Foundational Genetics

Find all genes that contribute to risk for or protection against Alzheimer’s disease; prioritize those with the greatest impact.

Alzheimer’s Genome Project™

Researchers: 
Funding year(s): 
2005 to 2016
Funding to date: 
$13,641,400

The goal of this project is to evaluate our new Alzheimer’s disease gene candidates for effects on Alzheimer’s pathology and related biological pathways, including APP processing, amyloid beta protein generation, tangle formation and cell death. These studies are being carried out as part of Phase II of the Alzheimer’s Genome Project (AGP) and entail functional analyses of the Alzheimer’s gene candidates identified in Phase I of the AGP. We have focused the Phase II studies on the novel Alzheimer’s genes known as ADAM10, ATXN1 and CD33, all identified in 2008 as part of Phase I of the AGP.

The functional studies, aimed at how these genes influence risk for Alzheimer’s, are carried out in both cell-based and animal models. We also have performed genetic follow-up and functional studies for AD-associated aberrations in the human genome, known as copy number variants (CNV). This has led to the identification of several CNVs in novel Alzheimer’s genes underlying the inheritance of cases of familial early-onset Alzheimer’s that were not explained by the known early-onset Alzheimer’s genes co-discovered by our lab in the 1980s and ’90s (amyloid precursor protein, presenilin 1 and presenilin 2).

The knowledge gained from how the newly identified Alzheimer’s genes (from Phase I) biologically increase or decrease risk for Alzheimer’s disease is being implemented to design new drug discovery efforts, also as part of Phase II of the AGP. Phase III of the AGP is being carried out parallel to Phase II and includes Whole Genome Sequencing of the human genomes of subjects from both early-onset and late-onset Alzheimer’s families. The goal of Phase III of the AGP is to identify all of the biologically relevant functional gene variants that influence risk for Alzheimer’s disease. Once identified, these gene variants will be analyzed using similar methods to those described here in Phase II of the AGP. A detailed description of Phase III of the AGP can be found in the section under “Whole Genome Sequencing of Alzheimer’s Disease Families.”

CIRCUITS: Production Center for Reference and Variation Gene-Regulatory Maps

Funding year(s): 
2016
Funding to date: 
$750,000

Alzheimer’s disease is a devastating neurodegenerative disorder, afflicting 1 in 3 dying seniors and costing $236 billion annually in the United States alone. Its prevalence is increasing rapidly in an aging population, and currently there is no cure. Recent genetic studies provide new hope for therapeutic avenues, but translating genetic results into therapeutics has been remarkably difficult, due primarily to the fact that most genetic mutations do not alter protein function directly, but instead affect the expression of nearby genes in subtle ways. Here, we seek to overcome this limitation by directly profiling the gene-regulatory differences in Alzheimer’s patients, to understand the cell types, regulatory regions, target genes and upstream regulators whose function is affected in disease. We profile epigenomic differences in Alzheimer’s disease across 600 individuals, we dissect the cell-type-specific action of these differences in neurons, astrocytes and microglial cells, and we map the detailed circuitry of brain regulatory regions across Alzheimer’s patients and controls. The resulting datasets will be released broadly to the scientific community, and also form the foundation for computational and experimental work by the Cure Alzheimer’s Fund’s CIRCUITS consortium, in order to translate the resulting datasets into mechanistic insights and new therapeutic avenues for Alzheimer’s.

CIRCUITS: Interpreting Alzheimer’s Disease-Associated Genetic Variation at Enhancer Regions

Funding year(s): 
2016
Funding to date: 
$189,610

Treating Alzheimer’s disease (AD) is one of the greatest challenges we face in the coming years; the disease has the potential to have an enormous impact on human health. Despite its importance, there still are no highly effective treatments for AD, due in large part to a limited understanding of the underlying disease mechanisms. Our laboratory, as a member of CIRCUITS (Consortium to Infer Regulatory Circuits and to Uncover Innovative Therapeutic Strategies), aims to make progress toward a cure using genomic approaches. Starting from recent insights into the genetic basis of Alzheimer’s disease, we will use a combination of machine learning and experimental techniques to systematically work toward the underlying biological processes, cell types, pathways and potential drug targets.

Regulation of Microglial Lysosome Acidification

Funding year(s): 
2016
Funding to date: 
$120,006

Microglia are the main immune cells of the central nervous system. They normally carry out diverse functions, including removal of dead cells and other debris from the brain. Under some circumstances they have been shown to degrade Alzheimer’s disease amyloid plaques in acidic organelles called lysosomes. We have shown that the acidity of microglial lysosomes is controlled by signaling processes, and that resting microglia in cell culture are ineffective at degrading amyloid because of poor lysosome acidification. In this project we will use modern optical imaging methods to measure the acidity of microglial lysosomes in living mice. We will test the hypothesis that mechanisms to regulate acidity that we have observed in cell culture also operate in vivo. Our goal is to manipulate these signaling processes to regulate degradation of amyloid plaques and inflammatory activation of microglia.

