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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.
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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.
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2
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Arbeev KG, Ukraintseva S, Bagley O, Duan H, Wu D, Akushevich I, Stallard E, Kulminski A, Christensen K, Feitosa MF, O’Connell JR, Parker D, Whitson H, Yashin AI. Interactions between genes involved in physiological dysregulation and axon guidance: role in Alzheimer's disease. Front Genet 2023; 14:1236509. [PMID: 37719713 PMCID: PMC10500346 DOI: 10.3389/fgene.2023.1236509] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/17/2023] [Indexed: 09/19/2023] Open
Abstract
Dysregulation of physiological processes may contribute to Alzheimer's disease (AD) development. We previously found that an increase in the level of physiological dysregulation (PD) in the aging body is associated with declining resilience and robustness to major diseases. Also, our genome-wide association study found that genes associated with the age-related increase in PD frequently represented pathways implicated in axon guidance and synaptic function, which in turn were linked to AD and related traits (e.g., amyloid, tau, neurodegeneration) in the literature. Here, we tested the hypothesis that genes involved in PD and axon guidance/synapse function may jointly influence onset of AD. We assessed the impact of interactions between SNPs in such genes on AD onset in the Long Life Family Study and sought to replicate the findings in the Health and Retirement Study. We found significant interactions between SNPs in the UNC5C and CNTN6, and PLXNA4 and EPHB2 genes that influenced AD onset in both datasets. Associations with individual SNPs were not statistically significant. Our findings, thus, support a major role of genetic interactions in the heterogeneity of AD and suggest the joint contribution of genes involved in PD and axon guidance/synapse function (essential for the maintenance of complex neural networks) to AD development.
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Affiliation(s)
- Konstantin G. Arbeev
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Svetlana Ukraintseva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Olivia Bagley
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Hongzhe Duan
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Deqing Wu
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Igor Akushevich
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Eric Stallard
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Alexander Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Kaare Christensen
- Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Mary F. Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Jeffrey R. O’Connell
- Division of Endocrinology, Diabetes and Nutrition and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Daniel Parker
- Duke Center for the Study of Aging and Human Development, Duke University, Durham, NC, United States
| | - Heather Whitson
- Duke Center for the Study of Aging and Human Development, Duke University, Durham, NC, United States
- Durham VA Geriatrics Research Education and Clinical Center, Durham, NC, United States
| | - Anatoliy I. Yashin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
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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.
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Wang H, Wang Q, Tan X, Wang J, Zhang J, Zheng M, Zhao G, Wen J. Estimation of genetic variability and identification of regions under selection based on runs of homozygosity in Beijing-You Chickens. Poult Sci 2022; 102:102342. [PMID: 36470032 PMCID: PMC9719870 DOI: 10.1016/j.psj.2022.102342] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
The genetic composition of populations is the result of a long-term process of selection and adaptation to specific environments and ecosystems. Runs of homozygosity (ROHs) are homozygous segments of the genome where the 2 haplotypes inherited from the parents are identical. The detection of ROH can be used to describe the genetic variability and quantify the level of inbreeding in an individual. Here, we investigated the occurrence and distribution of ROHs in 40 Beijing-You Chickens from the random breeding population (BJY_C) and 40 Beijing-You Chickens from the intramuscular fat (IMF) selection population (BJY_S). Principal component analysis (PCA) and maximum likelihood (ML) analyses showed that BJY_C was completely separated from the BJY_S. The nucleotide diversity of BJY_C was higher than that of BJY_S, and the decay rate of LD of BJY_C was faster. The ROHs were identified for a total of 7,101 in BJY_C and 9,273 in BJY_S, respectively. The ROH-based inbreeding estimate (FROH) of BJY_C was 0.079, which was significantly lower than that of BJY_S (FROH = 0.114). The results were the same as the estimates of the inbreeding coefficients calculated based on homozygosity (FHOM), the correlation between uniting gametes (FUNI), and the genomic relationship matrix (FGRM). Additionally, the distribution and number of ROH islands in chromosomes of BJY_C and BJY_S were significantly different. The ROH islands of BJY_S that included genes associated with lipid metabolism and fat deposition, such as CIDEA and S1PR1, were absent in BJY_C. However, GPR161 was detected in both populations, which is a candidate gene for the formation of the unique five-finger trait in Beijing-You chickens. Our findings contributed to the understanding of the genetic diversity of random or artificially selected populations, and allowed the accurate monitoring of population inbreeding using genomic information, as well as the detection of genomic regions that affect traits under selection.
