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Yuan X, Yang T, Xu T, Ren X, Huang S, Chen Y, Shi D, Li X. Expression pattern of ATG4C and its effect on early embryonic development of porcine oocytes. Theriogenology 2024; 225:9-15. [PMID: 38781849 DOI: 10.1016/j.theriogenology.2024.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/13/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024]
Abstract
Autophagy is essential for oocyte maturation and preimplantation embryo development. ATG4C, a member of the ATG4 family, plays a crucial role in the autophagy process. The effect of ATG4C on the early embryonic development in pig has not been studied. In this study, the expression patterns of ATG4C were explored using qRT-PCR and immunofluorescence staining. Different concentrations of serum were added to in vitro maturation (IVM) medium to investigate its effects on oocyte maturation and embryonic development. Finally, the developmental potential of parthenogenetic embryos was detected by downregulating ATG4C in MII stage oocytes under 0 % serum condition. The results revealed that ATG4C was highly expressed in porcine oocytes matured in vitro and in parthenogenetic embryos. Compared with the 10 % serum group, the cumulus cell expansion, first polar body (PB1) extrusion rate, and subsequent developmental competence of embryos were reduced in the 0 % and 5 % serum groups. The mRNA levels of LC3, ATG5, BECLIN1, TFAM, PGC1α, and PINK1 were significantly increased (P < 0.05) in the 0 % serum group. ATG4C was significantly upregulated in the embryos at the 1-cell, 2-cell, 8-cell, and 16-cell stages in the 0 % serum group (P < 0.05). Compared with the negative control group, downregulation of ATG4C significantly decreased the 4-cell, 8-cell, and blastocyst rates (P < 0.05), and the expression of genes related to autophagy, mitochondria, and zygotic genome activation (ZGA) was significantly decreased (P < 0.05). The relative fluorescence intensity of LC3 and mitochondrial content in the ATG4C siRNA group was significantly reduced (P < 0.05). Collectively, the results indicate that ATG4C is highly expressed in porcine oocytes matured in vitro and in early embryos, and inhibition of ATG4C effects embryonic developmental competence by decreasing autophagy, mitochondrial content, and ZGA under serum-free condition.
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Affiliation(s)
- Xi Yuan
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of animal science and technology, Guangxi University, Nanning, 530005, China
| | - Ting Yang
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of animal science and technology, Guangxi University, Nanning, 530005, China
| | - Tairan Xu
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of animal science and technology, Guangxi University, Nanning, 530005, China
| | - Xuan Ren
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of animal science and technology, Guangxi University, Nanning, 530005, China
| | - Shihai Huang
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Yuan Chen
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of animal science and technology, Guangxi University, Nanning, 530005, China
| | - Deshun Shi
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of animal science and technology, Guangxi University, Nanning, 530005, China
| | - Xiangping Li
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of animal science and technology, Guangxi University, Nanning, 530005, China.
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Parvaresh H, Paczek K, Al-Bari MAA, Eid N. Mechanistic insights into fasting-induced autophagy in the aging heart. World J Cardiol 2024; 16:109-117. [PMID: 38576517 PMCID: PMC10989221 DOI: 10.4330/wjc.v16.i3.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/01/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
Autophagy is a prosurvival mechanism for the clearance of accumulated abnormal proteins, damaged organelles, and excessive lipids within mammalian cells. A growing body of data indicates that autophagy is reduced in aging cells. This reduction leads to various diseases, such as myocardial hypertrophy, infarction, and atherosclerosis. Recent studies in animal models of an aging heart showed that fasting-induced autophagy improved cardiac function and longevity. This improvement is related to autophagic clearance of damaged cellular components via either bulk or selective autophagy (such as mitophagy). In this editorial, we summarize the mechanisms of autophagy in normal and aging hearts. In addition, the protective effect of fasting-induced autophagy in cardiac aging has been highlighted.
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Affiliation(s)
- Hannaneh Parvaresh
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Katarzyna Paczek
- Department of Chiropractic, International Medical University, Kuala Lumpur 57000, Malaysia
| | | | - Nabil Eid
- Department of Anatomy, Division of Human Biology, School of Medicine, International Medical University, Kuala Lumpur 57000, Malaysia.
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3
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Greene SM, Klein PR, Alcala GA, Bustamante I, Bordas B, Johnson A, Vu V, Uhm SY, Gould GG. Aging to 24 months increased C57BL/6J mouse social sniffing and hippocampal Neto1 levels, and impaired female spatial learning. Behav Processes 2023; 211:104929. [PMID: 37586617 DOI: 10.1016/j.beproc.2023.104929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Understanding how natural aging impacts rodent performance in translational behavior tests is critical to teasing apart impairments due to age-related decline from neurodegenerative disorder modeling. Reduced neuropilin and tolloid-like 1 (NETO1), an accessory protein of ionotropic glutamate receptors involved in synaptic plasticity, was associated with Alzheimer's disease, yet aging effects on Neto1 remain unclear. For these reasons, our goal was to characterize how Neto1 expression corresponded with social, repetitive, and spatial learning behaviors and stress response across the C57BL/6J mouse lifespan. We measured social preferences in three-chamber tests, and motor stereotypies by marble burying. Cognitive flexibility is typically assessed in the Morris water maze (MWM), wherein C57BL/6J mice exhibit deficits with age. However, fatigue or locomotor impairment may confound interpretation of MWM performance. Therefore, we used a less arduous water T-maze (WTM) to compare spatial learning flexibility in 2, 9-15, and 24-month-old male and female mice to test the hypothesis that deficits would emerge with age. In both sexes, 9-15-month-olds made more chamber entries during social preference tests, while 2-month-olds did less social sniffing than aged mice. No age or sex differences emerged in marble burying or serum corticosterone measurements. In 24-month-olds hippocampal Neto1was increased relative to 2-month-olds, and male cognitive flexibility was strong, while spatial learning and reversal learning of 24-month-old females was impaired in WTM irrespective of Neto1 expression. The WTM is a useful alternative assessment for cognitive flexibility deficits in aged mice, and the role of hippocampal Neto1 in promoting social sniffing is of interest.
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Affiliation(s)
- Susan M Greene
- Department of Cellular & Integrative Physiology, Center for Biomedical Neuroscience, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; University of the Incarnate Word, 4301 Broadway, San Antonio, TX 78209, USA
| | - Preston R Klein
- Department of Cellular & Integrative Physiology, Center for Biomedical Neuroscience, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Gloria-Andrea Alcala
- Department of Cellular & Integrative Physiology, Center for Biomedical Neuroscience, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; University of the Incarnate Word, 4301 Broadway, San Antonio, TX 78209, USA
| | - Isabela Bustamante
- Department of Cellular & Integrative Physiology, Center for Biomedical Neuroscience, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Trinity University, One Trinity Place, San Antonio, TX 78212, USA
| | - Blanka Bordas
- Department of Cellular & Integrative Physiology, Center for Biomedical Neuroscience, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Fralin Biomedical Research Institute at Virginia Tech Carilion, Virginia Tech, Roanoke, VA 24016, USA
| | - Alexia Johnson
- Department of Cellular & Integrative Physiology, Center for Biomedical Neuroscience, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Howard University, Washington D.C. 20059, USA
| | - Vy Vu
- Department of Cellular & Integrative Physiology, Center for Biomedical Neuroscience, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - So Yeon Uhm
- Department of Cellular & Integrative Physiology, Center for Biomedical Neuroscience, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Georgianna G Gould
- Department of Cellular & Integrative Physiology, Center for Biomedical Neuroscience, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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4
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Xie L, Xie L. Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning. PLoS Comput Biol 2023; 19:e1010974. [PMID: 37590332 PMCID: PMC10464998 DOI: 10.1371/journal.pcbi.1010974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/29/2023] [Accepted: 07/27/2023] [Indexed: 08/19/2023] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) are hetero-bifunctional molecules that induce the degradation of target proteins by recruiting an E3 ligase. PROTACs have the potential to inactivate disease-related genes that are considered undruggable by small molecules, making them a promising therapy for the treatment of incurable diseases. However, only a few hundred proteins have been experimentally tested for their amenability to PROTACs, and it remains unclear which other proteins in the entire human genome can be targeted by PROTACs. In this study, we have developed PrePROTAC, an interpretable machine learning model based on a transformer-based protein sequence descriptor and random forest classification. PrePROTAC predicts genome-wide targets that can be degraded by CRBN, one of the E3 ligases. In the benchmark studies, PrePROTAC achieved a ROC-AUC of 0.81, an average precision of 0.84, and over 40% sensitivity at a false positive rate of 0.05. When evaluated by an external test set which comprised proteins from different structural folds than those in the training set, the performance of PrePROTAC did not drop significantly, indicating its generalizability. Furthermore, we developed an embedding SHapley Additive exPlanations (eSHAP) method, which extends conventional SHAP analysis for original features to an embedding space through in silico mutagenesis. This method allowed us to identify key residues in the protein structure that play critical roles in PROTAC activity. The identified key residues were consistent with existing knowledge. Using PrePROTAC, we identified over 600 novel understudied proteins that are potentially degradable by CRBN and proposed PROTAC compounds for three novel drug targets associated with Alzheimer's disease.
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Affiliation(s)
- Li Xie
- Department of Computer Science, Hunter College, The City University of New York, New York City, New York, United States of America
| | - Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, New York City, New York, United States of America
- Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York City, New York, United States of America
- Helen and Robert Appel Alzheimer’s Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York City, New York, United States of America
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5
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Akiyama M, Sakaue S, Takahashi A, Ishigaki K, Hirata M, Matsuda K, Momozawa Y, Okada Y, Ninomiya T, Terao C, Murakami Y, Kubo M, Kamatani Y. Genome-wide association study reveals BET1L associated with survival time in the 137,693 Japanese individuals. Commun Biol 2023; 6:143. [PMID: 36737517 PMCID: PMC9898503 DOI: 10.1038/s42003-023-04491-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 01/17/2023] [Indexed: 02/05/2023] Open
Abstract
Human lifespan is reported to be heritable. Although previous genome-wide association studies (GWASs) have identified several loci, a limited number of studies have assessed the genetic associations with the real survival information on the participants. We conducted a GWAS to identify loci associated with survival time in the Japanese individuals participated in the BioBank Japan Project by carrying out sex-stratified GWASs involving 78,029 males and 59,664 females. Of them, 31,324 (22.7%) died during the mean follow-up period of 7.44 years. We found a novel locus associated with survival (BET1L; P = 5.89 × 10-9). By integrating with eQTL data, we detected a significant overlap with eQTL of BET1L in skeletal muscle. A gene-set enrichment analysis showed that genes related to the BCAR1 protein-protein interaction subnetwork influence survival time (P = 1.54 × 10-7). These findings offer the candidate genes and biological mechanisms associated with human lifespan.
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Affiliation(s)
- Masato Akiyama
- grid.509459.40000 0004 0472 0267Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan ,grid.509459.40000 0004 0472 0267Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan ,grid.177174.30000 0001 2242 4849Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582 Japan
| | - Saori Sakaue
- grid.509459.40000 0004 0472 0267Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan ,grid.509459.40000 0004 0472 0267Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan ,grid.136593.b0000 0004 0373 3971Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871 Japan
| | - Atsushi Takahashi
- grid.509459.40000 0004 0472 0267Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan ,grid.509459.40000 0004 0472 0267Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan ,grid.410796.d0000 0004 0378 8307Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Osaka, 564-8565 Japan
| | - Kazuyoshi Ishigaki
- grid.509459.40000 0004 0472 0267Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan ,grid.509459.40000 0004 0472 0267Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Makoto Hirata
- grid.26999.3d0000 0001 2151 536XLaboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Koichi Matsuda
- grid.26999.3d0000 0001 2151 536XLaboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Yukihide Momozawa
- grid.509459.40000 0004 0472 0267Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Yukinori Okada
- grid.509459.40000 0004 0472 0267Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan ,grid.509459.40000 0004 0472 0267Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan ,grid.136593.b0000 0004 0373 3971Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871 Japan ,grid.509459.40000 0004 0472 0267Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Toshiharu Ninomiya
- grid.177174.30000 0001 2242 4849Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Fukuoka, 812-8582 Japan
| | | | - Chikashi Terao
- grid.509459.40000 0004 0472 0267Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan ,grid.509459.40000 0004 0472 0267Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Yoshinori Murakami
- grid.26999.3d0000 0001 2151 536XDivision of Molecular Pathology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Michiaki Kubo
- grid.509459.40000 0004 0472 0267RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan. .,Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan. .,Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, 108-8639, Japan.
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Neumann GB, Korkuć P, Arends D, Wolf MJ, May K, König S, Brockmann GA. Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing. Front Genet 2023; 13:993959. [PMID: 36712857 PMCID: PMC9875303 DOI: 10.3389/fgene.2022.993959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind, DSN) are an endangered dual-purpose cattle breed originating from the North Sea region. The population comprises about 2,500 cattle and is considered one of the ancestral populations of the modern Holstein breed. The current study aimed at defining the breeds closest related to DSN cattle, characterizing their genomic diversity and inbreeding. In addition, the detection of selection signatures between DSN and Holstein was a goal. Relationship analyses using fixation index (FST), phylogenetic, and admixture analyses were performed between DSN and 68 other breeds from the 1000 Bull Genomes Project. Nucleotide diversity, observed heterozygosity, and expected heterozygosity were calculated as metrics for genomic diversity. Inbreeding was measured as excess of homozygosity (FHom) and genomic inbreeding (FRoH) through runs of homozygosity (RoHs). Region-wide FST and cross-population-extended haplotype homozygosity (XP-EHH) between DSN and Holstein were used to detect selection signatures between the two breeds, and RoH islands were used to detect selection signatures within DSN and Holstein. DSN showed a close genetic relationship with breeds from the Netherlands, Belgium, Northern Germany, and Scandinavia, such as Dutch Friesian Red, Dutch Improved Red, Belgian Red White Campine, Red White Dual Purpose, Modern Angler, Modern Danish Red, and Holstein. The nucleotide diversity in DSN (0.151%) was higher than in Holstein (0.147%) and other breeds, e.g., Norwegian Red (0.149%), Red White Dual Purpose (0.149%), Swedish Red (0.149%), Hereford (0.145%), Angus (0.143%), and Jersey (0.136%). The FHom and FRoH values in DSN were among the lowest. Regions with high FST between DSN and Holstein, significant XP-EHH regions, and RoH islands detected in both breeds harbor candidate genes that were previously reported for milk, meat, fertility, production, and health traits, including one QTL detected in DSN for endoparasite infection resistance. The selection signatures between DSN and Holstein provide evidence of regions responsible for the dual-purpose properties of DSN and the milk type of Holstein. Despite the small population size, DSN has a high level of diversity and low inbreeding. FST supports its relatedness to breeds from the same geographic origin and provides information on potential gene pools that could be used to maintain diversity in DSN.
