ATP1A2- and ATP1A3-associated early profound epileptic encephalopathy and polymicrogyria

Abstract

Constitutional heterozygous mutations of ATP1A2 and ATP1A3, encoding for two distinct isoforms of the Na+/K+-ATPase (NKA) alpha-subunit, have been associated with familial hemiplegic migraine (ATP1A2), alternating hemiplegia of childhood (ATP1A2/A3), rapid-onset dystonia-parkinsonism, cerebellar ataxia-areflexia-progressive optic atrophy, and relapsing encephalopathy with cerebellar ataxia (all ATP1A3). A few reports have described single individuals with heterozygous mutations of ATP1A2/A3 associated with severe childhood epilepsies. Early lethal hydrops fetalis, arthrogryposis, microcephaly, and polymicrogyria have been associated with homozygous truncating mutations in ATP1A2. We investigated the genetic causes of developmental and epileptic encephalopathies variably associated with malformations of cortical development in a large cohort and identified 22 patients with de novo or inherited heterozygous ATP1A2/A3 mutations. We characterized clinical, neuroimaging and neuropathological findings, performed in silico and in vitro assays of the mutations’ effects on the NKA-pump function, and studied genotype-phenotype correlations. Twenty-two patients harboured 19 distinct heterozygous mutations of ATP1A2 (six patients, five mutations) and ATP1A3 (16 patients, 14 mutations, including a mosaic individual). Polymicrogyria occurred in 10 (45%) patients, showing a mainly bilateral perisylvian pattern. Most patients manifested early, often neonatal, onset seizures with a multifocal or migrating pattern. A distinctive, ‘profound’ phenotype, featuring polymicrogyria or progressive brain atrophy and epilepsy, resulted in early lethality in seven patients (32%). In silico evaluation predicted all mutations to be detrimental. We tested 14 mutations in transfected COS-1 cells and demonstrated impaired NKA-pump activity, consistent with severe loss of function. Genotype-phenotype analysis suggested a link between the most severe phenotypes and lack of COS-1 cell survival, and also revealed a wide continuum of severity distributed across mutations that variably impair NKA-pump activity. We performed neuropathological analysis of the whole brain in two individuals with polymicrogyria respectively related to a heterozygous ATP1A3 mutation and a homozygous ATP1A2 mutation and found close similarities with findings suggesting a mainly neural pathogenesis, compounded by vascular and leptomeningeal abnormalities. Combining our report with other studies, we estimate that ∼5% of mutations in ATP1A2 and 12% in ATP1A3 can be associated with the severe and novel phenotypes that we describe here. Notably, a few of these mutations were associated with more than one phenotype. These findings assign novel, ‘profound’ and early lethal phenotypes of developmental and epileptic encephalopathies and polymicrogyria to the phenotypic spectrum associated with heterozygous ATP1A2/A3 mutations and indicate that severely impaired NKA pump function can disrupt brain morphogenesis.

Recurrent de novo single point mutation on the gene encoding Na+/K+ pump results in epilepsy

“…Mutations in ATP1A2 have been described in FHM2 and AHC1. These neurological disorders are dominantly inherited and are primarily caused by missense mutations (Chatron et al, 2019;Vetro et al, 2021). L764P, W887R, M731T, R689Q, D718N, P979L, E174K, C515Y, I286T, and T415M mutations occurred in families with FHM2 (De Fusco et al, 2003;Jurkat-Rott et al, 2004;Todt et al, 2005;Vanmolkot et al, 2003;Vanmolkot et al, 2007).…”

Dominantly acting variants in ARF3 have disruptive consequences on Golgi integrity and cause microcephaly recapitulated in zebrafish

“…Target enrichment kits, sequencing platforms, data analysis, and WES statistics are reported in Supplementary Table 2-6 and in the Supplementary Methods. WES data processing, read alignment to the GRCh37/hg19 version of genome assembly, and variant filtering and prioritization by allele frequency, predicted functional impact, and inheritance models were performed as previously reported [76][77][78][79][80] . WES data output is summarized in Supplementary Table…”

Genetically altered animal models forATP1A3-related disorders

“…PMG PMG is the most common developmental malformation of the cerebral cortex, characterised by abnormal folding and laminar organisation. Recently, de novo and familial mutations in ATP1A3 were found in patients affected by a severe form of PMG characterised by epilepsy and a global developmental delay (Miyatake et al, 2021;Smith et al, 2021;Vetro et al, 2021). PMG mutations include D801N, the most common mutation in AHC (Panagiotakaki et al, 2015), and L924P, which is also observed in early infantile epileptic encephalopathy (EIEE) (Arystarkhova et al, 2019).…”

“…A variety of mutations affecting the aspartic acid at position 801 (D801) can cause RDP, AHC or PMG. D801E and D801V are AHC-causing mutations (Panagiotakaki et al, 2015), whereas D801N can cause AHC and PMG (Panagiotakaki et al, 2015;Vetro et al, 2021), and D801Y can cause RDP and AHC (de Carvalho Aguiar et al, 2004;Viollet et al, 2015). Homozygous Atp1a3 D801Y mice die neonatally.…”