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Affiliation(s)
- Hailong Wang
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Qiao Wang
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Xiaodong Tan
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Jie Wang
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Jin Zhang
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Maiqing Zheng
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Guiping Zhao
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Jie Wen
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China.
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Belloy ME, Eger SJ, Le Guen Y, Napolioni V, Deters KD, Yang HS, Scelsi MA, Porter T, James SN, Wong A, Schott JM, Sperling RA, Laws SM, Mormino EC, He Z, Han SS, Altmann A, Greicius MD. KL∗VS heterozygosity reduces brain amyloid in asymptomatic at-risk APOE∗4 carriers. Neurobiol Aging 2021; 101:123-129. [PMID: 33610961 DOI: 10.1016/j.neurobiolaging.2021.01.008] [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: 09/17/2020] [Revised: 11/30/2020] [Accepted: 01/09/2021] [Indexed: 11/15/2022]
Abstract
KLOTHO∗VS heterozygosity (KL∗VSHET+) was recently shown to be associated with reduced risk of Alzheimer's disease (AD) in APOE∗4 carriers. Additional studies suggest that KL∗VSHET+ protects against amyloid burden in cognitively normal older subjects, but sample sizes were too small to draw definitive conclusions. We performed a well-powered meta-analysis across 5 independent studies, comprising 3581 pre-clinical participants ages 60-80, to investigate whether KL∗VSHET+ reduces the risk of having an amyloid-positive positron emission tomography scan. Analyses were stratified by APOE∗4 status. KL∗VSHET+ reduced the risk of amyloid positivity in APOE∗4 carriers (odds ratio = 0.67 [0.52-0.88]; p = 3.5 × 10-3), but not in APOE∗4 non-carriers (odds ratio = 0.94 [0.73-1.21]; p = 0.63). The combination of APOE∗4 and KL∗VS genotypes should help enrich AD clinical trials for pre-symptomatic subjects at increased risk of developing amyloid aggregation and AD. KL-related pathways may help elucidate protective mechanisms against amyloid accumulation and merit exploration for novel AD drug targets. Future investigation of the biological mechanisms by which KL interacts with APOE∗4 and AD are warranted.
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Affiliation(s)
- Michael E Belloy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
| | - Sarah J Eger
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Valerio Napolioni
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Kacie D Deters
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Hyun-Sik Yang
- Department of Neurology, Brigham and Women's Hospital, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marzia A Scelsi
- Centre for Medical Image Computing (CMIC), University College London, London, UK
| | - Tenielle Porter
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia; School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, Australia
| | - Sarah-Naomi James
- Medical Research Council Unit for Lifelong Health and Ageing, University College London, London, UK
| | - Andrew Wong
- Medical Research Council Unit for Lifelong Health and Ageing, University College London, London, UK
| | - Jonathan M Schott
- Dementia Research Centre, University College London Queen Square Institute of Neurology, University College London, London, UK; UK Dementia Research Institute, University College London, London, UK
| | - Reisa A Sperling
- Department of Neurology, Brigham and Women's Hospital, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Simon M Laws
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia; School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, Australia
| | - Elisabeth C Mormino
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Zihuai He
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA; Department of Medicine, Quantitative Sciences Unit, Stanford University, Stanford, CA, USA
| | - Summer S Han
- Department of Medicine, Quantitative Sciences Unit, Stanford University, Stanford, CA, USA; Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Andre Altmann
- Centre for Medical Image Computing (CMIC), University College London, London, UK
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
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