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Article ; Online: Genetic analyses in multiplex families confirms chromosome 5q35 as a risk locus for Alzheimer's Disease in individuals of African Ancestry.

Nuytemans, Karen / Rajabli, Farid / Jean-Francois, Melissa / Kurup, Jiji Thulaseedhara / Adams, Larry D / Starks, Takiyah D / Whitehead, Patrice L / Kunkle, Brian W / Caban-Holt, Allison / Haines, Jonathan L / Cuccaro, Michael L / Vance, Jeffery M / Byrd, Goldie S / Beecham, Gary W / Reitz, Christiane / Pericak-Vance, Margaret A

Neurobiology of aging

2023 Volume 133, Page(s) 125–133

Abstract: There is a paucity of genetic studies of Alzheimer Disease (AD) in individuals of African Ancestry, despite evidence suggesting increased risk of AD in the African American (AA) population. We performed whole-genome sequencing (WGS) and multipoint ... ...

Abstract	There is a paucity of genetic studies of Alzheimer Disease (AD) in individuals of African Ancestry, despite evidence suggesting increased risk of AD in the African American (AA) population. We performed whole-genome sequencing (WGS) and multipoint linkage analyses in 51 multi-generational AA AD families ascertained through the Research in African American Alzheimer Disease Initiative (REAAADI) and the National Institute on Aging Late Onset Alzheimer's disease (NIA-LOAD) Family Based Study. Variants were prioritized on minor allele frequency (<0.01), functional potential of coding and noncoding variants, co-segregation with AD and presence in multi-ancestry ADSP release 3 WGS data. We identified a significant linkage signal on chromosome 5q35 (HLOD=3.3) driven by nine families. Haplotype segregation analysis in the family with highest LOD score identified a 3'UTR variant in INSYN2B with the most functional evidence. Four other linked AA families harbor within-family shared variants located in INSYN2B's promoter or enhancer regions. This AA family-based finding shows the importance of diversifying population-level genetic data to better understand the genetic determinants of AD on a global scale.
MeSH term(s)	Humans ; Alzheimer Disease/genetics ; Alzheimer Disease/epidemiology ; Lod Score ; Genetic Linkage/genetics ; Haplotypes ; Chromosomes ; Genetic Predisposition to Disease/genetics
Language	English
Publishing date	2023-10-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	604505-4
ISSN	1558-1497 ; 0197-4580
ISSN (online)	1558-1497
ISSN	0197-4580
DOI	10.1016/j.neurobiolaging.2023.10.010
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Article: An Alzheimer's disease risk variant in

Cukier, Holly N / Duarte, Carolina L / Laverde-Paz, Mayra J / Simon, Shaina A / Van Booven, Derek J / Miyares, Amanda T / Whitehead, Patrice L / Hamilton-Nelson, Kara L / Adams, Larry D / Carney, Regina M / Cuccaro, Michael L / Vance, Jeffery M / Pericak-Vance, Margaret A / Griswold, Anthony J / Dykxhoorn, Derek M

bioRxiv : the preprint server for biology

2023

Abstract: A missense variant in the : Highlights: The AD risk variant TTC3 p.S1038C reduces the expression levels ... ...

Abstract	A missense variant in the Highlights: The AD risk variant TTC3 p.S1038C reduces the expression levels of
Language	English
Publishing date	2023-05-25
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.25.542316
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Article ; Online: An Alzheimer's disease risk variant in TTC3 modifies the actin cytoskeleton organization and the PI3K-Akt signaling pathway in iPSC-derived forebrain neurons.

Neurobiology of aging

2023 Volume 131, Page(s) 182–195

Abstract: A missense variant in the tetratricopeptide repeat domain 3 (TTC3) gene (rs377155188, p.S1038C, NM_003316.4:c 0.3113C>G) was found to segregate with disease in a multigenerational family with late-onset Alzheimer's disease. This variant was introduced ... ...

