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Hao Y, Li C, Wang H, Ming C. Effects of copy number variations on longevity in late-onset Alzheimer's disease patients: insights from a causality network analysis. Front Aging Neurosci 2023; 15:1241412. [PMID: 38020759 PMCID: PMC10652415 DOI: 10.3389/fnagi.2023.1241412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Alzheimer's disease (AD), particularly late-onset Alzheimer's disease (LOAD), is a prevalent form of dementia that significantly affects patients' cognitive and behavioral capacities and longevity. Although approximately 70 genetic risk factors linked with AD have been identified, their influence on patient longevity remains unclear. Further, recent studies have associated copy number variations (CNVs) with the longevity of healthy individuals and immune-related pathways in AD patients. This study aims to investigate the role of CNVs on the longevity of AD patients by integrating the Whole Genome Sequencing (WGS) and transcriptomics data from the Religious Orders Study/Memory and Aging Project (ROSMAP) cohort through causality network inference. Our comprehensive analysis led to the construction of a CNV-Gene-Age of Death (AOD) causality network. We successfully identified three key CNVs (DEL5006, mCNV14192, and DUP42180) and seven AD-longevity causal genes (PLGRKT, TLR1, PLAU, CALB2, SYTL2, OTOF, and NT5DC1) impacting AD patient longevity, independent of disease severity. This outcome emphasizes the potential role of plasminogen activation and chemotaxis in longevity. We propose several hypotheses regarding the role of identified CNVs and the plasminogen system on patient longevity. However, experimental validation is required to further corroborate these findings and uncover precise mechanisms. Despite these limitations, our study offers promising insights into the genetic influence on AD patient longevity and contributes to paving the way for potential therapeutic interventions.
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Affiliation(s)
- Yanan Hao
- Department of Public Health and Medicinal Administration, Faculty of Health Sciences, University of Macau, Macau, Macao SAR, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau, Macao SAR, China
| | - Chuhao Li
- Department of Public Health and Medicinal Administration, Faculty of Health Sciences, University of Macau, Macau, Macao SAR, China
| | - He Wang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Chen Ming
- Department of Public Health and Medicinal Administration, Faculty of Health Sciences, University of Macau, Macau, Macao SAR, China
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2
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Bellou E, Escott-Price V. Are Alzheimer's and coronary artery diseases genetically related to longevity? Front Psychiatry 2022; 13:1102347. [PMID: 36684006 PMCID: PMC9859055 DOI: 10.3389/fpsyt.2022.1102347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/12/2022] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION In the last decade researchers have attempted to investigate the shared genetic architecture of longevity and age-related diseases and assess whether the increased longevity in certain people is due to protective alleles in the risk genes for a particular condition or whether there are specific "longevity" genes increasing the lifespan independently of age-related conditions' risk genes. The aim of this study was to investigate the shared genetic component between longevity and two age-related conditions. METHODS We performed a cross-trait meta-analysis of publicly available genome-wide data for Alzheimer's disease, coronary artery disease and longevity using a subset-based approach provided by the R package ASSET. RESULTS Despite the lack of strong genetic correlation between longevity and the two diseases, we identified 38 genome-wide significant lead SNPs across 22 independent genomic loci. Of them 6 were found to be potentially shared among the three traits mapping to genes including DAB2IP, DNM2, FCHO1, CLPTM1, and SNRPD2. We also identified 19 novel genome-wide associations for the individual traits in this study. Functional annotations and biological pathway enrichment analyses suggested that pleiotropic variants are involved in clathrin-mediated endocytosis and plasma lipoprotein and neurotransmitter clearance processes. DISCUSSION In summary, we have been able to advance in the knowledge of the genetic overlap existing among longevity and the two most common age-related disorders.