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Affiliation(s)
- Guilherme B. Neumann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paula Korkuć
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Danny Arends
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, United Kingdom
| | - Manuel J. Wolf
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Gudrun A. Brockmann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,*Correspondence: Gudrun A. Brockmann,
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7
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Jaiswal MK. Editorial: Multi-omics, Epigenomics, and Computational Analysis of Neurodegenerative Disorders. Front Neurosci 2022; 16:930425. [PMID: 35873823 PMCID: PMC9297909 DOI: 10.3389/fnins.2022.930425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
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Tong X, Li WX, Liang J, Zheng Y, Dai SX. Two different aging paths in human blood revealed by integrated analysis of gene Expression, mutation and alternative splicing. Gene 2022; 829:146501. [PMID: 35452709 DOI: 10.1016/j.gene.2022.146501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/04/2022] [Accepted: 04/14/2022] [Indexed: 11/04/2022]
Abstract
Aging is a complex life process that human organs and tissues steadily and continuously decline. Aging has huge heterogeneity, which shows different aging rates among different individuals and in different tissues of the same individual. Many studies of aging are often contradictory and show little common signature. The integrated analysis of these transcriptome datasets will provide an unbiased global view of the aging process. Here, we integrated 8 transcriptome datasets including 757 samples from healthy human blood to study aging from three aspects of gene expression, mutations, and alternative splicing. Surprisingly, we found that transcriptome changes in blood are relatively independent of the chronological age. Further pseudotime analysis revealed two different aging paths (AgingPath1 and AgingPath2) in human blood. The differentially expressed genes (DEGs) along the two paths showed a limited overlap and are enriched in different biological processes. The mutations of DEGs in AgingPath1 are significantly increased in the aging process, while the opposite trend was observed in AgingPath2. Expression quantitative trait loci (eQTL) and splicing quantitative trait loci (sQTL) analysis identified 304 important mutations that can affect both gene expression and alternative splicing during aging. Finally, by comparison between aging and Alzheimer's disease, we identified 37 common DEGs in AgingPath1, AgingPath2 and Alzheimer's disease. These genes may contribute to the shift from aging state to Alzheimer's disease. In summary, this study revealed the two aging paths and the related genes and mutations, which provides a new insight into aging and aging-related disease.
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Affiliation(s)
- Xin Tong
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Wen-Xing Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Jihao Liang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Yang Zheng
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Shao-Xing Dai
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
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9
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Huan T, Nguyen S, Colicino E, Ochoa‐Rosales C, Hill WD, Brody JA, Soerensen M, Zhang Y, Baldassari A, Elhadad MA, Toshiko T, Zheng Y, Domingo‐Relloso A, Lee DH, Ma J, Yao C, Liu C, Hwang S, Joehanes R, Fornage M, Bressler J, van Meurs JB, Debrabant B, Mengel‐From J, Hjelmborg J, Christensen K, Vokonas P, Schwartz J, Gahrib SA, Sotoodehnia N, Sitlani CM, Kunze S, Gieger C, Peters A, Waldenberger M, Deary IJ, Ferrucci L, Qu Y, Greenland P, Lloyd‐Jones DM, Hou L, Bandinelli S, Voortman T, Hermann B, Baccarelli A, Whitsel E, Pankow JS, Levy D. Integrative analysis of clinical and epigenetic biomarkers of mortality. Aging Cell 2022; 21:e13608. [PMID: 35546478 PMCID: PMC9197414 DOI: 10.1111/acel.13608] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/03/2022] [Accepted: 03/24/2022] [Indexed: 01/28/2023] Open
Abstract
DNA methylation (DNAm) has been reported to be associated with many diseases and with mortality. We hypothesized that the integration of DNAm with clinical risk factors would improve mortality prediction. We performed an epigenome-wide association study of whole blood DNAm in relation to mortality in 15 cohorts (n = 15,013). During a mean follow-up of 10 years, there were 4314 deaths from all causes including 1235 cardiovascular disease (CVD) deaths and 868 cancer deaths. Ancestry-stratified meta-analysis of all-cause mortality identified 163 CpGs in European ancestry (EA) and 17 in African ancestry (AA) participants at p < 1 × 10-7 , of which 41 (EA) and 16 (AA) were also associated with CVD death, and 15 (EA) and 9 (AA) with cancer death. We built DNAm-based prediction models for all-cause mortality that predicted mortality risk after adjusting for clinical risk factors. The mortality prediction model trained by integrating DNAm with clinical risk factors showed an improvement in prediction of cancer death with 5% increase in the C-index in a replication cohort, compared with the model including clinical risk factors alone. Mendelian randomization identified 15 putatively causal CpGs in relation to longevity, CVD, or cancer risk. For example, cg06885782 (in KCNQ4) was positively associated with risk for prostate cancer (Beta = 1.2, PMR = 4.1 × 10-4 ) and negatively associated with longevity (Beta = -1.9, PMR = 0.02). Pathway analysis revealed that genes associated with mortality-related CpGs are enriched for immune- and cancer-related pathways. We identified replicable DNAm signatures of mortality and demonstrated the potential utility of CpGs as informative biomarkers for prediction of mortality risk.
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Affiliation(s)
- Tianxiao Huan
- The Framingham Heart StudyFraminghamMassachusettsUSA
- The Population Sciences BranchDivision of Intramural ResearchNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMarylandUSA
- Department of Ophthalmology and Visual SciencesUniversity of Massachusetts Medical SchoolWorcesterMassachusettsUSA
| | - Steve Nguyen
- Division of Epidemiology & Community HealthSchool of Public HealthUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Elena Colicino
- Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Carolina Ochoa‐Rosales
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
- Centro de Vida Saludable de la Universidad de ConcepciónConcepciónChile
| | - W. David Hill
- Department of PsychologyLothian Birth CohortsUniversity of EdinburghEdinburghUK
| | - Jennifer A. Brody
- Cardiovascular Health Research UnitDepartment of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Mette Soerensen
- Department of Public HealthEpidemiology, Biostatistics and BiodemographyUniversity of Southern DenmarkOdense CDenmark
- Department of Clinical Biochemistry and PharmacologyCenter for Individualized Medicine in Arterial DiseasesOdense University HospitalOdense CDenmark
- Department of Clinical GeneticsOdense University HospitalOdense CDenmark
| | - Yan Zhang
- Division of Clinical Epidemiology & Aging ResearchGerman Cancer Rsrch Ctr (DKFZ)HeidelbergGermany
| | - Antoine Baldassari
- Department of EpidemiologyGillings School of Global Public HealthUniversity of North CarolinaChapel HillNorth CarolinaUSA
| | - Mohamed Ahmed Elhadad
- Research Unit of Molecular EpidemiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- Institute of EpidemiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- German Research Center for Cardiovascular Disease (DZHK)Partner Site Munich Heart AllianceMunichGermany
| | - Tanaka Toshiko
- Translational Gerontology BranchNational Institute on AgingBaltimoreMarylandUSA
| | - Yinan Zheng
- Department of Preventive MedicineNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
| | - Arce Domingo‐Relloso
- Department of Chronic Diseases EpidemiologyNational Center for EpidemiologyCarlos III Health InstituteMadridSpain
- Department of Environmental Health SciencesColumbia University Mailman School of Public HealthNew YorkNew YorkUSA
- Department of Statistics and Operations ResearchUniversity of ValenciaValenciaSpain
| | - Dong Heon Lee
- The Framingham Heart StudyFraminghamMassachusettsUSA
- The Population Sciences BranchDivision of Intramural ResearchNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Jiantao Ma
- The Framingham Heart StudyFraminghamMassachusettsUSA
- The Population Sciences BranchDivision of Intramural ResearchNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMarylandUSA
- Nutrition Epidemiology and Data ScienceFriedman School of Nutrition Science and PolicyTufts UniversityBostonMassachusettsUSA
| | - Chen Yao
- The Framingham Heart StudyFraminghamMassachusettsUSA
- The Population Sciences BranchDivision of Intramural ResearchNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Chunyu Liu
- Department of BiostatisticsBoston University School of Public HealthBostonMassachusettsUSA
| | - Shih‐Jen Hwang
- The Framingham Heart StudyFraminghamMassachusettsUSA
- The Population Sciences BranchDivision of Intramural ResearchNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Roby Joehanes
- The Framingham Heart StudyFraminghamMassachusettsUSA
- The Population Sciences BranchDivision of Intramural ResearchNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Myriam Fornage
- Human Genetics CenterSchool of Public HealthUniversity of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Jan Bressler
- Department of Internal MedicineErasmusRotterdamthe Netherlands
| | | | - Birgit Debrabant
- Department of Public HealthEpidemiology, Biostatistics and BiodemographyUniversity of Southern DenmarkOdense CDenmark
| | - Jonas Mengel‐From
- Department of Public HealthEpidemiology, Biostatistics and BiodemographyUniversity of Southern DenmarkOdense CDenmark
- Department of Clinical GeneticsOdense University HospitalOdense CDenmark
| | - Jacob Hjelmborg
- Department of Public HealthEpidemiology, Biostatistics and BiodemographyUniversity of Southern DenmarkOdense CDenmark
| | - Kaare Christensen
- Department of Public HealthEpidemiology, Biostatistics and BiodemographyUniversity of Southern DenmarkOdense CDenmark
- Department of Clinical GeneticsOdense University HospitalOdense CDenmark
| | - Pantel Vokonas
- Veterans AffairsNormative Aging StudyBostonMassachusettsUSA
- Veterans AffairsBoston Healthcare SystemBostonMassachusettsUSA
- Boston University School of Public HealthBostonMassachusettsUSA
| | - Joel Schwartz
- Departments of Environmental Health and EpidemiologyHarvard TH Chan School of Public HealthBostonMassachusettsUSA
| | - Sina A. Gahrib
- Cardiovascular Health Research UnitDepartment of MedicineUniversity of WashingtonSeattleWashingtonUSA
- Department of PsychologyUniv of EdinburghEdinburghUK
| | - Nona Sotoodehnia
- Cardiovascular Health Research UnitDepartment of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Colleen M. Sitlani
- Cardiovascular Health Research UnitDepartment of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Sonja Kunze
- Research Unit of Molecular EpidemiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- Institute of EpidemiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
| | - Christian Gieger
- Research Unit of Molecular EpidemiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- Institute of EpidemiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- German Research Center for Cardiovascular Disease (DZHK)Partner Site Munich Heart AllianceMunichGermany
| | - Annette Peters
- Institute of EpidemiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- German Research Center for Cardiovascular Disease (DZHK)Partner Site Munich Heart AllianceMunichGermany
- German Center for Diabetes Research (DZD)München‐Neuherberg, NeuherbergGermany
- Institute of Medical Information Sciences, Biometry and EpidemiologyLudwig‐Maximilians‐UniversityMunichGermany
| | - Melanie Waldenberger
- Research Unit of Molecular EpidemiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- Institute of EpidemiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- German Research Center for Cardiovascular Disease (DZHK)Partner Site Munich Heart AllianceMunichGermany
| | - Ian J. Deary
- Division of PulmonaryCritical Care and Sleep MedicineCenter for Lung BiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Luigi Ferrucci
- Translational Gerontology BranchNational Institute on AgingBaltimoreMarylandUSA
| | - Yishu Qu
- Department of Preventive MedicineNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
| | - Philip Greenland
- Department of Preventive MedicineNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
| | - Donald M. Lloyd‐Jones
- Department of Preventive MedicineNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
| | - Lifang Hou
- Department of Preventive MedicineNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
| | | | - Trudy Voortman
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
| | - Brenner Hermann
- Division of Clinical Epidemiology & Aging ResearchGerman Cancer Rsrch Ctr (DKFZ)HeidelbergGermany
- Network Aging Research (NAR)University of HeidelbergHeidelbergGermany
| | - Andrea Baccarelli
- Precision Medicine ProgramDepartment of Environmental Health SciencesMailman School of Public HealthColumbia UniversityNew YorkNew YorkUSA
| | - Eric Whitsel
- Department of EpidemiologyGillings School of Global Public HealthUniversity of North CarolinaChapel HillNorth CarolinaUSA
- Department of MedicineSchool of MedicineUniversity of North CarolinaChapel HillNorth CarolinaUSA
| | - James S. Pankow
- Division of Epidemiology & Community HealthSchool of Public HealthUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Daniel Levy
- The Framingham Heart StudyFraminghamMassachusettsUSA
- The Population Sciences BranchDivision of Intramural ResearchNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMarylandUSA
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10
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Chang X, Zhou YF, Wang L, Liu J, Yuan JM, Khor CC, Heng CK, Pan A, Koh WP, Dorajoo R. Genetic associations with healthy ageing among Chinese adults. NPJ AGING 2022; 8:6. [PMID: 35927272 PMCID: PMC9158790 DOI: 10.1038/s41514-022-00086-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 04/04/2022] [Indexed: 12/15/2022]
Abstract
The genetic basis of overall healthy ageing, especially among the East-Asian population is understudied. We conducted a genome-wide association study among 1618 Singapore Chinese elderly participants (65 years or older) ascertained to have aged healthily and compared their genome-wide genotypes to 6221 participants who did not age healthily, after a 20-year follow-up. Two genetic variants were identified (PMeta < 2.59 × 10-8) to be associated with healthy aging, including the LRP1B locus previously associated in long-lived individuals without cognitive decline. Our study sheds additional insights on the genetic basis of healthy ageing.