Abstract	A missense variant in the tetratricopeptide repeat domain 3 (TTC3) gene (rs377155188, p.S1038C, NM_003316.4:c 0.3113C>G) was found to segregate with disease in a multigenerational family with late-onset Alzheimer's disease. This variant was introduced into induced pluripotent stem cells (iPSCs) derived from a cognitively intact individual using CRISPR genome editing, and the resulting isogenic pair of iPSC lines was differentiated into cortical neurons. Transcriptome analysis showed an enrichment for genes involved in axon guidance, regulation of actin cytoskeleton, and GABAergic synapse. Functional analysis showed that the TTC3 p.S1038C iPSC-derived neuronal progenitor cells had altered 3-dimensional morphology and increased migration, while the corresponding neurons had longer neurites, increased branch points, and altered expression levels of synaptic proteins. Pharmacological treatment with small molecules that target the actin cytoskeleton could revert many of these cellular phenotypes, suggesting a central role for actin in mediating the cellular phenotypes associated with the TTC3 p.S1038C variant.
MeSH term(s)	Humans ; Induced Pluripotent Stem Cells ; Phosphatidylinositol 3-Kinases ; Proto-Oncogene Proteins c-akt ; Alzheimer Disease/genetics ; Neurons ; Actin Cytoskeleton ; Late Onset Disorders ; Prosencephalon ; Signal Transduction/genetics ; Ubiquitin-Protein Ligases
Chemical Substances	Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; TTC3 protein, human (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2023-07-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	604505-4
ISSN	1558-1497 ; 0197-4580
ISSN (online)	1558-1497
ISSN	0197-4580
DOI	10.1016/j.neurobiolaging.2023.07.007
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Article: Generalizability of Tau and Amyloid Plasma Biomarkers in Alzheimer's Disease Cohorts of Diverse Genetic Ancestries.

Griswold, Anthony J / Rajabli, Farid / Gu, Tianjie / Arvizu, Jamie / Golightly, Charles G / Whitehead, Patrice L / Hamilton-Nelson, Kara L / Adams, Larry D / Sanchez, Jose Javier / Mena, Pedro R / Starks, Takiyah D / Illanes-Manrique, Maryenela / Silva, Concepcion / Bush, William S / Cuccaro, Michael L / Vance, Jeffery M / Cornejo-Olivas, Mario R / Feliciano-Astacio, Briseida E / Byrd, Goldie S /

Beecham, Gary W / Haines, Jonathan L / Pericak-Vance, Margaret A

medRxiv : the preprint server for health sciences

2024

Abstract: Introduction: Plasma phosphorylated threonine-181 of Tau and amyloid beta are biomarkers for differential diagnosis and preclinical detection of Alzheimer disease (AD). Given differences in AD risk across diverse populations, generalizability of ... ...

Abstract	Introduction: Plasma phosphorylated threonine-181 of Tau and amyloid beta are biomarkers for differential diagnosis and preclinical detection of Alzheimer disease (AD). Given differences in AD risk across diverse populations, generalizability of existing biomarker data is not assured. Methods: In 2,086 individuals of diverse genetic ancestries (African American, Caribbean Hispanic, and Peruvians) we measured plasma pTau-181 and Aβ42/Aβ40. Differences in biomarkers between cohorts and clinical diagnosis groups and the potential discriminative performance of the two biomarkers were assessed. Results: pTau-181 and Aβ42/Aβ40 were consistent across cohorts. Higher levels of pTau181 were associated with AD while Aβ42/Aβ40 had minimal differences. Correspondingly, pTau-181 had greater predictive value than Aβ42/Aβ40, however, the area under the curve differed between cohorts. Discussion: pTau-181 as a plasma biomarker for clinical AD is generalizable across genetic ancestries, but predictive value may differ. Combining genomic and biomarker data from diverse individuals will increase understanding of genetic risk and refine clinical diagnoses.
Language	English
Publishing date	2024-04-12
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.10.24305617
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Article ; Online: Ancestry-related differences in chromatin accessibility and gene expression of APOE ε4 are associated with Alzheimer's disease risk.

Alzheimer's & dementia : the journal of the Alzheimer's Association

2023 Volume 19, Issue 9, Page(s) 3902–3915

Abstract: Introduction: European local ancestry (ELA) surrounding apolipoprotein E (APOE) ε4 confers higher risk for Alzheimer's disease (AD) compared to African local ancestry (ALA). We demonstrated significantly higher APOE ε4 expression in ELA versus ALA in ... ...

