Bi-allelic ADARB1 Variants Associated with Microcephaly, Intellectual Disability, and Seizures

. 2020 Apr 02 ; 106 (4) : 467-483. [epub] 20200326

Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid32220291

Grantová podpora
UM1 HG008900 NHGRI NIH HHS - United States

Odkazy

PubMed 32220291
PubMed Central PMC7118584
DOI 10.1016/j.ajhg.2020.02.015
PII: S0002-9297(20)30057-4
Knihovny.cz E-zdroje

The RNA editing enzyme ADAR2 is essential for the recoding of brain transcripts. Impaired ADAR2 editing leads to early-onset epilepsy and premature death in a mouse model. Here, we report bi-allelic variants in ADARB1, the gene encoding ADAR2, in four unrelated individuals with microcephaly, intellectual disability, and epilepsy. In one individual, a homozygous variant in one of the double-stranded RNA-binding domains (dsRBDs) was identified. In the others, variants were situated in or around the deaminase domain. To evaluate the effects of these variants on ADAR2 enzymatic activity, we performed in vitro assays with recombinant proteins in HEK293T cells and ex vivo assays with fibroblasts derived from one of the individuals. We demonstrate that these ADAR2 variants lead to reduced editing activity on a known ADAR2 substrate. We also demonstrate that one variant leads to changes in splicing of ADARB1 transcript isoforms. These findings reinforce the importance of RNA editing in brain development and introduce ADARB1 as a genetic etiology in individuals with intellectual disability, microcephaly, and epilepsy.

Broad Center for Mendelian Genomics Broad Institute of MIT and Harvard Cambridge MA 02142 USA

Central European Institute of Technology Masaryk University Kamenice 735 5 A35 Brno 62500 Czech Republic

Department of Neuromuscular Disorders University College London Queen Square Institute of Neurology London WC1N 3BG UK

Department of Pediatrics Columbia University Medical Center New York NY 10032 USA

Division of Neurology Departments of Neurology and Pediatrics The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania Philadelphia PA 19104 USA; The Epilepsy NeuroGenetics Initiative Children's Hospital of Philadelphia Philadelphia PA 19104 USA

GeneDx Gaithersburg MD 20877 USA

Murdoch Children's Research Institute Melbourne 3052 Australia; Department of Pediatrics University of Melbourne Melbourne 3052 Australia; Department of Neurology Royal Children's Hospital Parkville 3052 Australia

Pediatric Genetics Unit Schneider Children's Medical Center of Israel Petah Tikva 49100 Israel

Raphael Recanati Genetic Institute Rabin Medical Center Beilinson Hospital Petah Tikva 49100 Israel; Sackler Faculty of Medicine Tel Aviv University Tel Aviv 6997801 Israel

Raphael Recanati Genetic Institute Rabin Medical Center Beilinson Hospital Petah Tikva 49100 Israel; Sackler Faculty of Medicine Tel Aviv University Tel Aviv 6997801 Israel; Felsenstein Medical Research Center Petah Tikva 49100 Israel

Sackler Faculty of Medicine Tel Aviv University Tel Aviv 6997801 Israel; Pediatric Neurology Unit Schneider Children's Medical Center of Israel Petah Tikva 49100 Israel

Victorian Clinical Genetics Services Melbourne 3052 Australia; Murdoch Children's Research Institute Melbourne 3052 Australia

Victorian Clinical Genetics Services Melbourne 3052 Australia; Murdoch Children's Research Institute Melbourne 3052 Australia; Department of Pediatrics University of Melbourne Melbourne 3052 Australia

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Sinigaglia K., Wiatrek D., Khan A., Michalik D., Sambrani N., Sedmík J., Vukić D., O’Connell M.A., Keegan L.P. ADAR RNA editing in innate immune response phasing, in circadian clocks and in sleep. Biochim. Biophys. Acta. Gene Regul. Mech. 2019;1862:356–369. PubMed

Licht K., Hartl M., Amman F., Anrather D., Janisiw M.P., Jantsch M.F. Inosine induces context-dependent recoding and translational stalling. Nucleic Acids Res. 2019;47:3–14. PubMed PMC

Jaikaran D.C., Collins C.H., MacMillan A.M. Adenosine to inosine editing by ADAR2 requires formation of a ternary complex on the GluR-B R/G site. J. Biol. Chem. 2002;277:37624–37629. PubMed

Poulsen H., Jorgensen R., Heding A., Nielsen F.C., Bonven B., Egebjerg J. Dimerization of ADAR2 is mediated by the double-stranded RNA binding domain. RNA. 2006;12:1350–1360. PubMed PMC

