1
|
Cukier HN, Simon SA, Tang E, Golightly CG, Laverde-Paz MJ, Adams LD, Starks TD, Vance JM, Cuccaro ML, Haines JL, Byrd GS, Pericak-Vance MA, Dykxhoorn DM. Generation of an induced pluripotent stem cell line (UMi043-A) from an African American patient with Alzheimer's disease carrying an ABCA7 deletion (p.Arg578Alafs). Stem Cell Res 2024; 76:103364. [PMID: 38422817 DOI: 10.1016/j.scr.2024.103364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/17/2024] [Accepted: 02/24/2024] [Indexed: 03/02/2024] Open
Abstract
The ATP-binding cassette, subfamily A (ABC1), member 7 (ABCA7) gene is associated with Alzheimer's disease (AD) risk in populations of African, Asian, and European ancestry1-5. Numerous ABCA7 mutations contributing to risk have been identified, including a 44 base pair deletion (rs142076058) specific to individuals of African ancestry and predicted to cause a frameshift mutation (p.Arg578Alafs) (Cukier et al., 2016). The UMi043-A human induced pluripotent stem cell line was derived from an African American individual with AD who is heterozygous for this deletion and is a resource to further investigate ABCA7 and how this African-specific deletion may influence disease pathology.
Collapse
Affiliation(s)
- Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Shaina A Simon
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Eugene Tang
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Charles G Golightly
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Mayra Juliana Laverde-Paz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Larry Deon Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Takiyah D Starks
- Social Sciences and Health Policy, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Goldie S Byrd
- Social Sciences and Health Policy, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| |
Collapse
|
2
|
Cukier HN, Duarte CL, Laverde-Paz MJ, Simon SA, Van Booven DJ, Miyares AT, Whitehead PL, Hamilton-Nelson KL, Adams LD, Carney RM, Cuccaro ML, Vance JM, Pericak-Vance MA, Griswold AJ, Dykxhoorn DM. An Alzheimer's disease risk variant in TTC3 modifies the actin cytoskeleton organization and the PI3K-Akt signaling pathway in iPSC-derived forebrain neurons. Neurobiol Aging 2023; 131:182-195. [PMID: 37677864 PMCID: PMC10538380 DOI: 10.1016/j.neurobiolaging.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/11/2023] [Indexed: 09/09/2023]
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.
Collapse
Affiliation(s)
- Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Carolina L Duarte
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mayra J Laverde-Paz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shaina A Simon
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derek J Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Amanda T Miyares
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; JJ Vance Memorial Summer Internship in Biological and Computational Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Regina M Carney
- Mental Health & Behavioral Science Service, Bruce W. Carter VA Medical Center, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.
| |
Collapse
|
3
|
Cukier HN, Duarte CL, Laverde-Paz MJ, Simon SA, Van Booven DJ, Miyares AT, Whitehead PL, Hamilton-Nelson KL, Adams LD, Carney RM, Cuccaro ML, Vance JM, Pericak-Vance MA, Griswold AJ, Dykxhoorn DM. An Alzheimer's disease risk variant in TTC3 modifies the actin cytoskeleton organization and the PI3K-Akt signaling pathway in iPSC-derived forebrain neurons. bioRxiv 2023:2023.05.25.542316. [PMID: 37292815 PMCID: PMC10246004 DOI: 10.1101/2023.05.25.542316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A missense variant in the tetratricopeptide repeat domain 3 ( TTC3 ) gene (rs377155188, p.S1038C, NM_003316.4:c.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 were 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 3D 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. Highlights The AD risk variant TTC3 p.S1038C reduces the expression levels of TTC3 The variant modifies the expression of AD specific genes BACE1 , INPP5F , and UNC5C Neurons with the variant are enriched for genes in the PI3K-Akt pathwayiPSC-derived neurons with the alteration have increased neurite length and branchingThe variant interferes with actin cytoskeleton and is ameliorated by Cytochalasin D.
Collapse
|
4
|
DeRosa BA, Simon SA, Cuccaro ML, Cukier HN, Vance JM, Vance MA, Dykxhoorn DM. Examining the impact of a rare protein‐truncating
SORL1
variant on AD pathology. Alzheimers Dement 2022. [DOI: 10.1002/alz.066993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Brooke A DeRosa
- John P. Hussman Institute for Human Genomics Miami FL USA
- University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. MacDonald Foundation Department of Human Genetics Miami FL USA
| | - Shaina A Simon
- John P. Hussman Institute for Human Genomics Miami FL USA
- University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. MacDonald Foundation Department of Human Genetics Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics Miami FL USA
- University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Holly N. Cukier
- John P. Hussman Institute for Human Genomics Miami FL USA
- University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. MacDonald Foundation Department of Human Genetics Miami FL USA
| | - Jeffery M. Vance
- University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
| | - Margaret A. Vance
- University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. MacDonald Foundation Department of Human Genetics Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Derek M. Dykxhoorn
- University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| |
Collapse
|
5
|
DeRosa BA, Hokayem JE, Artimovich E, Garcia-Serje C, Phillips AW, Van Booven D, Nestor JE, Wang L, Cuccaro ML, Vance JM, Pericak-Vance MA, Cukier HN, Nestor MW, Dykxhoorn DM. Author Correction: Convergent Pathways in Idiopathic Autism Revealed by Time Course Transcriptomic Analysis of Patient-Derived Neurons. Sci Rep 2022; 12:3445. [PMID: 35210532 PMCID: PMC8873475 DOI: 10.1038/s41598-022-07356-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Brooke A DeRosa
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.,Department of Medical & Molecular Genetics, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Jimmy El Hokayem
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | - Catherine Garcia-Serje
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | - Lily Wang
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.,Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.,John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Jefery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.,John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.,Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.,John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.,Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.,Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA. .,John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
| |
Collapse
|
6
|
Oron O, Rodgers JP, Vasquez ML, Celis K, Maddy KS, Chambers CM, Feliciano‐Astacio BE, Beecham GW, Cuccaro ML, Cukier HN, Blurton‐Jones M, Pericak‐Vance MA, Vance JM, Dykxhoorn DM. Transgenic
APOEε4/4
overexpression induces reactivity in astrocytes with a European
APOEε4/4
local ancestry, but not in astrocytes with an African
APOEε4/4
local ancestry. Alzheimers Dement 2021. [DOI: 10.1002/alz.056397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Oded Oron
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Joey P Rodgers
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Marina Lipkin Vasquez
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Katrina Celis
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Krisna S. Maddy
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Christopher M Chambers
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Holly N. Cukier
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| |
Collapse
|
7
|
Rajabli F, Feliciano-Astacio BE, Cukier HN, Wang L, Griswold AJ, Hamilton-Nelson KL, Adams LD, Rodriguez VC, Mena PR, Tejada S, Celis K, Whitehead PL, Van Booven DJ, Hofmann NK, Bussies PL, Prough M, Chinea A, Feliciano NI, Vardarajan BN, Reitz C, Lee JH, Prince MJ, Jimenez IZ, Mayeux RP, Acosta H, Dalgard CL, Haines JL, Vance JM, Cuccaro ML, Beecham GW, Pericak-Vance MA. Linkage of Alzheimer disease families with Puerto Rican ancestry identifies a chromosome 9 locus. Neurobiol Aging 2021; 104:115.e1-115.e7. [PMID: 33902942 DOI: 10.1016/j.neurobiolaging.2021.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/08/2021] [Accepted: 02/23/2021] [Indexed: 12/30/2022]
Abstract
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.
Collapse
Affiliation(s)
- Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Vanessa C Rodriguez
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Pedro R Mena
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sergio Tejada
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Katrina Celis
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derek J Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Natalia K Hofmann
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Parker L Bussies
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Angel Chinea
- Universidad Central del Caribe, Bayamón, PR, USA
| | - Nereida I Feliciano
- Hospital De Psiquiatría Estatal Dr. Ramón Fernández Marina-Centro Médico, San Juan, PR, USA
| | - Badri N Vardarajan
- Departments of Neurology, Psychiatry, and Epidemiology, Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Christiane Reitz
- Departments of Neurology, Psychiatry, and Epidemiology, Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Joseph H Lee
- Departments of Neurology, Psychiatry, and Epidemiology, Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Martin J Prince
- Department of Epidemiological Psychiatry, Centre for Public Mental Health, Institute of Psychiatry, King's College, London, UK
| | | | - Richard P Mayeux
- Departments of Neurology, Psychiatry, and Epidemiology, Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | | | - Clifton L Dalgard
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jonathan L Haines
- Department of Population & Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.
| |
Collapse
|
8
|
Laverde-Paz MJ, Nuytemans K, Wang L, Vance JM, Pericak-Vance MA, Dykxhoorn DM, Cukier HN. Derivation of stem cell line UMi028-A-2 containing a CRISPR/Cas9 induced Alzheimer's disease risk variant p.S1038C in the TTC3 gene. Stem Cell Res 2021; 52:102258. [PMID: 33626494 DOI: 10.1016/j.scr.2021.102258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 11/28/2022] Open
Abstract
The UMi028-A-2 human induced pluripotent stem cell line carries a homozygous mutation (rs377155188, C>G, p.S1038C) in the tetratricopeptide repeat domain 3 (TTC3) gene that was introduced via CRISPR/Cas9 genome editing. The line was originally derived from a neurologically normal male and has been thoroughly characterized following editing. The p.S1038C variant has been shown to potentially contribute to the risk of late onset Alzheimer's disease and is a resource to further investigate the consequences of TTC3 and this alteration in disease pathology.
