Mosaic trisomy of chromosome 1q in human brain tissue associates with unilateral polymicrogyria, very early-onset focal epilepsy, and severe developmental delay

Abstract

Polymicrogyria (PMG) is a developmental cortical malformation characterized by an excess of small and frustrane gyration and abnormal cortical lamination. PMG frequently associates with seizures. The molecular pathomechanisms underlying PMG development are not yet understood. About 40 genes have been associated with PMG, and small copy number variations have also been described in selected patients. We recently provided evidence that epilepsy-associated structural brain lesions can be classified based on genomic DNA methylation patterns. Here, we analyzed 26 PMG patients employing array-based DNA methylation profiling on formalin-fixed paraffin-embedded material. A series of 62 well-characterized non-PMG cortical malformations (focal cortical dysplasia type 2a/b and hemimegalencephaly), temporal lobe epilepsy, and non-epilepsy autopsy controls was used as reference cohort. Unsupervised dimensionality reduction and hierarchical cluster analysis of DNA methylation profiles showed that PMG formed a distinct DNA methylation class. Copy number profiling from DNA methylation data identified a uniform duplication spanning the entire long arm of chromosome 1 in 7 out of 26 PMG patients, which was verified by additional fluorescence in situ hybridization analysis. In respective cases, about 50% of nuclei in the center of the PMG lesion were 1q triploid. No chromosomal imbalance was seen in adjacent, architecturally normal-appearing tissue indicating mosaicism. Clinically, PMG 1q patients presented with a unilateral frontal or hemispheric PMG without hemimegalencephaly, a severe form of intractable epilepsy with seizure onset in the first months of life, and severe developmental delay. Our results show that PMG can be classified among other structural brain lesions according to their DNA methylation profile. One subset of PMG with distinct clinical features exhibits a duplication of chromosomal arm 1q.

Keywords: Brain development; Chromosome 1; Copy number variation; Cortical malformation; ID; Seizures.

Fig. 1

a UMAP and b hierarchical cluster analysis of PMG, reference MCD, non-MCD epilepsy, and no-seizure autopsy controls. Twenty-seven cases with histological diagnosis of PMG are indicated in light green. PMG cases formed a novel distinct methylation group. The color scheme for histopathological entities in (a) also applies to (b). c Copy number profiling analysis indicating duplication of chromosome arm 1q and FISH confirming brain somatic 1q triploid nuclei in the center of the lesion, but not in adjacent, architecturally normal-appearing tissue of the same patient. d 1q duplication in PMG patients associated with significantly earlier onset of seizures, but not longer duration of epilepsy before surgery. Chr chromosome, CTRL control, NCx neocortex, WM white matter, FCD focal cortical dysplasia, HME hemimegalencephaly, PMG polymicrogyria, TLE temporal lobe epilepsy, UMAP uniform manifold approximation and projection

Fig. 2

MRI and histology of representative PMG cases with and without brain mosaic 1q gain. a 15-year-old male patient (#6) with seizure onset at 3 months and an MRI-positive lesion in the right frontal lobe with cortical thickening and no hyperintense T2/FLAIR signal and no transmantle sign (arrow). b NeuN staining revealed abnormally folded sulci without pial opening. The cortical ribbon is small and mostly 4-layered. c GFAP-immunohistochemistry revealed protoplasmic astrocytic inclusions (blue arrow [28]). d 17-year-old male patient (#18) with seizure onset at 8 months and right hemimegalencephaly (asterisk). e Neocortical ribbon with small sulci without pial opening and nodular heterotopias in the white matter (black arrow; NeuN immunohistochemistry). f Dysmorphic neurons accumulating non-phosphorylated neurofilament protein (green arrows, SMI32 immunohistochemistry)