Biallelic PI4KA variants cause a novel neurodevelopmental syndrome with hypomyelinating leukodystrophy

Abstract

Phosphoinositides are lipids that play a critical role in processes such as cellular signalling, ion channel activity and membrane trafficking. When mutated, several genes that encode proteins that participate in the metabolism of these lipids give rise to neurological or developmental phenotypes. PI4KA is a phosphoinositide kinase that is highly expressed in the brain and is essential for life. Here we used whole exome or genome sequencing to identify 10 unrelated patients harbouring biallelic variants in PI4KA that caused a spectrum of conditions ranging from severe global neurodevelopmental delay with hypomyelination and developmental brain abnormalities to pure spastic paraplegia. Some patients presented immunological deficits or genito-urinary abnormalities. Functional analyses by western blotting and immunofluorescence showed decreased PI4KA levels in the patients' fibroblasts. Immunofluorescence and targeted lipidomics indicated that PI4KA activity was diminished in fibroblasts and peripheral blood mononuclear cells. In conclusion, we report a novel severe metabolic disorder caused by PI4KA malfunction, highlighting the importance of phosphoinositide signalling in human brain development and the myelin sheath.

Keywords: PI4KA; hypomyelinating leukodystrophy; inborn errors of metabolism; phosphoinositol; spastic paraplegia.

Figure 1

PI4KA variant features. (A) Family trees. Square = male; circle = female; filled symbols = affected individuals; open symbols = unaffected carriers; WT = wild-type allele. (B) Structure of PI4KA protein and the mutations identified in this study. Top: Missense/in-frame variants. Bottom: Loss-of-function variants. Light blue = α-solenoid domain; cyan = dimerization domain; dark blue = ‘cradle’ domain; dark purple = catalytic domain. (C) 3D representation of the PI4KA catalytic domain. Blue = PI4KA; green = TTC7B; pink = A1, PI4KA inhibitor occupying the ATP-binding space in the catalytic domain. The red balls represent the location of the missense/in-frame variants found in our cohort. Note the clustering of missense/in-frame variants near the catalytic site of PI4KA.

Figure 2

MRI features of patients harbouring biallelic PI4KA variants. Left: Axial T₁-weighted sequences. Middle: Axial T₂-weighted sequences. Right: Sagittal T₁-weighted sequences. Patients 1 and 2 exhibited diffuse hypomyelination, global white matter atrophy with posterior predominance, a thin corpus callosum and colpocephaly. Patient 1 also presented with brainstem and cerebellar hypoplasia. Patients 3 and 4 had diffuse hypomyelination with a thin corpus callosum and progressive cerebellar atrophy. Patient 4 also had brainstem atrophy. Patients 5–7 exhibited delayed myelination with mild ventriculomegaly. Patients 5 and 6 showed a dysplastic corpus callosum. Patient 6 had brainstem and cerebellar atrophy and Patient 7 exhibited atrophy of the cerebellar inferior lobe. Patient 8 showed bilateral perisylvian polymicrogyria. Patients 9 and 10 showed cervical spinal cord atrophy, and arachnoid cyst of the posterior fossa was observed in Patient 9, the images of whom were otherwise normal.

Figure 3

PI4KA activity evaluation. (A) Schematic representation of P4KA pathway. (B) Western blot of PI4KA protein and quantification. Patients’ fibroblasts (n = 5) and controls (CTL, n = 5). (C) Immunofluorescence of PI4KA protein and the head group of the lipid PI(4)P and (D) its quantification on a minimum of 100 cells. Patient’s fibroblasts (n = 5) and controls (CTL, n = 4). (E) Targeted lipidomics against phosphatidylinositol (PI), PIP and PIP2, in human PBMCs from control (CTL) children (n = 5), control adults (n = 5); and PI4KA deficient patients (n = 4). Data presented as mean ± SD. *P < 0.05, **P < 0.01, ***P < 0.001 (two-tailed Student’s t-test). Box plot centre line corresponds to the median, lower and upper limits to the first and third quartiles (25th and 75th percentiles), respectively, and whiskers to 1.5× the interquartile range.