Collapse
Affiliation(s)
- Mayra Juliana Laverde-Paz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136.
| |
Collapse
|
9
|
Wang L, Cukier HN, Rajabli F, Hofmann NK, Adams LD, Rodriguez VC, Mena PR, Garcia‐Serje C, Silva C, Feliciano NI, Feliciano‐Astacio BE, Acosta H, Vance JM, Beecham GW, Pericak‐Vance MA. Functional analysis of candidate genes identified through whole genome sequencing in Caribbean Hispanic families for late‐onset Alzheimer disease. Alzheimers Dement 2020. [DOI: 10.1002/alz.046017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Holly N. Cukier
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Natalia K. Hofmann
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Vanessa C. Rodriguez
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Pedro Ramon Mena
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Catherine Garcia‐Serje
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | | | | | | | | - Jeffery M. Vance
- Dr. John T. Macdonald Department of Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Gary W. Beecham
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | | |
Collapse
|
10
|
Dykxhoorn DM, Simon SA, Kunkle BW, Cuccaro ML, Vance JM, Cukier HN, Pericak‐Vance MA. Functional characterization of an Alzheimer disease‐associated deletion in SORL1. Alzheimers Dement 2020. [DOI: 10.1002/alz.045888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Shaina A. Simon
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Jeffery M. Vance
- Dr. John T. Macdonald Department of Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Holly N. Cukier
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | |
Collapse
|
11
|
Oron O, Maddy KS, Celis K, Cukier HN, Pericak‐Vance MA, Young J, Blurton‐Jones M, Griswold AJ, Vance JM, Dykxhoorn DM. African and European local ancestry surrounding Apolipoprotein E has a differential biological effect upon acute amyloid beta exposure in iPSC‐differentiated astrocytes. Alzheimers Dement 2020. [DOI: 10.1002/alz.045424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
| | | | - Katrina Celis
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Holly N. Cukier
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | | - Juan Young
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Mathew Blurton‐Jones
- Department of Neurobiology and Behavior University of California Irvine Irvine CA USA
| | - Anthony J. Griswold
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Jeffery M. Vance
- Dr. John T. Macdonald Department of Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| |
Collapse
|
12
|
Cukier HN, Laverde‐Paz J, Ramirez J, Adams LD, Starks TD, Vance JM, Cuccaro ML, Blurton‐Jones M, Haines JL, Byrd GS, Pericak‐Vance MA, Dykxhoorn DM. iPSC‐derived neurons and microglia with an African‐specific
ABCA7
frameshift deletion have impaired function. Alzheimers Dement 2020. [DOI: 10.1002/alz.046109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Holly N. Cukier
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Department of Neurology University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Department of Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Juliana Laverde‐Paz
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Juliana Ramirez
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Takiyah D. Starks
- Maya Angelou Center for Health Equity (MACHE)/Wake Forest School of Medicine Winston‐Salem NC USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Department of Neurology University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Department of Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Mathew Blurton‐Jones
- Department of Neurobiology and Behavior University of California, Irvine Irvine CA USA
| | | | - Goldie S. Byrd
- Maya Angelou Center for Health Equity (MACHE)/Wake Forest School of Medicine Winston Salem NC USA
| | - Margaret A Pericak‐Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Department of Neurology University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Department of Genetics University of Miami Miller School of Medicine Miami FL USA
| |
Collapse
|
13
|
Cukier HN, Griswold AJ, Hofmann NK, Gomez L, Whitehead PL, Abramson RK, Gilbert JR, Cuccaro ML, Dykxhoorn DM, Pericak-Vance MA. Three Brothers With Autism Carry a Stop-Gain Mutation in the HPA-Axis Gene NR3C2. Autism Res 2020; 13:523-531. [PMID: 32064789 DOI: 10.1002/aur.2269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/20/2019] [Accepted: 01/06/2020] [Indexed: 12/30/2022]
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.
Collapse
Affiliation(s)
- Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.,Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| | - Natalia K Hofmann
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Ruth K Abramson
- University of South Carolina School of Medicine, Columbia, South Carolina
| | - John R Gilbert
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.,Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| |
Collapse
|
14
|
Dykxhoorn DM, Cukier HN, Maddy KS, Adams LD, Starks TD, Celis K, Acosta H, Feliciano-Astacio BE, Byrd GS, Cuccaro ML, Beecham GW, Pericak-Vance MA, Vance JM. P3-206: INVESTIGATING ANCESTRY SPECIFIC DIFFERENCES IN APOE
FUNCTION USING INDUCED PLURIPOTENT STEM CELLS. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.06.3236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics; University of Miami; Miami FL USA
| | - Holly N. Cukier
- John P. Hussman Institute for Human Genomics; University of Miami; Miami FL USA
| | | | - Larry D. Adams
- John P. Hussman Institute for Human Genomics; University of Miami Miller School of Medicine; Miami FL USA
| | - Takiyah D. Starks
- Maya Angelou Center for Health Equity (MACHE)/Wake Forest School of Medicine; Winston-Salem NC USA
| | - Katrina Celis
- John P. Hussman Institute for Human Genomics; University of Miami Miller School of Medicine; Miami FL USA
| | | | | | - Goldie S. Byrd
- Maya Angelou Center for Health Equity (MACHE)/Wake Forest School of Medicine; Winston-Salem NC USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics; University of Miami Miller School of Medicine; Miami FL USA
| | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics; University of Miami Miller School of Medicine; Miami FL USA
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics; University of Miami Miller School of Medicine; Miami FL USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics; University of Miami Miller School of Medicine; Miami FL USA
| |
Collapse
|
15
|
Cukier HN, Nuytemans K, Strong TA, Laverde-Paz J, Eldabbas RA, Pericak-Vance MA, Dykxhoorn DM. UTILIZING CRISPR TO INVESTIGATE AN ETHNIC SPECIFIC DELETION IN ABCA7. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.06.2549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
16
|
Cukier HN, Johnson FS, Ramirez J, Whitehead PL, Adams LD, Carney RM, Vance JM, Cuccaro ML, Pericak-Vance MA, Dykxhoorn DM. P2‐114: A STEM CELL MODEL OF A RARE, SEGREGATING
TTC3
MUTATION. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.06.800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
17
|
DeRosa BA, El Hokayem J, Artimovich E, Garcia-Serje C, Phillips AW, Van Booven D, Nestor JE, Wang L, Cuccaro ML, Vance JM, Pericak-Vance MA, Cukier HN, Nestor MW, Dykxhoorn DM. Convergent Pathways in Idiopathic Autism Revealed by Time Course Transcriptomic Analysis of Patient-Derived Neurons. Sci Rep 2018; 8:8423. [PMID: 29849033 PMCID: PMC5976773 DOI: 10.1038/s41598-018-26495-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 05/15/2018] [Indexed: 12/14/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Brooke A DeRosa
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA.,Department of Medical & Molecular Genetics, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Jimmy El Hokayem
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA
| | - Elena Artimovich
- The Hussman Institute for Autism, Baltimore, Maryland, 21229, USA
| | - Catherine Garcia-Serje
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA
| | - Andre W Phillips
- The Hussman Institute for Autism, Baltimore, Maryland, 21229, USA
| | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA
| | | | - Lily Wang
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA.,Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA.,John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA.,John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA.,Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA.,John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA.,Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA
| | - Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA.,Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA
| | - Michael W Nestor
- The Hussman Institute for Autism, Baltimore, Maryland, 21229, USA.
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA. .,John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA.
| |
Collapse
|
18
|
Cukier HN, Kunkle BK, Hamilton KL, Rolati S, Kohli MA, Whitehead PL, Jaworski J, Vance JM, Cuccaro ML, Carney RM, Gilbert JR, Farrer LA, Martin ER, Beecham GW, Haines JL, Pericak-Vance MA. Exome Sequencing of Extended Families with Alzheimer's Disease Identifies Novel Genes Implicated in Cell Immunity and Neuronal Function. ACTA ACUST UNITED AC 2017; 7. [PMID: 29177109 PMCID: PMC5698805 DOI: 10.4172/2161-0460.1000355] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Objective Alzheimer’s disease (AD) is a neurodegenerative disorder for which more than 20 genetic loci have been implicated to date. However, studies demonstrate not all genetic factors have been identified. Therefore, in this study we seek to identify additional rare variants and novel genes potentially contributing to AD. Methods Whole exome sequencing was performed on 23 multi-generational families with an average of eight affected subjects. Exome sequencing was filtered for rare, nonsynonymous and loss-of-function variants. Alterations predicted to have a functional consequence and located within either a previously reported AD gene, a linkage peak (LOD>2), or clustering in the same gene across multiple families, were prioritized. Results Rare variants were found in known AD risk genes including AKAP9, CD33, CR1, EPHA1, INPP5D, NME8, PSEN1, SORL1, TREM2 and UNC5C. Three families had five variants of interest in linkage regions with LOD>2. Genes with segregating alterations in these peaks include CD163L1 and CLECL1, two genes that have both been implicated in immunity, CTNNA1, which encodes a catenin in the cerebral cortex and MIEF1, a gene that may induce mitochondrial dysfunction and has the potential to damage neurons. Four genes were identified with alterations in more than one family include PLEKHG5, a gene that causes Charcot-Marie-Tooth disease and THBS2, which promotes synaptogenesis. Conclusion Utilizing large families with a heavy burden of disease allowed for the identification of rare variants co-segregating with disease. Variants were identified in both known AD risk genes and in novel genes.
