Abstract
Idiopathic dilated cardiomyopathy (DCM) is a heritable, genetically heterogeneous disorder with variable age-dependent penetrance. We sought to identify the genetic underpinnings of syndromic, sporadic DCM in a newborn female diagnosed in utero. Postnatal evaluation revealed ventricular dilation and systolic dysfunction, bilateral cataracts, and mild facial dysmorphisms. Comprehensive metabolic and genetic testing, including chromosomal microarray, mitochondrial DNA and targeted RASopathy gene sequencing, and clinical whole exome sequencing for known cardiomyopathy genes was non-diagnostic. Following exclusion of asymptomatic DCM in the parents, trio-based whole exome sequencing was carried out on a research basis, filtering for rare, predicted deleterious de novo and recessive variants. An unreported de novo S75Y mutation was discovered in RRAGC, encoding Ras-related GTP binding C, an essential GTPase in nutrient-activated mechanistic target of rapamycin complex 1 (mTORC1) signaling. In silico protein modeling and molecular dynamics simulation predicted the mutation to disrupt ligand interactions and increase the GDP-bound state. Overexpression of RagCS75Y rendered AD293 cells partially insensitive to amino acid deprivation, resulting in increased mTORC1 signaling compared to wild-type RagC. These findings implicate mTORC1 dysregulation through a gain-of-function mutation in RagC as a novel molecular basis for syndromic forms of pediatric heart failure, and expand genotype–phenotype correlation in RASopathy-related syndromes.
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References
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR (2010) A method and server for predicting damaging missense mutations. Nat Methods 7:248–249. doi:10.1038/nmeth0410-248
Brauch KM, Karst ML, Herron KJ, de Andrade M, Pellikka PA, Rodeheffer RJ, Michels VV, Olson TM (2009) Mutations in ribonucleic acid binding protein gene cause familial dilated cardiomyopathy. J Am Coll Cardiol 54:930–941. doi:10.1016/j.jacc.2009.05.038
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennel TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498. doi:10.1038/ng.806
Dhandapany PS, Razzaque MA, Muthusami U, Kunnoth S, Edwards JJ, Mulero-Navarro S, Riess I, Pardo S, Sheng J, Rani DS, Rani B, Govindaraj P, Flex E, Yokota T, Furutani M, Nishizawa T, Nakanishi T, Robbins J, Limongelli G, Hajjar RJ, Lebeche D, Bahl A, Khullar M, Rathinavel A, Sadler KC, Tartaglia M, Matsuoka R, Thangaraj K, Gelb BD (2014) RAF1 mutations in childhood-onset dilated cardiomyopathy. Nat Genet 46:635–639. doi:10.1038/ng.2963
Efeyan A, Zoncu R, Chang S, Gumper I, Snitkin H, Wolfson RL, Kirak O, Sabatini DD, Sabatini DM (2013) Regulation of mTORC1 by the Rag GTPases is necessary for neonatal autophagy and survival. Nature 493:679–683. doi:10.1038/nature11745
Feig LA, Cooper GM (1988) Inhibition of NIH 3T3 cell proliferation by a mutant ras protein with preferential affinity for GDP. Mol Cell Biol 8:3235–3243
Gelb BD, Roberts AE, Tartaglia M (2015) Cardiomyopathies in Noonan syndrome and the other RASoapthies. Prog Pediatr Cardiol 39:13–19
Grant BJ, Rodrigues AP, ElSawy KM, McCammon JA, Caves LS (2006) Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics 22:2695–2696
Gressner AM, Wool IG (1974) The phosphorylation of liver ribosomal proteins in vivo. Evidence that only a single small subunit protein (S6) is phosphorylated. J Biol Chem 249:6917–6925
Hershberger RE, Morales A, Siegfried JD (2010) Clinical and genetic issues in dilated cardiomyopathy: a review for genetics professionals. Genet Med 12:655–667. doi:10.1097/GIM.0b013e3181f2481f
Hershberger RE, Hedges DJ, Morales A (2013) Dilated cardiomyopathy: the complexity of a diverse genetic architecture. Nat Rev Cardiol 10:531–547. doi:10.1038/nrcardio.2013
Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG (2012) ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 52:1757–1768. doi:10.1021/ci3001277
Kumar P, Henikoff S, Ng PC (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4:1073–1081. doi:10.1038/nprot.2009.86
Kushwaha S, Xu X (2012) Target of rapamycin (TOR)-based therapy for cardiomyopathy: evidence from zebrafish and human studies. Trends Cardiovasc Med 22:39–43. doi:10.1016/j.tcm.2012.06.009
Laplante M, Sabatini DM (2009) mTOR signaling at a glance. J Cell Sci 122(Pt20):3589–3594. doi:10.1242/jcs.051011
Long PA, Evans JM, Olson TM (2015a) Exome sequencing establishes diagnosis of Alström syndrome in an infant presenting with non-syndromic dilated cardiomyopathy. Am J Med Genet A 167A:886–890. doi:10.1002/ajmg.a.36994
Long PA, Larsen BT, Evans JM, Olson TM (2015b) Exome sequencing identified pathogenic and modifier mutations in a child with sporadic dilated cardiomyopathy. J Am Heart Assoc. doi:10.1161/JAHA.115.002443
Mackerell AD Jr, Feig M, Brooks CL 3rd (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 25:1400–1415
Marin TM, Keith K, Davies B, Conner DA, Guha P, Kalaitzidis D, Wu X, Lauriol J, Wang B, Bauer M, Bronson R, Franchini KG, Neel BG, Kontaridis MI (2011) Rapamycin reverses hypertrophic cardiomyopathy in a mouse model of LEOPARD syndrome-associated PTPN11 mutation. J Clin Invest 121:1026–1043. doi:10.1172/JCI44972
