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Published in: BMC Medical Genetics 1/2018

Open Access 01-12-2018 | Research article

Expanding the clinical phenotype of IARS2-related mitochondrial disease

Authors: Barbara Vona, Reza Maroofian, Emanuele Bellacchio, Maryam Najafi, Kyle Thompson, Ahmad Alahmad, Langping He, Najmeh Ahangari, Abolfazl Rad, Sima Shahrokhzadeh, Paulina Bahena, Falk Mittag, Frank Traub, Jebrail Movaffagh, Nafise Amiri, Mohammad Doosti, Reza Boostani, Ebrahim Shirzadeh, Thomas Haaf, Daria Diodato, Miriam Schmidts, Robert W. Taylor, Ehsan Ghayoor Karimiani

Published in: BMC Medical Genetics | Issue 1/2018

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Abstract

Background

IARS2 encodes a mitochondrial isoleucyl-tRNA synthetase, a highly conserved nuclear-encoded enzyme required for the charging of tRNAs with their cognate amino acid for translation. Recently, pathogenic IARS2 variants have been identified in a number of patients presenting broad clinical phenotypes with autosomal recessive inheritance. These phenotypes range from Leigh and West syndrome to a new syndrome abbreviated CAGSSS that is characterised by cataracts, growth hormone deficiency, sensory neuropathy, sensorineural hearing loss, and skeletal dysplasia, as well as cataract with no additional anomalies.

Methods

Genomic DNA from Iranian probands from two families with consanguineous parental background and overlapping CAGSSS features were subjected to exome sequencing and bioinformatics analysis.

Results

Exome sequencing and data analysis revealed a novel homozygous missense variant (c.2625C > T, p.Pro909Ser, NM_018060.3) within a 14.3 Mb run of homozygosity in proband 1 and a novel homozygous missense variant (c.2282A > G, p.His761Arg) residing in an ~ 8 Mb region of homozygosity in a proband of the second family. Patient-derived fibroblasts from proband 1 showed normal respiratory chain enzyme activity, as well as unchanged oxidative phosphorylation protein subunits and IARS2 levels. Homology modelling of the known and novel amino acid residue substitutions in IARS2 provided insight into the possible consequence of these variants on function and structure of the protein.