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Affiliation(s)
- Eftychia Bellou
- UK Dementia Research Institute, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Valentina Escott-Price
- Division of Neuroscience and Mental Health, School of Medicine, Cardiff University, Cardiff, United Kingdom
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3
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Dowden L, Tucker D, Morgan S, Uzun O, Syed YA. Contribution of Congenital Heart Disorders Associated With Copy Number Variants in Mediating Risk for Brain Developmental Disorders: Evidence From 20-Year Retrospective Cohort Study. Front Cardiovasc Med 2021; 8:655463. [PMID: 34336942 PMCID: PMC8319541 DOI: 10.3389/fcvm.2021.655463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022] Open
Abstract
Rare pathogenic copy number variants (CNVs) are genetic rearrangements that have been associated with an increased risk for congenital heart disorders (CHDs). However, the association of CNVs with atypical brain development, leading to neurodevelopmental disorders (NDDs), in the presence of CHDs remains unclear. We attempted to explore this association by establishing the prevalence and burden of CNVs associated with CHD in a Welsh population and by studying the effect of rare CNVs associated with CHDs in mediating the risk of NDDs. Toward this goal, we analyzed data from the Congenital Anomaly Register for Wales (CARIS), referred from hospitals in Wales between 1998 and 2018, which included 1,113 subjects in total. Of these, 785 subjects were included in the study following application of the exclusion criteria, and a total of 28 rare CNVs associated with CHD were analyzed. The findings from this cohort study identified 22q11.2 deletion as the most prominent CNV across the cohort. Our data demonstrates that the survival rate of the cohort after 3 years was 99.9%, and mortality fell significantly between 1 and 2 years and between 2 and 3 years [F(1,27) = 10, p = 0.0027; F(1,27) = 5.8, p = 0.0222]. Importantly, the data set revealed a positive correlation between the incidence of congenital heart disease and the incidence of neurodevelopmental abnormalities in patients with CNVs across the whole cohort [95% CI (0.4062, 0.8449), p < 0.0001, r = 0.6829]. Additionally, we identified significant CNVs that result in the co-morbidity of CHD and NDD and show that septal defects and global developmental delay are major congenital defects. Further research should identify a common molecular mechanism leading to the phenotypic comorbidity of CHDs and NDDs, arising from a common CNV, which can have an implication for improving risk classification and for fetal neuroprotection strategies in the affected children and in precision medicine.
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Affiliation(s)
- Luke Dowden
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom.,School of Bioscience, Cardiff University, Cardiff, United Kingdom
| | - David Tucker
- Knowledge Directorate, Public Health Wales, Swansea, United Kingdom
| | - Sian Morgan
- Department of Medical Genetics, University Hospital of Wales, Cardiff, United Kingdom
| | - Orhan Uzun
- Department of Fetal Cardiology, University Hospital of Wales, Cardiff, United Kingdom
| | - Yasir Ahmed Syed
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom.,School of Bioscience, Cardiff University, Cardiff, United Kingdom
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4
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Treaster S, Karasik D, Harris MP. Footprints in the Sand: Deep Taxonomic Comparisons in Vertebrate Genomics to Unveil the Genetic Programs of Human Longevity. Front Genet 2021; 12:678073. [PMID: 34163529 PMCID: PMC8215702 DOI: 10.3389/fgene.2021.678073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/12/2021] [Indexed: 01/09/2023] Open
Abstract
With the modern quality, quantity, and availability of genomic sequencing across species, as well as across the expanse of human populations, we can screen for shared signatures underlying longevity and lifespan. Knowledge of these mechanisms would be medically invaluable in combating aging and age-related diseases. The diversity of longevities across vertebrates is an opportunity to look for patterns of genetic variation that may signal how this life history property is regulated, and ultimately how it can be modulated. Variation in human longevity provides a unique window to look for cases of extreme lifespan within a population, as well as associations across populations for factors that influence capacity to live longer. Current large cohort studies support the use of population level analyses to identify key factors associating with human lifespan. These studies are powerful in concept, but have demonstrated limited ability to resolve signals from background variation. In parallel, the expanding catalog of sequencing and annotation from diverse species, some of which have evolved longevities well past a human lifespan, provides independent cases to look at the genomic signatures of longevity. Recent comparative genomic work has shown promise in finding shared mechanisms associating with longevity among distantly related vertebrate groups. Given the genetic constraints between vertebrates, we posit that a combination of approaches, of parallel meta-analysis of human longevity along with refined analysis of other vertebrate clades having exceptional longevity, will aid in resolving key regulators of enhanced lifespan that have proven to be elusive when analyzed in isolation.
