Potentially pathogenic alterations have been identified in individuals with autism spectrum disorders (ASDs) within a variety of key neurodevelopment genes. While this hints at a common ASD molecular ...etiology, gaps persist in our understanding of the neurodevelopmental mechanisms impacted by genetic variants enriched in ASD patients. Induced pluripotent stem cells (iPSCs) can model neurodevelopment in vitro, permitting the characterization of pathogenic mechanisms that manifest during corticogenesis. Taking this approach, we examined the transcriptional differences between iPSC-derived cortical neurons from patients with idiopathic ASD and unaffected controls over a 135-day course of neuronal differentiation. Our data show ASD-specific misregulation of genes involved in neuronal differentiation, axon guidance, cell migration, DNA and RNA metabolism, and neural region patterning. Furthermore, functional analysis revealed defects in neuronal migration and electrophysiological activity, providing compelling support for the transcriptome analysis data. This study reveals important and functionally validated insights into common processes altered in early neuronal development and corticogenesis and may contribute to ASD pathogenesis.
We previously demonstrated that in Alzheimer's disease (AD) patients, European apolipoprotein E (APOE) ε4 carriers express significantly more APOE ε4 in their brains than African AD carriers. We ...examined single nucleotide polymorphisms near APOE with significant frequency differences between African and European/Japanese APOE ε4 haplotypes that could contribute to this difference in expression through regulation. Two enhancer massively parallel reporter assay (MPRA) approaches were performed, supplemented with single fragment reporter assays. We used Capture C analyses to support interactions with the APOE promoter. Introns within TOMM40 showed increased enhancer activity in the European/Japanese versus African haplotypes in astrocytes and microglia. This region overlaps with APOE promoter interactions as assessed by Capture C analysis. Single variant analyses pinpoints rs2075650/rs157581, and rs59007384 as functionally different on these haplotypes. Identification of the mechanisms for differential regulatory function for APOE expression between African and European/Japanese haplotypes could lead to therapeutic targets for APOE ε4 carriers.
A PATIENT-DERIVED IPSC MODEL OF A RARE TTC3 MUTATION Dykxhoorn, Derek M.; Garcia-Serje, Catherine; Johnson, Francelethia of ...
Alzheimer's & dementia,
July 2017, 2017-07-00, Letnik:
13, Številka:
7
Journal Article
Background
Plasma concentrations of phosphorylated threonine‐181 of Tau (pTau181) and the ratio of amyloid beta isoforms Ab42/Ab40 are biomarkers for differential diagnosis and preclinical detection ...of Alzheimer disease (AD). However, measurement of these biomarkers is mostly from individuals of non‐Hispanic, European ancestry. Given differences in AD risk, generalizability of these findings is not assured in individuals of diverse ancestry. This study evaluates the utility of plasma pTau181 and Ab42/Ab40 in discriminating clinically diagnosed AD from cognitively intact, age‐matched controls in ancestrally diverse, admixed cohorts.
Method
We measured plasma pTau181 and Aβ42/Aβ40 with Simoa chemistry using the pTau181 AdvantageV2 and NEUROLOGY 3‐PLEX A assays, respectively. Our cohorts consisted of: 642 African Americans (162 AD and 480 cognitively intact (CI)), 906 Puerto Ricans (385 AD and 521 CI), 149 Peruvians (49 AD and 100 CI), 60 Cubans (26 AD and 34 CI), and 246 non‐Hispanic, European ancestry (22 AD and 224 CI). Linear mixed‐effect regression models adjusted for age, sex, population substructure and relatedness followed by Bonferroni correction was applied to identify differences across AD status. Diagnostic performance and construct receiver operator characteristic (ROC) curves were created from logistic regression models.
Result
Plasma pTau181 concentrations were increased in individuals with AD compared to CI (p < 2×10−16) taking into account all individuals and in each cohort separately (African Americans, p = 1.2×10−9; Puerto Ricans, p = 7.6×10−9; Peruvians, p = 0.02), and European ancestry, p = 2.2×10−8) except for the Cubans where there was a trend. There was no significant difference in the plasma Aβ42/Aβ40 ratio, however there was a trend towards a decreasing concentration in AD. Using the area under the ROC, pTau181 was more accurate at predicting status than the Aβ42/Aβ40 ratio, but the classification improved when both biomarkers were combined. The accuracy varied widely over the individual cohorts with AUC from 0.845 for African Americans to 0.683 for Peruvians.
Conclusion
These results suggest AD biomarkers are generalizable across ancestries, though the predictive value may differ depending on specific ancestral backgrounds. Ultimately, combining genomic and biomarker data from diverse individuals will increase understanding of genetic risk and refine clinical diagnoses in individuals of diverse ancestries.
Background
Plasma proteins, including phosphorylated threonine‐181 of Tau (pTau181) are used as biomarkers for differential diagnosis and preclinical detection of Alzheimer disease (AD). However, ...observation and measurement of these biomarkers are mostly from individuals of non‐Hispanic, European ancestry. Given differences in AD risk, generalizability of these findings is not assured in individuals of diverse ancestry. This study evaluates the utility of plasma pTau181 in discriminating clinically diagnosed AD from cognitively intact, age‐matched controls in ancestrally diverse, admixed cohorts.