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Affiliation(s)
- Xuling Chang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, 119074, Singapore
| | - Yan-Feng Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Ling Wang
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, 119074, Singapore
| | - An Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Woon-Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore.
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research (A*STAR), Singapore, 117609, Singapore.
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore.
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore.
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11
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Sharafeldin N, Zhang J, Singh P, Bosworth A, Chen Y, Patel SK, Wang X, Francisco L, Forman SJ, Wong FL, Ojesina AI, Bhatia S. Genome-wide variants and polygenic risk scores for cognitive impairment following blood or marrow transplantation. Bone Marrow Transplant 2022; 57:925-933. [PMID: 35379913 DOI: 10.1038/s41409-022-01642-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 11/10/2022]
Abstract
Cognitive impairment is prevalent in blood or marrow transplantation (BMT) recipients, albeit with inter-individual variability. We conducted a genome-wide association study of objective cognitive function assessed longitudinally in 239 adult BMT recipients for discovery and replicated in an independent cohort of 540 BMT survivors. Weighted genome-wide polygenic risk scores (PRS) were constructed using linkage disequilibrium pruned significant SNPs. Forty-four genome-wide significant SNPs were identified using additive (n = 3); codominant (n = 20) and genotype models (n = 21). Each additional copy of a risk allele was associated with a 0.28-point (p = 1.07 × 10-8) to a 1.82-point (p = 6.7 × 10-12) increase in a global deficit score. We replicated two SNPs (rs11634183 and rs12486041) with links to neural integrity. Patients in the top PRS quintile were at increased risk of cognitive impairment in discovery (RR = 1.95, 95%CI: 1.28-2.96, p = 0.002) and replication cohorts (OR = 1.84, 95%CI, 1.02-3.32, p = 0.043). Associations were stronger among individuals with lowest clinical risk for cognitive impairment. These findings support potential utility of PRS-based risk classification in the development of targeted interventions aimed at improving cognitive outcomes in BMT survivors.
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Affiliation(s)
- Noha Sharafeldin
- Institute for Cancer Outcomes and Survivorship, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Jianqing Zhang
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Purnima Singh
- Institute for Cancer Outcomes and Survivorship, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Yanjun Chen
- Institute for Cancer Outcomes and Survivorship, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Xuexia Wang
- Department of Mathematics, University of North Texas, Denton, TX, USA
| | - Liton Francisco
- Institute for Cancer Outcomes and Survivorship, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stephen J Forman
- Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, CA, USA
| | | | - Akinyemi I Ojesina
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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12
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Hwangbo N, Zhang X, Raftery D, Gu H, Hu SC, Montine TJ, Quinn JF, Chung KA, Hiller AL, Wang D, Fei Q, Bettcher L, Zabetian CP, Peskind E, Li G, Promislow DEL, Franks A. A Metabolomic Aging Clock Using Human Cerebrospinal Fluid. J Gerontol A Biol Sci Med Sci 2021; 77:744-754. [PMID: 34382643 PMCID: PMC8974344 DOI: 10.1093/gerona/glab212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Indexed: 01/13/2023] Open
Abstract
Quantifying the physiology of aging is essential for improving our understanding of age-related disease and the heterogeneity of healthy aging. Recent studies have shown that, in regression models using "-omic" platforms to predict chronological age, residual variation in predicted age is correlated with health outcomes, and suggest that these "omic clocks" provide measures of biological age. This paper presents predictive models for age using metabolomic profiles of cerebrospinal fluid (CSF) from healthy human subjects and finds that metabolite and lipid data are generally able to predict chronological age within 10 years. We use these models to predict the age of a cohort of subjects with Alzheimer's and Parkinson's disease and find an increase in prediction error, potentially indicating that the relationship between the metabolome and chronological age differs with these diseases. However, evidence is not found to support the hypothesis that our models will consistently overpredict the age of these subjects. In our analysis of control subjects, we find the carnitine shuttle, sucrose, biopterin, vitamin E metabolism, tryptophan, and tyrosine to be the most associated with age. We showcase the potential usefulness of age prediction models in a small data set (n = 85) and discuss techniques for drift correction, missing data imputation, and regularized regression, which can be used to help mitigate the statistical challenges that commonly arise in this setting. To our knowledge, this work presents the first multivariate predictive metabolomic and lipidomic models for age using mass spectrometry analysis of CSF.
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Affiliation(s)
- Nathan Hwangbo
- Department of Statistics and Applied Probability, University of California, Santa Barbara, USA
| | - Xinyu Zhang
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, USA
| | - Haiwei Gu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, USA
| | - Shu-Ching Hu
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA,Department of Neurology, University of Washington School of Medicine, Seattle, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Joseph F Quinn
- Portland Veterans Affairs Medical Center, Oregon, USA,Department of Neurology, Oregon Health and Science University, Portland, USA
| | - Kathryn A Chung
- Portland Veterans Affairs Medical Center, Oregon, USA,Department of Neurology, Oregon Health and Science University, Portland, USA
| | - Amie L Hiller
- Portland Veterans Affairs Medical Center, Oregon, USA,Department of Neurology, Oregon Health and Science University, Portland, USA
| | - Dongfang Wang
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, USA
| | - Qiang Fei
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, USA
| | - Lisa Bettcher
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, USA
| | - Cyrus P Zabetian
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA,Department of Neurology, University of Washington School of Medicine, Seattle, USA
| | - Elaine Peskind
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA,Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, USA
| | - Gail Li
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA,Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, USA
| | - Daniel E L Promislow
- Department of Biology, University of Washington, Seattle, USA,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, USA
| | - Alexander Franks
- Department of Statistics and Applied Probability, University of California, Santa Barbara, USA,Address correspondence to: Alexander Franks, PhD, Department of Statistics and Applied Probability, University of California, Santa Barbara, UCSB Statistics Department, 5607A South Hall, Santa Barbara, CA 93106, USA. E-mail:
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13
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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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14
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Torres GG, Nygaard M, Caliebe A, Blanché H, Chantalat S, Galan P, Lieb W, Christiansen L, Deleuze JF, Christensen K, Strauch K, Müller-Nurasyid M, Peters A, Nöthen MM, Hoffmann P, Flachsbart F, Schreiber S, Ellinghaus D, Franke A, Dose J, Nebel A. Exome-Wide Association Study Identifies FN3KRP and PGP as New Candidate Longevity Genes. J Gerontol A Biol Sci Med Sci 2021; 76:786-795. [PMID: 33491046 PMCID: PMC8087267 DOI: 10.1093/gerona/glab023] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Indexed: 12/19/2022] Open
Abstract
Despite enormous research efforts, the genetic component of longevity has remained largely elusive. The investigation of common variants, mainly located in intronic or regulatory regions, has yielded only little new information on the heritability of the phenotype. Here, we performed a chip-based exome-wide association study investigating 62 488 common and rare coding variants in 1248 German long-lived individuals, including 599 centenarians and 6941 younger controls (age < 60 years). In a single-variant analysis, we observed an exome-wide significant association between rs1046896 in the gene fructosamine-3-kinase-related-protein (FN3KRP) and longevity. Noteworthy, we found the longevity allele C of rs1046896 to be associated with an increased FN3KRP expression in whole blood; a database look-up confirmed this effect for various other human tissues. A gene-based analysis, in which potential cumulative effects of common and rare variants were considered, yielded the gene phosphoglycolate phosphatase (PGP) as another potential longevity gene, though no single variant in PGP reached the discovery p-value (1 × 10E−04). Furthermore, we validated the previously reported longevity locus cyclin-dependent kinase inhibitor 2B antisense RNA 1 (CDKN2B-AS1). Replication of our results in a French longevity cohort was only successful for rs1063192 in CDKN2B-AS1. In conclusion, we identified 2 new potential candidate longevity genes, FN3KRP and PGP which may influence the phenotype through their role in metabolic processes, that is, the reverse glycation of proteins (FN3KRP) and the control of glycerol-3-phosphate levels (PGP).
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Affiliation(s)
- Guillermo G Torres
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Germany
| | - Marianne Nygaard
- The Danish Twin Registry and The Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense C.,Department of Clinical Genetics, Odense University Hospital, Denmark
| | - Amke Caliebe
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Germany
| | - Hélène Blanché
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain (CEPH), Paris, France
| | - Sophie Chantalat
- Centre National de Recherche en Génomique Humaine CNRGH-CEA, Evry, France
| | - Pilar Galan
- Université Sorbonne Paris Cité-UREN, Unité de Recherche en Epidémiologie Nutritionelle, U557 Inserm, U1125 Inra, Bobigny, France
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Kiel University, University Hospital Schleswig-Holstein, Germany
| | - Lene Christiansen
- The Danish Twin Registry and The Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense C.,Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Jean-François Deleuze
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain (CEPH), Paris, France.,Centre National de Recherche en Génomique Humaine CNRGH-CEA, Evry, France
| | - Kaare Christensen
- The Danish Twin Registry and The Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense C.,Department of Clinical Genetics, Odense University Hospital, Denmark.,Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Denmark
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Germany.,Department of Internal Medicine I (Cardiology), Hospital of the LMU Munich, Germany
| | - Annette Peters
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | | | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Germany
| | - Friederike Flachsbart
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Germany
| | - Janina Dose
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Germany
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15
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Lencz T, Yu J, Khan RR, Flaherty E, Carmi S, Lam M, Ben-Avraham D, Barzilai N, Bressman S, Darvasi A, Cho JH, Clark LN, Gümüş ZH, Vijai J, Klein RJ, Lipkin S, Offit K, Ostrer H, Ozelius LJ, Peter I, Malhotra AK, Maniatis T, Atzmon G, Pe'er I. Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia. Neuron 2021; 109:1465-1478.e4. [PMID: 33756103 DOI: 10.1016/j.neuron.2021.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/16/2020] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
The identification of rare variants associated with schizophrenia has proven challenging due to genetic heterogeneity, which is reduced in founder populations. In samples from the Ashkenazi Jewish population, we report that schizophrenia cases had a greater frequency of novel missense or loss of function (MisLoF) ultra-rare variants (URVs) compared to controls, and the MisLoF URV burden was inversely correlated with polygenic risk scores in cases. Characterizing 141 "case-only" genes (MisLoF URVs in ≥3 cases with none in controls), the cadherin gene set was associated with schizophrenia. We report a recurrent case mutation in PCDHA3 that results in the formation of cytoplasmic aggregates and failure to engage in homophilic interactions on the plasma membrane in cultured cells. Modeling purifying selection, we demonstrate that deleterious URVs are greatly overrepresented in the Ashkenazi population, yielding enhanced power for association studies. Identification of the cadherin/protocadherin family as risk genes helps specify the synaptic abnormalities central to schizophrenia.
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Affiliation(s)
- Todd Lencz
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11550, USA; Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA.
| | - Jin Yu
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Raiyan Rashid Khan
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Erin Flaherty
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 9112102, Israel
| | - Max Lam
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Danny Ben-Avraham
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nir Barzilai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Susan Bressman
- Department of Neurology, Beth Israel Medical Center, New York, NY 10003, USA
| | - Ariel Darvasi
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Judy H Cho
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lorraine N Clark
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Taub Institute for Research of Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joseph Vijai
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Taub Institute for Research of Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Steven Lipkin
- Departments of Medicine, Genetic Medicine and Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Harry Ostrer
- Departments of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laurie J Ozelius
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anil K Malhotra
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11550, USA; Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; New York Genome Center, New York, NY 10013, USA
| | - Gil Atzmon
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Human Biology, Haifa University, Haifa, Israel
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY 10027, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.
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16
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Zhao X, Liang S, Wang N, Hong T, Sambou M, Fan J, Zhu M, Wang C, Hang D, Jiang Y, Dai J. Sex-Specific Associations of Testosterone and Genetic Factors With Health Span. Front Endocrinol (Lausanne) 2021; 12:773464. [PMID: 34899607 PMCID: PMC8655098 DOI: 10.3389/fendo.2021.773464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/26/2021] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Previous studies have suggested associations between testosterone, genetic factors, and a series of complex diseases, but the associations with the lifespan phenotype, such as health span, remain unclear. METHODS In this prospective cohort study, we analyzed 145,481 men and 147,733 women aged 38-73 years old from UK Biobank (UKB) to investigate the sex-specific associations of total testosterone (TT), free testosterone (FT), or polygenic risk score (PRS) with health span termination (HST) risk. At baseline, serum testosterone levels were measured. HST was defined by eight events strongly associated with longevity. PRS, an efficient tool combining the effect of common genetic variants to discriminate genetic risk of complex phenotypes, was constructed by 12 single-nucleotide polymorphisms related to health span from UKB (P ≤ 5.0 × 10-8). We used multivariable Cox regression models to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). RESULTS With a median follow-up time of 7.70 years, 26,748 (18.39%) men and 18,963 (12.84%) women had HST. TT was negatively associated with HST in men [HR per standard deviation (SD) increment of log-TT: 0.92, 95% CI: 0.88-0.97]. Inversely, both TT (HR per SD increment of log-TT: 1.05, 95% CI: 1.02-1.08) and FT (HR per SD increment of log-FT: 1.08, 95% CI: 1.05-1.11) presented an increased risk of HST in women. PRS was positively associated with HST risk (quintile 5 versus quintile 1, men, HR: 1.19, 95% CI: 1.15-1.24; women, HR: 1.21, 95% CI: 1.16-1.27). Moreover, men with high TT and low genetic risk showed the lowest HST risk (HR: 0.80, 95% CI: 0.73-0.88), whereas HST risk for women with both high TT and genetic risk increased obviously (HR: 1.32, 95% CI: 1.19-1.46). Similar joint effects were observed for FT in both genders. CONCLUSIONS We observed sex-specific associations that testosterone was negatively associated with HST risk in men and positively associated with HST risk in women. Genetic factors increased the HST risk, suggesting that participants with both high genetic risk and abnormal testosterone levels (high level in women or low level in men) should be the target for early intervention. Although our findings highlight the associations between testosterone and health span, further mechanistic studies and prospective trials are warranted to explore the causation behind.
