Ancestral origin of ApoE ε4 Alzheimer disease risk in Puerto Rican and African American populations

The ApoE ε4 allele is the most significant genetic risk factor for late-onset Alzheimer disease. The risk conferred by ε4, however, differs across populations, with populations of African ancestry showing lower ε4 risk compared to those of European or Asian ancestry. The cause of this heterogeneity in risk effect is currently unknown; it may be due to environmental or cultural factors correlated with ancestry, or it may be due to genetic variation local to the ApoE region that differs among populations. Exploring these hypotheses may lead to novel, population-specific therapeutics and risk predictions. To test these hypotheses, we analyzed ApoE genotypes and genome-wide array data in individuals from African American and Puerto Rican populations. A total of 1,766 African American and 220 Puerto Rican individuals with late-onset Alzheimer disease, and 3,730 African American and 169 Puerto Rican cognitively healthy individuals (> 65 years) participated in the study. We first assessed average ancestry across the genome (“global” ancestry) and then tested it for interaction with ApoE genotypes. Next, we assessed the ancestral background of ApoE alleles (“local” ancestry) and tested if ancestry local to ApoE influenced Alzheimer disease risk while controlling for global ancestry. Measures of global ancestry showed no interaction with ApoE risk (Puerto Rican: p-value = 0.49; African American: p-value = 0.65). Conversely, ancestry local to the ApoE region showed an interaction with the ApoE ε4 allele in both populations (Puerto Rican: p-value = 0.019; African American: p-value = 0.005). ApoE ε4 alleles on an African background conferred a lower risk than those with a European ancestral background, regardless of population (Puerto Rican: OR = 1.26 on African background, OR = 4.49 on European; African American: OR = 2.34 on African background, OR = 3.05 on European background). Factors contributing to the lower risk effect in the ApoE gene ε4 allele are likely due to ancestry-specific genetic factors near ApoE rather than non-genetic ethnic, cultural, and environmental factors

Using the Lens of Local Ancestry to Focus Risk in Alzheimer Disease (5420)

Objective: Our objective is to assess the effect of Southern European (SE) genetic ancestry on APOE gene using Caribbean Hispanic Puerto Rican (CHIPR) population Background: Alzheimer disease (AD) is a progressive neurodegenerative disease and occurs in all ethnic and racial groups. The APOE ɛ4 allele is a major risk factor for AD whose effect shows strong racial/ethnic differences. Among the non-Hispanic White populations APOE shows the strongest effect in North Europeans and has a relatively lower effect in SE populations. Hispanic/Latino populations with a large proportion of SE ancestry provides a unique opportunity to assess the role of SE ancestry in AD. Thus, our goal to assess the relevance of the SE genetic ancestry to the differential effect of the APOE using CHIPR population. Design/Methods: APOE and genome-wide genotyping were performed in 412 CHPR (231 cases, 181 controls). Local ancestry was calculated using SHAPEIT and RFMix. Global ancestry was assessed using GENESIS. Association between affection status and APOE genotype was analyzed using logistic regression models by adjusting for age, gender, and population substructure. Results: The admixture analysis showed that the origin of European ancestry in CHIPR is from SE. The distribution of the parental ancestries local to the APOE gene was 68% SE, 20% AF, and 12% AI. Logistic regression model showed significant association of the APOE ɛ4 risk allele with AD (CHIPR: OR = 1.9 CI:1.3–2.8, p-value = 4.4e-4). Conclusions: Our results showed that the effect of the ɛ4 risk allele in CHIPR with the dominantly (~67%) SE ancestral background is less than it was observed in overall NHW population and close to APOE effect observed in the population from the Iberian Peninsula. Our data support the findings that suggests an interaction between the genetic risk allele ɛ4 and ancestral backgrounds located around the genomic region of APOE gene. Disclosure: Dr. Rajabli has nothing to disclose. Dr. Feliciano-Astacio has nothing to disclose. Dr. Celis has nothing to disclose. Dr. Vance has received royalty, license fees, or contractual rights payments from Athena Diagnostics. Dr. Beecham has nothing to disclose. Dr. Pericak-Vance has nothing to disclose

Clinical characterization of a large Caribbean Hispanic family linked to chromosome 9 without ApoE4

