Phenotypic and genetic spectrum of ATP6V1A encephalopathy: a disorder of lysosomal homeostasis

Abstract

Vacuolar-type H+-ATPase (V-ATPase) is a multimeric complex present in a variety of cellular membranes that acts as an ATP-dependent proton pump and plays a key role in pH homeostasis and intracellular signalling pathways. In humans, 22 autosomal genes encode for a redundant set of subunits allowing the composition of diverse V-ATPase complexes with specific properties and expression. Sixteen subunits have been linked to human disease. Here we describe 26 patients harbouring 20 distinct pathogenic de novo missense ATP6V1A variants, mainly clustering within the ATP synthase α/β family-nucleotide-binding domain. At a mean age of 7 years (extremes: 6 weeks, youngest deceased patient to 22 years, oldest patient) clinical pictures included early lethal encephalopathies with rapidly progressive massive brain atrophy, severe developmental epileptic encephalopathies and static intellectual disability with epilepsy. The first clinical manifestation was early hypotonia, in 70%; 81% developed epilepsy, manifested as developmental epileptic encephalopathies in 58% of the cohort and with infantile spasms in 62%; 63% of developmental epileptic encephalopathies failed to achieve any developmental, communicative or motor skills. Less severe outcomes were observed in 23% of patients who, at a mean age of 10 years and 6 months, exhibited moderate intellectual disability, with independent walking and variable epilepsy. None of the patients developed communicative language. Microcephaly (38%) and amelogenesis imperfecta/enamel dysplasia (42%) were additional clinical features. Brain MRI demonstrated hypomyelination and generalized atrophy in 68%. Atrophy was progressive in all eight individuals undergoing repeated MRIs. Fibroblasts of two patients with developmental epileptic encephalopathies showed decreased LAMP1 expression, Lysotracker staining and increased organelle pH, consistent with lysosomal impairment and loss of V-ATPase function. Fibroblasts of two patients with milder disease, exhibited a different phenotype with increased Lysotracker staining, decreased organelle pH and no significant modification in LAMP1 expression. Quantification of substrates for lysosomal enzymes in cellular extracts from four patients revealed discrete accumulation. Transmission electron microscopy of fibroblasts of four patients with variable severity and of induced pluripotent stem cell-derived neurons from two patients with developmental epileptic encephalopathies showed electron-dense inclusions, lipid droplets, osmiophilic material and lamellated membrane structures resembling phospholipids. Quantitative assessment in induced pluripotent stem cell-derived neurons identified significantly smaller lysosomes. ATP6V1A-related encephalopathy represents a new paradigm among lysosomal disorders. It results from a dysfunctional endo-lysosomal membrane protein causing altered pH homeostasis. Its pathophysiology implies intracellular accumulation of substrates whose composition remains unclear, and a combination of developmental brain abnormalities and neurodegenerative changes established during prenatal and early postanal development, whose severity is variably determined by specific pathogenic variants.

Amelogenesis imperfecta: Next-generation sequencing sheds light on Witkop’s classification

“…Developmental and epileptic encephalopathy 93 is an autosomal dominant disorder with, among other features, delayed psychomotor and impaired intellectual developments, as well as early onset epilepsy. Additional clinical features like microcephaly and hypoplastic amelogenesis imperfecta were observed in epileptic encephalopathy ( Guerrini et al, 2022 ).…”

“…Since the discovery of the first gene underlying an amelogenesis imperfecta from mapping of AMELX in 1989 ( Lau et al, 1989 ) to its causative role in AI in 1990 ( Lagerström et al, 1990 ; 1991 ); more than 70 genes have been discovered as important for amelogenesis and its defects. The most recent ones are CLAUDIN 10 ( Sewerin et al, 2022 ) and ATP6V1A ( Guerrini et al, 2022 ) . Knowledge is evolving fast on amelogenesis ( Simmer et al, 2021 ) and enamel disturbances in rare diseases.…”

Proteomic and Bioinformatic Tools to Identify Potential Hub Proteins in the Audiogenic Seizure-Prone Hamster GASH/Sal

“…ATP6V1A (H + -transporting two-sector ATPase; underexpressed DEP with −2.17 FC) is part of a multimeric complex present in a variety of cellular membranes that acts as an ATP-dependent proton pump and plays a key role in pH homeostasis and intracellular signaling pathways. ATP6V1A variants, mainly clustering within the ATP synthase α/β family-nucleotide-binding domain, include early lethal encephalopathies and developmental encephalopathy in epilepsy [ 95 , 96 , 97 ]. Interestingly, several mutants of ATP6V1A , such as the p.Asp100Tyr, are characterized by reduced expression due to increased degradation; these mutations caused a defect in neurite elongation accompanied by loss of excitatory inputs, revealing that altered lysosomal homeostasis markedly affects neurite development and synaptic connectivity [ 95 ].…”

Astrocyte‐Derived Extracellular Vesicular miR‐143‐3p Dampens Autophagic Degradation of Endothelial Adhesion Molecules and Promotes Neutrophil Transendothelial Migration after Acute Brain Injury

“…This acidification process is crucial for lysosomal hydrolytic activity and autophagy. [ 40 , 44 , 45 ] Consistent with the downregulation of ATP6V1A, overexpression of miR‐143‐3p resulted in lysosomal de‐acidification (Figure 3I ). Moreover, this de‐acidification was accompanied by decreased enzymatic activities of CTSB and CTSD, which are two major lysosomal proteases (Figure 3J ).…”

“…Moreover, we investigated whether inhibiting the release of astrocytic EVs could suppress the increase in EVs‐miR‐143‐3p level in ICH mice. Neutral sphingomyelinase 2 (nSMase2), a product of the SMPD3 gene, is an essential enzyme for the synthesis and release of EVs [ .40 ] We specifically knockdown SMPD3 in astrocytes by stereotactically injecting AAV‐SMPD3‐shRNA that contains a GFAP‐specific promoter (Figure 2D ). Importantly, we found that after inhibiting the secretion of astrocytic EVs, the level of EVs‐miR‐143‐3p in brain pool was no longer elevated after ICH (Figure 2E ).…”