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Affiliation(s)
- Xiaoyu Zhao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuang Liang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Nanxi Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Tongtong Hong
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Muhammed Lamin Sambou
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jingyi Fan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
| | - Cheng Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
| | - Dong Hang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
| | - Yue Jiang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
- *Correspondence: Juncheng Dai,
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17
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Age-related hearing loss pertaining to potassium ion channels in the cochlea and auditory pathway. Pflugers Arch 2020; 473:823-840. [PMID: 33336302 PMCID: PMC8076138 DOI: 10.1007/s00424-020-02496-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/27/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022]
Abstract
Age-related hearing loss (ARHL) is the most prevalent sensory deficit in the elderly and constitutes the third highest risk factor for dementia. Lifetime noise exposure, genetic predispositions for degeneration, and metabolic stress are assumed to be the major causes of ARHL. Both noise-induced and hereditary progressive hearing have been linked to decreased cell surface expression and impaired conductance of the potassium ion channel KV7.4 (KCNQ4) in outer hair cells, inspiring future therapies to maintain or prevent the decline of potassium ion channel surface expression to reduce ARHL. In concert with KV7.4 in outer hair cells, KV7.1 (KCNQ1) in the stria vascularis, calcium-activated potassium channels BK (KCNMA1) and SK2 (KCNN2) in hair cells and efferent fiber synapses, and KV3.1 (KCNC1) in the spiral ganglia and ascending auditory circuits share an upregulated expression or subcellular targeting during final differentiation at hearing onset. They also share a distinctive fragility for noise exposure and age-dependent shortfalls in energy supply required for sustained surface expression. Here, we review and discuss the possible contribution of select potassium ion channels in the cochlea and auditory pathway to ARHL. We postulate genes, proteins, or modulators that contribute to sustained ion currents or proper surface expressions of potassium channels under challenging conditions as key for future therapies of ARHL.
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18
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Ren X, Kuan PF. RNAAgeCalc: A multi-tissue transcriptional age calculator. PLoS One 2020; 15:e0237006. [PMID: 32750074 PMCID: PMC7402472 DOI: 10.1371/journal.pone.0237006] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/16/2020] [Indexed: 12/12/2022] Open
Abstract
Biological aging reflects decline in physiological functions and is an effective indicator of morbidity and mortality. Numerous epigenetic age calculators are available, however biological aging calculators based on transcription remain scarce. Here, we introduce RNAAgeCalc, a versatile across-tissue and tissue-specific transcriptional age calculator. By performing a meta-analysis of transcriptional age signature across multi-tissues using the GTEx database, we identify 1,616 common age-related genes, as well as tissue-specific age-related genes. Based on these genes, we develop new across-tissue and tissue-specific age predictors. We show that our transcriptional age calculator outperforms other prior age related gene signatures as indicated by the higher correlation with chronological age as well as lower median and median error. Our results also indicate that both racial and tissue differences are associated with transcriptional age. Furthermore, we demonstrate that the transcriptional age acceleration computed from our within-tissue predictor is significantly correlated with mutation burden, mortality risk and cancer stage in several types of cancer from the TCGA database, and offers complementary information to DNA methylation age. RNAAgeCalc is available at http://www.ams.sunysb.edu/~pfkuan/softwares.html#RNAAgeCalc, both as Bioconductor and Python packages, accompanied by a user-friendly interactive Shiny app.
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Affiliation(s)
- Xu Ren
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
| | - Pei Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
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19
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Pulakat L, Chen HH. Pro-Senescence and Anti-Senescence Mechanisms of Cardiovascular Aging: Cardiac MicroRNA Regulation of Longevity Drug-Induced Autophagy. Front Pharmacol 2020; 11:774. [PMID: 32528294 PMCID: PMC7264109 DOI: 10.3389/fphar.2020.00774] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
Chronological aging as well as biological aging accelerated by various pathologies such as diabetes and obesity contribute to cardiovascular aging, and structural and functional tissue damage of the heart and vasculature. Cardiovascular aging in humans is characterized by structural pathologic remodeling including cardiac and vascular fibrosis, hypertrophy, stiffness, micro- and macro-circulatory impairment, left ventricular diastolic dysfunction precipitating heart failure with either reduced or preserved ejection fraction, and cardiovascular cell death. Cellular senescence, an important hallmark of aging, is a critical factor that impairs repair and regeneration of damaged cells in cardiovascular tissues whereas autophagy, an intracellular catabolic process is an essential inherent mechanism that removes senescent cells throughout life time in all tissues. Several recent reviews have highlighted the fact that all longevity treatment paradigms to mitigate progression of aging-related pathologies converge in induction of autophagy, activation of AMP kinase (AMPK) and Sirtuin pathway, and inhibition of mechanistic target of rapamycin (mTOR). These longevity treatments include health style changes such as caloric restriction, and drug treatments using rapamycin, the first FDA-approved longevity drug, as well as other experimental longevity drugs such as metformin, rapamycin, aspirin, and resveratrol. However, in the heart tissue, autophagy induction has to be tightly regulated since evidence show excessive autophagy results in cardiomyopathy and heart failure. Here we discuss emerging evidence for microRNA-mediated tight regulation of autophagy in the heart in response to treatment with rapamycin, and novel approaches to monitor autophagy progression in a temporal manner to diagnose and regulate autophagy induction by longevity treatments.
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Affiliation(s)
- Lakshmi Pulakat
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, United States.,Department of Medicine, Tufts University School of Medicine, Boston, MA, United States
| | - Howard H Chen
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, United States.,Department of Medicine, Tufts University School of Medicine, Boston, MA, United States
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20
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Abstract
In this review we critically summarize the evidence base and the progress to date regarding the genomic basis of periodontal disease and tooth morbidity (ie, dental caries and tooth loss), and discuss future applications and research directions in the context of precision oral health and care. Evidence for these oral/dental traits from genome-wide association studies first emerged less than a decade ago. Basic and translational research activities in this domain are now under way by multiple groups around the world. Key departure points in the oral health genomics discourse are: (a) some heritable variation exists for periodontal and dental diseases; (b) the environmental component (eg, social determinants of health and behavioral risk factors) has a major influence on the population distribution but probably interacts with factors of innate susceptibility at the person-level; (c) sizeable, multi-ethnic, well-characterized samples or cohorts with high-quality measures on oral health outcomes and genomics information are required to make decisive discoveries; (d) challenges remain in the measurement of oral health and disease, with current periodontitis and dental caries traits capturing only a part of the health-disease continuum, and are little or not informed by the underlying biology; (e) the substantial individual heterogeneity that exists in the clinical presentation and lifetime trajectory of oral disease can be identified and leveraged in a precision medicine framework or, if unappreciated, can hamper translational efforts. In this review we discuss how composite or biologically informed traits may offer improvements over clinically defined ones for the genomic interrogation of oral diseases. We demonstrate the utility of the results of genome-wide association studies for the development and testing of a genetic risk score for severe periodontitis. We conclude that exciting opportunities lie ahead for improvements in the oral health of individual patients and populations via advances in our understanding of the genomic basis of oral health and disease. The pace of new discoveries and their equitable translation to practice will largely depend on investments in the education and training of the oral health care workforce, basic and population research, and sustained collaborative efforts..
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Affiliation(s)
- Thiago Morelli
- Department of PeriodontologySchool of DentistryUniversity of North Carolina at Chapel HillChapel HillNorth Carolina, USA
| | - Cary S. Agler
- Department of Oral and Craniofacial Health SciencesSchool of DentistryUniversity of North Carolina at Chapel HillChapel HillNorth Carolina, USA
| | - Kimon Divaris
- Department of Pediatric DentistrySchool of DentistryUniversity of North Carolina at Chapel HillChapel HillNorth Carolina, USA
- Department of EpidemiologyGillings School of Global Public HealthUniversity of North Carolina at Chapel HillChapel HillNorth Carolina, USA
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21
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Belloy ME, Napolioni V, Greicius MD. A Quarter Century of APOE and Alzheimer's Disease: Progress to Date and the Path Forward. Neuron 2019; 101:820-838. [PMID: 30844401 DOI: 10.1016/j.neuron.2019.01.056] [Citation(s) in RCA: 301] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/08/2019] [Accepted: 01/27/2019] [Indexed: 12/11/2022]
Abstract
Alzheimer's disease (AD) is considered a polygenic disorder. This view is clouded, however, by lingering uncertainty over how to treat the quasi "monogenic" role of apolipoprotein E (APOE). The APOE4 allele is not only the strongest genetic risk factor for AD, it also affects risk for cardiovascular disease, stroke, and other neurodegenerative disorders. This review, based mostly on data from human studies, ranges across a variety of APOE-related pathologies, touching on evolutionary genetics and risk mitigation by ethnicity and sex. The authors also address one of the most fundamental question pertaining to APOE4 and AD: does APOE4 increase AD risk via a loss or gain of function? The answer will be of the utmost importance in guiding future research in AD.
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Affiliation(s)
- Michaël E Belloy
- Department of Neurology and Neurological Sciences, FIND Lab, Stanford University, Stanford, CA 94304, USA
| | - Valerio Napolioni
- Department of Neurology and Neurological Sciences, FIND Lab, Stanford University, Stanford, CA 94304, USA
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, FIND Lab, Stanford University, Stanford, CA 94304, USA.
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22
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Zhang Y, Saum KU, Schöttker B, Holleczek B, Brenner H. Methylomic survival predictors, frailty, and mortality. Aging (Albany NY) 2019. [PMID: 29514134 PMCID: PMC5892685 DOI: 10.18632/aging.101392] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Survival predictors are of potential use for informing on biological age and targeting prevention of aging-related morbidity. We assessed associations of 2 novel methylomic survival indicators, a methylation-based mortality risk score (MRscore) and the epigenetic clock-derived age acceleration (AA), with a well-known survival predictor, frailty index (FI), and compared the 3 indicators in mortality prediction. In a large population-based cohort with 14-year follow-up, we found both MRscore and AA to be independently associated with FI, but the association was much stronger for MRscore than for AA. Although all 3 indicators were individually associated with all-cause mortality, robust associations only persisted for MRscore and FI when simultaneously including the 3 indicators in regression models, with hazard ratios (95% CI) of 1.91 (1.63–2.22), 1.37 (1.25–1.51), and 1.05 (0.90–1.22), respectively, per standard deviation increase of MRscore, FI, and AA. Prediction error curves, Harrell’s C-statistics, and time-dependent AUCs all showed higher predictive accuracy for MRscore than for FI and AA. These findings were validated in independent samples. Our study demonstrates the ability of the MRscore to strongly enhance survival prediction beyond established markers of biological age, such as FI and AA, and it thus bears potential of a surrogate endpoint for clinical research and intervention.
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Affiliation(s)
- Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany
| | - Kai-Uwe Saum
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany.,Network Ageing Research, University of Heidelberg, Heidelberg 69115, Germany
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg D-69120, Germany
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23
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Zenin A, Tsepilov Y, Sharapov S, Getmantsev E, Menshikov LI, Fedichev PO, Aulchenko Y. Identification of 12 genetic loci associated with human healthspan. Commun Biol 2019; 2:41. [PMID: 30729179 PMCID: PMC6353874 DOI: 10.1038/s42003-019-0290-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 01/08/2019] [Indexed: 02/06/2023] Open
Abstract
Aging populations face diminishing quality of life due to increased disease and morbidity. These challenges call for longevity research to focus on understanding the pathways controlling healthspan. We use the data from the UK Biobank (UKB) cohort and observe that the risks of major chronic diseases increased exponentially and double every eight years, i.e., at a rate compatible with the Gompertz mortality law. Assuming that aging drives the acceleration in morbidity rates, we build a risk model to predict the age at the end of healthspan depending on age, gender, and genetic background. Using the sub-population of 300,447 British individuals as a discovery cohort, we identify 12 loci associated with healthspan at the whole-genome significance level. We find strong genetic correlations between healthspan and all-cause mortality, life-history, and lifestyle traits. We thereby conclude that the healthspan offers a promising new way to interrogate the genetics of human longevity.
