De novo mutations in childhood cases of sudden unexplained death that disrupt intracellular Ca ²⁺ regulation

Abstract

Sudden unexplained death in childhood (SUDC) is an understudied problem. Whole-exome sequence data from 124 “trios” (decedent child, living parents) was used to test for excessive de novo mutations (DNMs) in genes involved in cardiac arrhythmias, epilepsy, and other disorders. Among decedents, nonsynonymous DNMs were enriched in genes associated with cardiac and seizure disorders relative to controls (odds ratio = 9.76, P = 2.15 × 10−4). We also found evidence for overtransmission of loss-of-function (LoF) or previously reported pathogenic variants in these same genes from heterozygous carrier parents (11 of 14 transmitted, P = 0.03). We identified a total of 11 SUDC proband genotypes (7 de novo, 1 transmitted parental mosaic, 2 transmitted parental heterozygous, and 1 compound heterozygous) as pathogenic and likely contributory to death, a genetic finding in 8.9% of our cohort. Two genes had recurrent missense DNMs, RYR2 and CACNA1C. Both RYR2 mutations are pathogenic (P = 1.7 × 10−7) and were previously studied in mouse models. Both CACNA1C mutations lie within a 104-nt exon (P = 1.0 × 10−7) and result in slowed L-type calcium channel inactivation and lower current density. In total, six pathogenic DNMs can alter calcium-related regulation of cardiomyocyte and neuronal excitability at a submembrane junction, suggesting a pathway conferring susceptibility to sudden death. There was a trend for excess LoF mutations in LoF intolerant genes, where ≥1 nonhealthy sample in denovo-db has a similar variant (odds ratio = 6.73, P = 0.02); additional uncharacterized genetic causes of sudden death in children might be discovered with larger cohorts.

Proteomic differences in hippocampus and cortex of sudden unexplained death in childhood

“…Due to the increased risk of seizure associated with APOE genotype [ 41 , 44 ] and its impact on brain development [ 6 ], we evaluated APOE genotype in SUDC cases from previous WES [ 22 ]. Among the 19 SUDC cases, there was 1 APO E2/E3 case, 11 E3/E3, 5 E3/E4, and 2 E4/E4.…”

“…SUDC cases were included from those enrolled in the SUDCRRC from 2015 to 2018 with available brain tissue in the frontal cortex and hippocampus at the level of the lateral geniculate nucleus (LGN) [ 26 , 37 , 49 ]. SUDC cases were excluded ( n = 3) when post-autopsy ancillary analyses identified potential pathogenic whole-exome sequencing (WES) variants that may contribute to COD [ 22 ]. Under IRB approval, de-identified control cases were obtained through partnerships with various medical examiner and coroner offices that were examined from 2012 to 2017 ( n = 8).…”

“…Previous WES analyses in SUDC cases [ 22 ] were reviewed for APOE variants to determine significance in this population, as there is increased risk of seizure associated with APOE genotype [ 41 , 44 ], impact on brain development [ 6 ], and poor outcome after traumatic brain injury [ 34 ]. Briefly, GATK Haplotype caller with depth ≥ 10 and alternate counts ≥ 5 was used to annotate variants.…”

“…There have been few molecular studies in SUDC and several related studies in sudden unexpected infant death (SUID) cases (< 1 year of age). Genetic variants may influence SUDC risk, particularly neurological and/or cardiomyopathies [ 8 , 22 , 24 , 29 , 52 ]. De novo mutations that occur post-zygotically can result in somatic mosaicism and occur in SUDC and SUDEP cases, which can influence brain development in the form of abnormal neuronal migration, brain overgrowth disorders, as well as epileptic encephalopathies, intellectual disability, autism, and neuropsychiatric diseases [ 10 , 23 ].…”

Children with Critical Illness Carry Risk Variants Despite Non-Diagnostic Whole Exome Sequencing

“…To test the null hypothesis that our cohort contained an expected number of de novo variants in genes without a disease association, we utilized denovolyzeR. [44][45][46] denovolyzeR is an R package which analyzes the rate of de novo variants in a dataset and compares it to an expected variant rate to assess enrichment.…”