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Affiliation(s)
- Stephen Treaster
- Department of Orthopaedics, Boston Children's Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Ramat Gan, Israel.,Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, United States
| | - Matthew P Harris
- Department of Orthopaedics, Boston Children's Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
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5
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Mortillo M, Mulle JG. A cross-comparison of cognitive ability across 8 genomic disorders. Curr Opin Genet Dev 2021; 68:106-116. [PMID: 34082144 DOI: 10.1016/j.gde.2021.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/01/2021] [Accepted: 04/08/2021] [Indexed: 12/23/2022]
Abstract
Genomic disorders result from rearrangement of the human genome. Most genomic disorders are caused by copy number variants (CNV), deletions or duplications of several hundred kilobases. Many CNV loci are associated with autism, schizophrenia, and most commonly, intellectual disability (ID). However, there is little comparison of cognitive ability measures across these CNV disorders. This study aims to understand whether existing data can be leveraged for a cross-comparison of cognitive ability among multiple CNV. We found there is a lack of harmonization among assessment instruments and little standardization for reporting summary data across studies. Despite these limitations, we identified a differential impact of CNV loci on cognitive ability. Our data suggest that future cross-comparisons of CNV disorders will reveal meaningful differences across the phenotypic spectrum, especially if standardized phenotypic assessment is achieved.
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Affiliation(s)
- Michael Mortillo
- Department of Human Genetics, Emory University, Atlanta, GA, United States
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University, Atlanta, GA, United States.
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6
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Zhu Y, Liang Y, Khan AH, Dong M, Wan Y, Sun Z, Zeng Y, Nie C, Tian XL. Allelic distribution of ABO gene in Chinese centenarians. Aging Med (Milton) 2020; 3:195-204. [PMID: 33103040 PMCID: PMC7574633 DOI: 10.1002/agm2.12122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Objective Human ABO blood groups are determined by the alleles A, B, and O (O01 and O02) of the ABO gene and have been linked to the risks for cardiovascular diseases and cancers that affect lifespan. We examined the genetic associations of the ABO gene and blood groups with longevity. Methods We inspected the frequencies of the A, B, O, and O02 alleles in a large Chinese centenarian population (n = 2201) and in middle‐aged controls (n = 2330). The single nucleotide polymorphisms were selected as allele A (rs507666), B (rs8176743, rs8176746, and rs8176749), O (rs687289), and O02 (rs688976, rs549446, and rs512770). Results Supported by allelic and genotypic association studies, the frequencies of blood types A, B, O, and AB in centenarian versus control participants were not statistically different: 0.2821 versus 0.2781 (χ2 = 0.09, P = 0.76), 0.2867 versus 0.3060 (χ2 = 2.03, P = 0.15), 0.3380 versus 0.3159 (χ2 = 2.52, P = 0.11), and 0.0859 versus 0.0910 (χ2 = 0.37, P = 0.54), respectively. Sex had little effect on these distributions. Conclusion Integrated with other previous reports, we conclude from this large Chinese cohort that genetic variants of the ABO gene and blood groups are not associated with longevity.
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Affiliation(s)
- Ying Zhu
- Human Aging Research Institute (HARI) School of Life Science, and Jiangxi Key Laboratory of Human Aging Nanchang University Nanchang China.,First Affiliated Hospital of Gannan Medical University Ganzhou China
| | - Yu Liang
- Human Aging Research Institute (HARI) School of Life Science, and Jiangxi Key Laboratory of Human Aging Nanchang University Nanchang China
| | - Abdul Haseeb Khan
- Human Aging Research Institute (HARI) School of Life Science, and Jiangxi Key Laboratory of Human Aging Nanchang University Nanchang China
| | | | - Yiqi Wan
- Human Aging Research Institute (HARI) School of Life Science, and Jiangxi Key Laboratory of Human Aging Nanchang University Nanchang China
| | - Zhichao Sun
- Human Aging Research Institute (HARI) School of Life Science, and Jiangxi Key Laboratory of Human Aging Nanchang University Nanchang China
| | - Yi Zeng
- Center for the Study of Aging and Human Development Medical School of Duke University Durham North Carolina USA.,Center for Healthy Aging and Development Studies National School of Development Peking University Beijing China
| | - Chao Nie
- BGI Shenzhen Shenzhen China.,BGI Education Center University of Chinese Academy of Sciences Shenzhen China
| | - Xiao-Li Tian
- Human Aging Research Institute (HARI) School of Life Science, and Jiangxi Key Laboratory of Human Aging Nanchang University Nanchang China
