African descent populations have a lower Alzheimer disease risk from ApoE ε4 compared to other populations. Ancestry analysis showed that the difference in risk between African and European populations lies in the ancestral genomic background surrounding the ApoE locus (local ancestry). Identifying the mechanism(s) of this protection could lead to greater insight into the etiology of Alzheimer disease and more personalized therapeutic intervention. Our objective is to follow up the local ancestry finding and identify the genetic variants that drive this risk difference and result in a lower risk for developing Alzheimer disease in African ancestry populations. We performed association analyses using a logistic regression model with the ApoE ε4 allele as an interaction term and adjusted for genome-wide ancestry, age, and sex. Discovery analysis included imputed SNP data of 1,850 Alzheimer disease and 4,331 cognitively intact African American individuals. We performed replication analyses on 63 whole genome sequenced Alzheimer disease and 648 cognitively intact Ibadan individuals. Additionally, we reproduced results using whole-genome sequencing of 273 Alzheimer disease and 275 cognitively intact admixed Puerto Rican individuals. A further comparison was done with SNP imputation from an additional 8,463 Alzheimer disease and 11,365 cognitively intact non-Hispanic White individuals. We identified a significant interaction between the ApoE ε4 allele and the SNP rs10423769_A allele, (β = -0.54,SE = 0.12,p-value = 7.50x10-6) in the discovery data set, and replicated this finding in Ibadan (β = -1.32,SE = 0.52,p-value = 1.15x10-2) and Puerto Rican (β = -1.27,SE = 0.64,p-value = 4.91x10-2) individuals. The non-Hispanic Whites analyses showed an interaction trending in the “protective” direction but failing to pass a 0.05 significance threshold (β = -1.51,SE = 0.84,p-value = 7.26x10-2). The presence of the rs10423769_A allele reduces the odds ratio for Alzheimer disease risk from 7.2 for ApoE ε4/ε4 carriers lacking the A allele to 2.1 for ApoE ε4/ε4 carriers with at least one A allele. This locus is located approximately 2 mB upstream of the ApoE locus, in a large cluster of pregnancy specific beta-1 glycoproteins on chromosome 19 and lies within a long noncoding RNA, ENSG00000282943. This study identified a new African-ancestry specific locus that reduces the risk effect of ApoE ε4 for developing Alzheimer disease. The mechanism of the interaction with ApoEε4 is not known but suggests a novel mechanism for reducing the risk for ε4 carriers opening the possibility for potential ancestry-specific therapeutic intervention.

Introduction Puerto Ricans, the second largest Latino group in the continental US, are underrepresented in genomic studies of Alzheimer disease (AD). To increase representation of this group in genomic studies of AD, we developed a multisource ascertainment approach to enroll AD patients, and their family members living in Puerto Rico (PR) as part of the Alzheimer’s Disease Sequencing Project (ADSP), an international effort to advance broader personalized/precision medicine initiatives for AD across all populations. Methods The Puerto Rico Alzheimer Disease Initiative (PRADI) multisource ascertainment approach was developed to recruit and enroll Puerto Rican adults aged 50 years and older for a genetic research study of AD, including individuals with cognitive decline (AD, mild cognitive impairment), their similarly, aged family members, and cognitively healthy unrelated individuals age 50 and up. Emphasizing identification and relationship building with key stakeholders, we conducted ascertainment across the island. In addition to reporting on PRADI ascertainment, we detail admixture analysis for our cohort by region, group differences in age of onset, cognitive level by region, and ascertainment source. Results We report on 674 individuals who met standard eligibility criteria [282 AD-affected participants (42% of the sample), 115 individuals with mild cognitive impairment (MCI) (17% of the sample), and 277 cognitively healthy individuals (41% of the sample)]. There are 43 possible multiplex families (10 families with 4 or more AD-affected members and 3 families with 3 AD-affected members). Most individuals in our cohort were ascertained from the Metro, Bayamón, and Caguas health regions. Across health regions, we found differences in ancestral backgrounds, and select clinical traits. Discussion The multisource ascertainment approach used in the PRADI study highlights the importance of enlisting a broad range of community resources and providers. Preliminary results provide important information about our cohort that will be useful as we move forward with ascertainment. We expect that results from the PRADI study will lead to a better understanding of genetic risk for AD among this population.