Collapse
Affiliation(s)
- H N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - B K Kunkle
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - K L Hamilton
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - S Rolati
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - M A Kohli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - P L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - J Jaworski
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - J M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - M L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - R M Carney
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Mental Health and Behavioral Sciences Service, Miami Veterans Affairs, Miami, FL, USA
| | - J R Gilbert
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - L A Farrer
- Departments of Medicine, Neurology, Ophthalmology, Genetics and Genomics, Epidemiology and Biostatistics, Boston University, Boston, MA, USA
| | - E R Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - G W Beecham
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - J L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - M A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA.,John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| |
Collapse
|
19
|
Cuccaro ML, Reitz C, Beecham GW, Cukier HN, Celis K, Deon Adams L, Starks T, Joseph N, Whitehead PL, Hamilton‐Nelson KL, Reyes‐Dumeyer D, Byfield G, Bennett DA, Rosenberg RN, Boeve BF, Sweet RA, Cruchaga C, Haines JL, Vance JM, Byrd GS, Mayeux R, Pericak‐Vance MA. [P3–094]: RESOURCE OF MULTIPLEX AFRICAN AMERICAN FAMILIES FOR WHOLE‐GENOME SEQUENCING. Alzheimers Dement 2017. [DOI: 10.1016/j.jalz.2017.06.1304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of MedicineMiamiFLUSA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Cukier HN, Mehta N, Ramirez J, Rolati S, Whitehead PL, Deon Adams L, Celis K, Carney R, Vance JM, Cuccaro ML, Byrd GS, Pericak‐Vance MA, Dykxhoorn DM. [P2–114]: PATIENT‐DERIVED IPSC MODEL OF AN
ABCA7
FRAMESHIFT DELETION ASSOCIATED WITH ALZHEIMER's DISEASE IN AFRICAN AMERICANS. Alzheimers Dement 2017. [DOI: 10.1016/j.jalz.2017.06.764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
21
|
Cuccaro ML, Carney RM, Zhang Y, Bohm C, Kunkle BW, Vardarajan BN, Whitehead PL, Cukier HN, Mayeux R, St George-Hyslop P, Pericak-Vance MA. SORL1 mutations in early- and late-onset Alzheimer disease. Neurol Genet 2016; 2:e116. [PMID: 27822510 PMCID: PMC5082932 DOI: 10.1212/nxg.0000000000000116] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/23/2016] [Indexed: 11/18/2022]
Abstract
Objective: To characterize the clinical and molecular effect of mutations in the sortilin-related receptor (SORL1) gene. Methods: We performed whole-exome sequencing in early-onset Alzheimer disease (EOAD) and late-onset Alzheimer disease (LOAD) families followed by functional studies of select variants. The phenotypic consequences associated with SORL1 mutations were characterized based on clinical reviews of medical records. Functional studies were completed to evaluate β-amyloid (Aβ) production and amyloid precursor protein (APP) trafficking associated with SORL1 mutations. Results: SORL1 alterations were present in 2 EOAD families. In one, a SORL1 T588I change was identified in 4 individuals with AD, 2 of whom had parkinsonian features. In the second, an SORL1 T2134 alteration was found in 3 of 4 AD cases, one of whom had postmortem Lewy bodies. Among LOAD cases, 4 individuals with either SORL1 A528T or T947M alterations had parkinsonian features. Functionally, the variants weaken the interaction of the SORL1 protein with full-length APP, altering levels of Aβ and interfering with APP trafficking. Conclusions: The findings from this study support an important role for SORL1 mutations in AD pathogenesis by way of altering Aβ levels and interfering with APP trafficking. In addition, the presence of parkinsonian features among select individuals with AD and SORL1 mutations merits further investigation.
Collapse
Affiliation(s)
- Michael L Cuccaro
- John P. Hussman Institute for Human Genomics (M.L.C., R.M.C., B.W.K., P.L.W., H.N.C., M.A.P.-V.), University of Miami Miller School of Medicine, FL; Mental Health & Behavioral Science Service (R.M.C.), Bruce W. Carter VA Medical Center, Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Tanz Centre for Research in Neurodegenerative Diseases and Department of Medicine (Y.Z., C.B., P.S.G.-H.), University of Toronto, Ontario, Canada; Cambridge Institute for Medical Research (P.S.G.-H.), Department of Clinical Neurosciences, University of Cambridge, United Kingdom; and Dr. John T. Macdonald Foundation Department of Human Genetics (M.L.C., M.A.P.-V.), Miller School of Medicine, University of Miami, FL
| | - Regina M Carney
- John P. Hussman Institute for Human Genomics (M.L.C., R.M.C., B.W.K., P.L.W., H.N.C., M.A.P.-V.), University of Miami Miller School of Medicine, FL; Mental Health & Behavioral Science Service (R.M.C.), Bruce W. Carter VA Medical Center, Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Tanz Centre for Research in Neurodegenerative Diseases and Department of Medicine (Y.Z., C.B., P.S.G.-H.), University of Toronto, Ontario, Canada; Cambridge Institute for Medical Research (P.S.G.-H.), Department of Clinical Neurosciences, University of Cambridge, United Kingdom; and Dr. John T. Macdonald Foundation Department of Human Genetics (M.L.C., M.A.P.-V.), Miller School of Medicine, University of Miami, FL
| | - Yalun Zhang
- John P. Hussman Institute for Human Genomics (M.L.C., R.M.C., B.W.K., P.L.W., H.N.C., M.A.P.-V.), University of Miami Miller School of Medicine, FL; Mental Health & Behavioral Science Service (R.M.C.), Bruce W. Carter VA Medical Center, Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Tanz Centre for Research in Neurodegenerative Diseases and Department of Medicine (Y.Z., C.B., P.S.G.-H.), University of Toronto, Ontario, Canada; Cambridge Institute for Medical Research (P.S.G.-H.), Department of Clinical Neurosciences, University of Cambridge, United Kingdom; and Dr. John T. Macdonald Foundation Department of Human Genetics (M.L.C., M.A.P.-V.), Miller School of Medicine, University of Miami, FL
| | - Christopher Bohm
- John P. Hussman Institute for Human Genomics (M.L.C., R.M.C., B.W.K., P.L.W., H.N.C., M.A.P.-V.), University of Miami Miller School of Medicine, FL; Mental Health & Behavioral Science Service (R.M.C.), Bruce W. Carter VA Medical Center, Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Tanz Centre for Research in Neurodegenerative Diseases and Department of Medicine (Y.Z., C.B., P.S.G.-H.), University of Toronto, Ontario, Canada; Cambridge Institute for Medical Research (P.S.G.-H.), Department of Clinical Neurosciences, University of Cambridge, United Kingdom; and Dr. John T. Macdonald Foundation Department of Human Genetics (M.L.C., M.A.P.-V.), Miller School of Medicine, University of Miami, FL
| | - Brian W Kunkle
- John P. Hussman Institute for Human Genomics (M.L.C., R.M.C., B.W.K., P.L.W., H.N.C., M.A.P.-V.), University of Miami Miller School of Medicine, FL; Mental Health & Behavioral Science Service (R.M.C.), Bruce W. Carter VA Medical Center, Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Tanz Centre for Research in Neurodegenerative Diseases and Department of Medicine (Y.Z., C.B., P.S.G.-H.), University of Toronto, Ontario, Canada; Cambridge Institute for Medical Research (P.S.G.-H.), Department of Clinical Neurosciences, University of Cambridge, United Kingdom; and Dr. John T. Macdonald Foundation Department of Human Genetics (M.L.C., M.A.P.-V.), Miller School of Medicine, University of Miami, FL
| | - Badri N Vardarajan
- John P. Hussman Institute for Human Genomics (M.L.C., R.M.C., B.W.K., P.L.W., H.N.C., M.A.P.-V.), University of Miami Miller School of Medicine, FL; Mental Health & Behavioral Science Service (R.M.C.), Bruce W. Carter VA Medical Center, Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Tanz Centre for Research in Neurodegenerative Diseases and Department of Medicine (Y.Z., C.B., P.S.G.-H.), University of Toronto, Ontario, Canada; Cambridge Institute for Medical Research (P.S.G.-H.), Department of Clinical Neurosciences, University of Cambridge, United Kingdom; and Dr. John T. Macdonald Foundation Department of Human Genetics (M.L.C., M.A.P.-V.), Miller School of Medicine, University of Miami, FL
