In recent years, genome-wide association studies (GWAS) have identified 28 genomic regions that associate with risk for late-onset Alzheimer’s disease. Most of these hits are in non-coding regions, leaving scientists wondering how they influence disease. Now, researchers led by David Bennett, Rush University Medical Center, Chicago, report specific DNA methylation patterns in five of these loci in people who died with pathological AD. The postmortem analysis was published in the November 3 JAMA Neurology online. “These data clearly reinforce the implication that these five loci are involved in AD,” Jean-Charles Lambert, a geneticist at INSERM, Lille, France, wrote to Alzforum in an email. Lambert was not involved in the study. Though the results need to be replicated, this type of data might ultimately help determine which genes are responsible for GWAS signals, he wrote.
In DNA, methyl groups are added to cytosine (C) bases, often ones that lie next to a guanine (G) at a CpG site. The modification generally silences transcription, though sometimes it enhances it. Recently, Bennett’s group reported that methylation changes at 71 CpG sites across the genome tracked with amyloid plaque burden in postmortem brains (see Aug 2014 news story). In general, greater methylation accompanied more plaques. Interestingly, CpGs from the ABCA7 and BIN1 regions—which contain reported AD-risk variants—were among those found. The researchers wondered if other AD risk genes are abnormally methylated as well.
First author Lei Yu and colleagues analyzed tissue samples of 740 brain donors from the Religious Orders Study and the Rush Memory and Aging Project. On average, people were 88 years old when they died. Aβ plaque and tau pathology in 447 justified a pathological diagnosis of Alzheimer’s. The researchers extracted DNA from the gray matter in the dorsolateral prefrontal cortex—which includes neurons, microglia, endothelial cells, and other cell types. Using a commercial methylation array, Yu determined which of 500 or so sites within 100 kilobases of the AD-linked loci sported a methyl group.
The researchers first looked to see whether differences in methylation of CpGs in those loci associated with a diagnosis of AD. At each of five loci—SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1—between two and 19 sites significantly correlated with disease. For the most part, more methylation correlated with a higher risk of AD. Next, the researchers asked if there was any relationship between methylation and plaques and tangles. Overall methylation in the five loci varied both with Aβ load and density of tau tangles, though not necessarily at the same nucleotides. To find out whether and how these changes in methylation translated to altered gene transcription, they looked at the level of mRNAs for each gene in the brain extracts. For most, transcription was correlated weakly, if at all.
The study is unique in that it combines knowledge about genetic influences on Alzheimer’s with methylation data to begin to nail down some of the key suspects’ pathology, said Marilyn Miller, National Institute on Aging, Bethesda, Maryland. “It’s pretty clear from these data that the disruption of methylation is a part of the pathology of Alzheimer’s disease,” she told Alzforum.
The findings do not totally mesh with GWAS data. In several cases, the methylation site that associated with AD pathology lay near, but not in, a gene implicated by GWAS. That was true for sites near HLA-DRB5, ABCA7, and BIN1. This finding fits with the idea that GWAS just approximate the area of the genome associated with disease, said Bennett. Further studies can help pinpoint the exact genes responsible he said. Co-author Philip De Jager, Brigham and Women’s Hospital, Boston, emphasized that these methylation effects occur independently of the previously reported AD-associated SNPs. The group disregarded CpGs in those SNPs to avoid technical artifacts in the data.
Taken together, the results suggest that altered methylation plays a role in Alzheimer’s disease, said Bennett. Since only some loci experience changes, the epigenome appears to affect AD in specific and complex ways, the authors wrote. An accompanying editorial by Bryan Traynor and Alan Renton, National Institute on Aging, praised the work, saying it provided compelling evidence implicating DNA methylation in the pathogenesis of Alzheimer’s. However, they wondered about causality. Since Yu and colleagues examined postmortem brains, methylation changes might have accumulated during disease, rather than initiating it. Bennett agreed that issue remains unresolved, but noted their previous study found that the methylation changes, including those in ABCA7 and BIN1, correlated with neuritic plaque burden in people who remained cognitively normal. That the new methylation hits lie near previously identified GWAS polymorphisms implies that they could drive disease, added De Jager.
Methylation usually alters gene transcription, so why did the methylation patterns that associated with AD have little to no impact on RNA expression? The researchers are unsure, but suspect that RNA degradation in the postmortem sample may have led to spurious results. In addition, many other factors, such as histone modification, feedback regulation, and microRNAs, contribute to levels of gene expression, said Bennett. Methylation is just one small piece of that puzzle. In future studies, he aims to figure out how methylation fits into the bigger picture of RNA expression by testing how other factors affect transcription.
Traynor and Renton also point out that the researchers were examining methylation in cells that had survived until the patient died. For that reason, their methylation status may not represent that of the cells that succumbed. Bennett agreed, and said future research will have to sort that out.—Gwyneth Dickey Zakaib
- Chang L, Wang Y, Ji H, Dai D, Xu X, Jiang D, Hong Q, Ye H, Zhang X, Zhou X, Liu Y, Li J, Chen Z, Li Y, Zhou D, Zhuo R, Zhang Y, Yin H, Mao C, Duan S, Wang Q. Elevation of peripheral BDNF promoter methylation links to the risk of Alzheimer's disease. PLoS One. 2014;9(11):e110773. Epub 2014 Nov 3 PubMed.
- Li L, Zhang C, Zi X, Tu Q, Guo K. Epigenetic modulation of Cdk5 contributes to memory deficiency induced by amyloid fibrils. Exp Brain Res. 2015 Jan;233(1):165-73. Epub 2014 Sep 19 PubMed.
- Wood H. Alzheimer disease: AD-susceptible brain regions exhibit altered DNA methylation. Nat Rev Neurol. 2014 Oct;10(10):548. Epub 2014 Sep 2 PubMed.
- Piaceri I, Raspanti B, Tedde A, Bagnoli S, Sorbi S, Nacmias B. Epigenetic modifications in Alzheimer's disease: cause or effect?. J Alzheimers Dis. 2015;43(4):1169-73. PubMed.
- Lim AS, Srivastava GP, Yu L, Chibnik LB, Xu J, Buchman AS, Schneider JA, Myers AJ, Bennett DA, De Jager PL. 24-hour rhythms of DNA methylation and their relation with rhythms of RNA expression in the human dorsolateral prefrontal cortex. PLoS Genet. 2014 Nov;10(11):e1004792. Epub 2014 Nov 6 PubMed.
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- Yu L, Chibnik LB, Srivastava GP, Pochet N, Yang J, Xu J, Kozubek J, Obholzer N, Leurgans SE, Schneider JA, Meissner A, De Jager PL, Bennett DA. Association of Brain DNA methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 with pathological diagnosis of Alzheimer disease. JAMA Neurol. 2015 Jan;72(1):15-24. PubMed.
- Traynor BJ, Renton AE. Exploring the epigenetics of Alzheimer disease. JAMA Neurol. 2015 Jan;72(1):8-9. PubMed.