African origin haplotype protective for Alzheimer's disease in APOE ε4 carriers: exploring potential mechanisms

Abstract

APOEε4 is the strongest genetic risk factor for Alzheimer's disease (AD) with approximately 50% of AD patients carrying at least one APOEε4 allele. Our group identified a protective interaction between APOEε4 with the African-specific A allele of rs10423769, which reduces the AD risk effect of APOEε4 homozygotes by approximately 75%. The protective variant lies 2Mb from APOE in a region of segmental duplications (SD) of chromosome 19 containing a cluster of pregnancy specific beta-1 glycoprotein genes (PSGs) and a long non-coding RNA. Using both short and long read sequencing, we demonstrate that rs10423769_A allele lies within a unique single haplotype inside this region of segmental duplication. We identified the protective haplotype in all African ancestry populations studied, including both West and East Africans, suggesting the variant has an old origin. Long-read sequencing identified both structural and DNA methylation differences between the protective rs10423769_A allele and non-protective haplotypes. An expanded variable number tandem repeat (VNTR) containing multiple MEF2 family transcription factor binding motifs was found associated with the protective haplotype (p-value = 2.9e-10). These findings provide novel insights into the mechanisms of this African-origin protective variant for AD in APOEε4 carriers and supports the importance of including all ancestries in AD research.

Figure 1.

UCSC browser view of surrounding region of rs10423769_A alelle (marked by vertical red line). The annotation of segmental duplication includes all non-allelic intrachromosomal and interchromosomal alignments greater than 1 kb and with more than 90% of sequence identity, excluding common repeats or satellite sequences.

Figure 2.

Haplotype blocks identified in 1,962 individuals carrying at least one rs10423769_A allele using Haploview 4.2 and ADSP. Lines between blocks indicate co-occurrence of adjacent haplotypes in individuals with line thickness representing frequency of co-occurrence across individuals. Haplotype block frequencies are shown in the right of each block (≥ 0.05). Multiallelic D' is shown on the bottom of crossing areas, which represents the level of recombination between blocks. Blocks with D' > 0.8 were considered the same haplotype. Rs10423769 is marked by an orange box. The 21kb (chr19:43099521-43120243) minimum shared haplotype is marked by a red box and the 11 kb extended haplotype (chr19:43121359- 43132912) is marked by blue boxes.

Figure 3.

Population-specific frequency of the minimum shared haplotype harboring the rs10423769_A allele in 1000G. LD pruned haplotype across 10 blocks determined by Haploview are shown. Frequencies were calculated with the tool LDhap from LDlink web-based application.

Figure 4.

Read the coverage and map of the 21 kb minimum shared haplotype from two representative individuals homozygous for either the rs10423769_A or rs10423769_G alleles. The green star marker represents the rs10423769_A allele, and all other listed markers are in LD>0.95 with rs10423769_A. Colored lines represent IGV consensus SNPs: A, green; C, blue; T, red; G, orange.

Figure 5.

VNTR length correlation with rs10423769 haplotype (p-value = 2.944e-10).

Figure 6.

Motif analysis of the expanded VNTR allele associated with rs10423769_A. A. 29 bp Repetitive sequence identified by MEME Suite . B. MEF2 family of TF binding motifs with FIMO motif finding tool q-value ^,.

Figure 7.

Allele-specific differential methylation analysis in the rs10423769_A allele 21 kb minimum shared haplotype and surrounding region using 5 brain samples heterozygous for rs10423769. The dotted line indicates FDR <0.01. “Methylation diff” refers to the difference in mean methylation levels between the rs10423769_A and rs10423769_G haplotypes. “Methylation diff” is shown for DMP with FDR < 0.01.