Search for Female-Specific Genetic Factors Contributing to Risk for Alzheimer’s Disease

Researchers: 
Funding year(s): 
2016
Funding to date: 
$375,000

This multidimensional investigation will seek to elucidate sex-linked factors that determine Alzheimer’s disease risk, age of onset and rate of progression, powerful information that would contribute to the pursuit of a cure for both sexes. Women make up more than two-thirds of the Alzheimer’s patient population, yet very little is known or understood about why this is the case or what it means about the disease’s mechanisms of action, risk factors and progression. Epidemiological evidence suggests that a woman at age 65 faces almost twice the risk of developing Alzheimer’s disease in her lifetime and nearly three times at age 75 than does a man of the same age, differences that are not explained by age of expected mortality alone. We propose to carry out a comprehensive, family-based association meta-analysis of all three AD family sample Whole Genome Sequencing (WGS) datasets separately for each sex, an important and novel investigation since virtually no AD genome-wide association study carried out to date has considered sex-based differences. More specifically, we also will calculate the overall genetic component explained by each of the >47 million single nucleotide variants (SNV) identified in the National Institute of Mental Health WGS project and proceed to estimate the genetic correlation/overlap between males and females. More specific appreciation of the factors that increase or decrease risk of disease, age of onset and rate of progression would benefit both sexes, yet the collection, analysis and publication of scientific data have not yet caught up to this recognized need. Common gender-specific lifestyles, X-linked genetic variants, female hormonal profiles over the lifecycle and other differences offer compelling subjects for investigation as contributing factors.

Impact of Inflammasome Deactivation on Alzheimer’s Disease

Funding year(s): 
2016
Funding to date: 
$75,000

This research proposal from the Dixit laboratory, which will be pursued in interdisciplinary collaboration with the lab of Dr. Rudy Tanzi at Massachusetts General Hospital (MGH), emanates from our original findings that NLRP3 inflammasome activation in microglia controls age-related inflammation in the central nervous system (CNS) and that CD33-dependent inhibition of amyloid-beta uptake by microglia reduces IL-1beta to protect against AD. Inflammasome is a high molecular weight protein complex that assembles in the cytosol of microglia and myeloid-lineage cells upon encounter with ‘damage-associated molecular patterns’ such as amyloids, lipotoxic fatty acids or extracellular ATP derived from necrotic cells. Upon assembly, this causes caspase-1 dependent release of pro-inflammatory cytokines IL-1beta, IL-18 and a special form of cell death called pyroptosis1.

Studies from our lab have identified that the NLRP3 inflammasome controls development of inflammation-associated degenerative diseases during aging. Consistent with our data, independent studies also have demonstrated the increased activation of NLRP3 inflammasome in AD in humans and that genetic loss of NLRP3 protects against dementia in APP/PS1 mouse model. Although it is established that inflammation plays a pivotal role in development of Alzheimer’s disease (AD), the therapeutic approaches that impact specific innate immune mechanisms in the microglia remain to be identified. Interestingly, our preliminary results show that a subset of elderly are protected from age-related inflammation and microglial activation despite the presence of amyloid-beta plaques. This implies there must be endogenous protective mechanisms that maintain homeostasis in aging by preventing the sensing of aberrant Abeta deposits in microglia resulting in reduced inflammatory damage. Therefore, the long-term goal of this proposal is to identify and harness anti-inflammasome regulators as therapeutic targets to prevent or treat AD.

This proposal is based on our discovery that ketone metabolite beta-hydroxybutyrate (BHB) and NLRP3 inflammasome constitutes an immunometabolic checkpoint of binary opposition—endogenous polar signals that work in concert to regulate the innate immune response. Ketone bodies, BHB and acetoacetate (AcAc) support mammalian survival during periods of starvation by serving as a source of ATP in tricarboxylic acid (TCA) cycle for brain function. Intriguingly, we have found that macrophages and microglia highly express the key ketogenic enzyme 3-Hydroxy-3-MethylGlutaryl-CoA Lyase (HMGCL). This suggests that microglia can produce ketone bodies and that local levels of BHB in brain may function as a regulatory metabolite that restrains the runaway inflammasome activation. In addition, this suggests that medium-chain triglycerides (MCTs), which can cross the blood-brain barrier, serve as substrates for production of BHB in microglia. Given MCTs are under investigation to lower AD severity, the mechanism of microglial-derived BHB as regulatory anti-inflammasome metabolite has high clinical impact. Thus, based on our findings, the central hypothesis of this project is that ketogenic substrate switch underlies the regulatory microglial responses that protects against AD by inhibition of CD33 and deactivation of the NLRP3 inflammasome. The corollary is that elevating CNS ketogenesis and BHB signaling may serve as an anti-inflammatory intervention against AD.