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7
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Zhao X, Liu X, Zhang A, Chen H, Huo Q, Li W, Ye R, Chen Z, Liang L, Liu QA, Shen J, Jin X, Li W, Nygaard M, Liu X, Hou Y, Ni T, Bolund L, Gottschalk W, Tao W, Gu J, Tian XL, Yang H, Wang J, Xu X, Lutz MW, Min J, Zeng Y, Nie C. The correlation of copy number variations with longevity in a genome-wide association study of Han Chinese. Aging (Albany NY) 2019; 10:1206-1222. [PMID: 29883365 PMCID: PMC6046244 DOI: 10.18632/aging.101461] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 05/30/2018] [Indexed: 12/13/2022]
Abstract
Copy number variations (CNVs) have been shown to cause numerous diseases, however, their roles in human lifespan remain elusive. In this study, we investigate the association of CNVs with longevity by comparing the Han Chinese genomes of long-lived individuals from 90 to 117 years of age and the middle-aged from 30 to 65. Our data demonstrate that the numbers of CNVs, especially deletions, increase significantly in a direct correlation with longevity. We identify eleven CNVs that strongly associate with longevity; four of them locate in the chromosome bands, 7p11.2, 20q13.33, 19p12 and 8p23.3 and overlap partially with the CNVs identified in long-lived Danish or U.S. populations, while the other seven have not been reported previously. These CNV regions encode nineteen known genes, and some of which have been shown to affect aging-related phenotypes such as the shortening of telomere length (ZNF208), the risk of cancer (FOXA1, LAMA5, ZNF716), and vascular and immune-related diseases (ARHGEF10, TOR2A, SH2D3C). In addition, we found several pathways enriched in long-lived genomes, including FOXA1 and FOXA transcription factor networks involved in regulating aging or age-dependent diseases such as cancer. Thus, our study has identified longevity-associated CNV regions and their affected genes and pathways. Our results suggest that the human genome structures such as CNVs might play an important role in determining a long life in human.
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Affiliation(s)
- Xin Zhao
- BGI Shenzhen, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.,College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xiaomin Liu
- BGI Shenzhen, Shenzhen 518083, China.,School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | | | - Huashuai Chen
- Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham NC 27710, USA.,Center for Healthy Aging and Development Studies, Raissun Institute for Advanced Studies, National School of Development, Peking University, Beijing 10080, China.,Business School of Xiangtan University, Xiangtan 411105, China
| | - Qing Huo
- BGI Shenzhen, Shenzhen 518083, China
| | | | - Rui Ye
- BGI Shenzhen, Shenzhen 518083, China
| | | | | | | | - Juan Shen
- BGI Shenzhen, Shenzhen 518083, China
| | - Xin Jin
- BGI Shenzhen, Shenzhen 518083, China
| | - Wenwen Li
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Marianne Nygaard
- The Danish Aging Research Center, Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C 5000, Denmark
| | - Xiao Liu
- BGI Shenzhen, Shenzhen 518083, China
| | - Yong Hou
- BGI Shenzhen, Shenzhen 518083, China
| | - Ting Ni
- State Key Laboratory of Genetics Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Lars Bolund
- BGI Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - William Gottschalk
- Department of Neurology, Medical Center, Duke University, Durham, NC 27704, USA
| | - Wei Tao
- School of Life Sciences, Peking University, Beijing 100080, China
| | - Jun Gu
- School of Life Sciences, Peking University, Beijing 100080, China
| | - Xiao-Li Tian
- Department of Human Population Genetics, Human Aging Research Institute and School of Life Science Nanchang University, Nanchang 330000, China
| | | | - Jian Wang
- BGI Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI Shenzhen, Shenzhen 518083, China
| | - Michael W Lutz
- Department of Neurology, Medical Center, Duke University, Durham, NC 27704, USA
| | - Junxia Min
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yi Zeng
- Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham NC 27710, USA.,Center for Healthy Aging and Development Studies, Raissun Institute for Advanced Studies, National School of Development, Peking University, Beijing 10080, China
| | - Chao Nie
- BGI Shenzhen, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
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8
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Ershova ES, Malinovskaya EM, Konkova MS, Veiko RV, Umriukhin PE, Martynov AV, Kutsev SI, Veiko NN, Kostyuk SV. Copy Number Variation of Human Satellite III (1q12) With Aging. Front Genet 2019; 10:704. [PMID: 31447880 PMCID: PMC6692473 DOI: 10.3389/fgene.2019.00704] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/03/2019] [Indexed: 12/31/2022] Open
Abstract
