Identification of a specific APOE transcript and functional elements associated with Alzheimer's disease

Abstract

Background: The APOE gene is the strongest genetic risk factor for late-onset Alzheimer's Disease (LOAD). However, the gene regulatory mechanisms at this locus remain incompletely characterized.

Methods: To identify novel AD-linked functional elements within the APOE locus, we integrated SNP variants with multi-omics data from human postmortem brains including 2,179 RNA-seq samples from 3 brain regions and two ancestries (European and African), 667 DNA methylation samples, and ChIP-seq samples. Additionally, we plotted the expression trajectory of APOE transcripts in human brains during development.

Results: We identified an AD-linked APOE transcript (jxn1.2.2) particularly observed in the dorsolateral prefrontal cortex (DLPFC). The APOE jxn1.2.2 transcript is associated with brain neuropathological features, cognitive impairment, and the presence of the APOE4 allele in DLPFC. We prioritized two independent functional SNPs (rs157580 and rs439401) significantly associated with jxn1.2.2 transcript abundance and DNA methylation levels. These SNPs are located within active chromatin regions and affect brain-related transcription factor-binding affinities. The two SNPs shared effects on the jxn1.2.2 transcript between European and African ethnic groups.

Conclusion: The novel APOE functional elements provide potential therapeutic targets with mechanistic insight into the disease etiology.

Keywords: APOE; Alzheimer’s disease; Postmortem brain; SNP; Transcript.

Fig. 1

Overview of APOE study in human postmortem brain (A) and novel AD risk factors (genetic, transcriptomic, and epigenetic elements) and their relative position at the APOE locus (B). Brain collection: ROSMAP, The Religious Orders Study and the Memory and Aging Project; LIBD, Lieber Institute for Brain Development. Ancestry: EA, European Ancestry; AA, African American. Brain region: DLPFC, dorsolateral prefrontal cortex; PCC, posterior cingulate cortex; AC, anterior cingulate cortex. Green boxes represent exons; blue boxes represent untranslated regions (UTRs); Me represents methylation site; peaks represent active chromatin regions; 3 solid blue lines represent genomic DNA

Fig. 2

APOE jxn1.2.2 transcript is associated with Alzheimer’s disease (AD). A jxn1.2.2 expression (red) is the top hit compared to other transcripts at the APOE locus (blue) in the ROSMAP brain DLPFC region. The association of AD risk SNP, rs157580, with APOE gene level and its 3 transcripts (jxn1.2.1, jxn1.2.2, and jxn1.2.3) in ROSMAP considering global ancestry (B). Association of jxn1.2.2 and AD risk SNP in LIBD European ancestry (C) and African American (D). E Local ancestry analysis at the APOE locus

Fig. 3

Differential expression of APOE at gene level and transcripts level. A Differential expression of APOE exon-exon junctions across different diagnosis criteria among diverse ethnic groups (European ancestry [EA] and African ancestry [AA]). BP, bipolar disorders; SZ, schizophrenia; MDD, major depression disorders. The dashed line indicates the threshold of p-value = 0.05. Bigger red dots are jxn1.2.2. B Differential analysis of APOE at gene and junction level between AD and controls in BRAAK diagnosis. Differential analysis of jxn1.2.2 transcript in CERAD diagnosis (C), APOE4 carriers vs. non-carriers (D). E APOE gene and transcripts expression during brain development in brain DLPFC region in European ancestry. F APOE gene and transcripts expression during brain development in brain DLPFC region in African American ancestry

Fig. 4

Genotypic impact of candidate SNPs on DNA methylation levels in ROSMAP DLPFC. A Association of the candidate AD risk SNPs with CpG sites. B The association of the AD-linked CpGs is not affected by the APOE 2&4 allele by conditional analysis

Fig. 5

Candidate SNPs at the APOE locus located within active chromatin affect transcriptional factors (TFs)’ binding affinity. Left panel: (A) rs439401, (B) rs1871046, and (C) rs157580 are co-localized with H3K9ac ChIP-seq peak from human postmortem brains. Right panel: Recognition sites of TFs involved in Alzheimer’s disease are influenced by the 3 SNPs. The red dash box indicates the binding site of each SNP. D Linkage disequilibrium of candidate SNPs with other SNPs spanning APOE, including the two APOE2,3,4-determining SNPs