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Epigenetic Dysregulation of Enhancers in Neurons Drive Alzheimer's Disease, Study Finds

Article In Brief

Investigators found that the brains of people with Alzheimer's show a progressive loss of important epigenetic marks on enhancers, which regulate gene expression, and the loss is accelerated making their brain cells act older than they are and leaving them vulnerable to the disease.

A team of scientists from Van Andel Research Institute (VARI) in Michigan has identified abnormal epigenetic activity in neurons from patients who died and had mild-to-severe Alzheimer's disease (AD).

[Epigenetics involve events that regulate gene expression, which can include age, environment/lifestyle, and disease states. These events can activate gene expression or silence it, and this impacts the function of cells.]

The novel finding in the current study, published in Nature Communications on May 21, suggests that AD could be stalled by targeting specific epigenetic enhancers that regulate gene expression. The scientists discovered that some of these epigenetic changes were apparent very early on, before AD pathology emerged in neurons, and that patients with severe AD pathology had the most epigenetic changes in their neurons.

Epigenetic signals change with age, which led the Michigan scientists to question whether these changes were associated with the most significant risk factor in Alzheimer's: old age.

Figure

Proposed model displaying the contribution of enhancer dysregulation to the development and progression of AD. In aging, neurons gradually lose CpH methylation at enhancers, especially at enhancers regulating genes involved in the early cell cycle. Aging and other AD risk factors that trigger improper attempts of neurons to enter the cell cycle promotes the formation of neurofibrillary tangles in the AD brain and is neurotoxic. In AD neurons there is also a hypomethylation of enhancers in DSCAML1 that occurs early in disease. Enhancers in DSCAML1 activate BACE1 expression, which leads to the increased production of the amyloid-beta peptides. Amyloid-beta peptides promote an accelerated loss of DNA methylation at enhancers in AD neurons, thereby facilitating aberrant cell cycle reactivation. Amyloid-beta peptides also form plaques, which fuels the spread of neurofibrillary tangle pathology across the brain. Consequently, epigenetic changes at enhancers in AD neurons contributes to the pathology, neurodegeneration, and cognitive symptoms of AD.

“Scientists have had a very gene-centric view of disease,” said the senior author of the study, Viviane Labrie, PhD, an assistant professor at VARI. “But we are now learning a lot about elements outside of the genes that fine-tune what is going on inside the DNA sequence.”

The investigative team examined epigenetic marks at enhancers in AD neurons. Enhancers, which sit outside of the genes, work like a volume dial to turn up or turn down how much protein is made by specific genes. Epigenetic marks control the activity of enhancers by regulating access to DNA. Environmental factors and aging alter the levels of epigenetic marks, which in turn can affect the function of these enhancers, explained Dr. Labrie. She and her colleagues hope that their discoveries can be used to develop new prevention and treatment strategies for AD.

Study Design, Findings

To explore these research questions, the scientists turned to two federal databases: the Roadmap Epigenomics Project and Encyclopedia of DNA Elements or ENCODE. The datasets were built by a public research consortium with the charge of identifying all of the functional elements in the mouse and human genome.

Dr. Labrie and her colleagues looked at 30,000 enhancers that are present in neurons in the brain to determine whether there were differences in the normal aging brain and the brains of people with mild, moderate, or severe AD. First, they mapped out the expression of the genes in the neurons, and then they observed what happens to a neuron as it moves from a healthy state to a diseased one.

They used a fine-mapping technique to look at DNA methylation of neuronal enhancers across the genome. They measured the amount of DNA methylation, which provides a readout of whether the enhancers are on or off. They also analyzed 3-dimensional DNA maps so they can see the interactions between genes and their enhancers. This helped them identify gene targets affected in AD.

Two very important findings emerged: there was a widespread overactivation of many enhancers in the neurons from AD brains. And there was a significant loss of DNA methylation, which is necessary to silence enhancers. Many of these enhancers were kicking into activation, affecting the cell division cycle.

Reactivation of the cell cycle is a toxic event in the life of a neuron that doesn't divide. They also observed a dysregulation of genes involved in the formation of amyloid plaques and related to the progression of tau pathology, which coincided with the reactivation of cell division processes. In other words, they were able to model events that explain three primary theories of what triggers AD: the accumulation of amyloid plaques, tau tangles, and cell cycle reactivation. This study links all three events to the progression of AD.

The research team identified 1,224 enhancer regions with altered DNA methylation in the prefrontal cortical neurons from 101 individual autopsy samples of patients with mild, moderate, or severe pathology. Many neurons were from people who died with no evidence of AD pathology.

There are two primary locations for DNA methylation in the DNA of neurons: the CpG and CpH sites. Most of the 1,224 hypomethylated enhancers were at the CpH sites in AD neurons. (CpH methylation is abundant only in neurons and in embryonic stem cells.)