Background The ancestral genetic heterogeneity (admixture) of Caribbean Hispanics makes studies of this population critical to discovering ancestry‐specific genetic factors in Alzheimer's disease. As part of the Puerto Rican Alzheimer Disease Initiative (PRADI), we ascertained 80+ multigenerational families with multiple AD family members and reported linkage to 9p21. Here we present the clinical phenotype of the largest 9p21 linked family. Method The 18 members of this family were screened using neuropsychological test (e.g., CDR, 3MS), history of medical conditions, Apolipoprotein e4 were obtained and AD diagnosis was done by a panel of experts. Results were reported as frequencies and percentage and the associations were determined using Chi‐square. Result The family consisted of 17 participating family members, 76% females, a mean age of 70 years (SD=14 years). 1 participant was diagnosed with Parkinson’s disease, 6 with AD possible diagnosis, 1 as MCI and 6 were cognitively normal. No known causal genes for AD were observed through whole genome sequencing. The prevalence for APOE genotypes, 2/2, 2/3, 2/4 and 3/3, were 6%, 47%, 6% and 41% respectively. None of the AD cases in the family had an APOE4 allele. The average age of onset of AD cases was 79 years (SD=12 years) with a minimum of 60 years and maximum of 90 years. The average 3MS score for the cases was 49/100 (SD=33) and 90/100 (SD=4) for controls. CDR scores for all controls were 0 and between 2 and 1 for all cases. Depression was present in 33% of the participants, 22% diagnosed with diabetes, 25% with high cholesterol and 44% with hypertension. Conclusion In this family, 8 individuals had neurodegenerative disorders, 5 of which had at least 1 APOE2 allele. The only APOE4 carrier is a unaffected participant (APOE 2/4) whose age at exam was 57 years. This supports a novel AD risk factor segregating in this family. Pedigree studies remain a useful tool to help unravel the pathophysiologic pathways involved in neurodegeneration

The Relationship of Alzheimer’s Disease, Stroke and Ancestry in the Puerto Rican Alzheimer Disease Population

Background The Puerto Rico Alzheimer and Related Dementias Initiatives (PRADI) patient cohort was developed to investigate AD and the associated genetics factors in the Puerto Rican population. PRADI recruitment was a snowball sampling, with both island‐wide geographic distribution, and extensions of the PR communities in the continental US. A prior analysis suggested that stroke is a contributing factor to AD in the PR population. In this study we further evaluated the association between stroke and AD, while considering also age, gender, and ancestry. Method We assessed 1063 elderly PR individuals for dementia and obtained a medical history. Affection status or mild cognitive impairment was established using standard AD clinical criteria (NINCDS‐ADRDA). Medical history was obtained by a self‐report or informant report. The global ancestry was assessed through the ADMIXTURE program. Differences between affected and cognitively unimpaired (CU) individuals were initially evaluated using a chi‐square test (for age, gender, global ancestry, and stroke) and a t‐test for the age at the exam time. Follow‐up analyses on stroke were performed using logistic regression with age‐at‐exam, gender, and global ancestry proportions as covariates in the model. Initially we assess how stroke is associated with AD, while accounting for age, sex, and global ancestry analysis without APOE, results on the first table. The first table is the model without APOE. Then a second tab turns it around and looks at what factors are associated with Stroke, in the context of AD. Result In the PRADI population stroke is associated with an increased risk of AD dementia (p=0.012); this association persists even after accounting for APOE dosage (p=0.017). Additionally, age, gender and APOE dosage were all also associated with increased AD risk (p <0.05) (table 1). AD correlated with Stroke (p=0.013). Gender was also associated with stroke, with females having a decreased risk of stroke (p=0.0021). APOE dosage and ancestry proportions measured through ADMIXTURE approach were not associated with stroke (table 2). Conclusion Stroke was independently associated to AD after controlling for APOE dosage. In contrast, age and gender were associated with stroke whereas global ancestry and APOE dosage were not

ATAC-seq on iPSC derived astrocytes to assess chromatin accessibility differences between African and European local ancestry

Local ancestry (LA) surrounding the APOE4 allele is associated with an increased risk for Alzheimer Disease (AD) in European (EU) LA compared to African (AF) LA. We recently demonstrated that APOE4 has significantly higher expression in astrocytes in brain from EU compared to AF APOE4 LA carriers, but the specific molecular mechanism leading to this difference is not known. We investigated whether evaluating chromatin accessibility and gene expression profiles of inducible pluripotent stem cell (iPSC) derived astrocytes in the LA region in both AF and EU LA could lead us to identify potential regulatory factors affecting chromatin remodeling and expression of APOE. We assayed for Transposase Accessible Chromatin (ATAC-seq), and RNA-seq in three iPSC derived astrocytes from two AF LA and one EU LA individuals with AD. We processed the ATAC-seq data with the ENCODE ATAC-seq pipeline and called peaks using MACS2. An average of 692 peaks were detected in the LA region with no statistical difference between EU and AF LA. Interestingly, an African APOE4 homozygote LA astrocyte line with high APOE expression had an exclusive ATAC peak at the APOE promoter. Amongst the transcription factors (TFs) suggested to bind this differentially accessible peak in APOE are HNF4A and TEAD4. Both TFs had significantly increased expression in this astrocyte line compared to the other lines. Additionally, differential accessibility in this line include peaks in an intragenic enhancer of PVRL2 and the promoter of CBLC, both shown to be bound by HNF4A and both overexpressed in this cell line and one in the promoter of CYP2S1 with TEAD4 binding, which was also overexpressed. This study is one of the first studies to compare chromatin accessibility in AF and EU ancestries. It also represents initial efforts to investigate potential mechanisms and factors, using iPSC-derived cell lines, that could contribute to the differential expression we have previously reported in APOE4 between AF and EU LA brains. Our data suggest that elevated astrocytic expression of APOE4 is associated with rs