Introduction: Human satellite DNA is organized in long arrays in peri/centromeric heterochromatin. There is little information about satellite copy number variants (CNVs) in aging and replicative cell senescence (RS). Materials and Methods: Biotinylated pUC1.77 probe was used for the satellite III (f-SatIII) quantitation in leukocyte DNA by the non-radioactive quantitative hybridization for 557 subjects between 2 and 91 years old. The effect of RS and genotoxic stress (GS, 4 or 6 µM of K2CrO4) on the f-SatIII CNV was studied on the cultured human skin fibroblast (HSF) lines of five subjects. Results: f-SatIII in leukocyte and HSFs varies between 5.7 and 40 pg/ng of DNA. During RS, the f-SatIII content in HSFs increased. During GS, HSFs may increase or decrease f-SatIII content. Cells with low f-SatIII content have the greatest proliferative potential. F-SatIII CNVs in different individuals belonging to the different generations depend on year of their birth. Children (born in 2005-2015 years) differed significantly from the other age groups by low content and low coefficient of variation of f-SatIII. In the individuals born in 1912-1925 and living in unfavorable social conditions (FWW, the Revolution and the Russian Civil War, SWW), there is a significant disproportion in the content of f-SatIII. The coefficient of variation reaches the maximum values than in individuals born in the period from 1926 to 1975. In the group of people born in 1990-2000 (Chernobyl disaster, the collapse of the Soviet Union, and a sharp decline in the population living standard), again, there is a significant disproportion of individuals in the content of f-SatIII. A similar disproportion was observed in the analysis of a group of individuals born in 1926-1975 who in their youth worked for a long time in high-radioactive environment. Conclusion: In generations that were born and who lived in childhood in a period of severe social perturbations or in conditions of environmental pollution, we found a significant increase in leukocyte DNA f-SatIII variability. It is hypothesized that the change of the f-SatIII content in the blood cells reflects the body response to stress of different nature and intensity.
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Affiliation(s)
- Elizaveta S. Ershova
- Research Centre for Medical Genetics (RCMG), Moscow, Russia
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | | | | | - Roman V. Veiko
- Research Centre for Medical Genetics (RCMG), Moscow, Russia
| | - Pavel E. Umriukhin
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- P.K. Anokhin Institute of Normal Physiology, Moscow, Russia
| | | | | | | | - Svetlana V. Kostyuk
- Research Centre for Medical Genetics (RCMG), Moscow, Russia
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
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Morris BJ, Willcox BJ, Donlon TA. Genetic and epigenetic regulation of human aging and longevity. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1718-1744. [PMID: 31109447 PMCID: PMC7295568 DOI: 10.1016/j.bbadis.2018.08.039] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/02/2018] [Accepted: 08/28/2018] [Indexed: 02/06/2023]
Abstract
Here we summarize the latest data on genetic and epigenetic contributions to human aging and longevity. Whereas environmental and lifestyle factors are important at younger ages, the contribution of genetics appears more important in reaching extreme old age. Genome-wide studies have implicated ~57 gene loci in lifespan. Epigenomic changes during aging profoundly affect cellular function and stress resistance. Dysregulation of transcriptional and chromatin networks is likely a crucial component of aging. Large-scale bioinformatic analyses have revealed involvement of numerous interaction networks. As the young well-differentiated cell replicates into eventual senescence there is drift in the highly regulated chromatin marks towards an entropic middle-ground between repressed and active, such that genes that were previously inactive "leak". There is a breakdown in chromatin connectivity such that topologically associated domains and their insulators weaken, and well-defined blocks of constitutive heterochromatin give way to generalized, senescence-associated heterochromatin, foci. Together, these phenomena contribute to aging.
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Affiliation(s)
- Brian J Morris
- Basic & Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, University of Sydney, New South Wales 2006, Australia; Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI 96817, United States; Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Kuakini Medical Center Campus, Honolulu, HI 96813, United States.
| | - Bradley J Willcox
- Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI 96817, United States; Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Kuakini Medical Center Campus, Honolulu, HI 96813, United States.
| | - Timothy A Donlon
- Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI 96817, United States; Departments of Cell & Molecular Biology and Pathology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, United States.