Abstract	Introduction: European local ancestry (ELA) surrounding apolipoprotein E (APOE) ε4 confers higher risk for Alzheimer's disease (AD) compared to African local ancestry (ALA). We demonstrated significantly higher APOE ε4 expression in ELA versus ALA in AD brains from APOE ε4/ε4 carriers. Chromatin accessibility differences could contribute to these expression changes. Methods: We performed single nuclei assays for transposase accessible chromatin sequencing from the frontal cortex of six ALA and six ELA AD brains, homozygous for local ancestry and APOE ε4. Results: Our results showed an increased chromatin accessibility at the APOE ε4 promoter area in ELA versus ALA astrocytes. This increased accessibility in ELA astrocytes extended genome wide. Genes with increased accessibility in ELA in astrocytes were enriched for synapsis, cholesterol processing, and astrocyte reactivity. Discussion: Our results suggest that increased chromatin accessibility of APOE ε4 in ELA astrocytes contributes to the observed elevated APOE ε4 expression, corresponding to the increased AD risk in ELA versus ALA APOE ε4/ε4 carriers.
MeSH term(s)	Humans ; Apolipoprotein E4/genetics ; Alzheimer Disease/genetics ; Alzheimer Disease/complications ; Chromatin ; Heterozygote ; Gene Expression
Chemical Substances	Apolipoprotein E4 ; Chromatin
Language	English
Publishing date	2023-04-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2211627-8
ISSN	1552-5279 ; 1552-5260
ISSN (online)	1552-5279
ISSN	1552-5260
DOI	10.1002/alz.13075
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Article ; Online: Three Brothers With Autism Carry a Stop-Gain Mutation in the HPA-Axis Gene NR3C2.

Cukier, Holly N / Griswold, Anthony J / Hofmann, Natalia K / Gomez, Lissette / Whitehead, Patrice L / Abramson, Ruth K / Gilbert, John R / Cuccaro, Michael L / Dykxhoorn, Derek M / Pericak-Vance, Margaret A

Autism research : official journal of the International Society for Autism Research

2020 Volume 13, Issue 4, Page(s) 523–531

Abstract: Whole exome sequencing and copy-number variant analysis was performed on a family with three brothers diagnosed with autism. Each of the siblings shares an alteration in the nuclear receptor subfamily 3 group C member 2 (NR3C2) gene that is predicted to ... ...

Abstract	Whole exome sequencing and copy-number variant analysis was performed on a family with three brothers diagnosed with autism. Each of the siblings shares an alteration in the nuclear receptor subfamily 3 group C member 2 (NR3C2) gene that is predicted to result in a stop-gain mutation (p.Q919X) in the mineralocorticoid receptor (MR) protein. This variant was maternally inherited and provides further evidence for a connection between the NR3C2 and autism. Interestingly, the NR3C2 gene encodes the MR protein, a steroid hormone-regulated transcription factor that acts in the hypothalamic-pituitary-adrenal axis and has been connected to stress and anxiety, both of which are features often seen in individuals with autism. Autism Res 2020, 13: 523-531. © 2020 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Given the complexity of the genetics underlying autism, each gene contributes to risk in a relatively small number of individuals, typically less than 1% of all autism cases. Whole exome sequencing of three brothers with autism identified a rare variant in the nuclear receptor subfamily 3 group C member 2 gene that is predicted to strongly interfere with its normal function. This gene encodes the mineralocorticoid receptor protein, which plays a role in how the body responds to stress and anxiety, features that are often elevated in people diagnosed with autism. This study adds further support to the relevance of this gene as a risk factor for autism.
MeSH term(s)	Autism Spectrum Disorder/genetics ; Child, Preschool ; Humans ; Hypothalamo-Hypophyseal System ; Male ; Mutation/genetics ; Pituitary-Adrenal System ; Receptors, Mineralocorticoid/genetics ; Siblings
Chemical Substances	NR3C2 protein, human ; Receptors, Mineralocorticoid
Language	English
Publishing date	2020-02-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2481338-2
ISSN	1939-3806 ; 1939-3792
ISSN (online)	1939-3806
ISSN	1939-3792
DOI	10.1002/aur.2269
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Article ; Online: Genetic architecture of RNA editing regulation in Alzheimer's disease across diverse ancestral populations.

