dublin 1, Ireland.
- Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland.
| |
Collapse
|
69
|
McMillan HJ, Humphreys P, Smith A, Schwartzentruber J, Chakraborty P, Bulman DE, Beaulieu CL, Majewski J, Boycott KM, Geraghty MT. Congenital Visual Impairment and Progressive Microcephaly Due to Lysyl-Transfer Ribonucleic Acid (RNA) Synthetase (KARS) Mutations: The Expanding Phenotype of Aminoacyl-Transfer RNA Synthetase Mutations in Human Disease. J Child Neurol 2015; 30:1037-43. [PMID: 25330800 DOI: 10.1177/0883073814553272] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 09/07/2014] [Indexed: 12/20/2022]
Abstract
Aminoacyl-transfer ribonucleic acid (RNA) synthetases (ARSs) are a group of enzymes required for the first step of protein translation. Each aminoacyl-transfer RNA synthetase links a specific amino acid to its corresponding transfer RNA component within the cytoplasm, mitochondria, or both. Mutations in ARSs have been linked to a growing number of diseases. Lysyl-transfer RNA synthetase (KARS) links the amino acid lysine to its cognate transfer RNA. We report 2 siblings with severe infantile visual loss, progressive microcephaly, developmental delay, seizures, and abnormal subcortical white matter. Exome sequencing identified mutations within the KARS gene (NM_005548.2):c.1312C>T; p.Arg438Trp and c.1573G>A; p.Glu525Lys occurring within a highly conserved region of the catalytic domain. Our patients' phenotype is remarkably similar to a phenotype recently reported in glutaminyl-transfer RNA synthetase (QARS), another bifunctional ARS gene. This finding expands the phenotypic spectrum associated with mutations in KARS and draws attention to aminoacyl-transfer RNA synthetase as a group of enzymes that are increasingly being implicated in human disease.
Collapse
Affiliation(s)
- Hugh J McMillan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Peter Humphreys
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Amanda Smith
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Pranesh Chakraborty
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Dennis E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Chandree L Beaulieu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Jacek Majewski
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael T Geraghty
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
70
|
Mutations in the glutaminyl-tRNA synthetase gene cause early-onset epileptic encephalopathy. J Hum Genet 2014; 60:97-101. [PMID: 25471517 DOI: 10.1038/jhg.2014.103] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/10/2014] [Accepted: 11/13/2014] [Indexed: 11/08/2022]
Abstract
Aminoacylation is the process of attaching amino acids to their cognate tRNA, and thus is essential for the translation of mRNA into protein. This direct interaction of tRNA with amino acids is catalyzed by aminoacyl-tRNA synthetases. Using whole-exome sequencing, we identified compound heterozygous mutations [c.169T>C (p.Tyr57His) and c.1485dup (p.Lys496*)] in QARS, which encodes glutaminyl-tRNA synthetase, in two siblings with early-onset epileptic encephalopathy (EOEE). Recessive mutations in QARS, including the loss-of-function missense mutation p.Tyr57His, have been reported to cause intractable seizures with progressive microcephaly. The p.Lys496* mutation is novel and causes truncation of the QARS protein, leading to a deletion of part of the catalytic domain and the entire anticodon-binding domain. Transient expression of the p.Lys496* mutant in neuroblastoma 2A cells revealed diminished and aberrantly aggregated expression, indicating the loss-of-function nature of this mutant. Together with the previous report, our data suggest that abnormal aminoacylation is one of the underlying pathologies of EOEE.