Figure

“Taken together, enhancer abnormalities that promote plaques, tangles, and cell cycle reactivation appear to be paving the way for brain cell death in Alzheimers disease.”—DR. VIVIANE LABRIE

The researchers observed age-related CpH methylation in the normal brain, but it seemed highly accelerated in the aging brain with signs of AD pathology.

“Accelerated aging in neurons of AD patients could contribute to the disease process,” Dr. Labrie said.

The investigators then merged epigenetic and gene expression data, and that is when they could see pro-apoptotic reactivation of the cell cycle. Many of the enhancers that were off-kilter were regulating genes involved in the cell cycle and in the formation of toxic amyloid-beta plaques. The strongest changes that occurred were at the enhancers of BACE-1, a gene that plays a pivotal role in the accumulation of plaques. These molecular events occur early on, before the pathological or clinical signs of the disease emerged.

The group had access to data from Rush University Medical Center's longitudinal Alzheimer's study. They were able to use information—patient's medical histories, brain scans, and neuropsychological tests, and finally their autopsy material—to link the changes to how patients were progressing.

Many of the epigenetic changes were also associated with the rate of cognitive decline, suggesting that these changes could influence AD symptom progression.

“The enhancer changes we found also encourage the development of plaques, which act as gasoline for the spread of toxic tangles, propagating them through the brain like wildfire. Taken together, enhancer abnormalities that promote plaques, tangles, and cell cycle reactivation appear to be paving the way for brain cell death in Alzheimer's disease,” Dr. Labrie said.

The researchers are now working on designing systems to screen compounds to target enhancers.

Expert Commentary

“The epigenome may mediate the effect of life experiences and exposures that contribute to neurodegenerative and other diseases,” said Philip De Jager, MD, PhD, chief of the division of neuroimmunology at Columbia University Medical Center, who studies the epigenome.

“We are still in the early stages in understanding epigenetic effects and its importance in disease,” he added. “This group has shown that the genome is differentially methylated in response to Alzheimer's and have linked the genes to the location that is important in the disease.”

David A. Bennett, MD, director of the Rush Alzheimer's Disease Center and the Robert C. Borwell professor of neurological sciences at Rush University Medical Center, has also done a lot of work on the epigenome and collaborates with Dr. De Jager. They have reported many epigenomic differences in people with AD compared with older people without dementia.

“This is additional strong evidence for the field that DNA methylation is important for aging and Alzheimer's disease,” he said.

These are the early days of research, he said, adding that he hopes that the scientists examine different cell types. “There are a lot of important cell types in AD other than neurons. Also, methylation is one of a whole suite of epigenomic markers that need to be studied. Methylation does not work alone to control transcription.”

“This is a very interesting and well-executed study that highlights the relevance of epigenetics, and specifically changes in DNA methylation, in Alzheimer's disease etiopathogenesis,” added Ottavio Arancio, PhD, MD, director of the laboratory in neurophysiology and behavior of Taub Institute, also at Columbia University.

“DNA methylation is an under-investigated area of research that deserves more attention by the Alzheimer's disease research community. The investigators have unraveled dysregulation of enhancers in neurons at early stages of disease pathology. This is important because most of the studies in the field have been focused on the classical hallmarks of the disease, amyloid plaques, neurofibrillary tangles, and neuronal death. The study emphasized events occurring upstream of such classical hallmarks. The many failures in clinical trials against this devastating disorder beg for a change of strategy in the field, and early epigenetic changes offer the possibility of moving out of the classical disease hallmarks.”

Disclosures

Drs. Labrie, Bennett, and De Jagger reported no conflicts.

The Science Explained

WHAT IT IS

Epigenetics involve events—age, environment, lifestyle and disease states— that regulate gene expression. These events can activate gene expression or silence it and it impacts the function of cells.

HOW IT WORKS

One of the most common epigenetic processes is methylation. Proteins can't attach to activate genes if there are methyl groups blocking their entrance. There are other epigenetic processes such as chromatin modification, which can also alter gene expression.

HOW IT IS APPLIED

Scientists now understand that epigenetic events are critically important in understanding what is going wrong with cells and how it is impacting individuals. The field of epigenetics is rapidly expanding and scientists believe that the findings may be able to give rise to a richer understanding of these processes and to the development of new treatment targets.

Link Up for More Information

• Li P, Marshall L, Oh G, et al. Epigenetic dysregulation of enhancers in neuronsis associated with Alzheimer's disease pathology and cognitive symptoms https://www.nature.com/articles/s41467-019-10101-7. Nature Commun 2019;10 (1): 2246.
    • De Jager PL, Srivastava G, Bennett D. Alzheimer's disease: Early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci https://www.nature.com/articles/nn.3786. Nature Neurosci 2014; 17:1156–1163.
      • Lunnon K, Smith R, Hannon E, et al. Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease https://www.nature.com/articles/nn.3782. Nature Neurosci 2014;17:1164–1170.