Association of SPI1 Haplotypes with Altered SPI1 Gene Expression and Alzheimer's Disease Risk

Abstract

Background: Genetic studies reveal that single-nucleotide polymorphisms (SNPs) of SPI1 are associated with Alzheimer's disease (AD), while their effects in the Chinese population remain unclear.

Objective: We aimed to examine the AD-association of SPI1 SNPs in the Chinese population and investigate the underlying mechanisms of these SNPs in modulating AD risk.

Methods: We conducted a genetic analysis of three SPI1 SNPs (i.e., rs1057233, rs3740688, and rs78245530) in a Chinese cohort (n = 333 patients with AD, n = 721 normal controls). We also probed public European-descent AD cohorts and gene expression datasets to investigate the putative functions of those SNPs.

Results: We showed that SPI1 SNP rs3740688 is significantly associated with AD in the Chinese population (odds ratio [OR] = 0.72 [0.58-0.89]) and identified AD-protective SPI1 haplotypes β (tagged by rs1057233 and rs3740688) and γ (tagged by rs3740688 and rs78245530). Specifically, haplotypes β and γ are associated with decreased SPI1 gene expression level in the blood and brain tissues, respectively. The regulatory roles of these haplotypes are potentially mediated by changes in miRNA binding and the epigenetic landscape. Our results suggest that the AD-protective SPI1 haplotypes regulate pathways involved in immune and neuronal functions.

Conclusion: This study is the first to report a significant association of SPI1 with AD in the Chinese population. It also identifies SPI1 haplotypes that are associated with SPI1 gene expression and decreased AD risk.

Keywords: Alzheimer’s disease; SPI1; genetics; haplotype analysis; transcriptome.

Fig. 1

Identification of Alzheimer’s disease-protective SPI1 haplotypes. a) Linkage disequilibrium plot and haplotypes identified in the Hong Kong Chinese Alzheimer’s disease (AD) cohort. Cell color and labeled numbers in the upper and lower panels represent D’ and Pearson’s correlation coefficients (r²) between single-nucleotide polymorphisms (SNPs), respectively. Letters in upper and lower case denote major and minor alleles, respectively. b) AD-protective effects of the identified haplotypes in populations of Chinese and European descent. Dot size and filled color represent – log10(P) and Beta, respectively. ^**p < 0.01, ^*p < 0.05. c) Associations between haplotype γ and age of AD onset in APOE33 participants from the Late Onset Alzheimer’s Disease (LOAD) cohort. d) Associations between haplotype γ and Mini–Mental State Examination (MMSE) score in APOE33 participants from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset. ^**p < 0.01. CHN, Chinese; EUR, European descent; HR, hazard ratio.

Fig. 2

Effects of SPI1 haplotypes on the regulation of SPI1 transcript level. a–c) Associations between SPI1 haplotypes and SPI1 transcript level in (a) the cortex, (b) monocytes, and (c) macrophages from APOE33 donors. Rectangles and error bars denote the effect size and standard error, respectively. ^***p < 0.001, ^**p < 0.01, ^*p < 0.05. d) Epigenetic modification of the SNP-harboring region for the SPI1 haplotypes’ tag SNPs. Panels from top to bottom are the gene structure and coordinates of SPI1. Boxes and lines denote exons and introns, respectively. Red and yellow bars represent candidate cis-regulatory elements (ccREs) with high H3K4me3 and H3K27ac signals, respectively. Signals of DNase sequencing (DNase-seq), H3K4me3 chromatin immunoprecipitation sequencing (ChIP-seq), and H3K27ac ChIP-seq in the cerebral cortex. Signals of single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) in the cerebral cortex. Signals of DNase-seq, H3K4me3 ChIP-seq, and H3K27ac ChIP-seq in blood mononuclear cells. Please refer to Supplementary Figure 2 for all available biological replicates. Astro, astrocyte. ExN, excitatory neuron; InN, Inhibitory neuron; Micro, microglia; Oligo, oligodendrocyte; OPC, oligodendrocyte progenitor cell.

Fig. 3

Associations between haplotype γ and transcriptomic changes in the cerebral cortex in APOE33 donors. a) Volcano plot showing the associations between haplotype γ and cortical gene expression. b) Gene Ontology analysis of genes modulated by haplotype γ in the cerebral cortex. c) Protein–protein interaction network of genes involved in immune and neuronal functions. Nodes and edges denote genes and their interactions. Node shapes represent the ontology of corresponding genes. Node colors denote the effect size of haplotype γ on transcript level.