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics (M.L.C., R.M.C., B.W.K., P.L.W., H.N.C., M.A.P.-V.), University of Miami Miller School of Medicine, FL; Mental Health & Behavioral Science Service (R.M.C.), Bruce W. Carter VA Medical Center, Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Tanz Centre for Research in Neurodegenerative Diseases and Department of Medicine (Y.Z., C.B., P.S.G.-H.), University of Toronto, Ontario, Canada; Cambridge Institute for Medical Research (P.S.G.-H.), Department of Clinical Neurosciences, University of Cambridge, United Kingdom; and Dr. John T. Macdonald Foundation Department of Human Genetics (M.L.C., M.A.P.-V.), Miller School of Medicine, University of Miami, FL
| | - Holly N Cukier
- John P. Hussman Institute for Human Genomics (M.L.C., R.M.C., B.W.K., P.L.W., H.N.C., M.A.P.-V.), University of Miami Miller School of Medicine, FL; Mental Health & Behavioral Science Service (R.M.C.), Bruce W. Carter VA Medical Center, Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Tanz Centre for Research in Neurodegenerative Diseases and Department of Medicine (Y.Z., C.B., P.S.G.-H.), University of Toronto, Ontario, Canada; Cambridge Institute for Medical Research (P.S.G.-H.), Department of Clinical Neurosciences, University of Cambridge, United Kingdom; and Dr. John T. Macdonald Foundation Department of Human Genetics (M.L.C., M.A.P.-V.), Miller School of Medicine, University of Miami, FL
| | - Richard Mayeux
- John P. Hussman Institute for Human Genomics (M.L.C., R.M.C., B.W.K., P.L.W., H.N.C., M.A.P.-V.), University of Miami Miller School of Medicine, FL; Mental Health & Behavioral Science Service (R.M.C.), Bruce W. Carter VA Medical Center, Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Tanz Centre for Research in Neurodegenerative Diseases and Department of Medicine (Y.Z., C.B., P.S.G.-H.), University of Toronto, Ontario, Canada; Cambridge Institute for Medical Research (P.S.G.-H.), Department of Clinical Neurosciences, University of Cambridge, United Kingdom; and Dr. John T. Macdonald Foundation Department of Human Genetics (M.L.C., M.A.P.-V.), Miller School of Medicine, University of Miami, FL
| | - Peter St George-Hyslop
- John P. Hussman Institute for Human Genomics (M.L.C., R.M.C., B.W.K., P.L.W., H.N.C., M.A.P.-V.), University of Miami Miller School of Medicine, FL; Mental Health & Behavioral Science Service (R.M.C.), Bruce W. Carter VA Medical Center, Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Tanz Centre for Research in Neurodegenerative Diseases and Department of Medicine (Y.Z., C.B., P.S.G.-H.), University of Toronto, Ontario, Canada; Cambridge Institute for Medical Research (P.S.G.-H.), Department of Clinical Neurosciences, University of Cambridge, United Kingdom; and Dr. John T. Macdonald Foundation Department of Human Genetics (M.L.C., M.A.P.-V.), Miller School of Medicine, University of Miami, FL
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics (M.L.C., R.M.C., B.W.K., P.L.W., H.N.C., M.A.P.-V.), University of Miami Miller School of Medicine, FL; Mental Health & Behavioral Science Service (R.M.C.), Bruce W. Carter VA Medical Center, Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Tanz Centre for Research in Neurodegenerative Diseases and Department of Medicine (Y.Z., C.B., P.S.G.-H.), University of Toronto, Ontario, Canada; Cambridge Institute for Medical Research (P.S.G.-H.), Department of Clinical Neurosciences, University of Cambridge, United Kingdom; and Dr. John T. Macdonald Foundation Department of Human Genetics (M.L.C., M.A.P.-V.), Miller School of Medicine, University of Miami, FL
| |
Collapse
|
22
|
Abstract
Since the creation of induced Pluripotent Stem Cells (iPSCs) ten years ago, hundreds of publications have demonstrated their considerable impact on disease modeling and therapy. In this commentary, we will summarize key milestones, benefits and challenges in the iPSC field. Furthermore, we will highlight blood as an effective and easily accessible source for patient-specific iPSCs derivation in the context of work done in our laboratory and others.
Collapse
Affiliation(s)
- Jimmy El Hokayem
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, USA
| | - Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, USA.,Department of Neurology, University of Miami Miller School of Medicine, Miami, USA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, USA.,John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, USA
| |
Collapse
|
23
|
Dykxhoorn DM, Cukier HN, Kunkle BW, Vardarajan BN, Rolati S, Hamilton-Nelson KL, Kohli MA, Whitehead PL, Van Booven DJ, Lang R, Farrer LA, Cuccaro ML, Vance JM, Gilbert JR, Beecham GW, Martin ER, Carney RM, Mayeux R, Schellenberg GD, Byrd GS, Haines JL, Pericak-Vance MA. O1‐03‐02:
ABCA7
Frameshift Deletion Associated with Alzheimer’s Disease in African Americans. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Rosalyn Lang
- North Carolina A&T State UniversityGreensboroNC USA
| | | | | | | | | | | | - Eden R. Martin
- University of Miami Miller School of MedicineMiamiFL USA
| | | | | | | | | | | | | |
Collapse
|
24
|
Cukier HN, Kunkle BW, Rolati S, Whitehead PL, Vance JM, Cuccaro ML, Carney RM, Gilbert JR, Martin ER, Beecham GW, Haines JL, Pericak-Vance MA, Hamilton-Nelson KL. O1‐09‐02: Whole Exome Sequencing of Late Onset Multiplex Families Identifies Rare Coding Variants in Known and Novel Alzheimer’s Disease Genes. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of MiamiMiamiFL USA
| | | | | | | | | | - Regina M. Carney
- University of MiamiMiamiFL USA
- Miami VA Healthcare SystemMiamiFL USA
| | | | - Eden R. Martin
- University of Miami Miller School of MedicineMiamiFL USA
| | | | | | | | | |
Collapse
|
25
|
Kunkle BW, Vardarajan BN, Naj AC, Cukier HN, Dykxhoorn DM, Rolati S, Whitehead PL, Carney RM, Cuccaro ML, Vance JM, Genetics Consortium AD, Farrer LA, Haines JL, Schellenberg GD, Martin ER, Reitz C, Beecham GW, Mayeux R, Pericak-Vance MA. O1‐03‐03: Identification of Novel Candidate Genes for Early‐Onset Alzheimer's Disease Through Integrated Whole‐Exome Sequencing and Exome Chip Array Association Analysis. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Adam C. Naj
- University of Pennsylvania Perelman School of MedicinePhiladelphiaPA USA
| | | | | | | | | | | | | | | | | | | | | | | | - Eden R. Martin
- University of Miami Miller School of MedicineMiamiFL USA
| | | | | | | | | |
Collapse
|
26
|
Cukier HN, Kunkle BW, Vardarajan BN, Rolati S, Hamilton-Nelson KL, Kohli MA, Whitehead PL, Dombroski BA, Van Booven D, Lang R, Dykxhoorn DM, Farrer LA, Cuccaro ML, Vance JM, Gilbert JR, Beecham GW, Martin ER, Carney RM, Mayeux R, Schellenberg GD, Byrd GS, Haines JL, Pericak-Vance MA. ABCA7 frameshift deletion associated with Alzheimer disease in African Americans. Neurol Genet 2016; 2:e79. [PMID: 27231719 PMCID: PMC4871806 DOI: 10.1212/nxg.0000000000000079] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/31/2016] [Indexed: 11/24/2022]
Abstract
Objective: To identify a causative variant(s) that may contribute to Alzheimer disease (AD) in African Americans (AA) in the ATP-binding cassette, subfamily A (ABC1), member 7 (ABCA7) gene, a known risk factor for late-onset AD. Methods: Custom capture sequencing was performed on ∼150 kb encompassing ABCA7 in 40 AA cases and 37 AA controls carrying the AA risk allele (rs115550680). Association testing was performed for an ABCA7 deletion identified in large AA data sets (discovery n = 1,068; replication n = 1,749) and whole exome sequencing of Caribbean Hispanic (CH) AD families. Results: A 44-base pair deletion (rs142076058) was identified in all 77 risk genotype carriers, which shows that the deletion is in high linkage disequilibrium with the risk allele. The deletion was assessed in a large data set (531 cases and 527 controls) and, after adjustments for age, sex, and APOE status, was significantly associated with disease (p = 0.0002, odds ratio [OR] = 2.13 [95% confidence interval (CI): 1.42–3.20]). An independent data set replicated the association (447 cases and 880 controls, p = 0.0117, OR = 1.65 [95% CI: 1.12–2.44]), and joint analysis increased the significance (p = 1.414 × 10−5, OR = 1.81 [95% CI: 1.38–2.37]). The deletion is common in AA cases (15.2%) and AA controls (9.74%), but in only 0.12% of our non-Hispanic white cohort. Whole exome sequencing of multiplex, CH families identified the deletion cosegregating with disease in a large sibship. The deleted allele produces a stable, detectable RNA strand and is predicted to result in a frameshift mutation (p.Arg578Alafs) that could interfere with protein function. Conclusions: This common ABCA7 deletion could represent an ethnic-specific pathogenic alteration in AD.
