1
|
Li X, Lan F, Chen X, Yan Y, Li G, Wu G, Sun C, Yang N. Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding. BMC Genomics 2024; 25:638. [PMID: 38926812 PMCID: PMC11210043 DOI: 10.1186/s12864-024-10551-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 06/21/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The breeding of layers emphasizes the continual selection of egg-related traits, such as egg production, egg quality and eggshell, which enhance their productivity and meet the demand of market. As the breeding process continued, the genomic homozygosity of layers gradually increased, resulting in the emergence of runs of homozygosity (ROH). Therefore, ROH analysis can be used in conjunction with other methods to detect selection signatures and identify candidate genes associated with various important traits in layer breeding. RESULTS In this study, we generated whole-genome sequencing data from 686 hens in a Rhode Island Red population that had undergone fifteen consecutive generations of intensive artificial selection. We performed a genome-wide ROH analysis and utilized multiple methods to detect signatures of selection. A total of 141,720 ROH segments were discovered in whole population, and most of them (97.35%) were less than 3 Mb in length. Twenty-three ROH islands were identified, and they overlapped with some regions bearing selection signatures, which were detected by the De-correlated composite of multiple signals methods (DCMS). Sixty genes were discovered and functional annotation analysis revealed the possible roles of them in growth, development, immunity and signaling in layers. Additionally, two-tailed analyses including DCMS and ROH for 44 phenotypes of layers were conducted to find out the genomic differences between subgroups of top and bottom 10% phenotype of individuals. Combining the results of GWAS, we observed that regions significantly associated with traits also exhibited selection signatures between the high and low subgroups. We identified a region significantly associated with egg weight near the 25 Mb region of GGA 1, which exhibited selection signatures and has higher genomic homozygosity in the low egg weight subpopulation. This suggests that the region may be play a role in the decline in egg weight. CONCLUSIONS In summary, through the combined analysis of ROH, selection signatures, and GWAS, we identified several genomic regions that associated with the production traits of layers, providing reference for the study of layer genome.
Collapse
Affiliation(s)
- Xiaochang Li
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Fangren Lan
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaoman Chen
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Yiyuan Yan
- Beijing Engineering Research Centre of Layer, Beijing, 101206, China
| | - Guangqi Li
- Beijing Engineering Research Centre of Layer, Beijing, 101206, China
| | - Guiqin Wu
- Beijing Engineering Research Centre of Layer, Beijing, 101206, China
| | - Congjiao Sun
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
| | - Ning Yang
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
2
|
Tsitsipatis D, Martindale JL, Mazan‐Mamczarz K, Herman AB, Piao Y, Banskota N, Yang J, Cui L, Anerillas C, Chang M, Kaileh M, Munk R, Yang X, Ubaida‐Mohien C, Chia CW, Karikkineth AC, Zukley L, D'Agostino J, Abdelmohsen K, Basisty N, De S, Ferrucci L, Gorospe M. Transcriptomes of human primary skin fibroblasts of healthy individuals reveal age-associated mRNAs and long noncoding RNAs. Aging Cell 2023; 22:e13915. [PMID: 37462262 PMCID: PMC10652340 DOI: 10.1111/acel.13915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 09/27/2023] Open
Abstract
Changes in the transcriptomes of human tissues with advancing age are poorly cataloged. Here, we sought to identify the coding and long noncoding RNAs present in cultured primary skin fibroblasts collected from 82 healthy individuals across a wide age spectrum (22-89 years old) who participated in the GESTALT (Genetic and Epigenetic Signatures of Translational Aging Laboratory Testing) study of the National Institute on Aging, NIH. Using high-throughput RNA sequencing and a linear regression model, we identified 1437 coding RNAs (mRNAs) and 1177 linear and circular long noncoding (lncRNAs) that were differentially abundant as a function of age. Gene set enrichment analysis (GSEA) revealed select transcription factors implicated in coordinating the transcription of subsets of differentially abundant mRNAs, while long noncoding RNA enrichment analysis (LncSEA) identified RNA-binding proteins predicted to participate in the age-associated lncRNA profiles. In summary, we report age-associated changes in the global transcriptome, coding and noncoding, from healthy human skin fibroblasts and propose that these transcripts may serve as biomarkers and therapeutic targets in aging skin.