Collapse
|
71
|
Datt M, Sharma A. Evolutionary and structural annotation of disease-associated mutations in human aminoacyl-tRNA synthetases. BMC Genomics 2014; 15:1063. [PMID: 25476837 PMCID: PMC4298046 DOI: 10.1186/1471-2164-15-1063] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 11/20/2014] [Indexed: 11/10/2022] Open
Abstract
Background Mutation(s) in proteins are a natural byproduct of evolution but can also cause serious diseases. Aminoacyl-tRNA synthetases (aaRSs) are indispensable components of all cellular protein translational machineries, and in humans they drive translation in both cytoplasm and mitochondria. Mutations in aaRSs have been implicated in a plethora of diseases including neurological conditions, metabolic disorders and cancer. Results We have developed an algorithmic approach for genome-wide analyses of sequence substitutions that combines evolutionary, structural and functional information. This pipeline enabled us to super-annotate human aaRS mutations and analyze their linkage to health disorders. Our data suggest that in some but not all cases, aaRS mutations occur in functional and structural sectors where they can manifest their pathological effects by altering enzyme activity or causing structural instability. Further, mutations appear in both solvent exposed and buried regions of aaRSs indicating that these alterations could lead to dysfunctional enzymes resulting in abnormal protein translation routines by affecting inter-molecular interactions or by disruption of non-bonded interactions. Overall, the prevalence of mutations is much higher in mitochondrial aaRSs, and the two most often mutated aaRSs are mitochondrial glutamyl-tRNA synthetase and dual localized glycyl-tRNA synthetase. Out of 63 mutations annotated in this work, only 12 (~20%) were observed in regions that could directly affect aminoacylation activity via either binding to ATP/amino-acid, tRNA or by involvement in dimerization. Mutations in structural cores or at potential biomolecular interfaces account for ~55% mutations while remaining mutations (~25%) remain structurally un-annotated. Conclusion This work provides a comprehensive structural framework within which most defective human aaRSs have been structurally analyzed. The methodology described here could be employed to annotate mutations in other protein families in a high-throughput manner. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1063) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Amit Sharma
- Structural and Computational Biology group, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India.
| |
Collapse
|
72
|
Individual exome analysis in diagnosis and management of paediatric liver failure of indeterminate aetiology. J Hepatol 2014; 61:1056-63. [PMID: 25016221 PMCID: PMC4203706 DOI: 10.1016/j.jhep.2014.06.038] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/20/2014] [Accepted: 06/30/2014] [Indexed: 01/01/2023]
Abstract
BACKGROUND & AIMS In children with liver failure, as many as half remain of indeterminate aetiology. This hinders timely consideration of optimal treatment options. We posit that a significant subset of these children harbour known inherited metabolic liver diseases with atypical presentation or novel inborn errors of metabolism. We investigated the utility of whole-exome sequencing in three children with advanced liver disease of indeterminate aetiology. METHODS Patient 1 was a 10 year-old female diagnosed with Wilson disease but no detectable ATP7B mutations, and decompensated liver cirrhosis who underwent liver transplant and subsequently developed onset of neurodegenerative disease. Patient 2 was a full-term 2 day-old male with fatal acute liver failure of indeterminate aetiology. Patient 3 was an 8 year-old female with progressive syndromic cholestasis of unknown aetiology since age 3 months. RESULTS Unbiased whole-exome sequencing of germline DNA revealed homozygous mutations in MPV17 and SERAC1 as the disease causing genes in patient 1 and 2, respectively. This is the first demonstration of SERAC1 loss-of-function associated fatal acute liver failure. Patient 1 expands the phenotypic spectrum of the MPV17-related hepatocerebral mitochondrial DNA depletion syndrome. Patient 3 was found to have syndromic cholestasis due to bi-allelic NOTCH2 mutations. CONCLUSIONS Our findings validate the application of whole-exome sequencing in the diagnosis and management of children with advanced liver disease of indeterminate aetiology, with the potential to enhance optimal selection of treatment options and adequate counselling of families. Moreover, whole-exome sequencing revealed a hitherto unrecognized phenotypic spectrum of inherited metabolic liver diseases.