Conclusions

This study further expands the phenotypic spectrum of IARS2 pathogenic variants to include two patients (patients 2 and 3) with cataract and skeletal dysplasia and no other features of CAGSSS to the possible presentation of the defects in IARS2. Additionally, this study suggests that adult patients with CAGSSS may manifest central adrenal insufficiency and type II esophageal achalasia and proposes that a variable sensorineural hearing loss onset, proportionate short stature, polyneuropathy, and mild dysmorphic features are possible, as seen in patient 1. Our findings support that even though biallelic IARS2 pathogenic variants can result in a distinctive, clinically recognisable phenotype in humans, it can also show a wide range of clinical presentation from severe pediatric neurological disorders of Leigh and West syndrome to both non-syndromic cataract and cataract accompanied by skeletal dysplasia.
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Literature
1.
go back to reference Fujishima K, Kanai A. tRNA gene diversity in the three domains of life. Front Genet. 2014;5:142.CrossRef Fujishima K, Kanai A. tRNA gene diversity in the three domains of life. Front Genet. 2014;5:142.CrossRef
2.
go back to reference Antonellis A, Green ED. The role of aminoacyl-tRNA synthetases in genetic diseases. Annu Rev Genomics Hum Genet. 2008;9:87–107.CrossRef Antonellis A, Green ED. The role of aminoacyl-tRNA synthetases in genetic diseases. Annu Rev Genomics Hum Genet. 2008;9:87–107.CrossRef
3.
go back to reference Meyer-Schuman R, Antonellis A. Emerging mechanisms of aminoacyl-tRNA synthetase mutations in recessive and dominant human disease. Hum Mol Genet. 2017;26(R2):R114–r127.CrossRef Meyer-Schuman R, Antonellis A. Emerging mechanisms of aminoacyl-tRNA synthetase mutations in recessive and dominant human disease. Hum Mol Genet. 2017;26(R2):R114–r127.CrossRef
4.
go back to reference Florentz C, Sohm B, Tryoen-Toth P, Putz J, Sissler M. Human mitochondrial tRNAs in health and disease. Cell Mol Life Sci. 2003;60(7):1356–75.CrossRef Florentz C, Sohm B, Tryoen-Toth P, Putz J, Sissler M. Human mitochondrial tRNAs in health and disease. Cell Mol Life Sci. 2003;60(7):1356–75.CrossRef
5.
go back to reference Schwartzentruber J, Buhas D, Majewski J, Sasarman F, Papillon-Cavanagh S, Thiffault I, Sheldon KM, Massicotte C, Patry L, Simon M, et al. 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(11):1285–9.PubMed Schwartzentruber J, Buhas D, Majewski J, Sasarman F, Papillon-Cavanagh S, Thiffault I, Sheldon KM, Massicotte C, Patry L, Simon M, et al. 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(11):1285–9.PubMed
6.
go back to reference Liberfarb RM, Jackson AH, Eavey RD, Robb RM. Unique hereditary sensory and autonomic neuropathy with growth hormone deficiency. J Child Neurol. 1993;8(3):271–6.CrossRef Liberfarb RM, Jackson AH, Eavey RD, Robb RM. Unique hereditary sensory and autonomic neuropathy with growth hormone deficiency. J Child Neurol. 1993;8(3):271–6.CrossRef
7.
go back to reference Moosa S, Haagerup A, Gregersen PA, Petersen KK, Altmüller J, Thiele H, Nürnberg P, Cho TJ, Kim OH, Nishimura G, et al. Confirmation of CAGSSS syndrome as a distinct entity in a Danish patient with a novel homozygous mutation in IARS2. Am J Med Genet A. 2017;173(4):1102–8.CrossRef Moosa S, Haagerup A, Gregersen PA, Petersen KK, Altmüller J, Thiele H, Nürnberg P, Cho TJ, Kim OH, Nishimura G, et al. Confirmation of CAGSSS syndrome as a distinct entity in a Danish patient with a novel homozygous mutation in IARS2. Am J Med Genet A. 2017;173(4):1102–8.CrossRef
8.
go back to reference Li J, Leng Y, Han S, Yan L, Lu C, Luo Y, Zhang X, Cao LA-Ohoo: Clinical and genetic characteristics of Chinese patients with familial or sporadic pediatric cataract. Orphanet J Rare Dis. 2018;18;13(1):94. Li J, Leng Y, Han S, Yan L, Lu C, Luo Y, Zhang X, Cao LA-Ohoo: Clinical and genetic characteristics of Chinese patients with familial or sporadic pediatric cataract. Orphanet J Rare Dis. 2018;18;13(1):94.
10.
