A novel PTEN variant causing hemimegalencephaly and focal nodular heterotopias in the developing human brain

Brain development and subsequent brain function are highly sensitive to genetic mutations, which can result in severe neurodevelopmental malformations. Alterations in PTEN signaling cause a spectrum of developmental malformations and neurological diseases including epilepsy. To date, a detailed understanding of the neuropathological underpinnings of PTEN-associated brain malformations, particularly in fetuses, is missing. We have thus investigated a fetal case of hemimegalencephaly (HME), which is a rare disorder characterized by hemispheric overgrowth, developmental delay, and epileptic seizures. Our assessment of the male fetus includes genetic, radiologic, and histologic features and provides a comprehensive characterization of the cellular alterations in HME together with a genotypic correlation. Genetic analyses uncovered that hemispheric overgrowth was caused by a somatic second hit resulting in biallelic PTEN alteration in the affected brain tissue, although the unaffected hemisphere carried the same PTEN variant as the heterozygous germline variant. Based on the latter, we interpret that the PTEN mutation is not a dominant-negative variant. Within the outer subventricular zone of the enlarged cortex, we found small nodular heterotopias, which can be origins of focal epileptic seizures. Cell type-specific marker stainings revealed that the heterotopias consisted exclusively of SATB2⁺ glutamatergic projection neurons. Altogether, our analyses and findings contribute to a deeper understanding of the pathomechanisms of a novel PTEN variant driving a severe brain malformation.