Research Article: Whole exome sequence-based association analyses of plasma amyloid-β in African and European Americans; the Atherosclerosis Risk in Communities-Neurocognitive Study

Date Published: July 13, 2017

Publisher: Public Library of Science

Author(s): Jeannette Simino, Zhiying Wang, Jan Bressler, Vincent Chouraki, Qiong Yang, Steven G. Younkin, Sudha Seshadri, Myriam Fornage, Eric Boerwinkle, Thomas H. Mosley, Kristel Sleegers.


We performed single-variant and gene-based association analyses of plasma amyloid-β (aβ) concentrations using whole exome sequence from 1,414 African and European Americans. Our goal was to identify genes that influence plasma aβ42 concentrations and aβ42:aβ40 ratios in late middle age (mean = 59 years), old age (mean = 77 years), or change over time (mean = 18 years).

Plasma aβ measures were linearly regressed onto age, gender, APOE ε4 carrier status, and time elapsed between visits (fold-changes only) separately by race. Following inverse normal transformation of the residuals, seqMeta was used to conduct race-specific single-variant and gene-based association tests while adjusting for population structure. Linear regression models were fit on autosomal variants with minor allele frequencies (MAF)≥1%. T5 burden and Sequence Kernel Association (SKAT) gene-based tests assessed functional variants with MAF≤5%. Cross-race fixed effects meta-analyses were Bonferroni-corrected for the number of variants or genes tested.

Seven genes were associated with aβ in late middle age or change over time; no associations were identified in old age. Single variants in KLKB1 (rs3733402; p = 4.33×10-10) and F12 (rs1801020; p = 3.89×10-8) were significantly associated with midlife aβ42 levels through cross-race meta-analysis; the KLKB1 variant replicated internally using 1,014 additional participants with exome chip. ITPRIP, PLIN2, and TSPAN18 were associated with the midlife aβ42:aβ40 ratio via the T5 test; TSPAN18 was significant via the cross-race meta-analysis, whereas ITPRIP and PLIN2 were European American-specific. NCOA1 and NT5C3B were associated with the midlife aβ42:aβ40 ratio and the fold-change in aβ42, respectively, via SKAT in African Americans. No associations replicated externally (N = 725).

We discovered age-dependent genetic effects, established associations between vascular-related genes (KLKB1, F12, PLIN2) and midlife plasma aβ levels, and identified a plausible Alzheimer’s Disease candidate gene (ITPRIP) influencing cell death. Plasma aβ concentrations may have dynamic biological determinants across the lifespan; plasma aβ study designs or analyses must consider age.

Partial Text

Alzheimer’s disease (AD) is a major public health burden, afflicting 5.1 million Americans aged 65 or older; the number of cases is expected to triple by 2050, costing the nation $1.1 trillion [1]. Although there are no effective treatments to prevent, slow, or cure AD, researchers have made considerable progress in dissecting its genetic etiology and revealing biological pathways that may contain druggable targets. The International Genomics of Alzheimer’s Project leveraged results from genome-wide association studies (GWAS) of late-onset AD (LOAD) to identify candidate therapeutic targets in the immune response, endocytosis, cholesterol transport, and protein ubiquitination pathways [2]. GWAS and sequencing studies have nominated variants (representing ≈30 genes) from the whole allele frequency spectrum [3–7], yet there is a substantial proportion of LOAD heritability unexplained [6, 7]. The identification of additional therapeutic candidates is hindered by the reduced power of case-control outcomes [8].

The discovery analysis included 406 AAs and 1,008 EAs with whole exome sequence (Table 1; for summary statistics by cognitive status, see S2 and S3 Tables). Only one-third of AAs were male, whereas about half (47%) of EAs were male. Both races had similar age distributions, with the third visit corresponding to late middle age and the fifth visit corresponding to older age, and high APOE ε4 carriage rates compared to the general population (20–25%) [42]. In both AAs and EAs, mean aβ42 levels increased between visits and mean aβ42:aβ40 ratios decreased between visits. Although the third visit aβ42 levels differed between the races, the mean fold-changes were similar. The internal (ARIC exome chip) and external (FHS exome sequence) replication samples had lower APOE ε4 carriage rates (34% for ARIC AAs, 18% for ARIC EAs, and 22% for FHS EAs) than the discovery samples (S4 Table). The FHS replication sample included only EAs and had more males (52%) and higher midlife plasma aβ levels (both aβ42 and aβ42:aβ40 ratio) than all ARIC samples.

Leveraging late-midlife plasma aβ concentrations and fold-changes from a moderate-sized biracial sample enabled the identification of seven genes that were obscured in cross-sectional analyses of the elderly. These findings echoed those of the published GWAS meta-analysis of plasma aβ concentrations which failed to identify significant genetic variants in non-demented elderly participants [12]. Plasma aβ concentrations change with age, at least until dementia or brain plaques appear [22, 43], and could have a dynamic genetic architecture across the lifespan. Such age-dependent genetic associations have been reported for other complex traits, including blood pressure [44, 45] and lipids [46], and can represent genes that are active at specific ages or genes that are active across the age spectrum with varying effect magnitudes [45]. Accounting for age-dependent genetic effects, whether through model-based approaches or age stratification, can enhance gene discovery efforts and our understanding of intraindividual variation in plasma aβ levels [44–46]. Such analyses may suggest the optimal age range to capture particular facets of disease (e.g. AD, vascular) pathophysiology while negating the need for massive sample sizes.




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