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

<div><p>Objective</p><p>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).</p><p>Methods</p><p>Plasma aβ measures were linearly regressed onto age, gender, <i>APOE</i> 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.</p><p>Results</p><p>Seven genes were associated with aβ in late middle age or change over time; no associations were identified in old age. Single variants in <i>KLKB1</i> (rs3733402; p = 4.33x10^-10) and <i>F12</i> (rs1801020; p = 3.89x10^-8) were significantly associated with midlife aβ₄₂ levels through cross-race meta-analysis; the <i>KLKB1</i> variant replicated internally using 1,014 additional participants with exome chip. <i>ITPRIP</i>, <i>PLIN2</i>, and <i>TSPAN18</i> were associated with the midlife aβ₄₂:aβ₄₀ ratio via the T5 test; <i>TSPAN18</i> was significant via the cross-race meta-analysis, whereas <i>ITPRIP</i> and <i>PLIN2</i> were European American-specific. <i>NCOA1</i> and <i>NT5C3B</i> 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).</p><p>Conclusion</p><p>We discovered age-dependent genetic effects, established associations between vascular-related genes (<i>KLKB1</i>, <i>F12</i>, <i>PLIN2</i>) and midlife plasma aβ levels, and identified a plausible Alzheimer’s Disease candidate gene (<i>ITPRIP</i>) influencing cell death. Plasma aβ concentrations may have dynamic biological determinants across the lifespan; plasma aβ study designs or analyses must consider age.</p></div

Descriptive statistics of sequenced ARIC participants.

<p>Descriptive statistics of sequenced ARIC participants.</p

Significant gene-based (T5 and SKAT) results.

<p>Significant gene-based (T5 and SKAT) results.</p

Variants contributing to the significant T5 gene-based tests.

<p>This figure depicts the single-variant model results for variants contributing to the T5 tests of <i>ITPRIP</i>, <i>PLIN2</i>, and <i>TSPAN18</i> on the third visit aβ₄₂: aβ₄₀ ratio. One isoform was drawn unless the regions harboring variants differed substantially. Each contributing variant is labeled by name, single-variant association p-value, and direction of the minor allele effect (in parentheses). Variants with nominal (p<0.05) levels of association are in red. Overlapping variants in the two racial groups are encapsulated by a red box.</p

Effects of carrying a minor allele in <i>TSPAN18</i>, <i>ITPRIP</i>, and <i>PLIN2</i> on the third visit aβ₄₂: aβ₄₀ ratio in EAs.

<p>The plotted values are the inverse normal transformed ratios adjusted for age, gender, and <i>APOE ε</i>4 carriage status.</p

Significant single-variant results.

<p>Significant single-variant results.</p

Variants contributing to the significant SKAT gene-based tests.

<p>This figure displays the single-variant model results for variants contributing to the SKAT tests of <i>NCOA1</i> and <i>NT5C3B</i> on the third visit aβ₄₂: aβ₄₀ ratio and fold-change in aβ_42, respectively. One isoform was drawn unless the regions harboring variants differed substantially. Each contributing variant is labeled by name, single-variant association p-value, and direction of the minor allele effect. Variants with nominal (p<0.05) levels of association are in red. Overlapping variants in the two racial groups are encapsulated by a red box.</p

<i>KLKB1</i> and <i>F12</i> single-variant associations in ARIC participants with exome sequence.

<p> Panel A shows boxplots of the third visit aβ₄₂ levels and the fold-changes in aβ₄₂ stratified by the rs3733402 genotype in EAs. Panel B depicts the relative frequencies of the rs1801020 genotypes within each aβ₄₂ (visit 3) tertile in AAs and EAs. The plotted values are inverse normal transformed amyloid values adjusted for age, gender, time between visits (fold-change aβ₄₂ only), and <i>APOE</i> ε4 carriage status.</p

Additional file 1 of Multi-omics and pathway analyses of genome-wide associations implicate regulation and immunity in verbal declarative memory performance

Additional file 1: Supplemental Text. Table S1. Sample size and the number of SNPs in the paragraph delayed recall GWAS from each discovery and replication cohort. Table S2. Sample size and the number of SNPs in the word list delayed recall GWAS from each discovery and replication cohort. Table S3. Tissue-specific relationships between delayed recall test (PAR-dr and WL-dr) summary SNP associations and eQTLs and meQTLs. Table S4. Relationship Between Delayed Recall Summary Gene Associations and Transcription Factor Genes. Table S5. Significant Genes Associated with Paragraph Delayed Recall (PAR-dr) and Word List Delayed Recall (WL-dr). Table S6. Significant component genes in the six memory-associated pathways. Table S7. Homologous genes in memory-associated pathways for differential expression analysis. Figure S1. GWAS cohorts and microarray expression datasets. Figure S2. Design of the pathway analyses. Figure S3. Forest plots of significant pathway enrichment effects and p-values from discovery cohorts (Approach 1)

Age-dependent BMI loci.

<p>Effect estimates (beta ±95CI) per standard deviation in BMI and risk allele for loci showing age-differences in men & women ≤50y compared to men & women >50y. Loci are ordered by greater magnitude of effect in men & women ≤50y compared to men & women >50y. (95%CI: 95% confidence interval; BMI: body mass index; SD: standard deviation, *Newly identified loci).</p