- Email: [email protected]
Haplotypes at the MAPT locus associate with risk for LOAD and brain gene expression
Oral Sessions: O5-01: Basic Science: Genetics IV–The Role of Alzheimer’s Disease in Epigenetics and Transcriptomics Background: The apolipoprotein E gene (APOE) is the most highly established genetic risk factor for late-onset Alzheimer’s disease (AD); its ε4 allele has an odds ratio of 3.6, whereas all other genetic risk variants for late-onset AD have much smaller effects (AlzGene). In the past, research into APOE in AD has focused on apoE isoform-specific differences in the protein’s structure and function, which has generated vast, valuable insights and hypotheses. However, the precise mechanism by which apoE4 exerts its detrimental effect in AD remains incompletely understood. Independent genetic approaches and studies have consistently identified the APOE locus as harboring the strongest AD association signal within the human genome; thus, it is plausible that additional biological effects of this APOE locus, independent of apoE protein, also contribute to AD pathophysiology. Methods: We used the in silico analysis to search for functional elements of the APOE locus, and identified a distinct CpG island (CGI) in the APOE. We then performed the bisulfite pyrosequencing to detect the DNA methylation load of this CGI from postmortem brain of AD and control subjects. We also applied a methylation-accessible reporter assay to evaluate the transcriptional regulatory activity of this CGI. Results: A well-defined CGI comprised of 90 CpG dinucleotides coincides with APOE exon 4, and the two SNPs (rs429358 and rs7412) determining the ε2/ε3/ε4 alleles reside within this CGI. This APOE CGI is hyper-methylated in various tissues of postmortem brain. The methylated version of CGI has strong transcriptional regulatory activity, which can be modified according to the ε2/ ε3/ε4 alleles and can alter the promoter activity of multiple genes in the neighboring region, including APOE, TOMM40 and APOCI. Conclusions: We propose that the APOE CGI is a critical gene regulatory element, which drives an epigenetically imprinted transcriptional program at the APOE locus. This regulatory activity of APOE can be modulated by the ε2/ε3/ε4 allele variants and may have direct relevance to mechanisms of increased risk for AD resulting from inheritance of different APOE alleles. O5-01-04
EXPLORING THE EPIGENETIC ARCHITECTURE OF COGNITIVE RESILIENCE IN AGING: A DNA METHYLATION AND A GENETIC SCAN CONVERGE ON SEVERAL LOCI ASSOCIATED WITH RESILIENCE
Philip De Jager1, Gyan Srivastava1, Lori Chibnik1, Robert Wilson2, Julie Schneider3, David Bennett2, 1Brigham & Women’s Hospital, Boston, Massachusetts, United States; 2Rush University Medical Center, Chicago, Illinois, United States; 3RushUniversity Medical Center, Rush Alzheimer’s Disease Center, Chicago, Illinois, United States. Contact e-mail: [email protected] Background: Cognitive performance in older age is thought to be the result of competing forces, namely pathologic processes that decrease cognitive capacity and processes that mitigate the clinical expression of these pathologies. Currently, the molecular mechanisms that underlie these processes is not well understood. Here, we seek to identify loci in which genetic variation and/or chromatin state may contribute to this process of “cognitive resilience”. Methods: We base this investigation on a unique bank of frozen brains from subjects with longitudinal cognitive data collected in two prospective studies of aging: the Memory and Aging Project and the Religious Order Study. Each subject is non-demented at the time of entry into the study. A sample of dorsolateral prefrontal cortex was obtained from each of 748 subjects, which have genome-wide genotype data, and an Illumina Humanmethylation450 profile was generated, consisting of 486,428 CpG sites distributed throughout the genome for each cortical sample. Results: We performed both a methylome-wide scan and a genome-wide scan for cognitive resilience and integrated our two sets of results. In each scan, we seek loci in which methylation level or genetic variation relate to the last measure of global cognitive performance prior to death, after adjusting for the burden of amyloid, tangle, Lewy body, as well as micro- and macrovascular pathology found in each individual on post evaluation-mortem. Interestingly, top results of these two scans are converging: for example, cg15248943 (p¼5.8x10^-8) and rs13220815 (p¼3.3x10^-9) are found in the HS3ST3A1 locus. The TTLL7 locus is another example. Conclusions: Our approach to identify SNP and CpG associated with an individual’s ability to maintain cognitive
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performance in the face of all pathologies that we have characterized in our subjects is bearing fruit, and it appears that certain loci have both genetic variation and Methylation levels that influence cognitive resilience. O5-01-05
HAPLOTYPES AT THE MAPT LOCUS ASSOCIATE WITH RISK FOR LOAD AND BRAIN GENE EXPRESSION
