•A genome-wide significant linkage peak (HLOD=5.1) on 9p21 was found in PR Families for AD.•A rare missense variant in UNC13B segregates within PR families and is associated with AD risk in an ...independent case-control PR WGS dataset.•Our study demonstrated the importance of family-based design and WGS in genetic study of AD.
The genetic admixture of Caribbean Hispanics provides an opportunity to discover novel genetic factors in Alzheimer disease (AD). We sought to identify genetic variants for AD through a family-based design using the Puerto Rican (PR) Alzheimer Disease Initiative (PRADI). Whole-genome sequencing (WGS) and parametric linkage analysis were performed for 100 individuals from 23 multiplex PRADI families. Variants were prioritized by minor allele frequency (<0.01), functional potential combined annotation dependent depletion score (CADD) >10, and co-segregation with AD. Variants were further ranked using an independent PR case-control WGS dataset (PR10/66). A genome-wide significant linkage peak was found in 9p21 with a heterogeneity logarithm of the odds score (HLOD) >5.1, which overlaps with an AD linkage region from two published independent studies. The region harbors C9orf72, but no expanded repeats were observed in the families. Seven variants prioritized by the PRADI families also displayed evidence for association in the PR10/66 (p < 0.05), including a missense variant in UNC13B. Our study demonstrated the importance of family-based design and WGS in genetic study of AD.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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.
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.
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.
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.
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.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Background
Puerto Ricans, the second largest US Latino group, are underrepresented in genomic studies of Alzheimer disease (AD). We describe a multi‐source ascertainment approach, networking with ...community and governmental stakeholders, as part of the Puerto Rico (PR) Alzheimer Disease Initiative (PRADI) whose goal is to increase recruitment and retention of PR individuals in genomic research.The National Alzheimer’s disease Action Plan 2015‐2025 served as a framework for PRADI group that aims to fill two of the goals of the plan: increase research and education.
Method
We developed collaborative relationships with community and governmental organizations that serve the elderly and AD patients from 37/78 (47%) municipalities of PR to identify potential research participants. Trust and transparency were central to our interactions with community groups. We educated patients and caregivers about AD and their possible contribution to science. Bringing academia to the community encouraged participation. Additionally, we established relationships with multiple neurologists across PR caring for AD patients and their families. For recruitment and enrollment PRADI team members visited families in the homes, daycare facilities and clinics. All participants were assigned diagnoses by a clinical adjudication committee comprised of neurologists and neuropsychologists with expertise in AD and related dementias (ADRD)
Result
Since 2016 we have enrolled 1, 281 individuals. Among these 752 are unrelated individuals (193 AD, 170 mild cognitive impairment (MCI), 306 cognitively unimpaired (CU) and 83 with other diagnoses (OD). 529 individuals (195 AD, 76 MCI, 178 CU and 80 OD) were part of 155 multiplex AD families. Most families are from Eastern and Northern PR regions, reflecting dense population areas with large cities. Longitudinal follow‐up of the first 167 participants for diagnostic updates is complete. 64 individuals were ascertained in the continental US (cUS). Of the 167 individuals in the longitudinal follow‐up (3‐5 years), 7.2% progressed from either CU to MCI or AD, or MCI to AD.
Conclusion
The PRADI group multisource ascertainment approach enabled recruitment and retention of participants both in PR and the cUS. Longitudinal clinical data across the cohort further enriches the impact of genomic studies in a diverse population.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Abstract
Background
Alzheimer disease (AD) is the fourth leading cause of death in Puerto Rico. The Puerto Rican (PR) population has a high proportion of older adults (18%, over > 65), with 12.5% of ...them suffering from ADThese statistics highlight the need to investigate the genetic risk factors underlying AD in the PR population, as it could lead to the development of targeted treatments and therapies. Moreover, the ancestrally admixed makeup of the PR population provides an opportunity to assess the role of the European (∼67%), African (∼20%) and Amerindian (∼13%) ancestry in AD risk. We performed genome wide association analysis (GWAS) using whole genome sequence data to identify genetic risk/protective factors associated with AD in the PR population.
Method
The PR dataset includes WGS and phenotype data from 640 individuals, comprising 335 AD and 305 cognitively unimpaired (CU) controls. To account for the population substructure, we calculated the global ancestry (principal components) using EIGENSTRAT. We performed GWAS analyses with a generalized linear mixed‐model using the SAIGE software. The model included genotype, sex, age, and principal components (population substructure) as fixed effects and genetic relationship matrix as a random effect. The genetic relationship matrix was calculated based on genomic data and accounted for the relatedness among the individuals in the dataset.
Result
We identified four suggestive significant loci (P<1×10
−6
) associated with the risk of AD in PRs: NACC2 (pv = 4.8×10
−7
) on chromosome 9, SCN8A (pv = 9.3×10
−7
) on chromosome 12, FOXK2 (pv = 9.9×10
−7
) on chromosome 17, and APOEe4 (pv = 6.8×10
−8
) on chromosome 19. Eight additional AD loci with the same lead marker from European GWAS study (Bellenquez et al.) showed nominal significance: FERMT2 (pv = 6.2×10
−3
), TREM2 (pv = 8.0×10
−3
), CLU (pv = 1.8×10
−2
), RASGEF1C (pv = 2.4×10
−2
), ADAM17 (pv = 3.5×10
−2
), DOC2A (pv = 4.3×10
−2
), GRN (pv = 4.4×10
−2
) and SORL1 (pv = 5.1×10
−2
).
