Comparative gene expression studies in Alzheimer's disease and other conditions

More than 98% of the human genome is composed of noncoding DNA. It is postulated that much of the genetic variations that influence the risk of common and complex human diseases such as Alzheimer's disease and other neurodegenerative diseases will reside in noncoding, though functional and regulatory regions of the genome will alter disease risk by affecting gene expression.

If this hypothesis is correct, many functional, regulatory genetic variants or their proxies will associate with both disease risk and gene expression levels. Further, gene transcripts, which functional disease risk variants regulate, may show differential levels in subjects who have the disease either clinically or prodromally, compared with control subjects.

In support of this hypothesis, the lab has determined that genetic variants near many genetic risk loci for late-onset Alzheimer's disease associate with brain levels of nearby genes. Also, genetic variants that strongly associate with brain gene expression levels are enriched for human disease-associated variants, including those for late-onset Alzheimer's disease.

The lab has several ongoing projects that seek to harness this dual information on gene expression levels and disease risk. The goal is to identify and characterize novel genes, transcripts and genetic risk variants for late-onset Alzheimer's disease.

Learn more about these projects below.

1. Target pathway discovery in Alzheimer's disease using transcriptomics

The team has already determined that the strongest genetic risk variants for Alzheimer's disease — detected in genomic screens — also associate with the brain expression levels of genes located close to the strong risk variants. These findings suggest that genetic variants that confer a risk of Alzheimer's disease can be found by modifying the expression levels of genes in the brain.

Many genes exist in different forms, called isoforms, that result in different protein products with diverse functions. Identifying the precise changes in brain levels of these gene isoforms enhances the understanding of risk mechanisms in Alzheimer's disease and enables future novel therapeutic approaches.

In this project, the lab aims to uncover specific isoform level changes for the strongest Alzheimer's disease risk genes using donor brains of deceased people who had Alzheimer's disease. Also, researchers will identify the biological consequences of altering specific isoform levels for some of the risk genes by decreasing or increasing their levels in cellular models and investigating functional outcomes such as cell survival. The goal is to uncover changes to the gene isoform level that implicate novel pathways in Alzheimer's disease that may guide future drug discovery efforts and revolutionize therapeutic approaches.

2. A systems approach to targeting innate immunity in Alzheimer's disease

As part of a multi-institutional project co-led by Dr. Ertekin-Taner; Todd Golde, M.D., Ph.D., Emory University; and Nathan Price, Ph.D., Institute for Systems Biology, the lab is leading projects to identify potential therapeutic targets and novel biomarkers using multi-omics and computational systems biology approaches.

Using whole-genome sequencing, next-generation RNA sequencing and genome-wide genotypes, the team has identified:

• Novel pathways in Alzheimer's disease.
• Potential regulatory variants in innate immune genes.
• Distinct transcriptional networks implicated with cell-specific pathologies and characterized disease risk association.
• Transcriptional profiles of genes in innate immune pathways.

The vast amount of multi-omics data has been shared with the research community and used to nominate novel therapeutic targets for Alzheimer's disease.

The Mayo Clinic team aims to identify precise therapeutic targets, their potential mechanism of action and beneficial therapeutic direction by adding epigenetic profiling (H3K27ac and ATACseq) for 700 brain samples from 350 subjects and performing multiscale computational analyses followed by collaborative functional validations in model systems.