Collapse
Affiliation(s)
- Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Jennifer L. Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Krystyna Mazan‐Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Allison B. Herman
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Yulan Piao
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Nirad Banskota
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Jen‐Hao Yang
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Linna Cui
- Translational Gerontology Branch, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Ming‐Wen Chang
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Mary Kaileh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Xiaoling Yang
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Ceereena Ubaida‐Mohien
- Translational Gerontology Branch, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Chee W. Chia
- Clinical Research Core, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Ajoy C. Karikkineth
- Clinical Research Core, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Linda Zukley
- Clinical Research Core, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Jarod D'Agostino
- Clinical Research Core, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Nathan Basisty
- Translational Gerontology Branch, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research ProgramNational Institutes of HealthBaltimoreMarylandUSA
| |
Collapse
|
3
|
Maqoud F, Zizzo N, Attimonelli M, Tinelli A, Passantino G, Antonacci M, Ranieri G, Tricarico D. Immunohistochemical, pharmacovigilance, and omics analyses reveal the involvement of ATP-sensitive K + channel subunits in cancers: role in drug-disease interactions. Front Pharmacol 2023; 14:1115543. [PMID: 37180726 PMCID: PMC10167295 DOI: 10.3389/fphar.2023.1115543] [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: 12/04/2022] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Background: ATP-sensitive-K+ channels (KATP) are involved in diseases, but their role in cancer is poorly described. Pituitary macroadenoma has been observed in Cantu' syndrome (C.S.), which is associated with the gain-of-function mutations of the ABCC9 and KCNJ8 genes. We tested the role of the ABCC8/Sur1, ABCC9/Sur2A/B, KCNJ11/Kir6.2, and KCNJ8/Kir6.1 genes experimentally in a minoxidil-induced renal tumor in male rats and in the female canine breast cancer, a spontaneous animal model of disease, and in the pharmacovigilance and omics databases. Methods: We performed biopsies from renal tissues of male rats (N = 5) following a sub-chronic high dosing topical administration of minoxidil (0.777-77.7 mg/kg/day) and from breast tissues of female dogs for diagnosis (N = 23) that were analyzed by immunohistochemistry. Pharmacovigilance and omics data were extracted from EudraVigilance and omics databases, respectively. Results: An elevated immunohistochemical reactivity to Sur2A-mAb was detected in the cytosol of the Ki67+/G3 cells other than in the surface membrane in the minoxidil-induced renal tumor and the breast tumor samples. KCNJ11, KCNJ8, and ABCC9 genes are upregulated in cancers but ABCC8 is downregulated. The Kir6.2-Sur2A/B-channel opener minoxidil showed 23 case reports of breast cancer and one case of ovarian cancer in line with omics data reporting, respectively, and the negative and positive prognostic roles of the ABCC9 gene in these cancers. Sulfonylureas and glinides blocking the pancreatic Kir6.2-Sur1 subunits showed a higher risk for pancreatic cancer in line with the positive prognostic role of the ABCC8 gene but low risks for common cancers. Glibenclamide, repaglinide, and glimepiride show a lower cancer risk within the KATP channel blockers. The Kir6.2-Sur1 opener diazoxide shows no cancer reactions. Conclusion: An elevated expression of the Sur2A subunit was found in proliferating cells in two animal models of cancer. Immunohistochemistry/omics/pharmacovigilance data reveal the role of the Kir6.1/2-Sur2A/B subunits as a drug target in breast/renal cancers and in C.S.