Gardner, Olivia K / Van Booven, Derek / Wang, Lily / Gu, Tianjie / Hofmann, Natalia K / Whitehead, Patrice L / Nuytemans, Karen / Hamilton-Nelson, Kara L / Adams, Larry D / Starks, Takiyah D / Cuccaro, Michael L / Martin, Eden R / Vance, Jeffery M / Bush, William S / Byrd, Goldie S / Haines, Jonathan L / Beecham, Gary W / Pericak-Vance, Margaret A / Griswold, Anthony J

Human molecular genetics

2022 Volume 31, Issue 17, Page(s) 2876–2886

Abstract: Most Alzheimer's disease (AD)-associated genetic variants do not change protein coding sequence and thus likely exert their effects through regulatory mechanisms. RNA editing, the post-transcriptional modification of RNA bases, is a regulatory feature ... ...

Abstract	Most Alzheimer's disease (AD)-associated genetic variants do not change protein coding sequence and thus likely exert their effects through regulatory mechanisms. RNA editing, the post-transcriptional modification of RNA bases, is a regulatory feature that is altered in AD patients that differs across ancestral backgrounds. Editing QTLs (edQTLs) are DNA variants that influence the level of RNA editing at a specific site. To study the relationship of DNA variants genome-wide, and particularly in AD-associated loci, with RNA editing, we performed edQTL analyses in self-reported individuals of African American (AF) or White (EU) race with corresponding global genetic ancestry averaging 82.2% African ancestry (AF) and 96.8% European global ancestry (EU) in the two groups, respectively. We used whole-genome genotyping array and RNA sequencing data from peripheral blood of 216 AD cases and 212 age-matched, cognitively intact controls. We identified 2144 edQTLs in AF and 3579 in EU, of which 1236 were found in both groups. Among these, edQTLs in linkage disequilibrium (r2 > 0.5) with AD-associated genetic variants in the SORL1, SPI1 and HLA-DRB1 loci were associated with sites that were differentially edited between AD cases and controls. While there is some shared RNA editing regulatory architecture, most edQTLs had distinct effects on the rate of RNA editing in different ancestral populations suggesting a complex architecture of RNA editing regulation. Altered RNA editing may be one possible mechanism for the functional effect of AD-associated variants and may contribute to observed differences in the genetic etiology of AD between ancestries.
MeSH term(s)	Alzheimer Disease/genetics ; Alzheimer Disease/metabolism ; Black People ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; LDL-Receptor Related Proteins/metabolism ; Linkage Disequilibrium ; Membrane Transport Proteins/genetics ; Quantitative Trait Loci/genetics ; RNA Editing/genetics
Chemical Substances	LDL-Receptor Related Proteins ; Membrane Transport Proteins ; SORL1 protein, human
Language	English
Publishing date	2022-04-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1108742-0
ISSN	1460-2083 ; 0964-6906
ISSN (online)	1460-2083
ISSN	0964-6906
DOI	10.1093/hmg/ddac075
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Article ; Online: Admixture mapping identifies novel Alzheimer's disease risk regions in African Americans.

Alzheimer's & dementia : the journal of the Alzheimer's Association

2022 Volume 19, Issue 6, Page(s) 2538–2548

Abstract: Background: This study used admixture mapping to prioritize the genetic regions associated with Alzheimer's disease (AD) in African American (AA) individuals, followed by ancestry-aware regression analysis to fine-map the prioritized regions.: Methods! ...