Conclusion
This study identified three suggestive novel significant loci (NACC2, SCN8A, and FOXK2) associated with AD risk in PRs. In addition, GWAS study on PRs with a high proportion of European ancestry was able to replicate nine AD loci previously identified in European studies. These findings provide new insights into the genetic architecture of AD in the PR population.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Background
We 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.
Method
We 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.
Result
We 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.
Conclusion
These 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.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Background
With over 5.1 million individuals, the Puerto Rican population makes up over 1.5% of the US population and is the 2nd largest Hispanic/Latino population in the continental US. There are an ...estimated of 60,000 cases of AD on the island. The Puerto Rico Alzheimer's and Related Dementias Initiatives (PRADI) cohort will both leverage and complement existing AD Resources, the Alzheimer Disease Sequencing Project (ADSP) with the inclusion of a diverse and underrepresented population. At present, the cohort consists of a total of 935 total participants including individuals from 115 multiplex AD families. There are 418 cases of dementia, 217 mild cognitive impairment, and 300 unrelated and family‐based controls.
Method
We examined the most successful strategy to recruit cases and controls as well as multiplex families for both case/control and family‐based genetic studies. We began by engaging a wide range of stakeholders across the island. The core activities of our team include relationship building, partnership development and maintenance, and coalition building. For the community outreach, we utilize mass media like newspapers, radio interviews, and focal group presentations and engaged the following stakeholder groups: Alzheimer disease day care centers, elderly housing in San Juan, senior day care centers, non‐profit organizations, private neurology offices, and other community‐based organizations such as the Alzheimer’s Association.
Result
The percent of patients recruited through each stakeholder group were 45.76% (428/935) from community outreach, 34.33% (321/935) from private neurologist practices, 18.93% (177/935) from senior day care centers and 0.96% (9/935) from Alzheimer disease day care centers. The mean age and standard deviation of cases and controls were 78.22 years (±9.37) and 70.84 years (±7.92) respectively. Examining the data with respect to multiplex family structure, we found that 53.77% of the families (including the largest families) came from private physician referral.
Conclusion
Partnering with diverse stakeholders and building coalitions proved to be effective as an outreach method for recruitment. Private physicians remain an excellent source for the identification of multiplex AD families for family‐based genetics study. Outreach community‐based approaches are highly successful mechanisms to educate and engage participants in genetic research.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Abstract
Background
Genetic risk factors for Alzheimer disease (AD) demonstrate distinct effects across diverse ancestral populations. The ancestral heterogeneity (admixture) of Caribbean Hispanics ...from Puerto Rico (PR), makes studies of the PR population important in the discovery of ancestry‐specific factors in AD. To expand ongoing genomic investigations of AD in PR individuals, it is necessary to characterize functional downstream effects by studying gene expression and regulation. Here we characterized the differences in gene expression, splicing, and RNA editing of the protein coding transcriptome from peripheral blood in PR individuals. to identify case vs control differential expression, splicing, and RNA editing in this diverse population.
Method
Poly‐A selected RNA was from peripheral whole blood of 76 PR individuals over the age of 65 (39 AD, 37 cognitively normal controls) was sequenced and analyzed with a standard bioinformatics pipeline. Differential expression between PR cases and controls was calculated using DESeq2, alternative splicing using LeafCutter software, and RNA editing with REDITools and linear models. All analyses were adjusted for sex, age, and sequencing coverage. For each analysis, pathway enrichment analysis of Gene Ontology Biological Processes and KEGG gene sets were used to identify underlying biological pathways.
Result
A total of 761 genes (518 up‐regulated, 243 down‐regulated) were differentially expressed between PR AD and controls (adjusted p ≤ 0.05). At the transcript level, 561 genes had a significant (FDR ≤ 0.05) differential splicing event. We also identified 35,246 total RNA editing sites. While there was no significant difference globally, 422 sites in 159 genes showed nominally significant editing difference (p ≤ 0.05). These genes, isoforms, and RNA editing sites overlap little with previous investigations of the transcriptomes of Non‐Hispanic Whites and African‐American AD with only a few genes in common. However, pathway enrichment across all three PR transcriptomic analyses consistently reveals differences in both the adaptive and innate immune response pathways, consistent with other ancestries.
Conclusion
Transcriptomic analyses of diverse populations in AD, shows stark divergence at the single gene level. However, the convergence on immune molecular pathways suggest shared underlying disease etiology and the possibility of broad therapeutic options.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Abstract
Background
The
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.
Method
APOE
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.
Result
The 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).
Conclusion
We 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.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Background
To 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.
Method
Recombinant plasmids for testing overexpression (UNC13B) and promoter activity (ELAVL2) were made by site‐directed mutagenesis and transfected into the neuronal SH‐SY5Y.
Result
Two 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).
Conclusion
Two 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.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
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