Related publications

• Van der Lee SJ, Conway OJ, Jansen I, Carasquillo MM, Kleineidam L, van den Akker E, Hernández I, van Eijk KR, Stringa N, Chen JA, Zettergren A, Andlauer TFM, Diez-Fairen M, Simon-Sanchez J, Lleó A, et al. A nonsynonymous mutation in PLCG2 reduces the risk of Alzheimer's disease, dementia with Lewy bodies and frontotemporal dementia, and increases the likelihood of longevity. Acta Neuropathologica. 2019.
• Allen M, Wang X, Burgess JD, Watzlawik J, Serie DJ, Younkin CS, Nguyen T, Malphrus KG, Lincoln S, Carrasquillo MM, Ho C, Chakrabarty P, Strickland S, Murray ME, Swarup V, Geschwind DH, Seyfried NT, Dammer EB, Lah JJ, Levey AI, Golde TE, Funk C, Li H, Price ND, Petersen RC, Graff-Radford NR, Younkin SG, Dickson DW, Crook JR, Asmann YW, Ertekin-Taner N. Conserved brain myelination networks are altered in Alzheimer's and other neurodegenerative diseases. Alzheimer's & Dementia. 2018.
• Allen M, Wang X, Serie DJ, Strickland SL, Burgess JD, Koga S, Younkin CS, Nguyen TT, Malphrus KG, Lincoln SJ, Alamprese M, Zhu K, Chang R, Carrasquillo MM, Kouri N, Murray ME, Reddy JS, Funk C, Price ND, Golde TE, Younkin SG, Asmann YW, Crook JE, Dickson DW, Ertekin-Taner N. Divergent brain gene expression patterns associate with distinct cell-specific tau neuropathology traits in progressive supranuclear palsy. Acta Neuropathologica. 2018.
• Conway O, Carrasquillo MM, Wang X, Bredenberg JM, Reddy JS, Strickland SL, Younkin CS, Burgess JD, Allen M, Lincoln SJ, Nguyen T, Malphrus KG, Soto AI, Walton RL, Boeve BF, Petersen RC, Lucas JA, Ferman TJ, Cheshire WP, van Gerpen JA, Uitti RJ, Wszolek ZK, Ross OA, Dickson DW, Graff-Radford NR, Ertekin-Taner N. ABI3 and PLCG2 missense variants as risk factors for neurodegenerative diseases in Caucasians and African Americans. Molecular Neurodegeneration. 2018.
• Carrasquillo MM, Allen M, Burgess JD, Wang X, Strickland SL, Aryal S, Siuda J, Kachadoorian ML, Medway C, Younkin CS, Nair A, Wang C, Chanana P, Serie D, Nguyen T, Lincoln S, Malphrus KG, Morgan K, Golde TE, Price ND, White CC, De Jager PL, Bennett DA, Asmann YW, Crook JE, Petersen RC, Graff-Radford NR, Dickson DW, Younkin SG, Ertekin-Taner N. A candidate regulatory variant at the TREM gene cluster associates with decreased Alzheimer's disease risk and increased TREML1 and TREM2 brain gene expression. Alzheimer's & Dementia. 2017.
• Allen M, Carrasquillo MM, Funk C, Heavner BD, Zou F, Younkin CS, Burgess JD, Chai HS, Crook J, Eddy JA, Li H, Logsdon B, Peters MA, Dang KK, Wang X, Serie D, Wang C, Nguyen T, Lincoln S, Malphrus K, Bisceglio G, Li M, Golde TE, Mangravite LM, Asmann Y, Price ND, Petersen RC, Graff-Radford NR, Dickson DW, Younkin SG, Ertekin-Taner N. Human whole genome genotype and transcriptome data for Alzheimer's and other neurodegenerative diseases. Scientific Data. 2016.

3. Multi-omics approaches for biomarker discovery in Alzheimer's disease

The overarching goal of these studies is to identify genetically driven premorbid blood transcript biomarkers for Alzheimer's disease. Researchers in Dr. Ertekin-Taner's lab postulate that transcript-level changes that occur due to regulatory genetic variants, which also influence disease risk, can be detected prior to the development of clinical Alzheimer's disease. The underlying premise is that since disease risk variants are expected to be more frequent in the high-risk preclinical Alzheimer's disease population compared with controls, the downstream regulatory effects of transcript level changes also can be detected preclinically.

The strongest known genetic risk factor for late-onset Alzheimer's disease — apolipoprotein ε4 (APOE ε4) — is more common in subjects with mild cognitive impairment. This is a high-risk state considered to be a prodrome for Alzheimer's disease, especially for amnestic mild cognitive impairment. Although APOE ε4 reflects coding and not regulatory polymorphisms, if these observations apply to other disease risk variants, regulatory variants that influence Alzheimer's disease risk and associate with levels of gene transcripts will result in transcript-level differences. These include study participants with Alzheimer's disease versus controls and high-risk, preclinical subjects, such as amnestic mild cognitive impairment, versus controls.

If this hypothetical model is correct, it provides a strong rationale for using transcript levels as genetically driven biomarkers in preclinical Alzheimer's disease. This hypothesis is being tested in a project that Dr. Ertekin-Taner is conducting in her lab within the umbrella of the Accelerating Medicines Partnership Program for Alzheimer's Disease (AMP AD) consortium.

