Whole exome sequencing of Rett syndrome-like patients reveals the mutational diversity of the clinical phenotype.

Mario Lucariello,Joaquin Dopazo,Laura Roa,Silvia Vidal,Paola Jurado,Mauricio Saez,Judith Armstrong,Mercè Pineda,Esther Dalfó,Dori Huertas,Enrique Vidal,Manel Esteller

doi:10.1007/s00439-016-1721-3

Abstract

Classical Rett syndrome (RTT) is a neurodevelopmental disorder where most of cases carry MECP2 mutations. Atypical RTT variants involve mutations in CDKL5 and FOXG1. However, a subset of RTT patients remains that do not carry any mutation in the described genes. Whole exome sequencing was carried out in a cohort of 21 female probands with clinical features overlapping with those of RTT, but without mutations in the customarily studied genes. Candidates were functionally validated by assessing the appearance of a neurological phenotype in Caenorhabditis elegans upon disruption of the corresponding ortholog gene. We detected pathogenic variants that accounted for the RTT-like phenotype in 14 (66.6 %) patients. Five patients were carriers of mutations in genes already known to be associated with other syndromic neurodevelopmental disorders. We determined that the other patients harbored mutations in genes that have not previously been linked to RTT or other neurodevelopmental syndromes, such as the ankyrin repeat containing protein ANKRD31 or the neuronal acetylcholine receptor subunit alpha-5 (CHRNA5). Furthermore, worm assays demonstrated that mutations in the studied candidate genes caused locomotion defects. Our findings indicate that mutations in a variety of genes contribute to the development of RTT-like phenotypes.Electronic supplementary materialThe online version of this article (doi:10.1007/s00439-016-1721-3) contains supplementary material, which is available to authorized users.

Highlights

Around 90 % of the cases are explained by more than 800 reported mutations in the methyl CpG-binding protein 2 gene (MECP2) (RettBASE: MECP2 Variation Database) (Christodoulou et al 2003), which is located in the X chromosome and which causes most of the classical or typical forms of Rett syndrome (RTT) (Chahrour and Zoghbi 2007), and it was originally identified as encoding a protein that binds to methylated DNA (Lewis et al 1992)
We focused our analysis on de novo single nucleotide variants (SNVs) due to their known relevance in autism and mental retardation-related diseases (Vissers et al 2010)
We identified four mutations in genes such as HCN1 (Nava et al 2014) and GRIN2B (Endele et al 2010; Lemke et al 2014), which are associated with early infantile epileptic encephalopathy; SLC6A1, which is associated with epilepsy and myoclonic-atonic seizures (Carvill et al 2015); TCF4, which is associated with Pitt–Hopkins syndrome (Sweatt 2013); and SCN1A, which is associated with Dravet syndrome (Brunklaus and Zuberi 2014) (Table 2)

Summary

Introduction

RTT patients are asymptomatic during the first 6–18 months of life, but gradually develop severe motor, cognitive, and behavioral abnormalities that persist for life It is the second most common cause of intellectual disability in females after Down’s syndrome (Chahrour and Zoghbi 2007). 8 % of classic RTT and 42 % of variant RTT patients are MECP2 mutationnegative (Monros et al 2001; Percy 2008) Some of the latter group have mutations in other genes, such as that of the cyclin-dependent kinase-like 5 (CDKL5), which is described in individuals with an early seizure onset variant of RTT (Kalscheuer et al 2003) or the forkhead box G1 (FOXG1), which is responsible for the congenital variant of RTT (Ariani et al 2008). Generation sequencing (NGS) has emerged as a potentially powerful tool for the study of such genetic diseases (Zhu et al 2015)

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Conclusion