Collapse
Affiliation(s)
- Fatima Maqoud
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology Saverio de Bellis, I.R.C.C.S. Research Hospital, Milan, Italy
- Section of Pharmacology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Nicola Zizzo
- Section of Veterinary Pathology and Comparative Oncology, Department of Veterinary Medicine, University of Bari "Aldo Moro", Valenzano, Italy
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University "Aldo Moro" Bari, Bari, Italy
| | - Antonella Tinelli
- Section of Veterinary Pathology and Comparative Oncology, Department of Veterinary Medicine, University of Bari "Aldo Moro", Valenzano, Italy
| | - Giuseppe Passantino
- Section of Veterinary Pathology and Comparative Oncology, Department of Veterinary Medicine, University of Bari "Aldo Moro", Valenzano, Italy
| | - Marina Antonacci
- Section of Pharmacology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Girolamo Ranieri
- Department of Interventional Radiology and Integrated Medical Oncology, I.R.C.C.S. Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Domenico Tricarico
- Section of Pharmacology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari "Aldo Moro", Bari, Italy
| |
Collapse
|
4
|
Cheng X, Li X, Liu Y, Ma Y, Zhang R, Zhang Y, Fan C, Qu L, Ning Z. DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens. BMC Genomics 2023; 24:31. [PMID: 36658492 PMCID: PMC9854222 DOI: 10.1186/s12864-022-09100-8] [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: 08/07/2022] [Accepted: 12/26/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The quality of poultry eggshells is closely related to the profitability of egg production. Eggshell speckles reflect an important quality trait that influences egg appearance and customer preference. However, the mechanism of speckle formation remains poorly understood. In this study, we systematically compared serum immune and antioxidant indices of hens laying speckled and normal eggs. Transcriptome and methylome analyses were used to elucidate the mechanism of eggshell speckle formation. RESULTS The results showed that seven differentially expressed genes (DEGs) were identified between the normal and speckle groups. Gene set enrichment analysis (GSEA) revealed that the expressed genes were mainly enriched in the calcium signaling pathway, focal adhesion, and MAPK signaling pathway. Additionally, 282 differentially methylated genes (DMGs) were detected, of which 15 genes were associated with aging, including ARNTL, CAV1, and GCLC. Pathway analysis showed that the DMGs were associated with T cell-mediated immunity, response to oxidative stress, and cellular response to DNA damage stimulus. Integrative analysis of transcriptome and DNA methylation data identified BFSP2 as the only overlapping gene, which was expressed at low levels and hypomethylated in the speckle group. CONCLUSIONS Overall, these results indicate that aging- and immune-related genes and pathways play a crucial role in the formation of speckled eggshells, providing useful information for improving eggshell quality.
Collapse
Affiliation(s)
- Xue Cheng
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Xinghua Li
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yuchen Liu
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Ying Ma
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Ruiqi Zhang
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yalan Zhang
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Cuidie Fan
- Rongde Breeding Company Limited, Hebei, 053000 China
| | - Lujiang Qu
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Zhonghua Ning
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| |
Collapse
|
5
|
Liu JF, Wu Y, Yang YH, Wu SF, Liu S, Xu P, Yang JT. Phosphoproteome profiling of mouse liver during normal aging. Proteome Sci 2022; 20:12. [PMID: 35932011 PMCID: PMC9354360 DOI: 10.1186/s12953-022-00194-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 07/24/2022] [Indexed: 08/30/2023] Open
Abstract
Background Aging is a complex biological process accompanied by a time-dependent functional decline that affects most living organisms. Omics studies help to comprehensively understand the mechanism of aging and discover potential intervention methods. Old mice are frequently obese with a fatty liver. Methods We applied mass spectrometry-based phosphoproteomics to obtain a global phosphorylation profile of the liver in mice aged 2 or 18 months. MaxQuant was used for quantitative analysis and PCA was used for unsupervised clustering. Results Through phosphoproteome analysis, a total of 5,685 phosphosites in 2,335 proteins were filtered for quantitative analysis. PCA analysis of both the phosphoproteome and transcriptome data could distinguish young and old mice. However, from kinase prediction, kinase-substrate interaction analysis, and KEGG functional enrichment analysis done with phosphoproteome data, we observed high phosphorylation of fatty acid biosynthesis, β-oxidation, and potential secretory processes, together with low phosphorylation of the Egfr-Sos1-Araf/Braf-Map2k1-Mapk1 pathway and Ctnnb1 during aging. Proteins with differentially expressed phosphosites seemed more directly related to the aging-associated fatty liver phenotype than the differentially expressed transcripts. The phosphoproteome may reveal distinctive biological functions that are lost in the transcriptome. Conclusions In summary, we constructed a phosphorylation-associated network in the mouse liver during normal aging, which may help to discover novel antiaging strategies. Supplementary Information The online version contains supplementary material available at 10.1186/s12953-022-00194-2. The first phosphoproteome profiling of mouse livers during normal aging. A total of 5,685 phosphosites in 2,335 proteins were quantified in this study. A phosphorylation-regulated pathway network was constructed. Metabolism, secretion, and the cell cycle might be dysregulated during normal aging.