Mariet Allen1, Michaela Kachadoorian1, Zachary Quicksall1, Fanggeng Zou1, High Seng Chai2, Curtis Younkin1, Julia Crook1, Vernon Pankratz2, Minerva Carrasquillo1, Siddarth Krishnan1, Thuy Nguyen1, Li Ma1, Kimberly Malphrus1, Sarah Lincoln1, Gina Bisceglio1, Christopher Kolbert2, Jin Jen2, Ronald Petersen2, Neill Graff-Radford1, Dennis Dickson1, Steven Younkin1, Nilufer Ertekin-Taner2, 1Mayo Clinic, Jacksonville, Florida, United States; 2Mayo Clinic, Rochester, Minnesota, United States. Contact e-mail: [email protected] Background: Intracellular neurofibrillary tangles composed predominantly of tau protein are a classic neuropathological feature of AD. The MAPT gene (Chr17) encodes for tau, however the evidence for genetic involvement of this locus in LOAD etiology has been inconsistent. This may be because previous studies have generally used relatively small numbers of LOAD cases and controls, and/or have not investigated haplotypic variability at the locus in depth. We sought to examine well-established MAPT sub-haplotype-tagging variants in our large LOAD case-control series to determine their effect on risk for LOAD. We also hypothesized that some of the MAPT variants may confer disease risk by influencing brain expression levels of MAPT, based on our expression GWAS (eGWAS) and previous reports by others. Methods: We genotyped six SNPs which tag the most common MAPT locus haplotypes (frequencies >1%), in three Caucasian LOAD case-control series (Ncases¼2052; N-controls¼3,406). We measured MAPT expression levels in the cerebellum (N¼197) and temporal cortex (N¼202) of autopsied AD subjects as part of our eGWAS. The six SNPs and the estimated haplotypes were tested for: (I) association with LOAD risk using logistic regression and (II) gene expression of MAPT using linear regression; all analysis included appropriate covariates. Results: The H2 haplotype was significantly associated with decreased risk of LOAD (OR ¼ 0.80, p¼4.10E-04), and decreased MAPT expression in both brain regions (beta¼-0.16 to -0.49, p¼3.4E-03 to 8.70E-33). The most common H1 sub-haplotype (H1b) had nominally significant association with increased risk of LOAD (OR¼1.15, p¼0.046) and a global test for the 19 haplotypes identified in this study was significant (p ¼ 0.0123). Interestingly we do not find significant association for the H1c haplotype that has previously been implicated in LOAD (p ¼ 0.277). Conclusions: Our results strongly suggest that MAPT is a LOAD gene that has regulatory variants which confer LOAD risk by influencing its brain expression. Additional studies are needed to identify the precise mechanism of disease attributable to genetic variation at this locus. O5-01-06
RNA TRANSCRIPTION AND EDITING IN ALZHEIMER’S DISEASE
Crystal Humphries1, John Gilbert1, Martin Kohli2, Patrice L. Whitehead2, Deborah Mash3, Gary Beecham1, Margaret Pericak-Vance1, 1University of Miami, Miami, Florida, United States; 2John P. Hussman Institute of Human Genomics, University of Miami, Miami, Florida, United States; 3University of Miami, Department of Neurology, Miami, Florida, United States. Contact e-mail: [email protected] Background: A-to-I RNA editing is a post-transcriptional process that can affect RNAs’ secondary structure, change splice sites, and proteins by introducing nonsynonymous changes in transcripts. Changes in RNA editing are known to cause disruptions in neuronal functions and be altered in human disease. Studies have shown RNA editing differences in ALS, Schizophrenia and Bipolar Disorder. In this study we use RNA-Seq to demonstrate that RNA editing is also altered in Late Onset Alzheimer Disease (LOAD). Methods: RNA-Seq was performed on the HiSeq2000 using total RNA isolated from tissue sample from the temporal pole (BA: 38). Thirty age, race, and sex matched samples were sequenced: 10 each from LOAD, Diffuse Lewy-Body disease (DLB) and cognitively normal controls. RNA was
EXPLORING THE EPIGENETIC ARCHITECTURE OF COGNITIVE RESILIENCE IN AGING: A DNA METHYLATION AND A GENETIC SCAN CONVERGE ON SEVERAL LOCI ASSOCIATED WITH RESILIENCE
Philip De Jager1, Gyan Srivastava1, Lori Chibnik1, Robert Wilson2, Julie Schneider3, David Bennett2, 1Brigham & Women’s Hospital, Boston, Massachusetts, United States; 2Rush University Medical Center, Chicago, Illinois, United States; 3RushUniversity Medical Center, Rush Alzheimer’s Disease Center, Chicago, Illinois, United States. Contact e-mail: [email protected] Background: Cognitive performance in older age is thought to be the result of competing forces, namely pathologic processes that decrease cognitive capacity and processes that mitigate the clinical expression of these pathologies. Currently, the molecular mechanisms that underlie these processes is not well understood. Here, we seek to identify loci in which genetic variation and/or chromatin state may contribute to this process of “cognitive resilience”. Methods: We base this investigation on a unique bank of frozen brains from subjects with longitudinal cognitive data collected in two prospective studies of aging: the Memory and Aging Project and the Religious Order Study. Each subject is non-demented at the time of entry into the study. A sample of dorsolateral prefrontal cortex was obtained from each of 748 subjects, which have genome-wide genotype data, and