Abstract	Background: This study used admixture mapping to prioritize the genetic regions associated with Alzheimer's disease (AD) in African American (AA) individuals, followed by ancestry-aware regression analysis to fine-map the prioritized regions. Methods: We analyzed 10,271 individuals from 17 different AA datasets. We performed admixture mapping and meta-analyzed the results. We then used regression analysis, adjusting for local ancestry main effects and interactions with genotype, to refine the regions identified from admixture mapping. Finally, we leveraged in silico annotation and differential gene expression data to prioritize AD-related variants and genes. Results: Admixture mapping identified two genome-wide significant loci on chromosomes 17p13.2 (p = 2.2 × 10 Discussion: Our ancestry-aware regression approach showed that AA individuals have a lower risk of AD if they inherited African ancestry admixture block at the 17p13.2 locus. Highlights: We identified two genome-wide significant admixture mapping signals: on chromosomes 17p13.2 and 18q21.33, which are novel in African American (AA) populations. Our ancestry-aware regression approach showed that AA individuals have a lower risk of Alzheimer's disease (AD) if they inherited African ancestry admixture block at the 17p13.2 locus. We found that the overall proportion of African ancestry does not differ between the cases and controls that suggest African genetic ancestry alone is not likely to explain the AD prevalence difference between AA and non-Hispanic White populations.
MeSH term(s)	Humans ; Genetic Predisposition to Disease/genetics ; Black or African American/genetics ; Alzheimer Disease/genetics ; Chromosome Mapping/methods ; Genotype ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide/genetics ; Kinesins/genetics ; Protein Serine-Threonine Kinases/genetics
Chemical Substances	KIF1C protein, human ; Kinesins (EC 3.6.4.4) ; MINK1 protein, human (EC 2.7.11.1) ; Protein Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2022-12-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2211627-8
ISSN	1552-5279 ; 1552-5260
ISSN (online)	1552-5279
ISSN	1552-5260
DOI	10.1002/alz.12865
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Article: Use of local genetic ancestry to assess

Bussies, Parker L / Rajabli, Farid / Griswold, Anthony / Dorfsman, Daniel A / Whitehead, Patrice / Adams, Larry D / Mena, Pedro R / Cuccaro, Michael / Haines, Jonathan L / Byrd, Goldie S / Beecham, Gary W / Pericak-Vance, Margaret A / Young, Juan I / Vance, Jeffery M

Neurology. Genetics

2020 Volume 6, Issue 2, Page(s) e404

Abstract: Objective: Here, we re-examine : Methods: The : Results: The : Conclusions: Adjustment for LGA confirms ... ...

Abstract	Objective: Here, we re-examine Methods: The Results: The Conclusions: Adjustment for LGA confirms that
Language	English
Publishing date	2020-03-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2818607-2
ISSN	2376-7839
ISSN	2376-7839
DOI	10.1212/NXG.0000000000000404
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Article ; Online: Genetic variants in the SHISA6 gene are associated with delayed cognitive impairment in two family datasets.

Ramos, Jairo / Caywood, Laura J / Prough, Michael B / Clouse, Jason E / Herington, Sharlene D / Slifer, Susan H / Fuzzell, M Denise / Fuzzell, Sarada L / Hochstetler, Sherri D / Miskimen, Kristy L / Main, Leighanne R / Osterman, Michael D / Zaman, Andrew F / Whitehead, Patrice L / Adams, Larry D / Laux, Renee A / Song, Yeunjoo E / Foroud, Tatiana M / Mayeux, Richard P /

St George-Hyslop, Peter / Ogrocki, Paula K / Lerner, Alan J / Vance, Jeffery M / Cuccaro, Michael L / Haines, Jonathan L / Pericak-Vance, Margaret A / Scott, William K

Alzheimer's & dementia : the journal of the Alzheimer's Association

2022 Volume 19, Issue 2, Page(s) 611–620

Abstract: Introduction: Studies of cognitive impairment (CI) in Amish communities have identified sibships containing CI and cognitively unimpaired (CU) individuals. We hypothesize that CU individuals may carry protective alleles delaying age at onset (AAO) of CI. ...

Abstract	Introduction: Studies of cognitive impairment (CI) in Amish communities have identified sibships containing CI and cognitively unimpaired (CU) individuals. We hypothesize that CU individuals may carry protective alleles delaying age at onset (AAO) of CI. Methods: A total of 1522 individuals screened for CI were genotyped. The outcome studied was AAO for CI individuals or age at last normal exam for CU individuals. Cox mixed-effects models examined association between age and single nucleotide variants (SNVs). Results: Three SNVs were significantly associated (P < 5 × 10 Discussion: The replicated genome-wide significant association with AAO on chromosome 17 is located in the SHISA6 gene, which is involved in post-synaptic transmission in the hippocampus and is a biologically plausible candidate gene for Alzheimer's disease.
MeSH term(s)	Humans ; Alzheimer Disease/genetics ; Genome-Wide Association Study ; Genotype ; Cognitive Dysfunction/genetics ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2022-05-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2211627-8
ISSN	1552-5279 ; 1552-5260
ISSN (online)	1552-5279
ISSN	1552-5260
DOI	10.1002/alz.12686
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