Focus Area(s): 

SORLA Attenuates Abeta Toxicity Through Interactions With EphA4

Researchers: 
Funding year(s): 
2016
Funding to date: 
$150,000

SORLA is a genetic risk factor in Alzheimer’s disease (AD), but it is unclear how changes in SORLA abundance can trigger the onset of AD in the elderly. So far, studies have shown that SORLA can limit the amount of neurotoxic Abeta generated in the brain. However, since high levels of Abeta also are seen in aged individuals without symptoms of dementia or cognitive decline, neuroprotective mechanisms are likely in place to protect neurons from Abeta damage. We describe here that SORLA can limit the activation of a cell surface component EphA4 that is activated in the presence of Abeta, and which can damage synaptic function in the brain. Our preliminary results indicate that SORLA overexpression can limit Abeta-dependent activation of EphA4 in response to normal EphA4 activators such as Ephrin ligands, and Abeta in cultured neurons. Our pilot experiments indicate that mouse models overexpressing SORLA are less prone to Abeta injected into the mouse hippocampus. Our study here will confirm whether SORLA can limit toxic signals from EphA4 in response to Abeta, and whether molecular strategies to enhance SORLA/EphA4 interactions can further protect neurons from synaptic damage from Abeta. Together, this study may provide insight into a new pathway to protect neurons from Abeta damage, which may lead to strategies to improve cognition in AD patients.

Early Role of Microglia in Synapse Loss in Alzheimer’s Disease

Researchers: 
Funding year(s): 
2016 to 2017
Funding to date: 
$300,000

In Alzheimer’s disease (AD), synaptic connections are lost early and in specific areas of the brain, including the hippocampus, where memory is formed and stored; however, what makes synapses vulnerable in AD and other neurodegenerative diseases remains elusive. In the healthy developing brain, synaptic loss (also known as synaptic pruning) is a normal process required for proper brain development. We previously found a key role for a group of immune molecules called complement in synaptic pruning. These proteins localize to synapses during periods of active synapse elimination and are required for normal brain wiring. Interestingly, the function of complement proteins in the brain appears analogous to their function in the immune system: they “tag” cellular material to be eliminated. Synapses tagged with complement proteins are eliminated by microglia, resident immune cells that express complement receptors. We showed that synapse loss in AD mouse models is mediated by an abnormal reactivation of this developmental pruning pathway, and that blocking complement or microglial complement receptors resulted in protection of synapse loss and memory defects in AD models (Hong et al., Science 2016). We predict that proteins in this pruning pathway could serve as biomarkers in AD to detect the disease early. To test this hypothesis, we will determine whether complement and microglia localize to synapses in human brains of early stages of AD, and whether complement proteins are abnormally upregulated in the cerebrospinal fluid (CSF) of AD patients. Our preliminary data suggest that C1q, the initiating protein of the complement pathway, is associated with synapses in late stages of the disease. We plan to continue investigating the role of complement in earlier stages of human AD. Moreover, we aim to study the role of other microglial receptors in aberrant synapse loss. Recent genome-wide association studies have identified several microglial and complement proteins as AD susceptibility genes, including TREM2; however, it is not known whether TREM2 plays a role in synapse loss or dysfunction. Using established assays, we are investigating whether TREM2 acts as a receptor through which microglia engulf synapses in AD mouse models. We found that TREM2 is involved in activating microglia and may be involved in synaptic engulfment. Understanding the function of TREM2 and other immune-related risk genes in early synapse loss can provide novel insight into new biomarkers and therapeutic targets.

The Role of Meningeal Lymphatics in Cleansing the Brain: Implications for Alzheimer’s Disease

Researchers: 
Funding year(s): 
2016
Funding to date: 
$150,000

Blood vessels supply our organs with oxygen and nutrients. Another set of vessels, called the lymphatic vessels, perform other very important roles in the maintenance of tissues as they remove all the waste and toxic compounds the organ produces and also serve as a path for immune cells from organs back to the lymph nodes. The mammalian central nervous system (CNS) thus far has been considered one of the only organs devoid of lymphatic vessels, and it was not fully understood how toxic compounds are removed from the brain. Our group has identified and described the basic biology of a novel meningeal lymphatic vascular system that serves a tissue clearance function of the brain. Absence of meningeal lymphatics results in attenuated clearance of macromolecules from within the CNS. We will address the role of this main drainage pathway in regulation of Abeta removal, its dysfunction as a contributor to Alzheimer’s disease and finally, using a pharmacological approach, we will enhance its function and assess its effect on Alzheimer’s pathology.

Therapeutic Modulation of TREM2 Activity

Researchers: 
Funding year(s): 
2016
Funding to date: 
$150,000

There is strong evidence that inflammation occurs in different stages of Alzheimer’s disease (AD). Understanding this process can help us to design new therapeutic approaches. TREM2 is a protein directly related to the inflammation process that occurs in the brain of patients with AD. Mutations in this protein increase the risk to develop AD up to threefold. A fragment of this protein, namely soluble TREM2 (sTREM2), increases at very early stages of AD, and this increase occurs in parallel to an increase of biomarkers for neuronal cell death. We have evidence that increased sTREM2 reflects a protective response; however, this could not be maintained in later stages of AD.