Collapse
Affiliation(s)
- Jiang-Feng Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yue Wu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,School of Statistics and Data Science, Nankai University, Tianjin, 300071, China
| | - Ye-Hong Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Song-Feng Wu
- State Key Laboratory of ProteomicsResearch Unit of Proteomics & ResearchDevelopment of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Shu Liu
- State Key Laboratory of ProteomicsResearch Unit of Proteomics & ResearchDevelopment of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Ping Xu
- State Key Laboratory of ProteomicsResearch Unit of Proteomics & ResearchDevelopment of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China.
| | - Jun-Tao Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
| |
Collapse
|
6
|
Zhu W, Feng D, Shi X, Wei Q, Yang L. The Potential Role of Mitochondrial Acetaldehyde Dehydrogenase 2 in Urological Cancers From the Perspective of Ferroptosis and Cellular Senescence. Front Cell Dev Biol 2022; 10:850145. [PMID: 35517510 PMCID: PMC9065557 DOI: 10.3389/fcell.2022.850145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/21/2022] [Indexed: 12/21/2022] Open
Abstract
Overproduction of reactive oxygen species (ROS) and superlative lipid peroxidation promote tumorigenesis, and mitochondrial aldehyde dehydrogenase 2 (ALDH2) is associated with the detoxification of ROS-mediated lipid peroxidation-generated reactive aldehydes such as 4-hydroxy-2-nonenal (4-HNE), malondialdehyde, and acrolein due to tobacco smoking. ALDH2 has been demonstrated to be highly associated with the prognosis and chemoradiotherapy sensitivity of many types of cancer, including leukemia, lung cancer, head and neck cancer, esophageal cancer, hepatocellular cancer, pancreatic cancer, and ovarian cancer. In this study, we explored the possible relationship between ALDH2 and urological cancers from the aspects of ferroptosis, epigenetic alterations, proteostasis, mitochondrial dysfunction, and cellular senescence.
Collapse
Affiliation(s)
| | | | | | - Qiang Wei
- *Correspondence: Qiang Wei, ; Lu Yang,
| | - Lu Yang
- *Correspondence: Qiang Wei, ; Lu Yang,
| |
Collapse
|
7
|
Johnson AA, Shokhirev MN, Wyss-Coray T, Lehallier B. Systematic review and analysis of human proteomics aging studies unveils a novel proteomic aging clock and identifies key processes that change with age. Ageing Res Rev 2020; 60:101070. [PMID: 32311500 DOI: 10.1016/j.arr.2020.101070] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/23/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022]
Abstract
The development of clinical interventions that significantly improve human healthspan requires robust markers of biological age as well as thoughtful therapeutic targets. To promote these goals, we performed a systematic review and analysis of human aging and proteomics studies. The systematic review includes 36 different proteomics analyses, each of which identified proteins that significantly changed with age. We discovered 1,128 proteins that had been reported by at least two or more analyses and 32 proteins that had been reported by five or more analyses. Each of these 32 proteins has known connections relevant to aging and age-related disease. GDF15, for example, extends both lifespan and healthspan when overexpressed in mice and is additionally required for the anti-diabetic drug metformin to exert beneficial effects on body weight and energy balance. Bioinformatic enrichment analyses of our 1,128 commonly identified proteins heavily implicated processes relevant to inflammation, the extracellular matrix, and gene regulation. We additionally propose a novel proteomic aging clock comprised of proteins that were reported to change with age in plasma in three or more different studies. Using a large patient cohort comprised of 3,301 subjects (aged 18-76 years), we demonstrate that this clock is able to accurately predict human age.