go back to reference McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303.CrossRef McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303.CrossRef
11.
go back to reference Li H, Durbin R. Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics. 2010;26(5):589–95.CrossRef Li H, Durbin R. Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics. 2010;26(5):589–95.CrossRef
12.
go back to reference Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. A global reference for human genetic variation. Nature. 2015;526(7571):68–74.CrossRef Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. A global reference for human genetic variation. Nature. 2015;526(7571):68–74.CrossRef
13.
go back to reference Shihab HA, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR. Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. Hum Genomics. 2014;8:11.CrossRef Shihab HA, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR. Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. Hum Genomics. 2014;8:11.CrossRef
14.
go back to reference Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res. 2011;39(17):e118.CrossRef Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res. 2011;39(17):e118.CrossRef
15.
go back to reference Schwarz JM, Rödelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010;7(8):575–6.CrossRef Schwarz JM, Rödelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010;7(8):575–6.CrossRef
16.
go back to reference Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7(4):248–9.CrossRef Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7(4):248–9.CrossRef
17.
go back to reference Ng PC, Henikoff S. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet. 2006;7:61–80.CrossRef Ng PC, Henikoff S. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet. 2006;7:61–80.CrossRef
18.
go back to reference Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, et al. Analysis of protein-coding genetic variation in 60,706 humans. Natuere. 2016;536(7616):285–91.CrossRef Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, et al. Analysis of protein-coding genetic variation in 60,706 humans. Natuere. 2016;536(7616):285–91.CrossRef
19.
go back to reference Scott EM, Halees A, Itan Y, Spencer EG, He Y, Azab MA, Gabriel SB, Belkadi A, Boisson B, Abel L, et al. Characterization of greater middle eastern genetic variation for enhanced disease gene discovery. Nat Genet. 2016;48(9):1071–6.CrossRef Scott EM, Halees A, Itan Y, Spencer EG, He Y, Azab MA, Gabriel SB, Belkadi A, Boisson B, Abel L, et al. Characterization of greater middle eastern genetic variation for enhanced disease gene discovery. Nat Genet. 2016;48(9):1071–6.CrossRef
20.
go back to reference Akbari MR, Fattahi Z, Beheshtian M, Mohseni M, Poustchi H, Sellars E, Nezhadi H, Amini A, Arzhangi S, Jalalvand K, et al. Iranome: A human genome variation database of eight major ethnic groups that live in Iran and neighboring countries in the Middle East. Orlando: ASHG Annual Meeting; 2017. Akbari MR, Fattahi Z, Beheshtian M, Mohseni M, Poustchi H, Sellars E, Nezhadi H, Amini A, Arzhangi S, Jalalvand K, et al. Iranome: A human genome variation database of eight major ethnic groups that live in Iran and neighboring countries in the Middle East. Orlando: ASHG Annual Meeting; 2017.
21.
go back to reference Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Giron CG, et al. Ensembl 2018. Nucleic Acids Res. 2018;46(D1):D754–d761.CrossRef Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Giron CG, et al. Ensembl 2018. Nucleic Acids Res. 2018;46(D1):D754–d761.CrossRef
22.
go back to reference Landrum MJ, Lee JM, Benson M, Brown G, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Hoover J, et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 2016;44(D1):D862–8.CrossRef Landrum MJ, Lee JM, Benson M, Brown G, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Hoover J, et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 2016;44(D1):D862–8.CrossRef
23.
go back to reference Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN. The human gene mutation database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet. 2017;136(6):665–77.CrossRef Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN. The human gene mutation database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet. 2017;136(6):665–77.CrossRef