In this project, the team is measuring whole-transcriptome RNA and microRNA levels collected from plasma of elderly participants who have a diagnosis of incident mild cognitive impairment or incident Alzheimer's disease, or who are cognitively normal. Plasma samples collected longitudinally from each patient are being analyzed to identify:

• Preclinical biomarkers for Alzheimer's disease.
• Biomarkers of rate of decline.
• Biomarkers of clinical impairment.

4. Integrative translational discovery of vascular risk factors in aging and dementia

Dr. Ertekin-Taner's lab is leading studies focused on using multi-omics measures and systems biology approaches to identify novel genes and pathways associated with vascular risk factors for Alzheimer's disease. This project is part of the Molecular Mechanisms of the Vascular Etiology of Alzheimer's Disease (M2OVE-AD) consortium.

Genome-wide genotypes, RNA sequencing transcriptome measures and reduced representation bisulfite sequencing-based DNA methylation are being collected from brain tissue and blood samples along with rich cognitive and clinical data in two cohorts:

• A postmortem cohort of Alzheimer's disease cases scored for cerebral amyloid angiopathy.
• A prospective antemortem cohort with brain neuroimaging measures of microbleeds and infarcts.

Histone acetylation measures (H3K27ac) also are being collected for the postmortem cohort. Using genome-wide genotypes, we have identified an association of variants with cerebral amyloid angiopathy in the postmortem cohort and microbleeds and infarcts in the antemortem cohort. The team aims to integrate these initial genetic findings with other omics measures collected in these samples to further characterize observed associations. Gene expression and epigenomics measures also will be used independently to identify additional genes and pathways that are associated with measures of vascular pathology.

Brain tissue is composed of multiple cell types — neurons, astrocytes, microglia, endothelia and oligodendroglia — and subtypes of these. The team is conducting a study within this broader project that aims to generate gene expression profiles from these different cell types using neurosurgical brain tissue.

These cell types are being further characterized at the single-cell level using 10X genomics technology. The overall goals of this work are to determine which genes are predominantly expressed in certain cell types in the brain, identify and characterize cellular subtypes, and use this information to guide and improve the interpretation of bulk tissue expression profiling studies.

Related publication

• Carrasquillo MM, Reddy JS, Allen M, Reyes DA, McDonnel SK, Graff-Radford J, Kosel ML, Gregory JD, Nguyen T, Lincoln SJ, Malphrus KG, Crook JE, Jack Jr CR, Lowe VJ, Knopman DS, Petersen RC, Kantarci K, Bu G, Ertekin-Taner N. Genome-wide association study of cerebral microbleeds and infarction identifies candidate genes for vascular risk in dementia. Alzheimer's & Dementia. 2018.

5. Harnessing molecular networks of resilience for therapeutic discoveries in Alzheimer's disease

This project is led by Dr. Ertekin-Taner in collaboration with Hu Li, Ph.D., in the Department of Molecular Pharmacology and Experimental Therapeutics at Mayo Clinic's campus in Rochester, Minnesota.

Although protection from and resilience to Alzheimer's disease constitutes a fundamental aspect to understanding Alzheimer's disease pathophysiology, this is a relatively understudied area, and the molecular basis of resilience to Alzheimer's disease is largely unknown. We aim to fill this knowledge gap by studying cohorts resilient to Alzheimer's disease pathology and cognitive decline.

The team will leverage existing and generating novel molecular data to identify biological pathways that confer resilience to Alzheimer's disease. We seek to validate these pathways in experimental model systems and identify potential Alzheimer's disease therapeutics that promote resilience.

Dr. Ertekin-Taner's lab is leading these studies by integrating whole-genome sequence and whole-transcriptome gene expression data from blood (antemortem cohort) and brain (postmortem cohort) to identify novel genes and pathways associated with resilience to the development of Alzheimer's disease. Candidate resilience genes and pathways identified in the antemortem and postmortem cohorts will be validated in induced pluripotent stem cell-based models by the lab of Lihong Bu, M.D., Ph.D. They will be evaluated as potential drug targets using state-of-the-art, systems-based pharmacogenomics approaches by Dr. Li's group in close collaboration with Dr. Ertekin-Taner's lab.

These studies are expected to uncover networks and molecules of resilience and validate findings of other large-scale efforts to translate these discoveries to viable candidate drugs for Alzheimer's disease.