Collapse
|
8
|
Tobore TO. Towards a comprehensive theory of obesity and a healthy diet: The causal role of oxidative stress in food addiction and obesity. Behav Brain Res 2020; 384:112560. [DOI: 10.1016/j.bbr.2020.112560] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023]
|
9
|
Kimura M, Yokoyama A, Higuchi S. Aldehyde dehydrogenase-2 as a therapeutic target. Expert Opin Ther Targets 2019; 23:955-966. [DOI: 10.1080/14728222.2019.1690454] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Mitsuru Kimura
- National Hospital Organization Kurihama Medical and Addiction Center, Yokosuka, Kanagawa, Japan
| | - Akira Yokoyama
- National Hospital Organization Kurihama Medical and Addiction Center, Yokosuka, Kanagawa, Japan
| | - Susumu Higuchi
- National Hospital Organization Kurihama Medical and Addiction Center, Yokosuka, Kanagawa, Japan
| |
Collapse
|
10
|
Morris BJ, Willcox BJ, Donlon TA. Genetic and epigenetic regulation of human aging and longevity. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1718-1744. [PMID: 31109447 PMCID: PMC7295568 DOI: 10.1016/j.bbadis.2018.08.039] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/02/2018] [Accepted: 08/28/2018] [Indexed: 02/06/2023]
Abstract
Here we summarize the latest data on genetic and epigenetic contributions to human aging and longevity. Whereas environmental and lifestyle factors are important at younger ages, the contribution of genetics appears more important in reaching extreme old age. Genome-wide studies have implicated ~57 gene loci in lifespan. Epigenomic changes during aging profoundly affect cellular function and stress resistance. Dysregulation of transcriptional and chromatin networks is likely a crucial component of aging. Large-scale bioinformatic analyses have revealed involvement of numerous interaction networks. As the young well-differentiated cell replicates into eventual senescence there is drift in the highly regulated chromatin marks towards an entropic middle-ground between repressed and active, such that genes that were previously inactive "leak". There is a breakdown in chromatin connectivity such that topologically associated domains and their insulators weaken, and well-defined blocks of constitutive heterochromatin give way to generalized, senescence-associated heterochromatin, foci. Together, these phenomena contribute to aging.
Collapse
Affiliation(s)
- Brian J Morris
- Basic & Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, University of Sydney, New South Wales 2006, Australia; Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI 96817, United States; Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Kuakini Medical Center Campus, Honolulu, HI 96813, United States.
| | - Bradley J Willcox
- Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI 96817, United States; Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Kuakini Medical Center Campus, Honolulu, HI 96813, United States.
| | - Timothy A Donlon
- Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI 96817, United States; Departments of Cell & Molecular Biology and Pathology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, United States.
| |
Collapse
|
11
|
Aldehyde Dehydrogenase 2 (ALDH2) and Aging: Is There a Sensible Link? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1193:237-253. [DOI: 10.1007/978-981-13-6260-6_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
12
|
Genomic Approach to Understand the Association of DNA Repair with Longevity and Healthy Aging Using Genomic Databases of Oldest-Old Population. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:2984730. [PMID: 29854078 PMCID: PMC5960555 DOI: 10.1155/2018/2984730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 04/03/2018] [Indexed: 12/16/2022]
Abstract
Aged population is increasing worldwide due to the aging process that is inevitable. Accordingly, longevity and healthy aging have been spotlighted to promote social contribution of aged population. Many studies in the past few decades have reported the process of aging and longevity, emphasizing the importance of maintaining genomic stability in exceptionally long-lived population. Underlying reason of longevity remains unclear due to its complexity involving multiple factors. With advances in sequencing technology and human genome-associated approaches, studies based on population-based genomic studies are increasing. In this review, we summarize recent longevity and healthy aging studies of human population focusing on DNA repair as a major factor in maintaining genome integrity. To keep pace with recent growth in genomic research, aging- and longevity-associated genomic databases are also briefly introduced. To suggest novel approaches to investigate longevity-associated genetic variants related to DNA repair using genomic databases, gene set analysis was conducted, focusing on DNA repair- and longevity-associated genes. Their biological networks were additionally analyzed to grasp major factors containing genetic variants of human longevity and healthy aging in DNA repair mechanisms. In summary, this review emphasizes DNA repair activity in human longevity and suggests approach to conduct DNA repair-associated genomic study on human healthy aging.