an Illumina Humanmethylation450 profile was generated, consisting of 486,428 CpG sites distributed throughout the genome for each cortical sample. Results: We performed both a methylome-wide scan and a genome-wide scan for cognitive resilience and integrated our two sets of results. In each scan, we seek loci in which methylation level or genetic variation relate to the last measure of global cognitive performance prior to death, after adjusting for the burden of amyloid, tangle, Lewy body, as well as micro- and macrovascular pathology found in each individual on post evaluation-mortem. Interestingly, top results of these two scans are converging: for example, cg15248943 (p¼5.8x10^-8) and rs13220815 (p¼3.3x10^-9) are found in the HS3ST3A1 locus. The TTLL7 locus is another example. Conclusions: Our approach to identify SNP and CpG associated with an individual’s ability to maintain cognitive
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performance in the face of all pathologies that we have characterized in our subjects is bearing fruit, and it appears that certain loci have both genetic variation and Methylation levels that influence cognitive resilience. O5-01-05
HAPLOTYPES AT THE MAPT LOCUS ASSOCIATE WITH RISK FOR LOAD AND BRAIN GENE EXPRESSION
Mariet Allen1, Michaela Kachadoorian1, Zachary Quicksall1, Fanggeng Zou1, High Seng Chai2, Curtis Younkin1, Julia Crook1, Vernon Pankratz2, Minerva Carrasquillo1, Siddarth Krishnan1, Thuy Nguyen1, Li Ma1, Kimberly Malphrus1, Sarah Lincoln1, Gina Bisceglio1, Christopher Kolbert2, Jin Jen2, Ronald Petersen2, Neill Graff-Radford1, Dennis Dickson1, Steven Younkin1, Nilufer Ertekin-Taner2, 1Mayo Clinic, Jacksonville, Florida, United States; 2Mayo Clinic, Rochester, Minnesota, United States. Contact e-mail: [email protected] Background: Intracellular neurofibrillary tangles composed predominantly of tau protein are a classic neuropathological feature of AD. The MAPT gene (Chr17) encodes for tau, however the evidence for genetic involvement of this locus in LOAD etiology has been inconsistent. This may be because previous studies have generally used relatively small numbers of LOAD cases and controls, and/or have not investigated haplotypic variability at the locus in depth. We sought to examine well-established MAPT sub-haplotype-tagging variants in our large LOAD case-control series to determine their effect on risk for LOAD. We also hypothesized that some of the MAPT variants may confer disease risk by influencing brain expression levels of MAPT, based on our expression GWAS (eGWAS) and previous reports by others. Methods: We genotyped six SNPs which tag the most common MAPT locus haplotypes (frequencies >1%), in three Caucasian LOAD case-control series (Ncases¼2052; N-controls¼3,406). We measured MAPT expression levels in the cerebellum (N¼197) and temporal cortex (N¼202) of autopsied AD subjects as part of our eGWAS. The six SNPs and the estimated haplotypes were tested for: (I) association with LOAD risk using logistic regression and (II) gene expression of MAPT using linear regression; all analysis included appropriate covariates. Results: The H2 haplotype was significantly associated with decreased risk of LOAD (OR ¼ 0.80, p¼4.10E-04), and decreased MAPT expression in both brain regions (beta¼-0.16 to -0.49, p¼3.4E-03 to 8.70E-33). The most common H1 sub-haplotype (H1b) had nominally significant association with increased risk of LOAD (OR¼1.15, p¼0.046) and a global test for the 19 haplotypes identified in this study was significant (p ¼ 0.0123). Interestingly we do not find significant association for the H1c haplotype that has previously been implicated in LOAD (p ¼ 0.277). Conclusions: Our results strongly suggest that MAPT is a LOAD gene that has regulatory variants which confer LOAD risk by influencing its brain expression. Additional studies are needed to identify the precise mechanism of disease attributable to genetic variation at this locus. O5-01-06
RNA TRANSCRIPTION AND EDITING IN ALZHEIMER’S DISEASE
Crystal Humphries1, John Gilbert1, Martin Kohli2, Patrice L. Whitehead2, Deborah Mash3, Gary Beecham1, Margaret Pericak-Vance1, 1University of Miami, Miami, Florida, United States; 2John P. Hussman Institute of Human Genomics, University of Miami, Miami, Florida, United States; 3University of Miami, Department of Neurology, Miami, Florida, United States. Contact e-mail: [email protected] Background: A-to-I RNA editing is a post-transcriptional process that can affect RNAs’ secondary structure, change splice sites, and proteins by introducing nonsynonymous changes in transcripts. Changes in RNA editing are known to cause disruptions in neuronal functions and be altered in human disease. Studies have shown RNA editing differences in ALS, Schizophrenia and Bipolar Disorder. In this study we use RNA-Seq to demonstrate that RNA editing is also altered in Late Onset Alzheimer Disease (LOAD). Methods: RNA-Seq was performed on the HiSeq2000 using total RNA isolated from tissue sample from the temporal pole (BA: 38). Thirty age, race, and sex matched samples were sequenced: 10 each from LOAD, Diffuse Lewy-Body disease (DLB) and cognitively normal controls. RNA was