Functional analysis of candidate genes identified through whole genome sequencing in Caribbean Hispanic families for late‐onset Alzheimer disease

BackgroundTo identify LOAD risk genes in Puerto Ricans (PR), a population underrepresented in genetic studies, linkage analysis of whole genome sequencing (WGS) in 23 multiplex PR families identified a peak on chromosome 9p21 (MLOD = 3.9). The 1‐LOD unit down region spans from 31∼38Mb; identity‐by‐descent (IBD) sharing region spans from 23‐39 Mb. Two genes in the linkage region, UNC13B, located in the center of the linkage peak (35.1∼35.4 Mb), and ELAVL2 (23.7∼23.8 Mb), at the edge of the IBD sharing region, are of interest. Both genes have multiple rare variants with low minor allele frequencies (MAF) and high CADD scores that segregate with LOAD in the families. UNC13B encodes a protein involved in Ca2+ release at the synapse, and calcium dysfunction has been associated with LOAD. ELAVL2 encodes a neural‐specific protein involved in RNA processing.MethodRecombinant plasmids for testing overexpression (UNC13B) and promoter activity (ELAVL2) were made by site‐directed mutagenesis and transfected into the neuronal SH‐SY5Y.ResultTwo UNC13B missense variants, rs35199210 (Asp238Glu, CADD = 22, MAF = 0.5%) or rs41276043 (Phe1096Leu, CADD = 26.5, MAF = 0.5%) have been cloned into overexpression vectors and are currently being evaluated for their effect on Ca2+ release rates. One promoter variant rs542037226 (CADD = 16.6, MAF = 0.03%) in the ELAVL2 demonstrated strong activity (∼200x higher than the empty vector), and the rare allele showed reduced activity compared to the reference allele (10% reduction, p = 0.03).ConclusionTwo potential new LOAD genes with rare variants have been identified within the linkage 9p21 linkage peak. Using segregation and in‐silico analysis we have prioritized rare variants in each gene for testing. Successful demonstration of functional changes in the ELAVL2 variants provide support for this approach. Evaluation of UNC13B variants are underway. Those variants with functional effects will be further evaluated in our inducible pluripotent stem cell models

Southern European genetic ancestry shows reduced APOE E4 risk for Alzheimer disease in Caribbean Hispanic population

BackgroundThe APOE ε4 allele is a major risk factor for AD whose effect shows strong racial/ethnic differences. Among non‐Hispanic White (NHW) populations APOE shows the strongest effect in Northern European (NEu) (rs429358: OR = 3.32, CI:3.20‐3.45) and has a relatively lower effect in Southern European (SEu; i.e., Iberia, Italy, etc) populations (rs429358: OR = 2.27, CI:2.06–2.50). However, it is not clear if this difference in effect is due to genetic or environmental effects. Hispanic/Latino populations with a large proportion of SEu ancestry provide a unique opportunity to assess both global SEu ancestry (i.e., genome‐wide ancestry) and local SEu ancestry (chromosome/region specific ancestry) in populations with environments distinct from SEu. Our objective is to use data from a Caribbean Hispanic Puerto Rican (CHIPR) population to assess the role of SEu genetic ancestry and the APOE gene on Alzheimer disease (AD) risk.MethodAPOE and genome‐wide genotyping were performed in 412 CHIPR (231 cases, 181 controls). Local ancestry was calculated using SHAPEIT and RFMix. Global ancestry was assessed using GENESIS. Association between affection status and APOE genotype was analyzed using logistic regression models by adjusting for age, gender, and population substructure.ResultThe admixture analysis showed that CHIPR have a substantial SEu ancestral component (∼67%). At the APOE gene, the local ancestry was 68% SEu, 20% African, and 12% Amerindian. Logistic regression model showed a significant association of the APOE ε4 risk allele with AD (CHIPR: OR = 1.9 CI:1.3‐2.8, p‐value = 4.4e‐4).ConclusionWe found that the effect of the APOE ε4 risk allele in CHIPR with the high SEu ancestral background (∼67%) is similar to the effect observed in Southern European populations, despite having a distinct environment. Our results support the hypothesis that SEu genetic ancestry modulates the risk of APOE in CHIPRs. This suggests that subcontinental ancestry could also play an important role in modulating the risk for other known AD candidate. Studying the sub‐continental (NEu and SEu) ethnic disparity in the genetics of AD, provides critical information to advance the development of novel therapeutic measures