Chilibeck K.A., Wu T., Liang C., Schellenberg M.J., Gesner E.M., Lynch J.M., MacMillan A.M. FRET analysis of in vivo dimerization by RNA-editing enzymes. J. Biol. Chem. 2006;281:16530–16535. PubMed

Valente L., Nishikura K. RNA binding-independent dimerization of adenosine deaminases acting on RNA and dominant negative effects of nonfunctional subunits on dimer functions. J. Biol. Chem. 2007;282:16054–16061. PubMed PMC

Gallo A., Keegan L.P., Ring G.M., O’Connell M.A. An ADAR that edits transcripts encoding ion channel subunits functions as a dimer. EMBO J. 2003;22:3421–3430. PubMed PMC

Rice G.I., Kasher P.R., Forte G.M., Mannion N.M., Greenwood S.M., Szynkiewicz M., Dickerson J.E., Bhaskar S.S., Zampini M., Briggs T.A. Mutations in ADAR1 cause Aicardi-Goutières syndrome associated with a type I interferon signature. Nat. Genet. 2012;44:1243–1248. PubMed PMC

Livingston J.H., Lin J.P., Dale R.C., Gill D., Brogan P., Munnich A., Kurian M.A., Gonzalez-Martinez V., De Goede C.G., Falconer A. A type I interferon signature identifies bilateral striatal necrosis due to mutations in ADAR1. J. Med. Genet. 2014;51:76–82. PubMed

Miyamura Y., Suzuki T., Kono M., Inagaki K., Ito S., Suzuki N., Tomita Y. Mutations of the RNA-specific adenosine deaminase gene (DSRAD) are involved in dyschromatosis symmetrica hereditaria. Am. J. Hum. Genet. 2003;73:693–699. PubMed PMC

Kondo T., Suzuki T., Ito S., Kono M., Negoro T., Tomita Y. Dyschromatosis symmetrica hereditaria associated with neurological disorders. J. Dermatol. 2008;35:662–666. PubMed

Tojo K., Sekijima Y., Suzuki T., Suzuki N., Tomita Y., Yoshida K., Hashimoto T., Ikeda S. Dystonia, mental deterioration, and dyschromatosis symmetrica hereditaria in a family with ADAR1 mutation. Mov. Disord. 2006;21:1510–1513. PubMed

Aizawa H., Sawada J., Hideyama T., Yamashita T., Katayama T., Hasebe N., Kimura T., Yahara O., Kwak S. TDP-43 pathology in sporadic ALS occurs in motor neurons lacking the RNA editing enzyme ADAR2. Acta Neuropathol. 2010;120:75–84. PubMed

Kawahara Y., Ito K., Ito M., Tsuji S., Kwak S. Novel splice variants of human ADAR2 mRNA: skipping of the exon encoding the dsRNA-binding domains, and multiple C-terminal splice sites. Gene. 2005;363:193–201. PubMed

Gerber A., O’Connell M.A., Keller W. Two forms of human double-stranded RNA-specific editase 1 (hRED1) generated by the insertion of an Alu cassette. RNA. 1997;3:453–463. PubMed PMC

Lai F., Chen C.X., Carter K.C., Nishikura K. Editing of glutamate receptor B subunit ion channel RNAs by four alternatively spliced DRADA2 double-stranded RNA adenosine deaminases. Mol. Cell. Biol. 1997;17:2413–2424. PubMed PMC

Filippini A., Bonini D., Giacopuzzi E., La Via L., Gangemi F., Colombi M., Barbon A. Differential Enzymatic Activity of Rat ADAR2 Splicing Variants Is Due to Altered Capability to Interact with RNA in the Deaminase Domain. Genes (Basel) 2018;9:E79. PubMed PMC

Tan M.H., Li Q., Shanmugam R., Piskol R., Kohler J., Young A.N. Dynamic landscape and regulation of RNA editing in mammals. Nature. 2017;550:249–254. PubMed PMC

Sommer B., Köhler M., Sprengel R., Seeburg P.H. RNA editing in brain controls a determinant of ion flow in glutamate-gated channels. Cell. 1991;67:11–19. PubMed

Greger I.H., Khatri L., Kong X., Ziff E.B. AMPA receptor tetramerization is mediated by Q/R editing. Neuron. 2003;40:763–774. PubMed

Greger I.H., Khatri L., Ziff E.B. RNA editing at arg607 controls AMPA receptor exit from the endoplasmic reticulum. Neuron. 2002;34:759–772. PubMed