Collapse
Affiliation(s)
- Holly N Cukier
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Brian W Kunkle
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Badri N Vardarajan
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Sophie Rolati
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Martin A Kohli
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Beth A Dombroski
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Derek Van Booven
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Rosalyn Lang
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Lindsay A Farrer
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - John R Gilbert
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Regina M Carney
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Richard Mayeux
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Gerard D Schellenberg
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Goldie S Byrd
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Jonathan L Haines
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | | |
Collapse
|
27
|
Kohli MA, Cukier HN, Hamilton-Nelson KL, Rolati S, Kunkle BW, Whitehead PL, Züchner SL, Farrer LA, Martin ER, Beecham GW, Haines JL, Vance JM, Cuccaro ML, Gilbert JR, Schellenberg GD, Carney RM, Pericak-Vance MA. Segregation of a rare TTC3 variant in an extended family with late-onset Alzheimer disease. Neurol Genet 2016; 2:e41. [PMID: 27066578 PMCID: PMC4817909 DOI: 10.1212/nxg.0000000000000041] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/20/2015] [Indexed: 01/08/2023]
Abstract
OBJECTIVE The genetic risk architecture of Alzheimer disease (AD) is complex with single pathogenic mutations leading to early-onset AD, while both rare and common genetic susceptibility variants contribute to the more widespread late-onset AD (LOAD); we sought to discover novel genes contributing to LOAD risk. METHODS Whole-exome sequencing and genome-wide genotyping were performed on 11 affected individuals in an extended family with an apparent autosomal dominant pattern of LOAD. Variants of interest were then evaluated in a large cohort of LOAD cases and aged controls. RESULTS We detected a single rare, nonsynonymous variant shared in all 11 LOAD individuals, a missense change in the tetratricopeptide repeat domain 3 (TTC3) gene. The missense variant, rs377155188 (p.S1038C), is predicted to be damaging. Affecteds-only multipoint linkage analysis demonstrated that this region of TTC3 has a LOD score of 2.66 in this family. CONCLUSION The TTC3 p.S1038C substitution may represent a segregating, rare LOAD risk variant. Previous studies have shown that TTC3 expression is consistently reduced in LOAD patients and negatively correlated with AD neuropathology and that TTC3 is a regulator of Akt signaling, a key pathway disrupted in LOAD. This study demonstrates how utilizing whole-exome sequencing in a large, multigenerational family with a high incidence of LOAD could reveal a novel candidate gene.
Collapse
Affiliation(s)
- Martin A Kohli
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Holly N Cukier
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Sophie Rolati
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Brian W Kunkle
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Stephan L Züchner
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Lindsay A Farrer
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Jonathan L Haines
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - John R Gilbert
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Gerard D Schellenberg
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Regina M Carney
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| |
Collapse
|
28
|
DeRosa BA, Belle KC, Thomas BJ, Cukier HN, Pericak-Vance MA, Vance JM, Dykxhoorn DM. hVGAT-mCherry: A novel molecular tool for analysis of GABAergic neurons derived from human pluripotent stem cells. Mol Cell Neurosci 2015; 68:244-57. [PMID: 26284979 PMCID: PMC4593758 DOI: 10.1016/j.mcn.2015.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 07/30/2015] [Accepted: 08/10/2015] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND GABAergic synaptic transmission is known to play a critical role in the assembly of neuronal circuits during development and is responsible for maintaining the balance between excitatory and inhibitory signaling in the brain during maturation into adulthood. Importantly, defects in GABAergic neuronal function and signaling have been linked to a number of neurological diseases, including autism spectrum disorders, schizophrenia, and epilepsy. With patient-specific induced pluripotent stem cell (iPSC)-based models of neurological disease, it is now possible to investigate the disease mechanisms that underlie deficits in GABAergic function in affected human neurons. To that end, tools that enable the labeling and purification of viable GABAergic neurons from human pluripotent stem cells would be of great value. RESULTS To address the need for tools that facilitate the identification and isolation of viable GABAergic neurons from the in vitro differentiation of iPSC lines, a cell type-specific promoter-driven fluorescent reporter construct was developed that utilizes the human vesicular GABA transporter (hVGAT) promoter to drive the expression of mCherry specifically in VGAT-expressing neurons. The transduction of iPSC-derived forebrain neuronal cultures with the hVGAT promoter-mCherry lentiviral reporter construct specifically labeled GABAergic neurons. Immunocytochemical analysis of hVGAT-mCherry expression cells showed significant co-labeling with the GABAergic neuronal markers for endogenous VGAT, GABA, and GAD67. Expression of mCherry from the VGAT promoter showed expression in several cortical interneuron subtypes to similar levels. In addition, an effective and reproducible protocol was developed to facilitate the fluorescent activated cell sorting (FACS)-mediated purification of high yields of viable VGAT-positive cells. CONCLUSIONS These studies demonstrate the utility of the hVGAT-mCherry reporter construct as an effective tool for studying GABAergic neurons differentiated in vitro from human pluripotent stem cells. This approach could provide a means of obtaining large quantities of viable GABAergic neurons derived from disease-specific hiPSCs that could be used for functional assays or high-throughput screening of small molecule libraries.
Collapse
Affiliation(s)
- Brooke A DeRosa
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| | - Kinsley C Belle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| | - Blake J Thomas
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| | - Holly N Cukier
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| | - Margaret A Pericak-Vance
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| | - Jeffery M Vance
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| | - Derek M Dykxhoorn
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| |
Collapse
|
29
|
Cukier HN, Kunkle BW, Rolati S, Hamilton-Nelson KL, Kohli MA, Dombroski BA, Vardarajan BN, Whitehead PL, Booven DJ, Martin ER, Beecham GW, Farrer LA, Cuccaro ML, Vance JM, Mayeux R, Gilbert JR, Carney RM, Byrd GS, Haines JL, Schellenberg GD, Pericak-Vance MA, Lang R. P2‐013:
ABCA7
deletion associated with Alzheimer's disease in african americans. Alzheimers Dement 2015. [DOI: 10.1016/j.jalz.2015.06.549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Rosalyn Lang
- North Carolina A&T State UniversityGreensboroNCUSA
| | | |
Collapse
|
30
|
Kozol RA, Cukier HN, Zou B, Mayo V, De Rubeis S, Cai G, Griswold AJ, Whitehead PL, Haines JL, Gilbert JR, Cuccaro ML, Martin ER, Baker JD, Buxbaum JD, Pericak-Vance MA, Dallman JE. Two knockdown models of the autism genes SYNGAP1 and SHANK3 in zebrafish produce similar behavioral phenotypes associated with embryonic disruptions of brain morphogenesis. Hum Mol Genet 2015; 24:4006-23. [PMID: 25882707 DOI: 10.1093/hmg/ddv138] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 04/13/2015] [Indexed: 01/09/2023] Open
Abstract
Despite significant progress in the genetics of autism spectrum disorder (ASD), how genetic mutations translate to the behavioral changes characteristic of ASD remains largely unknown. ASD affects 1-2% of children and adults, and is characterized by deficits in verbal and non-verbal communication, and social interactions, as well as the presence of repetitive behaviors and/or stereotyped interests. ASD is clinically and etiologically heterogeneous, with a strong genetic component. Here, we present functional data from syngap1 and shank3 zebrafish loss-of-function models of ASD. SYNGAP1, a synaptic Ras GTPase activating protein, and SHANK3, a synaptic scaffolding protein, were chosen because of mounting evidence that haploinsufficiency in these genes is highly penetrant for ASD and intellectual disability (ID). Orthologs of both SYNGAP1 and SHANK3 are duplicated in the zebrafish genome and we find that all four transcripts (syngap1a, syngap1b, shank3a and shank3b) are expressed at the earliest stages of nervous system development with pronounced expression in the larval brain. Consistent with early expression of these genes, knockdown of syngap1b or shank3a cause common embryonic phenotypes including delayed mid- and hindbrain development, disruptions in motor behaviors that manifest as unproductive swim attempts, and spontaneous, seizure-like behaviors. Our findings indicate that both syngap1b and shank3a play novel roles in morphogenesis resulting in common brain and behavioral phenotypes.