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10
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Meucci S, Keilholz U, Heim D, Klauschen F, Cacciatore S. Somatic genome alterations in relation to age in lung squamous cell carcinoma. Oncotarget 2018; 9:32161-32172. [PMID: 30181806 PMCID: PMC6114948 DOI: 10.18632/oncotarget.25848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/12/2018] [Indexed: 12/31/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC) is the most common cause of global cancer-related mortality and the major risk factors is smoking consumption. By analyzing ∼500 LUSC samples from The Cancer Genome Atlas, we detected a higher mutational burden as well as a higher level of methylation changes in younger patients. The SNPs mutational profiling showed enrichments of smoking-related signature 4 and defective DNA mismatch repair (MMR)-related signature 6 in younger patients, while the defective DNA MMR signature 26 was enriched among older patients. Furthermore, gene set enrichment analysis was performed in order to explore functional effect of somatic alterations in relation to patient age. Extracellular Matrix-Receptor Interaction, Nucleotide Excision Repair and Axon Guidance seem crucial disrupted pathways in younger patients. We hypothesize that a higher sensitivity to smoking-related damages and the enrichment of defective DNA MMR related mutations may contribute to the higher mutational burden of younger patients. The two distinct age-related defective DNA MMR signatures 6 and 26 might be crucial mutational patterns in LUSC tumorigenesis which may develop distinct phenotypes. Our study provides indications of age-dependent differences in mutational backgrounds (SNPs and CNVs) as well as epigenetic patterns that might be relevant for age adjusted treatment approaches.
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Affiliation(s)
- Stefano Meucci
- Charité Comprehensive Cancer Center, Charité University Hospital, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité University Hospital, Berlin, Germany
| | - Daniel Heim
- Institut für Pathologie, Charité University Hospital, Berlin, Germany
| | | | - Stefano Cacciatore
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, England, UK
- International Centre for Genetic Engineering and Biotechnology, Cancer Genomics Group, Cape Town, South Africa
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11
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Bekpen C, Xie C, Nebel A, Tautz D. Involvement of SPATA31 copy number variable genes in human lifespan. Aging (Albany NY) 2018; 10:674-688. [PMID: 29676996 PMCID: PMC5940121 DOI: 10.18632/aging.101421] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/14/2018] [Indexed: 12/22/2022]
Abstract
The SPATA31 (alias FAM75A) gene family belongs to the core duplicon families that are thought to have contributed significantly to hominoid evolution. It is also among the gene families with the strongest signal of positive selection in hominoids. It has acquired new protein domains in the primate lineage and a previous study has suggested that the gene family has expanded its function into UV response and DNA repair. Here we show that over-expression of SPATA31A1 in fibroblast cells leads to premature senescence due to interference with aging-related transcription pathways. We show that there are considerable copy number differences for this gene family in human populations and we ask whether this could influence mutation rates and longevity in humans. We find no evidence for an influence on germline mutation rates, but an analysis of long-lived individuals (> 96 years) shows that they carry significantly fewer SPATA31 copies in their genomes than younger individuals in a control group. We propose that the evolution of SPATA31 copy number is an example for antagonistic pleiotropy by providing a fitness benefit during the reproductive phase of life, but negatively influencing the overall life span.
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Affiliation(s)
| | - Chen Xie
- Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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12
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Oluwole OA, Mahboubi K, Favetta LA, Revay T, Kroetsch T, King WA. Highly dynamic temporal changes of TSPY gene copy number in aging bulls. PLoS One 2017; 12:e0178558. [PMID: 28552978 PMCID: PMC5446161 DOI: 10.1371/journal.pone.0178558] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 05/15/2017] [Indexed: 12/30/2022] Open
Abstract
The Y-chromosomal TSPY gene is one of the highest copy number mammalian protein coding gene and represents a unique biological model to study various aspects of genomic copy number variations. This study investigated the age-related copy number variability of the bovine TSPY gene, a new and unstudied aspect of the biology of TSPY that has been shown to vary among cattle breeds, individual bulls and somatic tissues. The subjects of this prospective 30-month long study were 25 Holstein bulls, sampled every six months. Real-time quantitative PCR was used to determine the relative TSPY copy number (rTSPY CN) and telomere length in the DNA samples extracted from blood. Twenty bulls showed an altered rTSPY CN after 30 months, although only 9 bulls showed a significant change (4 significant increase while 5 significant decrease, P<0.01). The sequential sampling provided the flow of rTSPY CN over six observations in 30 months and wide-spread variation of rTSPY CN was detected. Although a clear trend of the direction of change was not identifiable, the highly dynamic changes of individual rTSPY CN in aging bulls were observed here for the first time. In summary we have observed a highly variable rTSPY CN in bulls over a short period of time. Our results suggest the importance of further long term studies of the dynamics of rTSPY CN variablility.