Collapse
|
13
|
Yan S, Wu G. Could ALDH2 *2 be the reason for low incidence and mortality of ovarian cancer for East Asia women? Oncotarget 2017; 9:12503-12512. [PMID: 29552329 PMCID: PMC5844765 DOI: 10.18632/oncotarget.23605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/16/2017] [Indexed: 12/15/2022] Open
Abstract
It is curious that East Asian women have a low incidence and mortality of ovarian cancer in various epidemiological studies. Although different explanations were given, they appear unsubstantial. We notice that East Asian population usually are inactive aldehyde dehydrogenase 2 mutation (ALDH2 * 2) carriers, and ALDH plays an important role in the resistance of ovarian cancer to chemotherapeutics, especially in ovarian cancer stem cells. Therefore, we hypothesize whether ALDH2 mutation is the major reason for low incidence and mortality of ovarian cancer in East Asian women, and use the evidence from literature, transcriptomic data with average 5-year overall survival to confirm our hypothesis.
Collapse
Affiliation(s)
- Shaomin Yan
- Bioscience and Technology Research Center, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, China
| | - Guang Wu
- Bioscience and Technology Research Center, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, China
| |
Collapse
|
14
|
Park SC. Serendipity in search for longevity from experiences of Hansen people. TRANSLATIONAL MEDICINE OF AGING 2017. [DOI: 10.1016/j.tma.2017.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
15
|
Donlon TA, Morris BJ, He Q, Chen R, Masaki KH, Allsopp RC, Willcox DC, Tranah GJ, Parimi N, Evans DS, Flachsbart F, Nebel A, Kim DH, Park J, Willcox BJ. Association of Polymorphisms in Connective Tissue Growth Factor and Epidermal Growth Factor Receptor Genes With Human Longevity. J Gerontol A Biol Sci Med Sci 2017; 72:1038-1044. [PMID: 27365368 PMCID: PMC5861942 DOI: 10.1093/gerona/glw116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 06/07/2016] [Indexed: 12/19/2022] Open
Abstract
Growth pathways play key roles in longevity. The present study tested single-nucleotide polymorphisms (SNPs) in the connective tissue growth factor gene (CTGF) and the epidermal growth factor receptor gene (EGFR) for association with longevity. Comparison of allele and genotype frequencies of 12 CTGF SNPs and 41 EGFR SNPs between 440 American men of Japanese ancestry aged ≥95 years and 374 men of average life span revealed association with longevity at the p < .05 level for 2 SNPs in CTGF and 7 in EGFR. Two in CTGF and two in EGFR remained significant after Bonferroni correction. The SNPs of both CTGF and EGFR were in a haplotype block in each respective gene. Haplotype analysis confirmed the suggestive association found by χ2 analysis. We noted an excess of heterozygotes among the longevity cases, consistent with heterozygote advantage in living to extreme old age. No associations of the most significant SNPs were observed in whites or Koreans. In conclusion, the present findings indicate that genetic variation in CTGF and EGFR may contribute to the attainment of extreme old age in Japanese. More research is needed to confirm that genetic variation in CTGF and EGFR contributes to the attainment of extreme old age across human populations.