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Background Understanding the effects of genetic factors that drive Alzheimer’s Disease (AD) pathogenesis, including genetic differences across diverse ancestral populations, will drive discovery of novel pharmacological targets. Weighted gene co‐expression network analysis (WGCNA) is a powerful method for finding gene clusters (modules) with correlated expression, relating these modules to phenotypes, and thus identifying key upstream regulatory elements. To study networks of transcriptional dysregulation in AD across ancestries, we performed WGCNA in African‐American (AA), Non‐Hispanic White (NHW), and Puerto Rican (PR) populations. Method RNA sequencing was performed on peripheral blood specimens from 275 AD cases (115 AA, 121 NHW, 39 PR) and 276 age and sex matched controls (119 AA, 120 NHW, 37 PR), all over age 65. We performed WGCNA and calculated the correlation between each co‐expression module and AD affection status within each ancestry group, adjusting for sex, age, and sequencing batch. Ingenuity Pathway Analysis (IPA) was used to identify enriched pathways and upstream regulators. Result We identified 13 co‐expression modules that were significantly associated with AD. Across all ancestries, modules were enriched for pathways related to endocytosis and inflammation. These modules largely differed between African and European ancestry, though there was some overlap in the admixed PR population. Only one module had significantly decreased expression in cases across all three ancestries. It was enriched for immune signaling pathways and showed especially strong enrichment (p = 1.09*10−19) for upstream regulation by granulocyte‐colony stimulating factor (G‐CSF). G‐CSF activates JAK2 and STAT1, which were central hub genes within this module, as were AD‐associated genes CR1 and TLR4. G‐CSF acts as a cytokine, hormone, and neurotrophic factor. In AD mouse models, G‐CSF decreases brain amyloid burden and reverses cognitive impairment. A recombinant form of G‐CSF is approved for use in neutropenia and has completed Phase II clinical trials for the treatment of AD (NCT01617577, NCT03656042). A current Phase II trial for the closely related GM‐CSF is ongoing (NCT01409915). Conclusion Through analyses of multiple populations, we have identified AD‐associated gene expression networks. Though these networks largely differ by ancestral background, convergence on pathways relevant to AD pathology suggest that shared underlying disease etiology can be targeted pharmacologically.

BackgroundWe previously reported strong linkage on chromosome 9p21 in multiplex Alzheimer disease (AD) families from Puerto Rico. Nine families had the highest linkage contribution. 3/9 families shared seven coding variants with displayed evidence for AD association in similar ancestral. Although these variants reside in genes with neuronal expression and functionality, they do not explain the linkage signal in all families. Here, we performed a fine‐mapping analysis to identify non‐coding variants that can contribute to the AD trait previously observed.MethodWe analyzed whole genome sequencing (WGS) from 9 families, 43 AD and 15 cognitively intact individuals. Chromatin interaction and cis‐regulatory element (CREs) were used to prioritized relevant non‐coding variants. Induced pluripotent stem cells (iPSC) derived neurons were generated from five individuals for characterization.ResultWe found an average of 300,000 non‐coding variants per family. Following filtering steps including segregation, allele frequency and chromatin association, we identified ∼400 variants per family. These variants were analyzed using the CREs derived from ENCODE, which left us with 31 (8%) variants falling in promoters. 5/31 variants were shared among four or more families, and fall in the promoter of genes FBXO10, ACO1, NDUFB6 and DNAJA1. Six families shared variants in FBXO10 making it our top candidate gene, a F‐box protein family with a role in apoptosis and immunity. Interestingly, another F‐box protein (FBXL7) has been associated with AD in a Caribbean Hispanic population.ConclusionThese results reiterate the importance of family‐based studies and fine‐mapping as a resourceful tool to identified functional variants in AD. Transcriptomic profile and functional characterization of iPSC derived neurons will aid to understand the implication of prioritized genes in the linkage association previously observed.