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Affiliation(s)
- Olutobi A. Oluwole
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
| | - Kiana Mahboubi
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
| | - Laura A. Favetta
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
| | - Tamas Revay
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
- * E-mail:
| | | | - William Allan King
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
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13
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In vivo and in vitro ageing results in accumulation of de novo copy number variations in bulls. Sci Rep 2017; 7:1631. [PMID: 28487564 PMCID: PMC5431667 DOI: 10.1038/s41598-017-01793-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 04/03/2017] [Indexed: 11/24/2022] Open
Abstract
We have identified de novo copy number variations (CNVs) generated in bulls as they age. Blood samples from eight bulls were collected and SNP arrayed in a prospective design over 30 months allowing us to differentiate de novo CNVs from constant CNVs that are present throughout the sampling period. Quite remarkably, the total number of CNVs doubled over the 30-month period, as we observed an almost equal number of de novo and constant CNVs (107 and 111, respectively, i.e. 49% and 51%). Twice as many de novo CNVs emerged during the second half of the sampling schedule as in the first part. It suggests a dynamic generation of de novo CNVs in the bovine genome that becomes more frequent as the age of the animal progresses. In a second experiment de novo CNVs were detected through in vitro ageing of bovine fibroblasts by sampling passage #5, #15 and #25. De novo CNVs also became more frequent, but the proportion of them was only ~25% of the total number of CNVs (21 out of 85). Temporal generation of de novo CNVs resulted in increasing genome coverage. Genes and quantitative trait loci overlapping de novo CNVs were further investigated for ageing related functions.
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Andriani GA, Vijg J, Montagna C. Mechanisms and consequences of aneuploidy and chromosome instability in the aging brain. Mech Ageing Dev 2017; 161:19-36. [PMID: 27013377 PMCID: PMC5490080 DOI: 10.1016/j.mad.2016.03.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/17/2016] [Accepted: 03/19/2016] [Indexed: 01/31/2023]
Abstract
Aneuploidy and polyploidy are a form of Genomic Instability (GIN) known as Chromosomal Instability (CIN) characterized by sporadic abnormalities in chromosome copy numbers. Aneuploidy is commonly linked to pathological states. It is a hallmark of spontaneous abortions and birth defects and it is observed virtually in every human tumor, therefore being generally regarded as detrimental for the development or the maturation of tissues under physiological conditions. Polyploidy however, occurs as part of normal physiological processes during maturation and differentiation of some mammalian cell types. Surprisingly, high levels of aneuploidy are present in the brain, and their frequency increases with age suggesting that the brain is able to maintain its functionality in the presence of high levels of mosaic aneuploidy. Because somatic aneuploidy with age can reach exceptionally high levels, it is likely to have long-term adverse effects in this organ. We describe the mechanisms accountable for an abnormal DNA content with a particular emphasis on the CNS where cell division is limited. Next, we briefly summarize the types of GIN known to date and discuss how they interconnect with CIN. Lastly we highlight how several forms of CIN may contribute to genetic variation, tissue degeneration and disease in the CNS.
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Affiliation(s)
- Grasiella A Andriani
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department Ophthalmology and Visual Science, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department of Pathology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA.
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15
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Somatically acquired structural genetic differences: a longitudinal study of elderly Danish twins. Eur J Hum Genet 2016; 24:1506-10. [PMID: 27094753 DOI: 10.1038/ejhg.2016.34] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 02/26/2016] [Accepted: 03/18/2016] [Indexed: 11/08/2022] Open
Abstract
Structural genetic variants like copy number variants (CNVs) comprise a large part of human genetic variation and may be inherited as well as somatically acquired. Recent studies have reported the presence of somatically acquired structural variants in the human genome and it has been suggested that they may accumulate in elderly individuals. To further explore the presence and the age-related acquisition of somatic structural variants in the human genome, we investigated CNVs acquired over a period of 10 years in 86 elderly Danish twins as well as CNV discordances between co-twins of 18 monozygotic twin pairs. Furthermore, the presence of mosaic structural variants was explored. We identified four mosaic acquired uniparental disomy events on chromosome 4q and 14q in the follow-up samples from four individuals, and our study thereby supports the increasing prevalence of somatic mosaic variants with age.
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