Salpietro V., Dixon C.L., Guo H., Bello O.D., Vandrovcova J., Efthymiou S., Maroofian R., Heimer G., Burglen L., Valence S., SYNAPS Study Group AMPA receptor GluA2 subunit defects are a cause of neurodevelopmental disorders. Nat. Commun. 2019;10:3094. PubMed PMC

Slavov D., Gardiner K. Phylogenetic comparison of the pre-mRNA adenosine deaminase ADAR2 genes and transcripts: conservation and diversity in editing site sequence and alternative splicing patterns. Gene. 2002;299:83–94. PubMed

Philippakis A.A., Azzariti D.R., Beltran S., Brookes A.J., Brownstein C.A., Brudno M., Brunner H.G., Buske O.J., Carey K., Doll C. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum. Mutat. 2015;36:915–921. PubMed PMC

Sobreira N., Schiettecatte F., Valle D., Hamosh A. GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum. Mutat. 2015;36:928–930. PubMed PMC

Retterer K., Juusola J., Cho M.T., Vitazka P., Millan F., Gibellini F., Vertino-Bell A., Smaoui N., Neidich J., Monaghan K.G. Clinical application of whole-exome sequencing across clinical indications. Genet. Med. 2016;18:696–704. PubMed

Zhu N., Gonzaga-Jauregui C., Welch C.L., Ma L., Qi H., King A.K., Krishnan U., Rosenzweig E.B., Ivy D.D., Austin E.D. Exome Sequencing in Children With Pulmonary Arterial Hypertension Demonstrates Differences Compared With Adults. Circ Genom Precis Med. 2018;11:e001887. PubMed PMC

Heale B.S., Keegan L.P., McGurk L., Michlewski G., Brindle J., Stanton C.M., Caceres J.F., O’Connell M.A. Editing independent effects of ADARs on the miRNA/siRNA pathways. EMBO J. 2009;28:3145–3156. PubMed PMC

Kishore S., Khanna A., Stamm S. Rapid generation of splicing reporters with pSpliceExpress. Gene. 2008;427:104–110. PubMed PMC

Livak K.J., Schmittgen T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001;25:402–408. PubMed

Stefl R., Oberstrass F.C., Hood J.L., Jourdan M., Zimmermann M., Skrisovska L., Maris C., Peng L., Hofr C., Emeson R.B., Allain F.H. The solution structure of the ADAR2 dsRBM-RNA complex reveals a sequence-specific readout of the minor groove. Cell. 2010;143:225–237. PubMed PMC

Matthews M.M., Thomas J.M., Zheng Y., Tran K., Phelps K.J., Scott A.I., Havel J., Fisher A.J., Beal P.A. Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity. Nat. Struct. Mol. Biol. 2016;23:426–433. PubMed PMC

Aurora R., Srinivasan R., Rose G.D. Rules for alpha-helix termination by glycine. Science. 1994;264:1126–1130. PubMed

Masliah G., Barraud P., Allain F.H. RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence. Cell. Mol. Life Sci. 2013;70:1875–1895. PubMed PMC

Mannion N.M., Greenwood S.M., Young R., Cox S., Brindle J., Read D., Nellåker C., Vesely C., Ponting C.P., McLaughlin P.J. The RNA-editing enzyme ADAR1 controls innate immune responses to RNA. Cell Rep. 2014;9:1482–1494. PubMed PMC

Daniel C., Widmark A., Rigardt D., Öhman M. Editing inducer elements increases A-to-I editing efficiency in the mammalian transcriptome. Genome Biol. 2017;18:195. PubMed PMC

McMillan N.A., Carpick B.W., Hollis B., Toone W.M., Zamanian-Daryoush M., Williams B.R. Mutational analysis of the double-stranded RNA (dsRNA) binding domain of the dsRNA-activated protein kinase, PKR. J. Biol. Chem. 1995;270:2601–2606. PubMed

Ramos A., Grünert S., Adams J., Micklem D.R., Proctor M.R., Freund S., Bycroft M., St Johnston D., Varani G. RNA recognition by a Staufen double-stranded RNA-binding domain. EMBO J. 2000;19:997–1009. PubMed PMC

Sansam C.L., Wells K.S., Emeson R.B. Modulation of RNA editing by functional nucleolar sequestration of ADAR2. Proc. Natl. Acad. Sci. USA. 2003;100:14018–14023. PubMed PMC

Desterro J.M.P., Keegan L.P., Lafarga M., Berciano M.T., O’Connell M., Carmo-Fonseca M. Dynamic association of RNA-editing enzymes with the nucleolus. J. Cell Sci. 2003;116:1805–1818. PubMed

Raponi M., Kralovicova J., Copson E., Divina P., Eccles D., Johnson P., Baralle D., Vorechovsky I. Prediction of single-nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 6. Hum. Mutat. 2011;32:436–444. PubMed