24.
go back to reference Kobayashi YA-O, Yang S, Nykamp K, Garcia J, Lincoln SE, Topper SE: Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Genome Med. 2017;6;9(1):13. Kobayashi YA-O, Yang S, Nykamp K, Garcia J, Lincoln SE, Topper SE: Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Genome Med. 2017;6;9(1):13.
25.
go back to reference Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG. Primer3--new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115.CrossRef Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG. Primer3--new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115.CrossRef
26.
go back to reference Thompson K, Majd H, Dallabona C, Reinson K, King MS, Alston CL, He L, Lodi T, Jones SA, Fattal-Valevski A, et al. Recurrent De novo dominant mutations in SLC25A4 cause severe early-onset mitochondrial disease and loss of mitochondrial DNA copy number. Am J Hum Genet. 2016;99(4):860–76.CrossRef Thompson K, Majd H, Dallabona C, Reinson K, King MS, Alston CL, He L, Lodi T, Jones SA, Fattal-Valevski A, et al. Recurrent De novo dominant mutations in SLC25A4 cause severe early-onset mitochondrial disease and loss of mitochondrial DNA copy number. Am J Hum Genet. 2016;99(4):860–76.CrossRef
27.
go back to reference Kirby DM, Thorburn DR, Turnbull DM, Taylor RW. Biochemical assays of respiratory chain complex activity. Methods Cell Biol. 2007;80:93–119.CrossRef Kirby DM, Thorburn DR, Turnbull DM, Taylor RW. Biochemical assays of respiratory chain complex activity. Methods Cell Biol. 2007;80:93–119.CrossRef
28.
go back to reference Nagata K, Randall A, Baldi P. SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations. Proteins. 2012;80(1):142–53.CrossRef Nagata K, Randall A, Baldi P. SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations. Proteins. 2012;80(1):142–53.CrossRef
29.
go back to reference Xu S, Gu X, Pan H, Zhu H, Gong F, Li Y, Xing Y. Reference ranges for serum IGF-1 and IGFBP-3 levels in Chinese children during childhood and adolescence. Endocr J. 2010;57(3):221–8.CrossRef Xu S, Gu X, Pan H, Zhu H, Gong F, Li Y, Xing Y. Reference ranges for serum IGF-1 and IGFBP-3 levels in Chinese children during childhood and adolescence. Endocr J. 2010;57(3):221–8.CrossRef
30.
go back to reference Mazzoli M, Van Camp G, Newton V, Giarbini N, Declau F, Parving A. Recommendations for the description of genetic and audiological data for families with nonsyndromic hereditary hearing impairment. Audiol Med. 2003;1:148–50.CrossRef Mazzoli M, Van Camp G, Newton V, Giarbini N, Declau F, Parving A. Recommendations for the description of genetic and audiological data for families with nonsyndromic hereditary hearing impairment. Audiol Med. 2003;1:148–50.CrossRef
31.
go back to reference Jabbour S, Harissi-Dagher M. Recessive mutation in a nuclear-encoded mitochondrial tRNA Synthetase associated with infantile cataract, congenital neurotrophic keratitis, and orbital myopathy. Cornea. 2016;35(6):894–6.CrossRef Jabbour S, Harissi-Dagher M. Recessive mutation in a nuclear-encoded mitochondrial tRNA Synthetase associated with infantile cataract, congenital neurotrophic keratitis, and orbital myopathy. Cornea. 2016;35(6):894–6.CrossRef
32.
go back to reference Charmandari E, Nicolaides NC, Chrousos GP. Adrenal insufficiency. Lancet. 2014;383(9935):2152–67.CrossRef Charmandari E, Nicolaides NC, Chrousos GP. Adrenal insufficiency. Lancet. 2014;383(9935):2152–67.CrossRef
33.
go back to reference Gockel HR, Schumacher J, Gockel I, Lang H, Haaf T, Nöthen MM. Achalasia: will genetic studies provide insights? Hum Genet. 2010;128(4):353–64.CrossRef Gockel HR, Schumacher J, Gockel I, Lang H, Haaf T, Nöthen MM. Achalasia: will genetic studies provide insights? Hum Genet. 2010;128(4):353–64.CrossRef
34.