Collapse
|
73
|
Schwartzentruber J, Buhas D, Majewski J, Sasarman F, Papillon-Cavanagh S, Thiffault I, Thiffaut I, Sheldon KM, Massicotte C, Patry L, Simon M, Zare AS, McKernan KJ, Michaud J, Boles RG, Deal CL, Desilets V, Shoubridge EA, Samuels ME. Mutation in the nuclear-encoded mitochondrial isoleucyl-tRNA synthetase IARS2 in patients with cataracts, growth hormone deficiency with short stature, partial sensorineural deafness, and peripheral neuropathy or with Leigh syndrome. Hum Mutat 2014; 35:1285-9. [PMID: 25130867 DOI: 10.1002/humu.22629] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 07/10/2014] [Indexed: 01/28/2023]
Abstract
Mutations in the nuclear-encoded mitochondrial aminoacyl-tRNA synthetases are associated with a range of clinical phenotypes. Here, we report a novel disorder in three adult patients with a phenotype including cataracts, short-stature secondary to growth hormone deficiency, sensorineural hearing deficit, peripheral sensory neuropathy, and skeletal dysplasia. Using SNP genotyping and whole-exome sequencing, we identified a single likely causal variant, a missense mutation in a conserved residue of the nuclear gene IARS2, encoding mitochondrial isoleucyl-tRNA synthetase. The mutation is homozygous in the affected patients, heterozygous in carriers, and absent in control chromosomes. IARS2 protein level was reduced in skin cells cultured from one of the patients, consistent with a pathogenic effect of the mutation. Compound heterozygous mutations in IARS2 were independently identified in a previously unreported patient with a more severe mitochondrial phenotype diagnosed as Leigh syndrome. This is the first report of clinical findings associated with IARS2 mutations.
Collapse
|
74
|
Unexpected genetic heterogeneity for primary ciliary dyskinesia in the Irish Traveller population. Eur J Hum Genet 2014; 23:210-7. [PMID: 24824133 DOI: 10.1038/ejhg.2014.79] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/22/2014] [Accepted: 04/04/2014] [Indexed: 02/07/2023] Open
Abstract
We present a study of five children from three unrelated Irish Traveller families presenting with primary ciliary dyskinesia (PCD). As previously characterized disorders in the Irish Traveller population are caused by common homozygous mutations, we hypothesised that all three PCD families shared the same recessive mutation. However, exome sequencing showed that there was no pathogenic homozygous mutation common to all families. This finding was supported by histology, which showed that each family has a different type of ciliary defect; transposition defect (family A), nude epithelium (family B) and absence of inner and outer dynein arms (family C). Therefore, each family was analysed independently using homozygosity mapping and exome sequencing. The affected siblings in family A share a novel 1 bp duplication in RSPH4A (NM_001161664.1:c.166dup; p.Arg56Profs*11), a radial-spoke head protein involved in ciliary movement. In family B, we identified three candidate genes (CCNO, KCNN3 and CDKN1C), with a 5-bp duplication in CCNO (NM_021147.3:c.258_262dup; p.Gln88Argfs*8) being the most likely cause of ciliary aplasia. This is the first study to implicate CCNO, a DNA repair gene reported to be involved in multiciliogenesis, in PCD. In family C, we identified a ∼3.5-kb deletion in DYX1C1, a neuronal migration gene previously associated with PCD. This is the first report of a disorder in the relatively small Irish Traveller population to be caused by >1 disease gene. Our study identified at least three different PCD genes in the Irish Traveller population, highlighting that one cannot always assume genetic homogeneity, even in small consanguineous populations.
Collapse
|
75
|
van Meel E, Wegner DJ, Cliften P, Willing MC, White FV, Kornfeld S, Cole FS. Rare recessive loss-of-function methionyl-tRNA synthetase mutations presenting as a multi-organ phenotype. BMC MEDICAL GENETICS 2013; 14:106. [PMID: 24103465 PMCID: PMC3852179 DOI: 10.1186/1471-2350-14-106] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 09/30/2013] [Indexed: 11/26/2022]
Abstract
Background Methionyl-tRNA synthetase (MARS) catalyzes the ligation of methionine to its cognate transfer RNA and therefore plays an essential role in protein biosynthesis. Methods We used exome sequencing, aminoacylation assays, homology modeling, and immuno-isolation of transfected MARS to identify and characterize mutations in the methionyl-tRNA synthetase gene (MARS) in an infant with an unexplained multi-organ phenotype. Results We identified compound heterozygous mutations (F370L and I523T) in highly conserved regions of MARS. The parents were each heterozygous for one of the mutations. Aminoacylation assays documented that the F370L and I523T MARS mutants had 18 ± 6% and 16 ± 6%, respectively, of wild-type activity. Homology modeling of the human MARS sequence with the structure of E. coli MARS showed that the F370L and I523T mutations are in close proximity to each other, with residue I523 located in the methionine binding pocket. We found that the F370L and I523T mutations did not affect the association of MARS with the multisynthetase complex. Conclusion This infant expands the catalogue of inherited human diseases caused by mutations in aminoacyl-tRNA synthetase genes.