Collapse
Affiliation(s)
- Timothy A Donlon
- Department of Research, Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS), Kuakini Medical Center, Hawaii
- Department of Cell and Molecular Biology and Department of Pathology, John A. Burns School of Medicine, University of Hawaii Manoa, Honolulu
| | - Brian J Morris
- Department of Research, Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS), Kuakini Medical Center, Hawaii
- Basic & Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, University of Sydney, New South Wales, Australia
- Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu
| | - Qimei He
- Department of Research, Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS), Kuakini Medical Center, Hawaii
| | - Randi Chen
- Department of Research, Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS), Kuakini Medical Center, Hawaii
| | - Kamal H Masaki
- Department of Research, Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS), Kuakini Medical Center, Hawaii
- Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu
| | - Richard C Allsopp
- Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii Manoa, Honolulu, Hawaii
| | - D Craig Willcox
- Department of Research, Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS), Kuakini Medical Center, Hawaii
- Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu
- Department of Human Welfare, Okinawa International University, Japan
| | - Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco
| | - Neeta Parimi
- California Pacific Medical Center Research Institute, San Francisco
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco
| | | | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Germany
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Joobae Park
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Bradley J Willcox
- Department of Research, Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS), Kuakini Medical Center, Hawaii
- Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu
| |
Collapse
|
16
|
Wu Y, Hannigan M, Zhan L, Madri JA, Huang CK. -NOD Mice Having a Lyn Tyrosine Kinase Mutation Exhibit Abnormal Neutrophil Chemotaxis. J Cell Physiol 2017; 232:1689-1695. [PMID: 27591397 DOI: 10.1002/jcp.25583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/01/2016] [Indexed: 12/14/2022]
Abstract
Neutrophils from NOD (Non-Obese Diabetic) mice exhibited reduced migration speed, decreased frequency of directional changes, and loss of directionality during chemotaxis (compared to wild-type [WT] C57BL/6 mice). Additionally, F-actin of chemotaxing NOD neutrophils failed to orient toward the chemoattractant gradient and NOD neutrophil adhesion was impaired. A point mutation near the autophosphorylation site of Lyn in NOD mice was identified. Point mutations of G to A (G1412 in LynA and G1199 in LynB) cause a change of amino acid E393 (glutamic acid) to K (lysine) in LynA (E393 →K) (E372 of LynB), affecting fMLP-induced tyrosine phosphorylation. These data indicate that the Lyn mutation in NOD neutrophils is likely responsible for dysregulation of neutrophil adhesion and directed migration, implying the role of Lyn in modulating diabetic patient's susceptibility to bacterial and fungal infections. J. Cell. Physiol. 232: 1689-1695, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Yue Wu
- Department of Immunology, University of Connecticut Health Center, Farmington, Connecticut.,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Michael Hannigan
- Department of Immunology, University of Connecticut Health Center, Farmington, Connecticut
| | - Lijun Zhan
- Department of Immunology, University of Connecticut Health Center, Farmington, Connecticut
| | - Joseph A Madri
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Chi-Kuang Huang
- Department of Immunology, University of Connecticut Health Center, Farmington, Connecticut
| |
Collapse
|
17
|
Lorenzo PI, Fuente-Martín E, Brun T, Cobo-Vuilleumier N, Jimenez-Moreno CM, G Herrera Gomez I, López Noriega L, Mellado-Gil JM, Martin-Montalvo A, Soria B, Gauthier BR. PAX4 Defines an Expandable β-Cell Subpopulation in the Adult Pancreatic Islet. Sci Rep 2015; 5:15672. [PMID: 26503027 PMCID: PMC4622080 DOI: 10.1038/srep15672] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/01/2015] [Indexed: 12/31/2022] Open
Abstract
PAX4 is a key regulator of pancreatic islet development whilst in adult acute overexpression protects β-cells against stress-induced apoptosis and stimulates proliferation. Nonetheless, sustained PAX4 expression promotes β-cell dedifferentiation and hyperglycemia, mimicking β-cell failure in diabetic patients. Herein, we study mechanisms that allow stringent PAX4 regulation endowing favorable β-cell adaptation in response to changing environment without loss of identity. To this end, PAX4 expression was monitored using a mouse bearing the enhanced green fluorescent protein (GFP) and cre recombinase construct under the control of the islet specific pax4 promoter. GFP was detected in 30% of islet cells predominantly composed of PAX4-enriched β-cells that responded to glucose-induced insulin secretion. Lineage tracing demonstrated that all islet cells were derived from PAX4+ progenitor cells but that GFP expression was confined to a subpopulation at birth which declined with age correlating with reduced replication. However, this GFP+ subpopulation expanded during pregnancy, a state of active β-cell replication. Accordingly, enhanced proliferation was exclusively detected in GFP+ cells consistent with cell cycle genes being stimulated in PAX4-overexpressing islets. Under stress conditions, GFP+ cells were more resistant to apoptosis than their GFP- counterparts. Our data suggest PAX4 defines an expandable β-cell sub population within adult islets.