Method
We measured pTau181 with Simoa chemistry using the pTau181 AdvantageV2 on the Quanterix HD‐X. Our cohorts consisted of 642 African Americans (162 AD and 480 controls), 906 Puerto Ricans (385 AD and 521 controls), 149 Peruvians (49 AD and 100 controls), 60 Cubans (26 AD and 34 controls), 246 individuals of non‐Hispanic, European ancestry (22 AD and 224 controls), and 58 autopsy confirmed AD cases of European ancestry with plasma isolated from EDTA blood tubes. Samples were randomized, measurements performed in duplicate, and non‐parametric Kruskal‐Wallis tests used to detect differences in biomarker concentrations between cases and controls in each cohort.
Result
Median pTau levels in cases was higher than controls in all cohorts assayed: African Americans (2.30±1.14pg/mL vs 1.15±2.99pg/mL, pcorr=2.0x10‐27); Puerto Ricans (2.33±1.82pg/mL vs 1.44±1.21pg/mL, pcorr=8.2x10‐32); Peruvians (2.63±1.64pg/mL vs 2.13±1.42pg/mL, pcorr=0.02); Cubans (2.09±1.16pg/mL vs 1.35±0.67pg/mL, pcorr=0.02); and European ancestry (2.40pg/mL±0.78pg/mL vs 1.54pg/mL ±1.44pg/mL, pcorr=0.02). The pTau levels in the autopsy confirmed cases (2.96±2.29 pg/mL) were not significantly higher than AD cases in the other ancestries.
Conclusion
This study suggests pTau181 as a biomarker is generalizable across genetic ancestries, though potential sex and age effects remain to be determined. Ultimately, combining genomic and biomarker data, including pTau181 and other AD related plasma biomarkers such as Aβ40 and Aβ42, from diverse individuals will increase understanding of genetic risk and refine clinical diagnoses in individuals of diverse ancestries.
We previously demonstrated that in Alzheimer’s disease (AD)
patients, European apolipoprotein E (
APOE
)
ε
4 carriers express significantly more
APOEε
4 in their brains than African AD carriers. We
...examined single nucleotide polymorphisms near
APOE
with
significant frequency differences between African and European/Japanese
APOE ε
4 haplotypes that could contribute to this
difference in expression through regulation. Two enhancer massively parallel
reporter assay (MPRA) approaches were performed, supplemented with single
fragment reporter assays. We used Capture C analyses to support interactions
with the
APOE
promoter. Introns within
TOMM40
showed increased enhancer activity in the European/Japanese versus African
haplotypes in astrocytes and microglia. This region overlaps with
APOE
promoter interactions as assessed by Capture C
analysis. Single variant analyses pinpoints rs2075650/rs157581, and rs59007384
as functionally different on these haplotypes. Identification of the mechanisms
for differential regulatory function for
APOE
expression
between African and European/Japanese haplotypes could lead to therapeutic
targets for
APOE ε
4 carriers.
Background
Plasma proteins as biomarkers for the differential diagnosis of AD from other similar neurodegenerative disorders, as well as the identification of preclinical AD, has recently been well ...supported across several large AD cohorts. However, these are composed primarily of individuals of non‐Hispanic European ancestry. Few studies have been performed in African‐American or Hispanic/Latinx AD populations to determine if plasma biomarkers are also useful in these populations. Given the differences in AD risk loci found across ancestries, the application of these biomarkers in diverse populations is not assured. Therefore, the aim of this study is to explore the utility of plasma biomarkers in AD, MCI and at‐risk family members from diverse ancestral backgrounds.
Method
As part of ongoing initiatives to understand AD in individuals of diverse ancestry, we are measuring the plasma level of biomarkers in a cohort of more than 3,000 individuals. This includes: 999 African Americans (248 AD cases, 591 controls, 160 MCI), 581 Puerto Ricans (223 AD cases, 208 controls, 150 MCI), 1052 Puerto Ricans in families (411 AD cases, 413 controls, 228 MCI), 98 Cubans (23 AD cases, 39 controls, 36 MCI), and 117 Peruvians (33 AD cases, 75 controls, 9 MCI). We will also have data on autopsy confirmed European AD cases (37) and a cohort of Amish individuals (∼400 AD cases, ∼200 MCI, and ∼500 controls). Plasma proteins tested are Aβ42, Aβ40, total Tau, and p‐Tau181 using Simoa chemistry assays (Quanterix HD‐X). All measurements are performed in duplicate and data analysis performed using HD‐X Analyzer Software v1.6.
Result
Measurement and analysis of biomarkers in this diverse dataset is currently underway and will be completed in a few months. These results will allow a direct comparison of biomarker analysis related to AD diagnosis between European, African, and Amerindian ancestries. Moreover, a family‐based design for over 1000 Puerto Rican individuals will be the first to identify potential heritable trends in biomarker levels.
Conclusion
This study is critical to being to understand how plasma biomarkers for AD may vary across diverse ancestries and whether previous findings will be generalizable and useful for all individuals, regardless of ancestry.
Abstract
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 Ca
2+
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 Ca
2+
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.
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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