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Affiliation(s)
- Aleksandr Zenin
- Gero LLC, Novokuznetskaya street 24/2, Moscow, Russia 119017
| | - Yakov Tsepilov
- Novosibirsk State University, Pirogova 2, Novosibirsk, Russia 630090
- Institute of Cytology and Genetics SB RAS, Lavrentyeva ave. 10, Novosibirsk, Russia 630090
| | - Sodbo Sharapov
- Novosibirsk State University, Pirogova 2, Novosibirsk, Russia 630090
- Institute of Cytology and Genetics SB RAS, Lavrentyeva ave. 10, Novosibirsk, Russia 630090
| | | | - L. I. Menshikov
- Gero LLC, Novokuznetskaya street 24/2, Moscow, Russia 119017
- National Research Center “Kurchatov Institute”, 1, Akademika Kurchatova pl., Moscow, Russia 123182
| | - Peter O. Fedichev
- Gero LLC, Novokuznetskaya street 24/2, Moscow, Russia 119017
- Moscow Institute of Physics and Technology, Institutskii per. 9, Dolgoprudny, Moscow Russia 141700
| | - Yurii Aulchenko
- Novosibirsk State University, Pirogova 2, Novosibirsk, Russia 630090
- Institute of Cytology and Genetics SB RAS, Lavrentyeva ave. 10, Novosibirsk, Russia 630090
- PolyOmica, Het Vlaggeschip 61, 5237PA ‘s-Hertogenbosch, The Netherlands
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, Scotland EH8 9AG UK
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24
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Li J, Zhang D, Wiersma M, Brundel BJJM. Role of Autophagy in Proteostasis: Friend and Foe in Cardiac Diseases. Cells 2018; 7:cells7120279. [PMID: 30572675 PMCID: PMC6316637 DOI: 10.3390/cells7120279] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/13/2018] [Accepted: 12/18/2018] [Indexed: 12/11/2022] Open
Abstract
Due to ageing of the population, the incidence of cardiovascular diseases will increase in the coming years, constituting a substantial burden on health care systems. In particular, atrial fibrillation (AF) is approaching epidemic proportions. It has been identified that the derailment of proteostasis, which is characterized by the loss of homeostasis in protein biosynthesis, folding, trafficking, and clearance by protein degradation systems such as autophagy, underlies the development of common cardiac diseases. Among various safeguards within the proteostasis system, autophagy is a vital cellular process that modulates clearance of misfolded and proteotoxic proteins from cardiomyocytes. On the other hand, excessive autophagy may result in derailment of proteostasis and therefore cardiac dysfunction. Here, we review the interplay between autophagy and proteostasis in the healthy heart, discuss the imbalance between autophagy and proteostasis during cardiac diseases, including AF, and finally explore new druggable targets which may limit cardiac disease initiation and progression.
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Affiliation(s)
- Jin Li
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, 1081 HV Amsterdam, The Netherlands.
| | - Deli Zhang
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, 1081 HV Amsterdam, The Netherlands.
| | - Marit Wiersma
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, 1081 HV Amsterdam, The Netherlands.
| | - Bianca J J M Brundel
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, 1081 HV Amsterdam, The Netherlands.
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25
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Mekli K, Stevens A, Marshall AD, Arpawong TE, Phillips DF, Tampubolon G, Lee J, Prescott CA, Nazroo JY, Pendleton N. Frailty Index associates with GRIN2B in two representative samples from the United States and the United Kingdom. PLoS One 2018; 13:e0207824. [PMID: 30475886 PMCID: PMC6258126 DOI: 10.1371/journal.pone.0207824] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/05/2018] [Indexed: 02/07/2023] Open
Abstract
The concept of frailty has been used in the clinical and research field for more than two decades. It is usually described as a clinical state of heightened vulnerability to poor resolution of homeostasis after a stressor event, which thereby increases the risk of adverse outcomes, including falls, delirium, disability and mortality. Here we report the results of the first genome-wide association scan and comparative gene ontology analyses where we aimed to identify genes and pathways associated with the deficit model of frailty. We used a discovery-replication design with two independent, nationally representative samples of older adults. The square-root transformed Frailty Index (FI) was the outcome variable, and age and sex were included as covariates. We report one hit exceeding genome-wide significance: the rs6765037 A allele was significantly associated with a decrease in the square-root transformed FI score in the Discovery sample (beta = -0.01958, p = 2.14E-08), without confirmation in the Replication sample. We also report a nominal replication: the rs7134291 A allele was significantly associated with a decrease in the square-root transformed FI score (Discovery sample: beta = -0.01021, p = 1.85E-06, Replication sample: beta = -0.005013, p = 0.03433). These hits represent the KBTBD12 and the GRIN2B genes, respectively. Comparative gene ontology analysis identified the pathways ‘Neuropathic pain signalling in dorsal horn neurons’ and the ‘GPCR-Mediated Nutrient Sensing in Enteroendocrine Cells’, exceeding the p = 0.01 significance in both samples, although this result does not survive correction for multiple testing. Considering the crucial role of GRIN2B in brain development, synaptic plasticity and cognition, this gene appears to be a potential candidate to play a role in frailty. In conclusion, we conducted genome-wide association scan and pathway analyses and have identified genes and pathways with potential roles in frailty. However, frailty is a complex condition. Therefore, further research is required to confirm our results and more thoroughly identify relevant biological mechanisms.
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Affiliation(s)
- Krisztina Mekli
- Cathie Marsh Institute for Social Research, The University of Manchester, Manchester, United Kingdom
- * E-mail:
| | - Adam Stevens
- Division of Developmental Biology and Medicine, The University of Manchester, Manchester, United Kingdom
| | - Alan D. Marshall
- School of Social and Political Science, The University of Edinburgh, Edinburgh, United Kingdom
| | - Thalida E. Arpawong
- Department of Psychology, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, United States of America
| | - Drystan F. Phillips
- Dornsife Center for Economic and Social Research, University of Southern California, Los Angeles, CA, United States of America
- RAND Corporation, Santa Monica, CA, United States of America
| | - Gindo Tampubolon
- Institute for Social Change, The University of Manchester, Manchester, United Kingdom
| | - Jinkook Lee
- Dornsife Center for Economic and Social Research, University of Southern California, Los Angeles, CA, United States of America
- RAND Corporation, Santa Monica, CA, United States of America
| | - Carol A. Prescott
- Department of Psychology, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, United States of America
- Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States of America
| | - James Y. Nazroo
- Cathie Marsh Institute for Social Research, The University of Manchester, Manchester, United Kingdom
| | - Neil Pendleton
- Division of Neuroscience and Experimental Psychology, The University of Manchester, Manchester, United Kingdom
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Kent SJ, Flexner C. Ageing in patients with chronic HIV infection: impact of hypercoagulation. AIDS Res Ther 2018; 15:22. [PMID: 30474565 PMCID: PMC6260879 DOI: 10.1186/s12981-018-0211-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/09/2018] [Indexed: 12/30/2022] Open
Abstract
Ageing is the result of biological events that progressively and irreversibly compromise the function of vital organs and eventually result in death. There is a general perception that ageing is accelerated in people living with HIV, with an increasing body of evidence to support this view. With the introduction of effective antiretroviral therapy, the life expectancy of people living with HIV has improved. Since people with HIV are living longer than previously, while also ageing faster than the general population, there is an increase in HIV-positive patients living with age-related comorbidities. This brief overview of ageing and HIV discusses aspects of the complications of HIV infection as they impact the ageing process. How diseases of age affect patients with HIV provides clues to help unravel the interactions between HIV and ageing that ultimately should help clinicians understand the basis of ‘normal’ ageing and manage ageing HIV-positive patients more effectively.
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Yashin AI, Arbeev KG, Wu D, Arbeeva LS, Bagley O, Stallard E, Kulminski AM, Akushevich I, Fang F, Wojczynski MK, Christensen K, Newman AB, Boudreau RM, Province MA, Thielke S, Perls TT, An P, Elo I, Ukraintseva SV. Genetics of Human Longevity From Incomplete Data: New Findings From the Long Life Family Study. J Gerontol A Biol Sci Med Sci 2018; 73:1472-1481. [PMID: 30299504 PMCID: PMC6175028 DOI: 10.1093/gerona/gly057] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Indexed: 02/04/2023] Open
Abstract
The special design of the Long Life Family Study provides a unique opportunity to investigate the genetics of human longevity by analyzing data on exceptional lifespans in families. In this article, we performed two series of genome wide association studies of human longevity which differed with respect to whether missing lifespan data were predicted or not predicted. We showed that the use of predicted lifespan is most beneficial when the follow-up period is relatively short. In addition to detection of strong associations of SNPs in APOE, TOMM40, NECTIN2, and APOC1 genes with longevity, we also detected a strong new association with longevity of rs1927465, located between the CYP26A1 and MYOF genes on chromosome 10. The association was confirmed using data from the Health and Retirement Study. We discuss the biological relevance of the detected SNPs to human longevity.
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Affiliation(s)
- Anatoliy I Yashin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina,Address correspondence to: Anatoliy I. Yashin, PhD, Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina. E-mail:
| | - Konstantin G Arbeev
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
| | - Deqing Wu
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
| | - Liubov S Arbeeva
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Olivia Bagley
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
| | - Eric Stallard
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
| | - Igor Akushevich
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
| | - Fang Fang
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
| | - Mary K Wojczynski
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri
| | - Kaare Christensen
- Department of Epidemiology, University of Southern Denmark, Odense, Denmark
| | - Anne B Newman
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Robert M Boudreau
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michael A Province
- Department of Genetics, Washington University in St Louis, St Louis, Missouri
| | | | - Thomas T Perls
- Medical Center, Boston University, Boston, Massachusetts
| | - Ping An
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri
| | - Irma Elo
- Department of Sociology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Svetlana V Ukraintseva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
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Abstract
Longer human lives have led to a global burden of late-life disease. However, some older people experience little ill health, a trait that should be extended to the general population. Interventions into lifestyle, including increased exercise and reduction in food intake and obesity, can help to maintain healthspan. Altered gut microbiota, removal of senescent cells, blood factors obtained from young individuals and drugs can all improve late-life health in animals. Application to humans will require better biomarkers of disease risk and responses to interventions, closer alignment of work in animals and humans, and increased use of electronic health records, biobank resources and cohort studies.
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Hook M, Roy S, Williams EG, Bou Sleiman M, Mozhui K, Nelson JF, Lu L, Auwerx J, Williams RW. Genetic cartography of longevity in humans and mice: Current landscape and horizons. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2718-2732. [PMID: 29410319 PMCID: PMC6066442 DOI: 10.1016/j.bbadis.2018.01.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/24/2018] [Accepted: 01/28/2018] [Indexed: 12/14/2022]
Abstract
Aging is a complex and highly variable process. Heritability of longevity among humans and other species is low, and this finding has given rise to the idea that it may be futile to search for DNA variants that modulate aging. We argue that the problem in mapping longevity genes is mainly one of low power and the genetic and environmental complexity of aging. In this review we highlight progress made in mapping genes and molecular networks associated with longevity, paying special attention to work in mice and humans. We summarize 40 years of linkage studies using murine cohorts and 15 years of studies in human populations that have exploited candidate gene and genome-wide association methods. A small but growing number of gene variants contribute to known longevity mechanisms, but a much larger set have unknown functions. We outline these and other challenges and suggest some possible solutions, including more intense collaboration between research communities that use model organisms and human cohorts. Once hundreds of gene variants have been linked to differences in longevity in mammals, it will become feasible to systematically explore gene-by-environmental interactions, dissect mechanisms with more assurance, and evaluate the roles of epistasis and epigenetics in aging. A deeper understanding of complex networks-genetic, cellular, physiological, and social-should position us well to improve healthspan.
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Affiliation(s)
- Michael Hook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Suheeta Roy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Evan G Williams
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland
| | - Maroun Bou Sleiman
- Interfaculty Institute of Bioengineering, Laboratory of Integrative and Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - James F Nelson
- Department of Cellular and Integrative Physiology and Barshop Institute for Longevity and Aging Studies, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Johan Auwerx
- Interfaculty Institute of Bioengineering, Laboratory of Integrative and Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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30
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Shi R, Guberman M, Kirshenbaum LA. Mitochondrial quality control: The role of mitophagy in aging. Trends Cardiovasc Med 2018; 28:246-260. [DOI: 10.1016/j.tcm.2017.11.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 12/25/2022]
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31
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Castillo E, Leon J, Mazzei G, Abolhassani N, Haruyama N, Saito T, Saido T, Hokama M, Iwaki T, Ohara T, Ninomiya T, Kiyohara Y, Sakumi K, LaFerla FM, Nakabeppu Y. Comparative profiling of cortical gene expression in Alzheimer's disease patients and mouse models demonstrates a link between amyloidosis and neuroinflammation. Sci Rep 2017; 7:17762. [PMID: 29259249 PMCID: PMC5736730 DOI: 10.1038/s41598-017-17999-3] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 12/05/2017] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, characterized by accumulation of amyloid β (Aβ) and neurofibrillary tangles. Oxidative stress and inflammation are considered to play an important role in the development and progression of AD. However, the extent to which these events contribute to the Aβ pathologies remains unclear. We performed inter-species comparative gene expression profiling between AD patient brains and the App NL-G-F/NL-G-F and 3xTg-AD-H mouse models. Genes commonly altered in App NL-G-F/NL-G-F and human AD cortices correlated with the inflammatory response or immunological disease. Among them, expression of AD-related genes (C4a/C4b, Cd74, Ctss, Gfap, Nfe2l2, Phyhd1, S100b, Tf, Tgfbr2, and Vim) was increased in the App NL-G-F/NL-G-F cortex as Aβ amyloidosis progressed with exacerbated gliosis, while genes commonly altered in the 3xTg-AD-H and human AD cortices correlated with neurological disease. The App NL-G-F/NL-G-F cortex also had altered expression of genes (Abi3, Apoe, Bin2, Cd33, Ctsc, Dock2, Fcer1g, Frmd6, Hck, Inpp5D, Ly86, Plcg2, Trem2, Tyrobp) defined as risk factors for AD by genome-wide association study or identified as genetic nodes in late-onset AD. These results suggest a strong correlation between cortical Aβ amyloidosis and the neuroinflammatory response and provide a better understanding of the involvement of gender effects in the development of AD.
