Improving Genetic Diagnostic Yield in Familial and Sporadic Cerebral Cavernous Malformations

Abstract

Cerebral cavernous malformations (CCMs) are vascular lesions in the brain associated with risk of haemorrhages and seizures. While the majority are sporadic and driven by somatic pathogenic variants in PIK3CA and MAP3K3, around 20% are familial cases with germline pathogenic variants in one of three CCM (1/2/3) genes. We performed deep phenotyping and genetic analysis of nine multiplex families and ten sporadic individuals with CCM. High depth exome or genome sequencing was performed on paired CCM tissue and blood of familial and sporadic cases. Chromosomal microarray analysis or droplet digital PCR were employed for validation, with the latter also being used to screen for recurrent pathogenic variants in CCM tissue. Clinical and surgical outcomes were correlated with genotype. We solved all 9 multiplex families identifying germline pathogenic variants in CCM1 (KRIT1) or CCM2. Of these, one-third (n=3/9) were single or multiple exon deletions or splice site variants, all in KRIT1. In four of these families, we identified second hit recurrent somatic pathogenic PIK3CA variants in two-thirds (n=4/6) of family members with CCM tissue available for testing. Most familial cases had multiple supra- and infra-tentorial CCMs and were more likely to have symptomatic intracerebral haemorrhages. In a high proportion (n=8/10) of sporadic individuals we detected recurrent somatic CCM2, PIK3CA or MAP3K3 pathogenic variants in CCM tissue, consistent with prior studies. The sporadic cases all presented with seizures and had a single lesion, which was in the temporal lobe in 8/10 individuals, likely reflecting recruitment through an epilepsy surgery centre. All familial cases were solved because we screened for small copy number changes or deep non-coding variants that would not be detected on standard clinical genetic testing. We expanded on the recently described phenomenon of second hit somatic variants in the CCM tissue of some familial cases. We found a somatic variant in 80% of sporadic cases. Genetic diagnosis provides potential eligibility for precision medicine therapies to treat rapidly growing CCMs, such as the clinically approved mTOR pathway inhibitor Sirolimus.