Collapse
Affiliation(s)
- Eline van Meel
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St, Louis, MO 63110, USA.
| | | | | | | | | | | | | |
Collapse
|
76
|
Abstract
INTRODUCTION In the last 10 years the field of mitochondrial genetics has widened, shifting the focus from rare sporadic, metabolic disease to the effects of mitochondrial DNA (mtDNA) variation in a growing spectrum of human disease. The aim of this review is to guide the reader through some key concepts regarding mitochondria before introducing both classic and emerging mitochondrial disorders. SOURCES OF DATA In this article, a review of the current mitochondrial genetics literature was conducted using PubMed (http://www.ncbi.nlm.nih.gov/pubmed/). In addition, this review makes use of a growing number of publically available databases including MITOMAP, a human mitochondrial genome database (www.mitomap.org), the Human DNA polymerase Gamma Mutation Database (http://tools.niehs.nih.gov/polg/) and PhyloTree.org (www.phylotree.org), a repository of global mtDNA variation. AREAS OF AGREEMENT The disruption in cellular energy, resulting from defects in mtDNA or defects in the nuclear-encoded genes responsible for mitochondrial maintenance, manifests in a growing number of human diseases. AREAS OF CONTROVERSY The exact mechanisms which govern the inheritance of mtDNA are hotly debated. GROWING POINTS Although still in the early stages, the development of in vitro genetic manipulation could see an end to the inheritance of the most severe mtDNA disease.
Collapse
Affiliation(s)
| | - Gavin Hudson
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| |
Collapse
|
77
|
Wong LJC. Challenges of bringing next generation sequencing technologies to clinical molecular diagnostic laboratories. Neurotherapeutics 2013; 10:262-72. [PMID: 23269496 PMCID: PMC3625389 DOI: 10.1007/s13311-012-0170-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Molecular diagnosis of complex dual genome mitochondrial disorders is a challenge. It requires the identification of deleterious mutations in one of the ~1,500 nuclear genes and the mitochondrial genome. If the molecular defect is in the mitochondrial genome, quantification of degree of mutation load (heteroplasmy) in affected tissues is important. Due to the extreme clinical and genetic heterogeneity, conventional sequence analysis of the candidate genes one-by-one is impractical, if not impossible. The newly developed massively parallel next generation sequencing (NGS) technique, that allows simultaneous sequence analysis of multiple target genes, when appropriately validated with deep coverage and proper quality controls, can be used as an effective comprehensive diagnostic approach in CLIA certified clinical laboratories.
Collapse
Affiliation(s)
- Lee-Jun C Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, NAB 2015, Houston, TX 77030, USA.
| |
Collapse
|
78
|
Next generation molecular diagnosis of mitochondrial disorders. Mitochondrion 2013; 13:379-87. [PMID: 23473862 DOI: 10.1016/j.mito.2013.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/31/2013] [Accepted: 02/04/2013] [Indexed: 12/21/2022]
Abstract
Mitochondrial disorders are by far the most genetically heterogeneous group of diseases, involving two genomes, the 16.6k b mitochondrial genome and ~1500 genes encoded in the nuclear genome. For maternally inherited mitochondrial DNA disorders, a complete molecular diagnosis requires several different methods for the detection and quantification of mtDNA point mutations and large deletions. For mitochondrial disorders caused by autosomal recessive, dominant, and X-linked nuclear genes, the diagnosis has relied on clinical, biochemical, and molecular studies to point to a group of candidate genes followed by stepwise Sanger sequencing of the candidate genes one-by-one. The development of Next Generation Sequencing (NGS) has revolutionized the diagnostic approach. Using massively parallel sequencing (MPS) analysis of the entire mitochondrial genome, mtDNA point mutations and deletions can be detected and quantified in one single step. The NGS approach also allows simultaneous analyses of a group of genes or the whole exome, thus, the mutations in causative gene(s) can be identified in one-step. New approaches make genetic analyses much faster and more efficient. Huge amounts of sequencing data produced by the new technologies brought new challenges to bioinformatics, analytical pipelines, and interpretation of numerous novel variants. This article reviews the clinical utility of next generation sequencing for the molecular diagnoses of complex dual genome mitochondrial disorders.
Collapse
|