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Affiliation(s)
- Erika Castillo
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Julio Leon
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.,Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Guianfranco Mazzei
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Nona Abolhassani
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Naoki Haruyama
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Saitama, Japan
| | - Takaomi Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Saitama, Japan
| | - Masaaki Hokama
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.,Department of Neurosurgery, Japan Community Health Care Organization Kyushu Hospital, Kitakyushu, 806-8501, Japan
| | - Toru Iwaki
- Department of Neuropathology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tomoyuki Ohara
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Toshiharu Ninomiya
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yutaka Kiyohara
- Hisayama Research Institute for Lifestyle Diseases, Hisayama, Fukuoka, Japan
| | - Kunihiko Sakumi
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Frank M LaFerla
- Department of Neurobiology and Behavior, University of California, Irvine, CA, 92697, USA
| | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
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32
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Dougherty M, Lazar J, Klein JC, Diaz K, Gobillot T, Grunblatt E, Hasle N, Lawrence D, Maurano M, Nelson M, Olson G, Srivatsan S, Shendure J, Keene CD, Bird T, Horwitz MS, Marshall DA. Genome sequencing in a case of Niemann-Pick type C. Cold Spring Harb Mol Case Stud 2017; 2:a001222. [PMID: 27900365 PMCID: PMC5111003 DOI: 10.1101/mcs.a001222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Adult-onset Niemann–Pick disease type C (NPC) is an infrequent presentation of a rare neurovisceral lysosomal lipid storage disorder caused by autosomal recessive mutations in NPC1 (∼95%) or NPC2 (∼5%). Our patient was diagnosed at age 33 when he presented with a 10-yr history of difficulties in judgment, concentration, speech, and coordination. A history of transient neonatal jaundice and splenomegaly with bone marrow biopsy suggesting a lipid storage disorder pointed to NPC; biochemical (“variant” level cholesterol esterification) and ultrastructural studies in adulthood confirmed the diagnosis. Genetic testing revealed two different missense mutations in the NPC1 gene—V950M and N1156S. Symptoms progressed over >20 yr to severe ataxia and spasticity, dementia, and dysphagia with aspiration leading to death. Brain autopsy revealed mild atrophy of the cerebrum and cerebellum. Microscopic examination showed diffuse gray matter deposition of balloon neurons, mild white matter loss, extensive cerebellar Purkinje cell loss with numerous “empty baskets,” and neurofibrillary tangles predominantly in the hippocampal formation and transentorhinal cortex. We performed whole-genome sequencing to examine whether the patient harbored variants outside of the NPC1 locus that could have contributed to his late-onset phenotype. We focused analysis on genetic modifiers in pathways related to lipid metabolism, longevity, and neurodegenerative disease. We identified no rare coding variants in any of the pathways examined nor was the patient enriched for genome-wide association study (GWAS) single-nucleotide polymorphisms (SNPs) associated with longevity or altered lipid metabolism. In light of these findings, this case provides support for the V950M variant being sufficient for adult-onset NPC disease.
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Affiliation(s)
- Max Dougherty
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA;; Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA
| | - John Lazar
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA;; Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Jason C Klein
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA;; Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Karina Diaz
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Theodore Gobillot
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Eli Grunblatt
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Nicholas Hasle
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Daniel Lawrence
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Megan Maurano
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Maria Nelson
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Gregory Olson
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Sanjay Srivatsan
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA;; Howard Hughes Medical Institute, Seattle, Washington 98195, USA
| | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Thomas Bird
- Department of Neurology, University of Washington, Seattle, Washington 98105, USA;; Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Marshall S Horwitz
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Desiree A Marshall
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
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Singh J, Minster RL, Schupf N, Kraja A, Liu Y, Christensen K, Newman AB, Kammerer CM. Genomewide Association Scan of a Mortality Associated Endophenotype for a Long and Healthy Life in the Long Life Family Study. J Gerontol A Biol Sci Med Sci 2017; 72:1411-1416. [PMID: 28329217 DOI: 10.1093/gerona/glx011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Indexed: 01/21/2023] Open
Abstract
Background Identification of genes or fundamental biological pathways that regulate aging phenotypes and longevity could lead to possible interventions to increase healthy longevity. Methods Using data from the Long Life Family Study, we performed genomewide association analyses on an endophenotype construct, LF1, comprising a linear combination of traits across health domains. LF1 primarily reflected traits from the pulmonary and physical activity domains. Results We detected a significant association between LF1 and a locus on chromosome 10p15 (p-value = 4.65 × 10-8) and suggestive evidence (p-value < 5 × 10-6) for association on chromosomes 1, 2, 8, 12, 15, 18, and 22. Using data from the Health, Aging and Body Composition Study, we subsequently replicated the association for the 1p13 region near the NBPF6 locus (p-value = 3.65 × 10-4). Conclusions Our analyses indicate that loci influencing a healthy aging endophenotype construct predominantly comprised of pulmonary and physical function domains may be located on chromosome 1p13 near the NBPF6 locus. Further investigation of this possible locus and other suggestive loci may reveal novel biological pathways that influence healthy aging.
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Affiliation(s)
- Jatinder Singh
- Department of Human Genetics, University of Pittsburgh, Pennsylvania
| | - Ryan L Minster
- Department of Human Genetics, University of Pittsburgh, Pennsylvania
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, New York
| | - Aldi Kraja
- Division of Statistical Genomics, School of Medicine, Washington University in St. Louis, Missouri
| | - YongMei Liu
- Department of Epidemiology & Prevention, Wake Forest University Health Sciences, Winston-Salem, North Carolina
| | - Kaare Christensen
- The Danish Aging Research Center, University of Southern Denmark; Department of Clinical Biochemistry and Pharmacology and Department of Clinical Genetics, Odense University Hospital, Denmark
| | - Anne B Newman
- Department of Epidemiology, University of Pittsburgh, Pennsylvania
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Eline Slagboom P, van den Berg N, Deelen J. Phenome and genome based studies into human ageing and longevity: An overview. Biochim Biophys Acta Mol Basis Dis 2017; 1864:2742-2751. [PMID: 28951210 DOI: 10.1016/j.bbadis.2017.09.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 12/13/2022]
Abstract
Human ageing is an extremely personal process leading across the life course of individuals to large population heterogeneity in the decline of functional capacity, health and lifespan. The extremes of this process are witnessed by the healthy vital 100-year-olds on one end and the 60-year-olds suffering from multiple morbid conditions on the other end of the spectrum. Molecular studies into the basis of this heterogeneity have focused on a range of endpoints and methodological approaches. The phenotype definitions most prominently investigated in these studies are either lifespan-related or biomarker based indices of the biological ageing rate of individuals and their tissues. Unlike for many complex, age-related diseases, consensus on the ultimate set of multi-biomarker ageing or lifespan-related phenotypes for genetic and genomic studies has not been reached yet. Comparable to animal models, hallmarks of age-related disease risk, healthy ageing and longevity include immune and metabolic pathways. Potentially novel genomic regions and pathways have been identified among many (epi)genomic studies into chronological age and studies into human lifespan regulation, with APOE and FOXO3A representing yet the most robust loci. Functional analysis of a handful of genes in cell-based and animal models is ongoing. The way forward in human ageing and longevity studies seems through improvements in the interpretation of the biology of the genome, in application of computational and systems biology, integration with animal models and by harmonization of repeated phenotypic and omics measures in longitudinal and intervention studies. This article is part of a Special Issue entitled: Model Systems of Aging - edited by "Houtkooper Riekelt".
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Affiliation(s)
- P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
| | - Niels van den Berg
- Department of Molecular Epidemiology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
| | - Joris Deelen
- Department of Molecular Epidemiology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands; Max Planck Institute for Biology of Ageing; Joseph-Stelzmann-Str. 9b, D-50931 Köln (Cologne), Germany.
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35
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Mozhui K, Snively BM, Rapp SR, Wallace RB, Williams RW, Johnson KC. Genetic Analysis of Mitochondrial Ribosomal Proteins and Cognitive Aging in Postmenopausal Women. Front Genet 2017; 8:127. [PMID: 28983317 PMCID: PMC5613226 DOI: 10.3389/fgene.2017.00127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/04/2017] [Indexed: 11/24/2022] Open
Abstract
Genes encoding mitochondrial ribosomal proteins (MRPs) have been linked to aging and longevity in model organisms (i.e., mice, Caenorhabditis elegans). Here we evaluated if the MRPs have conserved effects on aging traits in humans. We utilized data from 4,504 participants of the Women's Health Initiative Memory Study (WHIMS) who had both longitudinal cognitive data and genetic data. Two aging phenotypes were considered: (1) gross lifespan (time to all-cause mortality), and (2) cognitive aging (longitudinal rate of change in modified mini-mental state scores). We tested genetic association with variants in 78 members of the MRP gene family. Genetic association tests were done at the single nucleotide polymorphism (SNP) level, and at gene-set level using two distinct procedures (GATES and MAGMA). We included SNPs in APOE and adjusted the tests for the APOE-ε4 allele, a known risk factor for dementia. The strongest association signal is for the known cognitive aging SNP, rs429358, in APOE (p-value = 5 × 10-28 for cognitive aging; p-value = 0.03 for survival). We found no significant association between the MRPs and survival time. For cognitive aging, we detected SNP level association for rs189661478 in MRPL23 (p-value < 9 × 10-6). Furthermore, the gene-set analysis showed modest but significant association between the MRP family and cognitive aging. In conclusion, our results indicate a potential pathway-level association between the MRPs and cognitive aging that is independent of the APOE locus. We however did not detect association between the MRPs and lifespan.
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Affiliation(s)
- Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science CenterMemphis, TN, United States
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science CenterMemphis, TN, United States
| | - Beverly M. Snively
- Department of Biostatistical Sciences, Wake Forest University School of MedicineWinston-Salem, NC, United States
| | - Stephen R. Rapp
- Department of Psychiatry and Behavioral Medicine, Wake Forest University School of MedicineWinston-Salem, NC, United States
| | - Robert B. Wallace
- Department of Epidemiology, University of Iowa College of Public HealthIowa City, IA, United States
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science CenterMemphis, TN, United States
| | - Karen C. Johnson
- Department of Preventive Medicine, University of Tennessee Health Science CenterMemphis, TN, United States
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36
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McDaid AF, Joshi PK, Porcu E, Komljenovic A, Li H, Sorrentino V, Litovchenko M, Bevers RPJ, Rüeger S, Reymond A, Bochud M, Deplancke B, Williams RW, Robinson-Rechavi M, Paccaud F, Rousson V, Auwerx J, Wilson JF, Kutalik Z. Bayesian association scan reveals loci associated with human lifespan and linked biomarkers. Nat Commun 2017; 8:15842. [PMID: 28748955 PMCID: PMC5537485 DOI: 10.1038/ncomms15842] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 05/08/2017] [Indexed: 02/07/2023] Open
Abstract
The enormous variation in human lifespan is in part due to a myriad of sequence variants, only a few of which have been revealed to date. Since many life-shortening events are related to diseases, we developed a Mendelian randomization-based method combining 58 disease-related GWA studies to derive longevity priors for all HapMap SNPs. A Bayesian association scan, informed by these priors, for parental age of death in the UK Biobank study (n=116,279) revealed 16 independent SNPs with significant Bayes factor at a 5% false discovery rate (FDR). Eleven of them replicate (5% FDR) in five independent longevity studies combined; all but three are depleted of the life-shortening alleles in older Biobank participants. Further analysis revealed that brain expression levels of nearby genes (RBM6, SULT1A1 and CHRNA5) might be causally implicated in longevity. Gene expression and caloric restriction experiments in model organisms confirm the conserved role for RBM6 and SULT1A1 in modulating lifespan.
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Affiliation(s)
- Aaron F McDaid
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne 1010, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland
| | - Eleonora Porcu
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
| | - Andrea Komljenovic
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.,Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Hao Li
- Laboratory of Integrative and Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Vincenzo Sorrentino
- Laboratory of Integrative and Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Maria Litovchenko
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.,Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Roel P J Bevers
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.,Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Sina Rüeger
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne 1010, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
| | - Murielle Bochud
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne 1010, Switzerland
| | - Bart Deplancke
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.,Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Marc Robinson-Rechavi
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.,Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Fred Paccaud
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne 1010, Switzerland
| | - Valentin Rousson
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne 1010, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative and Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne 1010, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
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Stegeman R, Weake VM. Transcriptional Signatures of Aging. J Mol Biol 2017; 429:2427-2437. [PMID: 28684248 DOI: 10.1016/j.jmb.2017.06.019] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/02/2017] [Accepted: 06/28/2017] [Indexed: 12/31/2022]
Abstract
Genome-wide studies of aging have identified subsets of genes that show age-related changes in expression. Although the types of genes that are age regulated vary among different tissues and organisms, some patterns emerge from these large data sets. First, aging is associated with a broad induction of stress response pathways, although the specific genes and pathways involved differ depending on cell type and species. In contrast, a wide variety of functional classes of genes are downregulated with age, often including tissue-specific genes. Although the upregulation of age-regulated genes is likely to be governed by stress-responsive transcription factors, questions remain as to why particular genes are susceptible to age-related transcriptional decline. Here, we discuss recent findings showing that splicing is misregulated with age. While defects in splicing could lead to changes in protein isoform levels, they could also impact gene expression through nonsense-mediated decay of intron-retained transcripts. The discovery that splicing is misregulated with age suggests that other aspects of gene expression, such as transcription elongation, termination, and polyadenylation, must also be considered as potential mechanisms for age-related changes in transcript levels. Moreover, the considerable variation between genome-wide aging expression studies indicates that there is a critical need to analyze the transcriptional signatures of aging in single-cell types rather than whole tissues. Since age-associated decreases in gene expression could contribute to a progressive decline in cellular function, understanding the mechanisms that determine the aging transcriptome provides a potential target to extend healthy cellular lifespan.
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Affiliation(s)
- R Stegeman
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - V M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN 47907, USA.
