Genome-wide association and multi-omics studies identify MGMT as a novel risk gene for Alzheimer's disease among women

Abstract

Introduction: Variants in the tau gene (MAPT) region are associated with breast cancer in women and Alzheimer's disease (AD) among persons lacking apolipoprotein E ε4 (ε4-).

Methods: To identify novel genes associated with tau-related pathology, we conducted two genome-wide association studies (GWAS) for AD, one among 10,340 ε4- women in the Alzheimer's Disease Genetics Consortium (ADGC) and another in 31 members (22 women) of a consanguineous Hutterite kindred.

Results: We identified novel associations of AD with MGMT variants in the ADGC (rs12775171, odds ratio [OR] = 1.4, P = 4.9 × 10^-8) and Hutterite (rs12256016 and rs2803456, OR = 2.0, P = 1.9 × 10^-14) datasets. Multi-omics analyses showed that the most significant and largest number of associations among the single nucleotide polymorphisms (SNPs), DNA-methylated CpGs, MGMT expression, and AD-related neuropathological traits were observed among women. Furthermore, promoter capture Hi-C analyses revealed long-range interactions of the MGMT promoter with MGMT SNPs and CpG sites.

Discussion: These findings suggest that epigenetically regulated MGMT expression is involved in AD pathogenesis, especially in women.

Keywords: MGMT; gene expression; genome‐wide association study; methylation; tau.

Figure 1.

Minimum pedigree linking the five cases (shown as filled black symbols) in the Hutterites. APOE genotypes are shown below each case and the kinship coefficient of the parents are shown over the double horizontal bars connecting the parents of each case (equivalent to the inbreeding coefficient of each case). The double horizontal bars indicate that the marriage was consanguineous. The minimum pedigree includes only those relatives needed to connect the five cases in the minimum number of steps.

Figure 2.

Genetic association of Alzheimer disease (AD) with MGMT in the ADGC datasets (A and B) and in the Hutterites (C). A. Locus-zoom plot showing the association of AD with SNPs in the MGMT region in the ADGC datasets. The SNP with the lowest P-value (rs12775171) is indicated with a purple diamond. Computed estimates of linkage disequilibrium (r²) of SNPs in this region with rs1277517 are color-coded according to the key. B. Forest plot of the association of AD with rs12775171 among the APOE ε4- women within each ADGC dataset and in the toal sample (META). The ADGC-8 dataset includes eight individual GWAS datasets (ACT2, BIOCARD, CHAP2, EAS, NBB, RMAYO, UKS, and WASHU2) each containing < 50 subjects. The odds ratio (shaded symbol) and 95% confidence interval (represented by horizontal line) are plotted on the x-axis. C. Locus-zoom plot showing the association of AD with SNPs in the MGMT region in the Hutterites. Significance level is shown as the -log₁₀(p-value). Computed estimates of linkage disequilibrium (r²) of SNPs in this region with the two most significant SNPs, rs12256016 (left panel) and rs2803456 (right panel), are color-coded according to the key. Recombination rates among adjacent SNPs are indicated with vertical blue lines.

Figure 2.

Genetic association of Alzheimer disease (AD) with MGMT in the ADGC datasets (A and B) and in the Hutterites (C). A. Locus-zoom plot showing the association of AD with SNPs in the MGMT region in the ADGC datasets. The SNP with the lowest P-value (rs12775171) is indicated with a purple diamond. Computed estimates of linkage disequilibrium (r²) of SNPs in this region with rs1277517 are color-coded according to the key. B. Forest plot of the association of AD with rs12775171 among the APOE ε4- women within each ADGC dataset and in the toal sample (META). The ADGC-8 dataset includes eight individual GWAS datasets (ACT2, BIOCARD, CHAP2, EAS, NBB, RMAYO, UKS, and WASHU2) each containing < 50 subjects. The odds ratio (shaded symbol) and 95% confidence interval (represented by horizontal line) are plotted on the x-axis. C. Locus-zoom plot showing the association of AD with SNPs in the MGMT region in the Hutterites. Significance level is shown as the -log₁₀(p-value). Computed estimates of linkage disequilibrium (r²) of SNPs in this region with the two most significant SNPs, rs12256016 (left panel) and rs2803456 (right panel), are color-coded according to the key. Recombination rates among adjacent SNPs are indicated with vertical blue lines.

Figure 2.

Genetic association of Alzheimer disease (AD) with MGMT in the ADGC datasets (A and B) and in the Hutterites (C). A. Locus-zoom plot showing the association of AD with SNPs in the MGMT region in the ADGC datasets. The SNP with the lowest P-value (rs12775171) is indicated with a purple diamond. Computed estimates of linkage disequilibrium (r²) of SNPs in this region with rs1277517 are color-coded according to the key. B. Forest plot of the association of AD with rs12775171 among the APOE ε4- women within each ADGC dataset and in the toal sample (META). The ADGC-8 dataset includes eight individual GWAS datasets (ACT2, BIOCARD, CHAP2, EAS, NBB, RMAYO, UKS, and WASHU2) each containing < 50 subjects. The odds ratio (shaded symbol) and 95% confidence interval (represented by horizontal line) are plotted on the x-axis. C. Locus-zoom plot showing the association of AD with SNPs in the MGMT region in the Hutterites. Significance level is shown as the -log₁₀(p-value). Computed estimates of linkage disequilibrium (r²) of SNPs in this region with the two most significant SNPs, rs12256016 (left panel) and rs2803456 (right panel), are color-coded according to the key. Recombination rates among adjacent SNPs are indicated with vertical blue lines.

Figure 3.

Association summary statistics among Omics data including MGMT SNPs (or their proxies) significantly associated with AD risk in the ADGC (colored in red) and Hutterite (colored in green or blue) datasets, methylation of adjacent CpG sites, MGMT expression, and AD-related neuropathological traits in the total ROSMAP sample, as well as in subgroups stratified sex and APOE ε4 carrier status (ε4+ or ε4-). Only significant results are shown. Rs11596752 and rs11016864 are proxy SNPs for rs2803456 and rs12256016 (LD r² > 0.8). CpG IDs are serially numbered 1–5 based on their base pair positions: cg07646467 (CpG1), cg09450835 (CpG2), cg02634492 (CpG3), cg05596517 (CpG4), and cg01419164 (CpG5). Red and blue arrows indicate positive and negative effect directions, respectively. Dashed black arrows signify inferred relationships based on the pcHi-C results assuming DNA containing AD-associated alleles render the chromatin to be less accessible leading to reduced MGMT expression.

Figure 4.

Regulatory landscape of MGMT locus. A. Chromatin looping interactions emanating from the MGMT and EBF3 promoters in human iPSCs-derived neurons at three stages of differentiation. PCHi-C interactions are displayed as gray arcs. Interactions between MGMT and EBF3 promoters with SNPs are represented by arcs highlighted in blue (Hutterites) and orange (ADGC). Green arcs highlight interactions between MGMT and EBF3 promoters with CpGs. The yellow and green strip highlight the interaction with SNPs and CpGs, respectively. B. Magnified view of the MGMT locus with chromatin state annotations from the Roadmap Epigenomics Project (REP). Colored bars indicate chromatin state annotations from tissues profiled by the REP, including neuronal cells: neuronal progenitors (epigenome identifiers E007), brain anterior caudate (E068), and brain germinal matrix (E070); and non-neuronal cells: IMR90 fetal lung (E017), small intestine (E109), primary T-cells (E043 and E045), fetal heart (E083), and pancreatic islets (E087).