Cell type-specificity of mosaic chromosome 1q gain resolved by single-nucleus RNA-seq in a case of pharmacoresistant epilepsy associated with hyaline protoplasmic astrocytopathy
Introduction: Mosaic gain of chromosome 1q (chr1q) is a recently described driver of malformation of cortical development (MCD) and pharmacoresistant epilepsy. Hyaline protoplasmic astrocytopathy of the neocortex is a rare neuropathological finding seen in cases of pharmacoresistant epilepsy with focal cortical dysplasia or other MCD. The cell-type specificity of mosaic chr1q gain in the brain is unknown, and no data exists on the molecular signatures of hyaline protoplasmic astrocytopathy. Methods: We present a child with pharmacoresistant epilepsy who underwent epileptic focus resections at age 3 and 5 years and was found to have mosaic chr1q gain and hyaline protoplasmic astrocytopathy with partial reduction in seizure burden after the second surgery. We performed single-nucleus RNA-sequencing (snRNA-seq) of brain tissue from the second resection. Results: Remarkably, snRNA-seq showed increased expression of chr1q genes only in select populations of neurons and astrocytes. Differentially expressed genes correlating with inferred chr1q gain included AKT3 and genes associated with cell adhesion or migration. A subcluster of astrocytes demonstrated enrichment for synapse-associated transcripts, possibly linked to the astrocytic inclusions observed in hyaline protoplasmic astrocytopathy. Discussion: snRNA-seq may be used to infer the cell type-specificity of mosaic chromosomal copy number variations and identify associated gene expression alterations, which in the case of chr1q gain may involve aberrations in cell migration. Future studies using spatial profiling could yield further insights on the molecular signatures of hyaline protoplasmic astrocytopathy. Overall design: Single-nucleus RNA-seq using the 10x platform (v3 chemistry) of a single sample of fresh frozen surgically resected brain tissue from the right frontal lobe