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Sebastiani P, Bae H, Gurinovich A, Soerensen M, Puca A, Perls TT. Limitations and risks of meta-analyses of longevity studies. Mech Ageing Dev 2017; 165:139-146. [PMID: 28143747 PMCID: PMC5533653 DOI: 10.1016/j.mad.2017.01.008] [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: 10/05/2016] [Revised: 01/21/2017] [Accepted: 01/23/2017] [Indexed: 11/22/2022]
Abstract
Searching for genetic determinants of human longevity has been challenged by the rarity of data sets with large numbers of individuals who have reached extreme old age, inconsistent definitions of the phenotype, and the difficulty of defining appropriate controls. Meta-analysis - a statistical method to summarize results from different studies - has become a common tool in genetic epidemiology to accrue large sample sizes for powerful genetic association studies. In conducting a meta-analysis of studies of human longevity however, particular attention must be made to the definition of cases and controls (including their health status) and on the effect of possible confounders such as sex and ethnicity upon the genetic effect to be estimated. We will show examples of how a meta-analysis can inflate the false negative rates of genetic association studies or it can bias estimates of the association between a genetic variant and extreme longevity.
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Affiliation(s)
- Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118, United States.
| | - Harold Bae
- College of Public Health and Human Sciences, Oregon State University, 151 Milam Hall, Corvallis, OR, United States.
| | - Anastasia Gurinovich
- Bioinformatics Program, Boston University, 44 Cummington Mall, Boston, MA 02215, United States.
| | - Mette Soerensen
- The Danish Aging Research Center, Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, J.B. Winsloews Vej 9 B, St., 5000 Odense C, Denmark.
| | - Annibale Puca
- IRCCS MultiMedica, 20138 Milan (Mi), Italy; University of Salerno, Department of Medicine and Surgery, 84081 Baronissi, SA, Italy.
| | - Thomas T Perls
- Geriatrics Section, Department of Medicine, Boston University School of Medicine & Boston Medical Center, 88 E Newton St., Boston, MA 02118, United States.
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Abstract
: The increased prevalence of age-related comorbidities and mortality is worrisome in ageing HIV-infected patients. Here, we aim to analyse the different ageing mechanisms with regard to HIV infection. Ageing results from the time-dependent accumulation of random cellular damage. Epigenetic modifications and mitochondrial DNA haplogroups modulate ageing. In antiretroviral treatment-controlled patients, epigenetic clock appears to be advanced, and some haplogroups are associated with HIV infection severity. Telomere shortening is enhanced in HIV-infected patients because of HIV and some nucleoside analogue reverse transcriptase inhibitors. Mitochondria-related oxidative stress and mitochondrial DNA mutations are increased during ageing and also by some nucleoside analogue reverse transcriptase inhibitors. Overall, increased inflammation or 'inflammageing' is a major driver of ageing and could result from cell senescence with secreted proinflammatory mediators, altered gut microbiota, and coinfections. In HIV-infected patients, the level of inflammation and innate immunity activation is enhanced and related to most comorbidities and to mortality. This status could result, in addition to age, from the virus itself or viral protein released from reservoirs, from HIV-enhanced gut permeability and dysbiosis, from antiretroviral treatment, from frequent cytomegalovirus and hepatitis C virus coinfections, and also from personal and environmental factors, as central fat accumulation or smoking. Adaptive immune activation and immunosenescence are associated with comorbidities and mortality in the general population but are less predictive in HIV-infected patients. Biomarkers to evaluate ageing in HIV-infected patients are required. Numerous systemic or cellular inflammatory, immune activation, oxidative stress, or senescence markers can be tested in serum or peripheral blood mononuclear cells. The novel European Study to Establish Biomarkers of Human Ageing MARK-AGE algorithm, evaluating the biological age, is currently assessed in HIV-infected patients and reveals an advanced biological age. Some enhanced inflammatory or innate immune activation markers are interesting but still not validated for the patient's follow-up. To be able to assess patients' biological age is an important objective to improve their healthspan.
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Dozmorov MG, Coit P, Maksimowicz-McKinnon K, Sawalha AH. Age-associated DNA methylation changes in naive CD4 + T cells suggest an evolving autoimmune epigenotype in aging T cells. Epigenomics 2017; 9:429-445. [PMID: 28322571 DOI: 10.2217/epi-2016-0143] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AIM We sought to define age-associated DNA methylation changes in naive CD4+ T cells. MATERIALS & METHODS Naive CD4+ T cells were collected from 74 healthy individuals (age 19-66 years), and age-related DNA methylation changes were characterized. RESULTS We identified 11,431 age-associated CpG sites, 57% of which were hypermethylated with age. Hypermethylated sites were enriched in CpG islands and repressive transcription factor binding sites, while hypomethylated sites showed T cell specific enrichment in active enhancers marked by H3K27ac and H3K4me1. Our data emphasize cancer-related DNA methylation changes with age, and also reveal age-associated hypomethylation in immune-related pathways, such as T cell receptor signaling, FCγR-mediated phagocytosis, apoptosis and the mammalian target of rapamycin signaling pathway. The MAPK signaling pathway was hypermethylated with age, consistent with a defective MAPK signaling in aging T cells. CONCLUSION Age-associated DNA methylation changes may alter regulatory mechanisms and signaling pathways that predispose to autoimmunity.
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Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Patrick Coit
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Center for Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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Zhang Y, Wilson R, Heiss J, Breitling LP, Saum KU, Schöttker B, Holleczek B, Waldenberger M, Peters A, Brenner H. DNA methylation signatures in peripheral blood strongly predict all-cause mortality. Nat Commun 2017; 8:14617. [PMID: 28303888 PMCID: PMC5357865 DOI: 10.1038/ncomms14617] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/17/2017] [Indexed: 12/27/2022] Open
Abstract
DNA methylation (DNAm) has been revealed to play a role in various diseases. Here we performed epigenome-wide screening and validation to identify mortality-related DNAm signatures in a general population-based cohort with up to 14 years follow-up. In the discovery panel in a case-cohort approach, 11,063 CpGs reach genome-wide significance (FDR<0.05). 58 CpGs, mapping to 38 well-known disease-related genes and 14 intergenic regions, are confirmed in a validation panel. A mortality risk score based on ten selected CpGs exhibits strong association with all-cause mortality, showing hazard ratios (95% CI) of 2.16 (1.10–4.24), 3.42 (1.81–6.46) and 7.36 (3.69–14.68), respectively, for participants with scores of 1, 2–5 and 5+ compared with a score of 0. These associations are confirmed in an independent cohort and are independent from the ‘epigenetic clock'. In conclusion, DNAm of multiple disease-related genes are strongly linked to mortality outcomes. The DNAm-based risk score might be informative for risk assessment and stratification. DNA methylation is modulated by environmental factors and has a role in many complex diseases. Here, the authors find that methylation at specific DNA sites is associated with all-cause mortality, and a methylation-based risk score may be informative for risk assessment and stratification.
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Affiliation(s)
- Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Research Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Center for Environmental Health, D-85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764 Neuherberg, Germany
| | - Jonathan Heiss
- Division of Clinical Epidemiology and Aging Research, German Research Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Lutz P Breitling
- Division of Clinical Epidemiology and Aging Research, German Research Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Kai-Uwe Saum
- Division of Clinical Epidemiology and Aging Research, German Research Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Research Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.,Network Ageing Research, University of Heidelberg, Bergheimer Strasse 20, D-69115 Heidelberg, Germany
| | - Bernd Holleczek
- Saarland Cancer Registry, Präsident Baltz Strasse 5, D-66119 Saarbrücken, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Center for Environmental Health, D-85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764 Neuherberg, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Center for Environmental Health, D-85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764 Neuherberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Research Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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Lin JF, Wu S, Juang JMJ, Chiang FT, Hsu LA, Teng MS, Cheng ST, Huang HL, Sun YC, Liu PY, Ko YL. IL1RL1 single nucleotide polymorphism predicts sST2 level and mortality in coronary and peripheral artery disease. Atherosclerosis 2017; 257:71-77. [DOI: 10.1016/j.atherosclerosis.2016.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/08/2016] [Accepted: 12/16/2016] [Indexed: 12/25/2022]
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Briggs CA, Chakroborty S, Stutzmann GE. Emerging pathways driving early synaptic pathology in Alzheimer's disease. Biochem Biophys Res Commun 2016; 483:988-997. [PMID: 27659710 DOI: 10.1016/j.bbrc.2016.09.088] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/13/2016] [Accepted: 09/17/2016] [Indexed: 11/25/2022]
Abstract
The current state of the AD research field is highly dynamic is some respects, while seemingly stagnant in others. Regarding the former, our current lack of understanding of initiating disease mechanisms, the absence of effective treatment options, and the looming escalation of AD patients is energizing new research directions including a much-needed re-focusing on early pathogenic mechanisms, validating novel targets, and investigating relevant biomarkers, among other exciting new efforts to curb disease progression and foremost, preserve memory function. With regard to the latter, the recent disappointing series of failed Phase III clinical trials targeting Aβ and APP processing, in concert with poor association between brain Aβ levels and cognitive function, have led many to call for a re-evaluation of the primacy of the amyloid cascade hypothesis. In this review, we integrate new insights into one of the earliest described signaling abnormalities in AD pathogenesis, namely intracellular Ca2+ signaling disruptions, and focus on its role in driving synaptic deficits - which is the feature that does correlate with AD-associated memory loss. Excess Ca2+release from intracellular stores such as the endoplasmic reticulum (ER) has been well-described in cellular and animal models of AD, as well as human patients, and here we expand upon recent developments in ER-localized release channels such as the IP3R and RyR, and the recent emphasis on RyR2. Consistent with ER Ca2+ mishandling in AD are recent findings implicating aspects of SOCE, such as STIM2 function, and TRPC3 and TRPC6 levels. Other Ca2+-regulated organelles important in signaling and protein handling are brought into the discussion, with new perspectives on lysosomal regulation. These early signaling abnormalities are discussed in the context of synaptic pathophysiology and disruptions in synaptic plasticity with a particular emphasis on short-term plasticity deficits. Overall, we aim to update and expand the list of early neuronal signaling abnormalities implicated in AD pathogenesis, identify specific channels and organelles involved, and link these to proximal synaptic impairments driving the memory loss in AD. This is all within the broader goal of identifying novel therapeutic targets to preserve cognitive function in AD.
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Affiliation(s)
- Clark A Briggs
- Department of Neuroscience, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, IL 60064, USA
| | - Shreaya Chakroborty
- Department of Neuroscience, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, IL 60064, USA
| | - Grace E Stutzmann
- Department of Neuroscience, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, IL 60064, USA.
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Brinkmeyer-Langford CL, Guan J, Ji G, Cai JJ. Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. Front Aging Neurosci 2016; 8:183. [PMID: 27536236 PMCID: PMC4971101 DOI: 10.3389/fnagi.2016.00183] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/15/2016] [Indexed: 11/13/2022] Open
Abstract
Human aging is associated with cognitive decline and an increased risk of neurodegenerative disease. Our objective for this study was to evaluate potential relationships between age and variation in gene expression across different regions of the brain. We analyzed the Genotype-Tissue Expression (GTEx) data from 54 to 101 tissue samples across 13 brain regions in post-mortem donors of European descent aged between 20 and 70 years at death. After accounting for the effects of covariates and hidden confounding factors, we identified 1446 protein-coding genes whose expression in one or more brain regions is correlated with chronological age at a false discovery rate of 5%. These genes are involved in various biological processes including apoptosis, mRNA splicing, amino acid biosynthesis, and neurotransmitter transport. The distribution of these genes among brain regions is uneven, suggesting variable regional responses to aging. We also found that the aging response of many genes, e.g., TP37 and C1QA, depends on individuals' genotypic backgrounds. Finally, using dispersion-specific analysis, we identified genes such as IL7R, MS4A4E, and TERF1/TERF2 whose expressions are differentially dispersed by aging, i.e., variances differ between age groups. Our results demonstrate that age-related gene expression is brain region-specific, genotype-dependent, and associated with both mean and dispersion changes. Our findings provide a foundation for more sophisticated gene expression modeling in the studies of age-related neurodegenerative diseases.