Cartegni L., Wang J., Zhu Z., Zhang M.Q., Krainer A.R. ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res. 2003;31:3568–3571. PubMed PMC

Smith P.J., Zhang C., Wang J., Chew S.L., Zhang M.Q., Krainer A.R. An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum. Mol. Genet. 2006;15:2490–2508. PubMed

McTague A., Howell K.B., Cross J.H., Kurian M.A., Scheffer I.E. The genetic landscape of the epileptic encephalopathies of infancy and childhood. Lancet Neurol. 2016;15:304–316. PubMed

Ambrosino P., Soldovieri M.V., Bast T., Turnpenny P.D., Uhrig S., Biskup S., Döcker M., Fleck T., Mosca I., Manocchio L. De novo gain-of-function variants in KCNT2 as a novel cause of developmental and epileptic encephalopathy. Ann. Neurol. 2018;83:1198–1204. PubMed

Duan H., Peng J., Kessi M., Yin F. De Novo KCNQ2 Mutation in One Case of Epilepsy of Infancy With Migrating Focal Seizures That Evolved to Infantile Spasms. Child Neurol. Open. 2018;5:X18767738. PubMed PMC

Freibauer A., Jones K. KCNQ2 mutation in an infant with encephalopathy of infancy with migrating focal seizures. Epileptic Disord. 2018;20:541–544. PubMed

Freilich E.R., Jones J.M., Gaillard W.D., Conry J.A., Tsuchida T.N., Reyes C., Dib-Hajj S., Waxman S.G., Meisler M.H., Pearl P.L. Novel SCN1A mutation in a proband with malignant migrating partial seizures of infancy. Arch. Neurol. 2011;68:665–671. PubMed PMC

Gorman K.M., Forman E., Conroy J., Allen N.M., Shahwan A., Lynch S.A., Ennis S., King M.D. Novel SMC1A variant and epilepsy of infancy with migrating focal seizures: Expansion of the phenotype. Epilepsia. 2017;58:1301–1302. PubMed

Howell K.B., McMahon J.M., Carvill G.L., Tambunan D., Mackay M.T., Rodriguez-Casero V., Webster R., Clark D., Freeman J.L., Calvert S. SCN2A encephalopathy: A major cause of epilepsy of infancy with migrating focal seizures. Neurology. 2015;85:958–966. PubMed PMC

Komulainen-Ebrahim J., Schreiber J.M., Kangas S.M., Pylkäs K., Suo-Palosaari M., Rahikkala E., Liinamaa J., Immonen E.V., Hassinen I., Myllynen P. Novel variants and phenotypes widen the phenotypic spectrum of GABRG2-related disorders. Seizure. 2019;69:99–104. PubMed

Poduri A., Heinzen E.L., Chitsazzadeh V., Lasorsa F.M., Elhosary P.C., LaCoursiere C.M., Martin E., Yuskaitis C.J., Hill R.S., Atabay K.D. SLC25A22 is a novel gene for migrating partial seizures in infancy. Ann. Neurol. 2013;74:873–882. PubMed PMC

Rizzo F., Ambrosino P., Guacci A., Chetta M., Marchese G., Rocco T., Soldovieri M.V., Manocchio L., Mosca I., Casara G. Characterization of two de novoKCNT1 mutations in children with malignant migrating partial seizures in infancy. Mol. Cell. Neurosci. 2016;72:54–63. PubMed

Štěrbová K., Vlčková M., Klement P., Neupauerová J., Staněk D., Zůnová H., Seeman P., Laššuthová P. Neonatal Onset of Epilepsy of Infancy with Migrating Focal Seizures Associated with a Novel GABRB3 Variant in Monozygotic Twins. Neuropediatrics. 2018;49:204–208. PubMed

Stödberg T., McTague A., Ruiz A.J., Hirata H., Zhen J., Long P., Farabella I., Meyer E., Kawahara A., Vassallo G. Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures. Nat. Commun. 2015;6:8038. PubMed PMC

Su D.J., Lu J.F., Lin L.J., Liang J.S., Hung K.L. SCN2A mutation in an infant presenting with migrating focal seizures and infantile spasm responsive to a ketogenic diet. Brain Dev. 2018;40:724–727. PubMed

Higuchi M., Maas S., Single F.N., Hartner J., Rozov A., Burnashev N., Feldmeyer D., Sprengel R., Seeburg P.H. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2. Nature. 2000;406:78–81. PubMed

Jia Z., Agopyan N., Miu P., Xiong Z., Henderson J., Gerlai R., Taverna F.A., Velumian A., MacDonald J., Carlen P. Enhanced LTP in mice deficient in the AMPA receptor GluR2. Neuron. 1996;17:945–956. PubMed