go back to reference Walters-Sen LC, Hashimoto S, Thrush DL, Reshmi S, Gastier-Foster JM, Astbury C, Pyatt RE. Variability in pathogenicity prediction programs: impact on clinical diagnostics. Mol Genet Genomic Med. 2015;3(2):99–110.CrossRef Walters-Sen LC, Hashimoto S, Thrush DL, Reshmi S, Gastier-Foster JM, Astbury C, Pyatt RE. Variability in pathogenicity prediction programs: impact on clinical diagnostics. Mol Genet Genomic Med. 2015;3(2):99–110.CrossRef
35.
go back to reference Sasarman F, Nishimura T, Thiffault I, Shoubridge EA. A novel mutation in YARS2 causes myopathy with lactic acidosis and sideroblastic anemia. Hum Mutat. 2012;33(8):1201–6.CrossRef Sasarman F, Nishimura T, Thiffault I, Shoubridge EA. A novel mutation in YARS2 causes myopathy with lactic acidosis and sideroblastic anemia. Hum Mutat. 2012;33(8):1201–6.CrossRef
36.
go back to reference Almalki A, Alston CL, Parker A, Simonic I, Mehta SG, He L, Reza M, Oliveira JM, Lightowlers RN, McFarland R, et al. Mutation of the human mitochondrial phenylalanine-tRNA synthetase causes infantile-onset epilepsy and cytochrome c oxidase deficiency. Biochim Biophys Acta. 2014;1842(1):56–64.CrossRef Almalki A, Alston CL, Parker A, Simonic I, Mehta SG, He L, Reza M, Oliveira JM, Lightowlers RN, McFarland R, et al. Mutation of the human mitochondrial phenylalanine-tRNA synthetase causes infantile-onset epilepsy and cytochrome c oxidase deficiency. Biochim Biophys Acta. 2014;1842(1):56–64.CrossRef
37.
go back to reference Oliveira R, Sommerville EW, Thompson K, Nunes J, Pyle A, Grazina M, Chinnery PF, Diogo L, Garcia P, Taylor RW. Lethal neonatal LTBL associated with Biallelic EARS2 variants: case report and review of the reported Neuroradiological features. JIMD Rep. 2017;33:61–8.CrossRef Oliveira R, Sommerville EW, Thompson K, Nunes J, Pyle A, Grazina M, Chinnery PF, Diogo L, Garcia P, Taylor RW. Lethal neonatal LTBL associated with Biallelic EARS2 variants: case report and review of the reported Neuroradiological features. JIMD Rep. 2017;33:61–8.CrossRef
38.
go back to reference Azevedo L, Mort M, Costa AC, Silva RM, Quelhas D, Amorim A, Cooper DN. Improving the in silico assessment of pathogenicity for compensated variants. Eur J Hum Genet. 2016;25(1):2–7.CrossRef Azevedo L, Mort M, Costa AC, Silva RM, Quelhas D, Amorim A, Cooper DN. Improving the in silico assessment of pathogenicity for compensated variants. Eur J Hum Genet. 2016;25(1):2–7.CrossRef
39.
go back to reference Konovalova S, Tyynismaa H. Mitochondrial aminoacyl-tRNA synthetases in human disease. Mol Genet Metab. 2013;108(4):206–11.CrossRef Konovalova S, Tyynismaa H. Mitochondrial aminoacyl-tRNA synthetases in human disease. Mol Genet Metab. 2013;108(4):206–11.CrossRef
40.
go back to reference Chow J, Rahman J, Achermann JC, Dattani MT, Rahman S. Mitochondrial disease and endocrine dysfunction. Nat Rev Endocrinol. 2017;13(2):92–104.CrossRef Chow J, Rahman J, Achermann JC, Dattani MT, Rahman S. Mitochondrial disease and endocrine dysfunction. Nat Rev Endocrinol. 2017;13(2):92–104.CrossRef
41.
go back to reference Parikh S, Goldstein A, Karaa A, Koenig MK, Anselm I, Brunel-Guitton C, Christodoulou J, Cohen BH, Dimmock D, Enns GM, et al. Patient care standards for primary mitochondrial disease: a consensus statement from the mitochondrial medicine society. Genet Med. 2017;19(12). Parikh S, Goldstein A, Karaa A, Koenig MK, Anselm I, Brunel-Guitton C, Christodoulou J, Cohen BH, Dimmock D, Enns GM, et al. Patient care standards for primary mitochondrial disease: a consensus statement from the mitochondrial medicine society. Genet Med. 2017;19(12).
Metadata
Title
Expanding the clinical phenotype of IARS2-related mitochondrial disease
Authors
Barbara Vona
Reza Maroofian
Emanuele Bellacchio
Maryam Najafi
Kyle Thompson
Ahmad Alahmad
Langping He
Najmeh Ahangari
Abolfazl Rad
Sima Shahrokhzadeh
Paulina Bahena
Falk Mittag
Frank Traub
Jebrail Movaffagh
Nafise Amiri
Mohammad Doosti
Reza Boostani
Ebrahim Shirzadeh
Thomas Haaf
Daria Diodato
Miriam Schmidts
Robert W. Taylor
Ehsan Ghayoor Karimiani
Publication date
01-12-2018
Publisher
BioMed Central
Published in
BMC Medical Genetics / Issue 1/2018
Electronic ISSN: 1471-2350
DOI
https://doi.org/10.1186/s12881-018-0709-3

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