Low-Allele-Frequency Somatic Variants in a Cohort of Sporadic Saccular "Berry" Cerebral Aneurysms

Subarachnoid hemorrhage from ruptured saccular intracranial aneurysms (IAs) is fatal in ≈50% of cases. Significant effort has been devoted to identifying the molecular pathogenesis of IAs to develop new therapies to treat or halt the progression of IAs.

Paired deep whole-exome sequencing was performed on the walls of sporadic IAs in a discovery set of 11 sporadic IAs from 10 unrelated patients and matching peripheral blood DNA. Somatic alterations unique to the IA tissue were characterized. Variants were validated with gene-targeted deep next-generation sequencing. The genetic landscape of a validation cohort of 68 IAs was analyzed by targeted deep sequencing of all altered genes detected in the discovery cohort as well as other genes associated with aneurysm formation.

Whole-exome sequencing revealed somatic variants in 7 of the 11 IA walls. These somatic variants were found at low allele frequencies (AFs), ranging from 2% to 19% at a consistent AF range within a sample, suggesting a cell-based population. Most coding somatic variants found were missense (91%). Notably, 2 IAs from 1 patient were included in the discovery set and both harbored unique somatic variants, not detected in the other sample. Similarly, a different aneurysm from a patient in the discovery cohort was included in the larger validation cohort and revealed a unique genotype. Saccular aneurysms harbored somatic variants in genes falling into several functional categories including angiogenesis (PKD1, XDH), DNA repair (SFB3, DCC, MLH1), extracellular matrix (FBN1, COL4A1, COL4A5, MMP8) and cancer genes (ERBb4 and PTCH1). Deep targeted sequencing of these genes in a larger cohort by next-generation sequencing revealed other somatic variants in 11 of the same genes in IA walls from 10 unrelated patients, similarly in low AFs. Another custom designed next-generation sequencing panel identified 7 other somatic variants in genes associated with IA formation. Notably, there were no common somatic variants among the 2 aneurysms from the same patient.

Saccular IAs harbor somatic low AF variants in coding genes predicted to alter protein function. AFs occurred in a similar range within and between samples, suggesting a cell- based population driving the pathogenesis of saccular IAs. Recurrent variants in genes known to be involved in IAs such as COL4A5 as well as novel genes (eg, ERBb4 and PABIR3) also suggests a new frontier for further research.