Brusa R., Zimmermann F., Koh D.-S., Feldmeyer D., Gass P., Seeburg P.H., Sprengel R. Early-onset epilepsy and postnatal lethality associated with an editing-deficient GluR-B allele in mice. Science. 1995;270:1677–1680. PubMed

Garncarz W., Tariq A., Handl C., Pusch O., Jantsch M.F. A high-throughput screen to identify enhancers of ADAR-mediated RNA-editing. RNA Biol. 2013;10:192–204. PubMed PMC

Tariq A., Garncarz W., Handl C., Balik A., Pusch O., Jantsch M.F. RNA-interacting proteins act as site-specific repressors of ADAR2-mediated RNA editing and fluctuate upon neuronal stimulation. Nucleic Acids Res. 2013;41:2581–2593. PubMed PMC

Bratt E., Ohman M. Coordination of editing and splicing of glutamate receptor pre-mRNA. RNA. 2003;9:309–318. PubMed PMC

Quinones-Valdez G., Tran S.S., Jun H.I., Bahn J.H., Yang E.W., Zhan L., Brümmer A., Wei X., Van Nostrand E.L., Pratt G.A. Regulation of RNA editing by RNA-binding proteins in human cells. Commun Biol. 2019;2:19. PubMed PMC

Bhogal B., Jepson J.E., Savva Y.A., Pepper A.S., Reenan R.A., Jongens T.A. Modulation of dADAR-dependent RNA editing by the Drosophila fragile X mental retardation protein. Nat. Neurosci. 2011;14:1517–1524. PubMed PMC

Filippini A., Bonini D., Lacoux C., Pacini L., Zingariello M., Sancillo L., Bosisio D., Salvi V., Mingardi J., La Via L. Absence of the Fragile X Mental Retardation Protein results in defects of RNA editing of neuronal mRNAs in mouse. RNA Biol. 2017;14:1580–1591. PubMed PMC

Marcucci R., Brindle J., Paro S., Casadio A., Hempel S., Morrice N., Bisso A., Keegan L.P., Del Sal G., O’Connell M.A. Pin1 and WWP2 regulate GluR2 Q/R site RNA editing by ADAR2 with opposing effects. EMBO J. 2011;30:4211–4222. PubMed PMC

Qi L., Song Y., Chan T.H.M., Yang H., Lin C.H., Tay D.J.T., Hong H., Tang S.J., Tan K.T., Huang X.X. An RNA editing/dsRNA binding-independent gene regulatory mechanism of ADARs and its clinical implication in cancer. Nucleic Acids Res. 2017;45:10436–10451. PubMed PMC

Shamay-Ramot A., Khermesh K., Porath H.T., Barak M., Pinto Y., Wachtel C., Zilberberg A., Lerer-Goldshtein T., Efroni S., Levanon E.Y., Appelbaum L. Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish. PLoS Genet. 2015;11:e1005702. PubMed PMC

Shelton P.M., Duran A., Nakanishi Y., Reina-Campos M., Kasashima H., Llado V., Ma L., Campos A., García-Olmo D., García-Arranz M. The Secretion of miR-200s by a PKCζ/ADAR2 Signaling Axis Promotes Liver Metastasis in Colorectal Cancer. Cell Rep. 2018;23:1178–1191. PubMed PMC

Macbeth M.R., Schubert H.L., Vandemark A.P., Lingam A.T., Hill C.P., Bass B.L. Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing. Science. 2005;309:1534–1539. PubMed PMC

Sorek R., Lev-Maor G., Reznik M., Dagan T., Belinky F., Graur D., Ast G. Minimal conditions for exonization of intronic sequences: 5′ splice site formation in alu exons. Mol. Cell. 2004;14:221–231. PubMed

Dichmann D.S., Walentek P., Harland R.M. The alternative splicing regulator Tra2b is required for somitogenesis and regulates splicing of an inhibitory Wnt11b isoform. Cell Rep. 2015;10:527–536. PubMed PMC

Storbeck M., Hupperich K., Gaspar J.A., Meganathan K., Martínez Carrera L., Wirth R., Sachinidis A., Wirth B. Neuronal-specific deficiency of the splicing factor Tra2b causes apoptosis in neurogenic areas of the developing mouse brain. PLoS ONE. 2014;9:e89020. PubMed PMC

Newell N.E. Cascade detection for the extraction of localized sequence features; specificity results for HIV-1 protease and structure-function results for the Schellman loop. Bioinformatics. 2011;27:3415–3422. PubMed

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