Collapse
Affiliation(s)
- Robert A Kozol
- Department of Biology, University of Miami, Coral Gables, FL, USA,
| | - Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Bing Zou
- Department of Biology, University of Miami, Coral Gables, FL, USA
| | - Vera Mayo
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Friedman Brain Institute and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA and
| | - Guiqing Cai
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Friedman Brain Institute and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA and
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - John R Gilbert
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - James D Baker
- Department of Biology, University of Miami, Coral Gables, FL, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Friedman Brain Institute and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA and
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Julia E Dallman
- Department of Biology, University of Miami, Coral Gables, FL, USA,
| |
Collapse
|
31
|
Cukier HN, Dueker ND, Slifer SH, Lee JM, Whitehead PL, Lalanne E, Leyva N, Konidari I, Gentry RC, Hulme WF, Booven DV, Mayo V, Hofmann NK, Schmidt MA, Martin ER, Haines JL, Cuccaro ML, Gilbert JR, Pericak-Vance MA. Exome sequencing of extended families with autism reveals genes shared across neurodevelopmental and neuropsychiatric disorders. Mol Autism 2014; 5:1. [PMID: 24410847 PMCID: PMC3896704 DOI: 10.1186/2040-2392-5-1] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 12/04/2013] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Autism spectrum disorders (ASDs) comprise a range of neurodevelopmental conditions of varying severity, characterized by marked qualitative difficulties in social relatedness, communication, and behavior. Despite overwhelming evidence of high heritability, results from genetic studies to date show that ASD etiology is extremely heterogeneous and only a fraction of autism genes have been discovered. METHODS To help unravel this genetic complexity, we performed whole exome sequencing on 100 ASD individuals from 40 families with multiple distantly related affected individuals. All families contained a minimum of one pair of ASD cousins. Each individual was captured with the Agilent SureSelect Human All Exon kit, sequenced on the Illumina Hiseq 2000, and the resulting data processed and annotated with Burrows-Wheeler Aligner (BWA), Genome Analysis Toolkit (GATK), and SeattleSeq. Genotyping information on each family was utilized in order to determine genomic regions that were identical by descent (IBD). Variants identified by exome sequencing which occurred in IBD regions and present in all affected individuals within each family were then evaluated to determine which may potentially be disease related. Nucleotide alterations that were novel and rare (minor allele frequency, MAF, less than 0.05) and predicted to be detrimental, either by altering amino acids or splicing patterns, were prioritized. RESULTS We identified numerous potentially damaging, ASD associated risk variants in genes previously unrelated to autism. A subset of these genes has been implicated in other neurobehavioral disorders including depression (SLIT3), epilepsy (CLCN2, PRICKLE1), intellectual disability (AP4M1), schizophrenia (WDR60), and Tourette syndrome (OFCC1). Additional alterations were found in previously reported autism candidate genes, including three genes with alterations in multiple families (CEP290, CSMD1, FAT1, and STXBP5). Compiling a list of ASD candidate genes from the literature, we determined that variants occurred in ASD candidate genes 1.65 times more frequently than in random genes captured by exome sequencing (P = 8.55 × 10-5). CONCLUSIONS By studying these unique pedigrees, we have identified novel DNA variations related to ASD, demonstrated that exome sequencing in extended families is a powerful tool for ASD candidate gene discovery, and provided further evidence of an underlying genetic component to a wide range of neurodevelopmental and neuropsychiatric diseases.
Collapse
Affiliation(s)
- Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
| | - Nicole D Dueker
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
| | - Susan H Slifer
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
| | - Joycelyn M Lee
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
| | - Eminisha Lalanne
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
| | - Natalia Leyva
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
| | - Ioanna Konidari
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
| | - Ryan C Gentry
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
| | - William F Hulme
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
| | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
| | - Vera Mayo
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
| | - Natalia K Hofmann
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
| | - Michael A Schmidt
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Jonathan L Haines
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232-0700, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - John R Gilbert
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB-314 (M860), Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| |
Collapse
|
32
|
Cukier HN, Lee JM, Ma D, Young JI, Mayo V, Butler BL, Ramsook SS, Rantus JA, Abrams AJ, Whitehead PL, Wright HH, Abramson RK, Haines JL, Cuccaro ML, Pericak-Vance MA, Gilbert JR. The expanding role of MBD genes in autism: identification of a MECP2 duplication and novel alterations in MBD5, MBD6, and SETDB1. Autism Res 2012; 5:385-97. [PMID: 23055267 DOI: 10.1002/aur.1251] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/02/2012] [Indexed: 01/09/2023]
Abstract
The methyl-CpG-binding domain (MBD) gene family was first linked to autism over a decade ago when Rett syndrome, which falls under the umbrella of autism spectrum disorders (ASDs), was revealed to be predominantly caused by MECP2 mutations. Since that time, MECP2 alterations have been recognized in idiopathic ASD patients by us and others. Individuals with deletions across the MBD5 gene also present with ASDs, impaired speech, intellectual difficulties, repetitive behaviors, and epilepsy. These findings suggest that further investigations of the MBD gene family may reveal additional associations related to autism. We now describe the first study evaluating individuals with ASD for rare variants in four autosomal MBD family members, MBD5, MBD6, SETDB1, and SETDB2, and expand our initial screening in the MECP2 gene. Each gene was sequenced over all coding exons and evaluated for copy number variations in 287 patients with ASD and an equal number of ethnically matched control individuals. We identified 186 alterations through sequencing, approximately half of which were novel (96 variants, 51.6%). We identified 17 ASD specific, nonsynonymous variants, four of which were concordant in multiplex families: MBD5 Tyr1269Cys, MBD6 Arg883Trp, MECP2 Thr240Ser, and SETDB1 Pro1067del. Furthermore, a complex duplication spanning of the MECP2 gene was identified in two brothers who presented with developmental delay and intellectual disability. From our studies, we provide the first examples of autistic patients carrying potentially detrimental alterations in MBD6 and SETDB1, thereby demonstrating that the MBD gene family potentially plays a significant role in rare and private genetic causes of autism.
Collapse
Affiliation(s)
- Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Griswold AJ, Ma D, Cukier HN, Nations LD, Schmidt MA, Chung RH, Jaworski JM, Salyakina D, Konidari I, Whitehead PL, Wright HH, Abramson RK, Williams SM, Menon R, Martin ER, Haines JL, Gilbert JR, Cuccaro ML, Pericak-Vance MA. Evaluation of copy number variations reveals novel candidate genes in autism spectrum disorder-associated pathways. Hum Mol Genet 2012; 21:3513-23. [PMID: 22543975 DOI: 10.1093/hmg/dds164] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Autism spectrum disorders (ASDs) are highly heritable, yet relatively few associated genetic loci have been replicated. Copy number variations (CNVs) have been implicated in autism; however, the majority of loci contribute to <1% of the disease population. Therefore, independent studies are important to refine associated CNV regions and discover novel susceptibility genes. In this study, a genome-wide SNP array was utilized for CNV detection by two distinct algorithms in a European ancestry case-control data set. We identify a significantly higher burden in the number and size of deletions, and disrupting more genes in ASD cases. Moreover, 18 deletions larger than 1 Mb were detected exclusively in cases, implicating novel regions at 2q22.1, 3p26.3, 4q12 and 14q23. Case-specific CNVs provided further evidence for pathways previously implicated in ASDs, revealing new candidate genes within the GABAergic signaling and neural development pathways. These include DBI, an allosteric binder of GABA receptors, GABARAPL1, the GABA receptor-associated protein, and SLC6A11, a postsynaptic GABA transporter. We also identified CNVs in COBL, deletions of which cause defects in neuronal cytoskeleton morphogenesis in model vertebrates, and DNER, a neuron-specific Notch ligand required for cerebellar development. Moreover, we found evidence of genetic overlap between ASDs and other neurodevelopmental and neuropsychiatric diseases. These genes include glutamate receptors (GRID1, GRIK2 and GRIK4), synaptic regulators (NRXN3, SLC6A8 and SYN3), transcription factor (ZNF804A) and RNA-binding protein FMR1. Taken together, these CNVs may be a few of the missing pieces of ASD heritability and lead to discovering novel etiological mechanisms.