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Affiliation(s)
| | - Jinting Guan
- Department of Automation, Xiamen UniversityXiamen, China
| | - Guoli Ji
- Department of Automation, Xiamen UniversityXiamen, China
- Innovation Center for Cell Signaling Network, Xiamen UniversityXiamen, China
| | - James J. Cai
- Department of Veterinary Integrative Biosciences, Texas A&M UniversityCollege Station, TX, USA
- Interdisciplinary Program in Genetics, Texas A&M UniversityCollege Station, TX, USA
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Marthandan S, Menzel U, Priebe S, Groth M, Guthke R, Platzer M, Hemmerich P, Kaether C, Diekmann S. Conserved genes and pathways in primary human fibroblast strains undergoing replicative and radiation induced senescence. Biol Res 2016; 49:34. [PMID: 27464526 PMCID: PMC4963952 DOI: 10.1186/s40659-016-0095-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/19/2016] [Indexed: 01/01/2023] Open
Abstract
Background Cellular senescence is induced either internally, for example by replication exhaustion and cell division, or externally, for example by irradiation. In both cases, cellular damages accumulate which, if not successfully repaired, can result in senescence induction. Recently, we determined the transcriptional changes combined with the transition into replicative senescence in primary human fibroblast strains. Here, by γ-irradiation we induced premature cellular senescence in the fibroblast cell strains (HFF and MRC-5) and determined the corresponding transcriptional changes by high-throughput RNA sequencing. Results Comparing the transcriptomes, we found a high degree of similarity in differential gene expression in replicative as well as in irradiation induced senescence for both cell strains suggesting, in each cell strain, a common cellular response to error accumulation. On the functional pathway level, “Cell cycle” was the only pathway commonly down-regulated in replicative and irradiation-induced senescence in both fibroblast strains, confirming the tight link between DNA repair and cell cycle regulation. However, “DNA repair” and “replication” pathways were down-regulated more strongly in fibroblasts undergoing replicative exhaustion. We also retrieved genes and pathways in each of the cell strains specific for irradiation induced senescence. Conclusion We found the pathways associated with “DNA repair” and “replication” less stringently regulated in irradiation induced compared to replicative senescence. The strong regulation of these pathways in replicative senescence highlights the importance of replication errors for its induction. Electronic supplementary material The online version of this article (doi:10.1186/s40659-016-0095-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shiva Marthandan
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany.
| | - Uwe Menzel
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute e.V. (HKI), Jena, Germany
| | - Steffen Priebe
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute e.V. (HKI), Jena, Germany
| | - Marco Groth
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Reinhard Guthke
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute e.V. (HKI), Jena, Germany
| | - Matthias Platzer
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Peter Hemmerich
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Christoph Kaether
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Stephan Diekmann
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
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Smita S, Lange F, Wolkenhauer O, Köhling R. Deciphering hallmark processes of aging from interaction networks. Biochim Biophys Acta Gen Subj 2016; 1860:2706-15. [PMID: 27456767 DOI: 10.1016/j.bbagen.2016.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/18/2016] [Accepted: 07/20/2016] [Indexed: 12/18/2022]
Abstract
BACKGROUND Aging is broadly considered to be a dynamic process that accumulates unfavourable structural and functional changes in a time dependent fashion, leading to a progressive loss of physiological integrity of an organism, which eventually leads to age-related diseases and finally to death. SCOPE OF REVIEW The majority of aging-related studies are based on reductionist approaches, focusing on single genes/proteins or on individual pathways without considering possible interactions between them. Over the last few decades, several such genes/proteins were independently analysed and linked to a role that is affecting the longevity of an organism. However, an isolated analysis on genes and proteins largely fails to explain the mechanistic insight of a complex phenotype due to the involvement and integration of multiple factors. MAJOR CONCLUSIONS Technological advance makes it possible to generate high-throughput temporal and spatial data that provide an opportunity to use computer-based methods. These techniques allow us to go beyond reductionist approaches to analyse large-scale networks that provide deeper understanding of the processes that drive aging. GENERAL SIGNIFICANCE In this review, we focus on systems biology approaches, based on network inference methods to understand the dynamics of hallmark processes leading to aging phenotypes. We also describe computational methods for the interpretation and identification of important molecular hubs involved in the mechanistic linkage between aging related processes. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
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Affiliation(s)
- Suchi Smita
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany; Oscar-Langendorff-Institute of Physiology, Rostock University Medical Center, Rostock, Germany.
| | - Falko Lange
- Oscar-Langendorff-Institute of Physiology, Rostock University Medical Center, Rostock, Germany.
| | - Olaf Wolkenhauer
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany; Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa.
| | - Rüdiger Köhling
- Oscar-Langendorff-Institute of Physiology, Rostock University Medical Center, Rostock, Germany.
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Yashin AI, Arbeev KG, Wu D, Arbeeva L, Kulminski A, Kulminskaya I, Akushevich I, Ukraintseva SV. How Genes Modulate Patterns of Aging-Related Changes on the Way to 100: Biodemographic Models and Methods in Genetic Analyses of Longitudinal Data. NORTH AMERICAN ACTUARIAL JOURNAL : NAAJ 2016; 20:201-232. [PMID: 27773987 PMCID: PMC5070546 DOI: 10.1080/10920277.2016.1178588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND AND OBJECTIVE To clarify mechanisms of genetic regulation of human aging and longevity traits, a number of genome-wide association studies (GWAS) of these traits have been performed. However, the results of these analyses did not meet expectations of the researchers. Most detected genetic associations have not reached a genome-wide level of statistical significance, and suffered from the lack of replication in the studies of independent populations. The reasons for slow progress in this research area include low efficiency of statistical methods used in data analyses, genetic heterogeneity of aging and longevity related traits, possibility of pleiotropic (e.g., age dependent) effects of genetic variants on such traits, underestimation of the effects of (i) mortality selection in genetically heterogeneous cohorts, (ii) external factors and differences in genetic backgrounds of individuals in the populations under study, the weakness of conceptual biological framework that does not fully account for above mentioned factors. One more limitation of conducted studies is that they did not fully realize the potential of longitudinal data that allow for evaluating how genetic influences on life span are mediated by physiological variables and other biomarkers during the life course. The objective of this paper is to address these issues. DATA AND METHODS We performed GWAS of human life span using different subsets of data from the original Framingham Heart Study cohort corresponding to different quality control (QC) procedures and used one subset of selected genetic variants for further analyses. We used simulation study to show that approach to combining data improves the quality of GWAS. We used FHS longitudinal data to compare average age trajectories of physiological variables in carriers and non-carriers of selected genetic variants. We used stochastic process model of human mortality and aging to investigate genetic influence on hidden biomarkers of aging and on dynamic interaction between aging and longevity. We investigated properties of genes related to selected variants and their roles in signaling and metabolic pathways. RESULTS We showed that the use of different QC procedures results in different sets of genetic variants associated with life span. We selected 24 genetic variants negatively associated with life span. We showed that the joint analyses of genetic data at the time of bio-specimen collection and follow up data substantially improved significance of associations of selected 24 SNPs with life span. We also showed that aging related changes in physiological variables and in hidden biomarkers of aging differ for the groups of carriers and non-carriers of selected variants. CONCLUSIONS . The results of these analyses demonstrated benefits of using biodemographic models and methods in genetic association studies of these traits. Our findings showed that the absence of a large number of genetic variants with deleterious effects may make substantial contribution to exceptional longevity. These effects are dynamically mediated by a number of physiological variables and hidden biomarkers of aging. The results of these research demonstrated benefits of using integrative statistical models of mortality risks in genetic studies of human aging and longevity.
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Affiliation(s)
- Anatoliy I. Yashin
- Professor, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A102E, Durham, NC 27705, USA. Tel.: (+1) 919-668-2713; Fax: (+1) 919-684-3861
| | - Konstantin G. Arbeev
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A102F, Durham, NC 27705, USA. Tel.: (+1) 919-668-2707; Fax: (+1) 919-684-3861
| | - Deqing Wu
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A104, Durham, NC 27705, USA. Tel.: (+1) 919-684-6126; Fax: (+1) 919-684-3861
| | - Liubov Arbeeva
- Statistician, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A102G, Durham, NC 27705, USA. Tel.: (+1) 919-613-0715; Fax: (+1) 919-684-3861
| | - Alexander Kulminski
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A106, Durham, NC 27705, USA. Tel.: (+1) 919-684-4962; Fax: (+1) 919-684-3861
| | - Irina Kulminskaya
- Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A102D, Durham, NC 27705, USA. Tel.: (+1) 919-681-8232; Fax: (+1) 919-684-3861
| | - Igor Akushevich
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A107, Durham, NC 27705, USA. Tel.: (+1) 919-668-2715; Fax: (+1) 919-684-3861
| | - Svetlana V. Ukraintseva
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A105, Durham, NC 27705, USA. Tel.: (+1) 919-668-2712; Fax: (+1) 919-684-3861
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Abstract
OBJECTIVE The aim of this study is to identify single-nucleotide polymorphisms (SNPs) influencing blood pressure (BP) response to the β-blocker atenolol. METHODS Genome-wide association analysis of BP response to atenolol monotherapy was performed in 233 white participants with uncomplicated hypertension in the pharmacogenomic evaluation of antihypertensive responses study. Forty-two polymorphisms with P less than 10 for association with either diastolic or systolic response to atenolol monotherapy were validated in four independent groups of hypertensive individuals (total n = 2114). RESULTS In whites, two polymorphisms near the gene PTPRD (rs12346562 and rs1104514) were associated with DBP response to atenolol (P = 3.2 × 10 and P = 5.9 × 10, respectively) with directionally opposite association for response to hydrochlorothiazide in another group of 228 whites (P = 0.0018 and P = 0.00012). A different polymorphism (rs10739150) near PTPRD was associated with response to atenolol in 150 black hypertensive individuals (P = 8.25 × 10). rs12346562 had a similar trend in association with response to bisoprolol (a different β-blocker) in 207 Finnish men in the genetics of drug responsiveness in essential hypertension study. In addition, an intronic single-nucleotide polymorphism (rs4742610) in the PTPRD gene was associated with resistant hypertension in whites and Hispanics in the international verapamil SR trandolapril study (meta-analysis P = 3.2 × 10). CONCLUSION PTPRD was identified as a novel locus potentially associated with BP response to atenolol and resistant hypertension in multiple ethnic groups.
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Shirakabe A, Ikeda Y, Sciarretta S, Zablocki DK, Sadoshima J. Aging and Autophagy in the Heart. Circ Res 2016; 118:1563-76. [PMID: 27174950 PMCID: PMC4869999 DOI: 10.1161/circresaha.116.307474] [Citation(s) in RCA: 298] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/15/2016] [Indexed: 12/15/2022]
Abstract
The aging population is increasing in developed countries. Because the incidence of cardiac disease increases dramatically with age, it is important to understand the molecular mechanisms through which the heart becomes either more or less susceptible to stress. Cardiac aging is characterized by the presence of hypertrophy, fibrosis, and accumulation of misfolded proteins and dysfunctional mitochondria. Macroautophagy (hereafter referred to as autophagy) is a lysosome-dependent bulk degradation mechanism that is essential for intracellular protein and organelle quality control. Autophagy and autophagic flux are generally decreased in aging hearts, and murine autophagy loss-of-function models develop exacerbated cardiac dysfunction that is accompanied by the accumulation of misfolded proteins and dysfunctional organelles. On the contrary, stimulation of autophagy generally improves cardiac function in mouse models of protein aggregation by removing accumulated misfolded proteins, dysfunctional mitochondria, and damaged DNA, thereby improving the overall cellular environment and alleviating aging-associated pathology in the heart. Increasing lines of evidence suggest that autophagy is required for many mechanisms that mediate lifespan extension, such as caloric restriction, in various organisms. These results raise the exciting possibility that autophagy may play an important role in combating the adverse effects of aging in the heart. In this review, we discuss the role of autophagy in the heart during aging, how autophagy alleviates age-dependent changes in the heart, and how the level of autophagy in the aging heart can be restored.
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Affiliation(s)
- Akihiro Shirakabe
- From the Department of Cell Biology and Molecular Medicine, Rutgers-New Jersey Medical School, Newark (A.S., Y.I., S.S., D.K.Z., J.S.); Department of Cardiovascular Medicine and Hypertension, Graduate School of Medical and Dental Science, Kagoshima University, Japan (Y.I.); Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy (S.S.); and Department of AngioCardioNeurology, IRCCS Neuromed, Pozzilli, Italy (S.S.)
| | - Yoshiyuki Ikeda
- From the Department of Cell Biology and Molecular Medicine, Rutgers-New Jersey Medical School, Newark (A.S., Y.I., S.S., D.K.Z., J.S.); Department of Cardiovascular Medicine and Hypertension, Graduate School of Medical and Dental Science, Kagoshima University, Japan (Y.I.); Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy (S.S.); and Department of AngioCardioNeurology, IRCCS Neuromed, Pozzilli, Italy (S.S.)
| | - Sebastiano Sciarretta
- From the Department of Cell Biology and Molecular Medicine, Rutgers-New Jersey Medical School, Newark (A.S., Y.I., S.S., D.K.Z., J.S.); Department of Cardiovascular Medicine and Hypertension, Graduate School of Medical and Dental Science, Kagoshima University, Japan (Y.I.); Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy (S.S.); and Department of AngioCardioNeurology, IRCCS Neuromed, Pozzilli, Italy (S.S.)
| | - Daniela K Zablocki
- From the Department of Cell Biology and Molecular Medicine, Rutgers-New Jersey Medical School, Newark (A.S., Y.I., S.S., D.K.Z., J.S.); Department of Cardiovascular Medicine and Hypertension, Graduate School of Medical and Dental Science, Kagoshima University, Japan (Y.I.); Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy (S.S.); and Department of AngioCardioNeurology, IRCCS Neuromed, Pozzilli, Italy (S.S.)
| | - Junichi Sadoshima
- From the Department of Cell Biology and Molecular Medicine, Rutgers-New Jersey Medical School, Newark (A.S., Y.I., S.S., D.K.Z., J.S.); Department of Cardiovascular Medicine and Hypertension, Graduate School of Medical and Dental Science, Kagoshima University, Japan (Y.I.); Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy (S.S.); and Department of AngioCardioNeurology, IRCCS Neuromed, Pozzilli, Italy (S.S.).
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Abstract
Adhesion G protein-coupled receptors (aGPCRs) have a long evolutionary history dating back to very basal unicellular eukaryotes. Almost every vertebrate is equipped with a set of different aGPCRs. Genomic sequence data of several hundred extinct and extant species allows for reconstruction of aGPCR phylogeny in vertebrates and non-vertebrates in general but also provides a detailed view into the recent evolutionary history of human aGPCRs. Mining these sequence sources with bioinformatic tools can unveil many facets of formerly unappreciated aGPCR functions. In this review, we extracted such information from the literature and open public sources and provide insights into the history of aGPCR in humans. This includes comprehensive analyses of signatures of selection, variability of human aGPCR genes, and quantitative traits at human aGPCR loci. As indicated by a large number of genome-wide genotype-phenotype association studies, variations in aGPCR contribute to specific human phenotypes. Our survey demonstrates that aGPCRs are significantly involved in adaptation processes, phenotype variations, and diseases in humans.
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Affiliation(s)
- Peter Kovacs
- Integrated Research and Treatment Center (IFB) AdiposityDiseases, Medical Faculty, University of Leipzig, Liebigstr. 21, Leipzig, 04103, Germany.
| | - Torsten Schöneberg
- Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig, 04103, Germany.
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