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. doi:10.1101/gr.107524.110
Michels VV, Moll PP, Miller FA, Tajik AJ, Chu JS, Driscoll DJ, Burnett JC, Rodeheffer RJ, Chesebro JH, Tazelaar HD (1992) The frequency of familial dilated cardiomyopathy in a series of patients with idiopathic dilated cardiomyopathy. N Engl J Med 326:77–82
Nedyalkova L, Tempel W, Tong Y, Crombet L, Zhong N, Guan X, Arrowsmith CH, Edwards AM, Bountra C, Weigelt J, Bochkarev A, Park H, Structural Genomics Consortium (2010) Crystal structure of the nucleotide-binding domain of Ras-related GTP-binding protein C. http://www.rcsb.org/pdb/explore.do?structureId=3LLU. Accessed 26 Feb 2016
Okosun J, Wolfson RL, Wang J, Araf S, Wilkins L, Castellano BM, Escudero-Ibarz L, Al Seraihi AF, Richter J, Bernhart SH, Efeyan A, Iqbal S, Matthews J, Clear A, Guerra-Assunção JA, Bödör C, Quentmeier H, Mansbridge C, Johnson P, Davies A, Strefford JC, Packham G, Barrans S, Jack A, Du MQ, Calaminici M, Lister TA, Auer R, Montoto S, Gribben JG, Siebert R, Chelala C, Zoncu R, Sabatini DM, Fitzgibbon J (2015) Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nat Genet 48:183–188. doi:10.1038/ng.3473
Olson TM, Chan DP (2013) Dilated cardiomyopathy. In: Allen HD, Driscoll DJ, Shaddy RE, Feltes TF (eds) Moss and Adams’ heart disease in infants, children, and adolescents: including the fetus and young adult, vol II, 8th edn. Wolters Kluwer Health/Lippincott Williams & Wilkins, Philadelphia, pp 1235–1246
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802
Pugh TJ, Kelly MA, Gowrisankar S, Hynes E, Seidman MA, Baxter SM, Bowser M, Harrison B, Aaron D, Mahanta LM, Lakdawala NK, McDermott G, White ET, Rehm HL, Lebo M, Funke BH (2014) The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing. Genet Med 16:601–608. doi:10.1038/gim.2013.204
Ramos FJ, Chen SC, Garelick MG, Dai DF, Liao CY, Schreiber KH, MacKay VL, An EH, Strong R, Ladiges WC, Rabinovitch PS, Kaeberlein M, Kennedy BK (2012) Rapamycin reverses elevated mTORC1 signaling in lamin A/C-deficient mice, rescues cardiac and skeletal muscle function, and extends survival. Sci Transl Med 4:144ra103. doi:10.1126/scitranslmed.3003802
Rauen KA (2013) The RASopathies. Annu Rev Genomics Hum Genet 14:355–369. doi:10.1146/annurev-genom-091212-153523
Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE, Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee (2007) ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007. Genet Med 10:294–300. doi:10.1097/GIM.0b013e31816b5cae
Sancak Y, Peterson TR, Shaul YD, Lindquist RA, Thoreen CC, Bar-Peled L, Sabatini DM (2008) The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1. Science 320:1496–1501. doi:10.1126/science.1157535
Sciarretta S, Volpe M, Sadoshima J (2014) Mammalian target of rapamycin signaling in cardiac physiology and disease. Circ Res 114:549–564. doi:10.1161/CIRCRESAHA.114.302022
Sun L, Dimitromanolakis A (2014) PREST-plus identifies pedigree errors and cryptic relatedness in the GAW18 sample using genome-wide SNP data. In: BMC proceedings 8 (Suppl 1 Genetic Analysis Workshop 18Vanessa Olmo) S23. doi:10.1186/1753-6561-8-S1-S23
The 1000 Genomes Consortium (2012) An integrated map of genetic variation from 1092 human genomes. Nature 491:56–65. doi:10.1038/nature11632
Towbin JA, Lowe AM, Colan SD, Sleeper LA, Orav EJ, Clunie S, Messere J, Cox GF, Lurie PR, Hsu D, Canter C, Wilkinson JD, Lipshultz SE (2006) Incidence, causes, and outcomes of dilated cardiomyopathy in children. JAMA 296:1867–1876
Yano T, Shimoshige S, Miki T, Tanno M, Mochizuki A, Fujito T, Yuda S, Muranaka A, Ogasawara M, Hashimoto A, Tsuchihashi K, Miura T (2015) Clinical impact of myocardial mTORC1 activation in nonischemic dilated cardiomyopathy. J Mol Cell Cardiol 91:6–9. doi:10.1016/j.yjmcc.2015.12.022
Zhang P, Shan T, Liang X, Deng C, Kuang S (2014) Mammalian target of rapamycin is essential for cardiomyocyte survival and heart development in mice. Biochem Biophys Res Commun 452:53–59. doi:10.1016/j.bbrc.2014.08.046
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We thank the family who participated in this study.
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National Institutes of Health: R01 HL071225 (T.M.O), RO1HL107304 (X.X.), and T32GM072474 (P.A.L.); American Heart Association: 14PRE18070007 (P.A.L.).
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This study was approved by the Mayo Clinic Institutional Review Board and all procedures were performed in accordance with the ethical standards of the 1964 Helsinki declaration and its later amendments. Informed consent was obtained from all individual participants included in the study.
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M. T. Zimmermann and M. Kim contributed equally to this work.
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Long, P.A., Zimmermann, M.T., Kim, M. et al. De novo RRAGC mutation activates mTORC1 signaling in syndromic fetal dilated cardiomyopathy. Hum Genet 135, 909–917 (2016). https://doi.org/10.1007/s00439-016-1685-3
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DOI: https://doi.org/10.1007/s00439-016-1685-3