Collapse
Affiliation(s)
- Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Hedges DJ, Hamilton-Nelson KL, Sacharow SJ, Nations L, Beecham GW, Kozhekbaeva ZM, Butler BL, Cukier HN, Whitehead PL, Ma D, Jaworski JM, Nathanson L, Lee JM, Hauser SL, Oksenberg JR, Cuccaro ML, Haines JL, Gilbert JR, Pericak-Vance MA. Evidence of novel fine-scale structural variation at autism spectrum disorder candidate loci. Mol Autism 2012; 3:2. [PMID: 22472195 PMCID: PMC3352055 DOI: 10.1186/2040-2392-3-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 04/02/2012] [Indexed: 01/11/2023] Open
Abstract
Background Autism spectrum disorders (ASD) represent a group of neurodevelopmental disorders characterized by a core set of social-communicative and behavioral impairments. Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the brain, acting primarily via the GABA receptors (GABR). Multiple lines of evidence, including altered GABA and GABA receptor expression in autistic patients, indicate that the GABAergic system may be involved in the etiology of autism. Methods As copy number variations (CNVs), particularly rare and de novo CNVs, have now been implicated in ASD risk, we examined the GABA receptors and genes in related pathways for structural variation that may be associated with autism. We further extended our candidate gene set to include 19 genes and regions that had either been directly implicated in the autism literature or were directly related (via function or ancestry) to these primary candidates. For the high resolution CNV screen we employed custom-designed 244 k comparative genomic hybridization (CGH) arrays. Collectively, our probes spanned a total of 11 Mb of GABA-related and additional candidate regions with a density of approximately one probe every 200 nucleotides, allowing a theoretical resolution for detection of CNVs of approximately 1 kb or greater on average. One hundred and sixty-eight autism cases and 149 control individuals were screened for structural variants. Prioritized CNV events were confirmed using quantitative PCR, and confirmed loci were evaluated on an additional set of 170 cases and 170 control individuals that were not included in the original discovery set. Loci that remained interesting were subsequently screened via quantitative PCR on an additional set of 755 cases and 1,809 unaffected family members. Results Results include rare deletions in autistic individuals at JAKMIP1, NRXN1, Neuroligin4Y, OXTR, and ABAT. Common insertion/deletion polymorphisms were detected at several loci, including GABBR2 and NRXN3. Overall, statistically significant enrichment in affected vs. unaffected individuals was observed for NRXN1 deletions. Conclusions These results provide additional support for the role of rare structural variation in ASD.
Collapse
Affiliation(s)
- Dale J Hedges
- Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10 Ave, M-860, Miami, FL 33136, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Salyakina D, Cukier HN, Lee JM, Sacharow S, Nations LD, Ma D, Jaworski JM, Konidari I, Whitehead PL, Wright HH, Abramson RK, Williams SM, Menon R, Haines JL, Gilbert JR, Cuccaro ML, Pericak-Vance MA. Copy number variants in extended autism spectrum disorder families reveal candidates potentially involved in autism risk. PLoS One 2011; 6:e26049. [PMID: 22016809 PMCID: PMC3189231 DOI: 10.1371/journal.pone.0026049] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 09/16/2011] [Indexed: 02/02/2023] Open
Abstract
Copy number variations (CNVs) are a major cause of genetic disruption in the human genome with far more nucleotides being altered by duplications and deletions than by single nucleotide polymorphisms (SNPs). In the multifaceted etiology of autism spectrum disorders (ASDs), CNVs appear to contribute significantly to our understanding of the pathogenesis of this complex disease. A unique resource of 42 extended ASD families was genotyped for over 1 million SNPs to detect CNVs that may contribute to ASD susceptibility. Each family has at least one avuncular or cousin pair with ASD. Families were then evaluated for co-segregation of CNVs in ASD patients. We identified a total of five deletions and seven duplications in eleven families that co-segregated with ASD. Two of the CNVs overlap with regions on 7p21.3 and 15q24.1 that have been previously reported in ASD individuals and two additional CNVs on 3p26.3 and 12q24.32 occur near regions associated with schizophrenia. These findings provide further evidence for the involvement of ICA1 and NXPH1 on 7p21.3 in ASD susceptibility and highlight novel ASD candidates, including CHL1, FGFBP3 and POUF41. These studies highlight the power of using extended families for gene discovery in traits with a complex etiology.
Collapse
Affiliation(s)
- Daria Salyakina
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Holly N. Cukier
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Joycelyn M. Lee
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Stephanie Sacharow
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Laura D. Nations
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Deqiong Ma
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - James M. Jaworski
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Ioanna Konidari
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Patrice L. Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Harry H. Wright
- Department of Neuropsychiatry, University of South Carolina School of Medicine, Columbia, South Carolina, United States of America
| | - Ruth K. Abramson
- Department of Neuropsychiatry, University of South Carolina School of Medicine, Columbia, South Carolina, United States of America
| | - Scott M. Williams
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ramkumar Menon
- Department of Epidemiology and Department of Obstetrics and Gynecology, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Jonathan L. Haines
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - John R. Gilbert
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- * E-mail:
| |
Collapse
|
36
|
Cukier HN, Salyakina D, Blankstein SF, Robinson JL, Sacharow S, Ma D, Wright HH, Abramson RK, Menon R, Williams SM, Haines JL, Cuccaro ML, Gilbert JR, Pericak-Vance MA. Microduplications in an autism multiplex family narrow the region of susceptibility for developmental disorders on 15q24 and implicate 7p21. Am J Med Genet B Neuropsychiatr Genet 2011; 156B:493-501. [PMID: 21480499 PMCID: PMC5490366 DOI: 10.1002/ajmg.b.31188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 03/04/2011] [Indexed: 11/08/2022]
Abstract
Copy number variations (CNVs) play a crucial role in the intricate genetics of autism spectrum disorders. A region on chromosome 15q24 vulnerable to both deletions and duplications has been previously implicated in a range of phenotypes including autism, Asperger's syndrome, delayed development, and mild to severe mental retardation. Prior studies have delineated a minimal critical region of approximately 1.33 Mb. In this study, a multiplex autism family was evaluated for CNVs using genotyping data from the Illumina 1 M BeadChip and analyzed with the PennCNV algorithm. Variants were then identified that co-segregate with autism features in this family. Here, we report autistic first cousins who carry two microduplications concordant with disease. Both duplications were inherited maternally and found to be identical by descent. The first is an approximately 10,000 base pair microduplication within the minimal region on 15q24 that falls across a single gene, ubiquitin-like 7. This is the smallest duplication in the region to result in a neuropsychiatric disorder, potentially narrowing the critical region for susceptibility to developmental and autism spectrum disorders. The second is a novel, 352 kb tandem duplication on 7p21 that replicates part of the neurexophilin 1 and islet cell autoantigen 1 genes. The breakpoint junction falls within the intronic regions of these genes and demonstrates a microhomology of four base pairs. Each of these microduplications may contribute to the complex etiology of autism spectrum disorders.
Collapse
Affiliation(s)
- Holly N. Cukier
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Daria Salyakina
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Sarah F. Blankstein
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Joycelyn L. Robinson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Stephanie Sacharow
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida,Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Deqiong Ma
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida,Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Harry H. Wright
- Department of Neuropsychiatry, University of South Carolina School of Medicine, Columbia, South Carolina
| | - Ruth K. Abramson
- Department of Neuropsychiatry, University of South Carolina School of Medicine, Columbia, South Carolina
| | - Ramkumar Menon
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia,Department of Obstetrics and Gynecology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Scott M. Williams
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee
| | - Jonathan L. Haines
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida,Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida
| | - John R. Gilbert
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida,Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida,Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida,Correspondence to: Margaret A. Pericak-Vance, Ph.D., Associate Dean for Human Genomic Programs, Dr. John T. Macdonald Foundation Professor of Human Genomics, Director, John P. Hussman Institute for Human Genomics, 1501 NW 10th Avenue, BRB-314 (M860), University of Miami, Miller School of Medicine, Miami, FL 33136.
| |
Collapse
|
37
|
Cukier HN, Rabionet R, Konidari I, Rayner-Evans MY, Baltos ML, Wright HH, Abramson RK, Martin ER, Cuccaro ML, Pericak-Vance MA, Gilbert JR. Novel variants identified in methyl-CpG-binding domain genes in autistic individuals. Neurogenetics 2010; 11:291-303. [PMID: 19921286 PMCID: PMC2941261 DOI: 10.1007/s10048-009-0228-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 10/26/2009] [Indexed: 12/01/2022]
Abstract
Misregulation of the methyl-CpG-binding protein 2 (MECP2) gene has been found to cause a myriad of neurological disorders including autism, mental retardation, seizures, learning disabilities, and Rett syndrome. We hypothesized that mutations in other members of the methyl-CpG-binding domain (MBD) family may also cause autistic features in individuals. We evaluated 226 autistic individuals for alterations in the four genes most homologous to MECP2: MBD1, MBD2, MBD3, and MBD4. A total of 46 alterations were identified in the four genes, including ten missense changes and two deletions that alter coding sequence. Several are either unique to our autistic population or cosegregate with affected individuals within a family, suggesting a possible relation of these variations to disease etiology. Variants include a R23M alteration in two affected half brothers which falls within the MBD domain of the MBD3 protein, as well as a frameshift in MBD4 that is predicted to truncate almost half of the protein. These results suggest that rare cases of autism may be influenced by mutations in members of the dynamic MBD protein family.
