Association of variants in HTRA1 and NOTCH3 with MRI-defined extremes of cerebral small vessel disease in older subjects

Abstract

We report a composite extreme phenotype design using distribution of white matter hyperintensities and brain infarcts in a population-based cohort of older persons for gene-mapping of cerebral small vessel disease. We demonstrate its application in the 3C-Dijon whole exome sequencing (WES) study (n = 1924, nWESextremes = 512), with both single variant and gene-based association tests. We used other population-based cohort studies participating in the CHARGE consortium for replication, using whole exome sequencing (nWES = 2,868, nWESextremes = 956) and genome-wide genotypes (nGW = 9924, nGWextremes = 3308). We restricted our study to candidate genes known to harbour mutations for Mendelian small vessel disease: NOTCH3, HTRA1, COL4A1, COL4A2 and TREX1. We identified significant associations of a common intronic variant in HTRA1, rs2293871 using single variant association testing (Pdiscovery = 8.21 × 10-5, Preplication = 5.25 × 10-3, Pcombined = 4.72 × 10-5) and of NOTCH3 using gene-based tests (Pdiscovery = 1.61 × 10-2, Preplication = 3.99 × 10-2, Pcombined = 5.31 × 10-3). Follow-up analysis identified significant association of rs2293871 with small vessel ischaemic stroke, and two blood expression quantitative trait loci of HTRA1 in linkage disequilibrium. Additionally, we identified two participants in the 3C-Dijon cohort (0.4%) carrying heterozygote genotypes at known pathogenic variants for familial small vessel disease within NOTCH3 and HTRA1. In conclusion, our proof-of-concept study provides strong evidence that using a novel composite MRI-derived phenotype for extremes of small vessel disease can facilitate the identification of genetic variants underlying small vessel disease, both common variants and those with rare and low frequency. The findings demonstrate shared mechanisms and a continuum between genes underlying Mendelian small vessel disease and those contributing to the common, multifactorial form of the disease.

Keywords: cerebral small vessel disease; exome sequencing study; extreme phenotype; lacunes of presumed vascular origin; white matter hyperintensity.

Figure 1

Schematic representation of the extreme SVD design in the 3C-Dijon study.

Figure 2

NOTCH3 protein modifying rare and low frequency variants in the 3C-Dijon extreme SVD cohort.

Figure 3

MRI images of participants carrying heterozygote genotypes at CADASIL and CARASIL causing mutations. (A) Baseline (1) and 4-year follow-up (2) MRI scans of a 65-year old female participant with extensive SVD, in whom a NOTCH3 EGFr domain cysteine-modifying mutation was found: NM_000435.2 (NOTCH3):c.C2353T:p.R785C. Images show lacunar infarcts and dilated perivascular spaces in basal ganglia and white matter, and WMH in the periventricular region and deep white matter; on the follow-up MRI scan WMH and dilated perivascular spaces burden had increased and WMH became visible in the anterior temporal lobes (yellow arrows), a typical location for CADASIL. This participant remained free of stroke and dementia until the end of her follow-up at age 77. Her MMSE score was 28 at baseline and 26 at 12 years follow-up (secondary school education but no high school). (B) Baseline MRI scan of a 74-year-old female participant with extensive SVD, in whom a heterozygous CARASIL causing mutation was found: NM_002775.4 (HTRA1):c.1108C > T (p.Arg370Ter). Images show WMH and lacunes in the pons and extensive WMH in the deep white matter and periventricular region (magenta arrows). This participant was free of stroke and dementia at baseline but was lost to follow-up. Her baseline MMSE score was 27 (primary school education).