Collapse
Affiliation(s)
- Holly N. Cukier
- John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Raquel Rabionet
- Genes and Disease Program, Centre de Regulació Genòmica and CIBER en Epidemiología y Salud Pública, Barcelona, Spain
| | - Ioanna Konidari
- John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Melissa Y. Rayner-Evans
- John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Mary L. Baltos
- John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Harry H. Wright
- University of South Carolina School of Medicine, Columbia, SC, USA
| | - Ruth K. Abramson
- University of South Carolina School of Medicine, Columbia, SC, USA
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - John R. Gilbert
- John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, Miami, FL 33136, USA
| |
Collapse
|
38
|
Ma DQ, Rabionet R, Konidari I, Jaworski J, Cukier HN, Wright HH, Abramson RK, Gilbert JR, Cuccaro ML, Pericak-Vance MA, Martin ER. Association and gene-gene interaction of SLC6A4 and ITGB3 in autism. Am J Med Genet B Neuropsychiatr Genet 2010; 153B:477-483. [PMID: 19588468 PMCID: PMC3735126 DOI: 10.1002/ajmg.b.31003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Autism is a heritable neurodevelopmental disorder with substantial genetic heterogeneity. Studies point to possible links between autism and two serotonin related genes: SLC6A4 and ITGB3 with a sex-specific genetic effect and interaction between the genes. Despite positive findings, inconsistent results have complicated interpretation. This study seeks to validate and clarify previous findings in an independent dataset taking into account sex, family-history (FH) and gene-gene effects. Family-based association analysis was performed within each gene. Gene-gene interactions were tested using extended multifactor dimensionality reduction (EMDR) and MDR-phenomics (MDR-P) using sex of affecteds and FH as covariates. No significant associations with individual SNPs were found in the datasets stratified by sex, but associations did emerge when we stratified by family history. While not significant in the overall dataset, nominally significant association was identified at RS2066713 (P = 0.006) within SLC6A4 in family-history negative (FH-) families, at RS2066713 (P = 0.038) in family-history positive (FH+) families but with the opposite risk allele as in the FH- families. For ITGB3, nominally significant association was identified at RS3809865 overall (P = 0.040) and within FH+ families (P = 0.031). However, none of the associations survived the multiple testing correction. MDR-P confirmed gene-gene effects using sex of affecteds (P = 0.023) and family history (P = 0.014, survived the multiple testing corrections) as covariates. Our results indicate the extensive heterogeneity within these two genes among families. The potential interaction between SLC6A4 and ITGB3 may be clarified using family history as an indicator of genetic architecture, illustrating the importance of covariates as markers of heterogeneity in genetic analyses.
Collapse
Affiliation(s)
- D Q Ma
- Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida
| | - R Rabionet
- Center for Genomic Regulation, Universitat Pompeu Fabra (CRG-UPF), Barcelona, Spain
| | - I Konidari
- Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida
| | - J Jaworski
- Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida
| | - H N Cukier
- Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida
| | - H H Wright
- School of Medicine, University of South Carolina, Columbia, South Carolina
| | - R K Abramson
- School of Medicine, University of South Carolina, Columbia, South Carolina
| | - J R Gilbert
- Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida
| | - M L Cuccaro
- Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida
| | - M A Pericak-Vance
- Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida
| | - E R Martin
- Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida
| |
Collapse
|
39
|
Cukier HN, Skaar DA, Rayner-Evans MY, Konidari I, Whitehead PL, Jaworski JM, Cuccaro ML, Pericak-Vance MA, Gilbert JR. Identification of chromosome 7 inversion breakpoints in an autistic family narrows candidate region for autism susceptibility. Autism Res 2010; 2:258-66. [PMID: 19877165 DOI: 10.1002/aur.96] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Chromosomal breaks and rearrangements have been observed in conjunction with autism and autistic spectrum disorders. A chromosomal inversion has been previously reported in autistic siblings, spanning the region from approximately 7q22.1 to 7q31. This family is distinguished by having multiple individuals with autism and associated disabilities. The region containing the inversion has been strongly implicated in autism by multiple linkage studies, and has been particularly associated with language defects in autism as well as in other disorders with language components. Mapping of the inversion breakpoints by FISH has localized the inversion to the region spanning approximately 99-108.75 Mb of chromosome 7. The proximal breakpoint has the potential to disrupt either the coding sequence or regulatory regions of a number of cytochrome P450 genes while the distal region falls in a relative gene desert. Copy number variant analysis of the breakpoint regions detected no duplication or deletion that could clearly be associated with disease status. Association analysis in our autism data set using single nucleotide polymorphisms located near the breakpoints showed no significant association with proximal breakpoint markers, but has identified markers near the distal breakpoint ( approximately 108-110 Mb) with significant associations to autism. The chromosomal abnormality in this family strengthens the case for an autism susceptibility gene in the chromosome 7q22-31 region and targets a candidate region for further investigation.
Collapse
Affiliation(s)
- Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Ma D, Salyakina D, Jaworski JM, Konidari I, Whitehead PL, Andersen AN, Hoffman JD, Slifer SH, Hedges DJ, Cukier HN, Griswold AJ, McCauley JL, Beecham GW, Wright HH, Abramson RK, Martin ER, Hussman JP, Gilbert JR, Cuccaro ML, Haines JL, Pericak-Vance MA. A genome-wide association study of autism reveals a common novel risk locus at 5p14.1. Ann Hum Genet 2009; 73:263-73. [PMID: 19456320 DOI: 10.1111/j.1469-1809.2009.00523.x] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although autism is one of the most heritable neuropsychiatric disorders, its underlying genetic architecture has largely eluded description. To comprehensively examine the hypothesis that common variation is important in autism, we performed a genome-wide association study (GWAS) using a discovery dataset of 438 autistic Caucasian families and the Illumina Human 1M beadchip. 96 single nucleotide polymorphisms (SNPs) demonstrated strong association with autism risk (p-value < 0.0001). The validation of the top 96 SNPs was performed using an independent dataset of 487 Caucasian autism families genotyped on the 550K Illumina BeadChip. A novel region on chromosome 5p14.1 showed significance in both the discovery and validation datasets. Joint analysis of all SNPs in this region identified 8 SNPs having improved p-values (3.24E-04 to 3.40E-06) than in either dataset alone. Our findings demonstrate that in addition to multiple rare variations, part of the complex genetic architecture of autism involves common variation.
Collapse
Affiliation(s)
- Deqiong Ma
- Miami Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Cukier HN, Pericak-Vance MA, Gilbert JR, Hedges DJ. Sample degradation leads to false-positive copy number variation calls in multiplex real-time polymerase chain reaction assays. Anal Biochem 2009; 386:288-90. [DOI: 10.1016/j.ab.2008.11.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Revised: 11/25/2008] [Accepted: 11/26/2008] [Indexed: 01/10/2023]
|
42
|
Abstract
The levels of methyl-CpG–binding protein 2 (MeCP2) are critical for normal post-natal development and function of the nervous system. Loss of function of MeCP2, a transcriptional regulator involved in chromatin remodeling, causes classic Rett syndrome (RTT) as well as other related conditions characterized by autism, learning disabilities, or mental retardation. Increased dosage of MeCP2 also leads to clinically similar neurological disorders and mental retardation. To identify molecular mechanisms capable of compensating for altered MeCP2 levels, we generated transgenic Drosophila overexpressing human MeCP2. We find that MeCP2 associates with chromatin and is phosphorylated at serine 423 in Drosophila, as is found in mammals. MeCP2 overexpression leads to anatomical (i.e., disorganized eyes, ectopic wing veins) and behavioral (i.e., motor dysfunction) abnormalities. We used a candidate gene approach to identify genes that are able to compensate for abnormal phenotypes caused by MeCP2 increased activity. These genetic modifiers include other chromatin remodeling genes (Additional sex combs, corto, osa, Sex combs on midleg, and trithorax), the kinase tricornered, the UBE3A target pebble, and Drosophila homologues of the MeCP2 physical interactors Sin3a, REST, and N-CoR. These findings demonstrate that anatomical and behavioral phenotypes caused by MeCP2 activity can be ameliorated by altering other factors that might be more amenable to manipulation than MeCP2 itself. Rett syndrome (RTT) is a progressive neurodevelopmental disorder that affects girls early in childhood and is caused by mutations in the MECP2 gene. Loss of MeCP2 function can also lead to clinically distinct conditions characterized by autism, learning disability, and mental retardation. Remarkably, increased levels of MeCP2 leads to related neurological disorders and mental retardation as well. These data emphasize the critical importance of regulating MeCP2 protein levels for normal post-natal development and function of the nervous system. MeCP2 is a protein that associates with chromatin and is thought to modulate gene expression. We have generated Drosophila that overexpress human MeCP2 to investigate the possibility that adjusting the activity of other genes may compensate for altered levels of MeCP2. In support of this hypothesis, we found a variety of modifier genes, including chromatin remodeling genes, that are able to ameliorate and/or aggravate the consequences of MeCP2 overexpression. These findings open the possibility of therapeutic avenues for RTT and related neuropsychiatric disorders by targeting proteins that are possibly easier to manipulate than MeCP2 itself.
Collapse
Affiliation(s)
- Holly N. Cukier
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alma M. Perez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ann L. Collins
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zhaolan Zhou
- Neurobiology Program, Children's Hospital Boston, Massachusetts, United States of America
- Departments of Neurology and Neurobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Huda Y. Zoghbi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Departments of Neuroscience and Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, United States of America
| | - Juan Botas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
| |
Collapse
|