Collapse
Affiliation(s)
- Petra I Lorenzo
- Pancreatic Islet Development and Regeneration Unit, Department of Stem Cells, CABIMER-Andalusian Center for Molecular Biology and Regenerative Medicine, Seville, Spain
| | - Esther Fuente-Martín
- Pancreatic Islet Development and Regeneration Unit, Department of Stem Cells, CABIMER-Andalusian Center for Molecular Biology and Regenerative Medicine, Seville, Spain
| | - Thierry Brun
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Nadia Cobo-Vuilleumier
- Pancreatic Islet Development and Regeneration Unit, Department of Stem Cells, CABIMER-Andalusian Center for Molecular Biology and Regenerative Medicine, Seville, Spain
| | - Carmen María Jimenez-Moreno
- Pancreatic Islet Development and Regeneration Unit, Department of Stem Cells, CABIMER-Andalusian Center for Molecular Biology and Regenerative Medicine, Seville, Spain
| | - Irene G Herrera Gomez
- Pancreatic Islet Development and Regeneration Unit, Department of Stem Cells, CABIMER-Andalusian Center for Molecular Biology and Regenerative Medicine, Seville, Spain
| | - Livia López Noriega
- Pancreatic Islet Development and Regeneration Unit, Department of Stem Cells, CABIMER-Andalusian Center for Molecular Biology and Regenerative Medicine, Seville, Spain
| | - José Manuel Mellado-Gil
- Pancreatic Islet Development and Regeneration Unit, Department of Stem Cells, CABIMER-Andalusian Center for Molecular Biology and Regenerative Medicine, Seville, Spain
| | - Alejandro Martin-Montalvo
- Pancreatic Islet Development and Regeneration Unit, Department of Stem Cells, CABIMER-Andalusian Center for Molecular Biology and Regenerative Medicine, Seville, Spain
| | - Bernat Soria
- Cellular Therapy of Diabetes Mellitus and its Complications, Department of Stem Cells, CABIMER-Andalusian Center for Molecular Biology and Regenerative Medicine, Seville, Spain.,CIBERDEM, Instituto Carlos III, Madrid, Spain
| | - Benoit R Gauthier
- Pancreatic Islet Development and Regeneration Unit, Department of Stem Cells, CABIMER-Andalusian Center for Molecular Biology and Regenerative Medicine, Seville, Spain
| |
Collapse
|
18
|
Puzzling role of genetic risk factors in human longevity: "risk alleles" as pro-longevity variants. Biogerontology 2015; 17:109-27. [PMID: 26306600 PMCID: PMC4724477 DOI: 10.1007/s10522-015-9600-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/19/2015] [Indexed: 02/07/2023]
Abstract
Complex diseases are major contributors to human mortality in old age. Paradoxically, many genetic variants that have been associated with increased risks of such diseases are found in genomes of long-lived people, and do not seem to compromise longevity. Here we argue that trade-off-like and conditional effects of genes can play central role in this phenomenon and in determining longevity. Such effects may occur as result of: (i) antagonistic influence of gene on the development of different health disorders; (ii) change in the effect of gene on vulnerability to death with age (especially, from “bad” to “good”); (iii) gene–gene interaction; and (iv) gene–environment interaction, among other factors. A review of current knowledge provides many examples of genetic factors that may increase the risk of one disease but reduce chances of developing another serious health condition, or improve survival from it. Factors that may increase risk of a major disease but attenuate manifestation of physical senescence are also discussed. Overall, available evidence suggests that the influence of a genetic variant on longevity may be negative, neutral or positive, depending on a delicate balance of the detrimental and beneficial effects of such variant on multiple health and aging related traits. This balance may change with age, internal and external environments, and depend on genetic surrounding. We conclude that trade-off-like and conditional genetic effects are very common and may result in situations when a disease “risk allele” can also be a pro-longevity variant, depending on context. We emphasize importance of considering such effects in both aging research and disease prevention.
Collapse
|
19
|
Yashin AI, Wu D, Arbeeva LS, Arbeev KG, Kulminski AM, Akushevich I, Kovtun M, Culminskaya I, Stallard E, Li M, Ukraintseva SV. Genetics of aging, health, and survival: dynamic regulation of human longevity related traits. Front Genet 2015; 6:122. [PMID: 25918517 PMCID: PMC4394697 DOI: 10.3389/fgene.2015.00122] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 03/16/2015] [Indexed: 11/13/2022] Open
Abstract
Background: The roles of genetic factors in human longevity would be better understood if one can use more efficient methods in genetic analyses and investigate pleiotropic effects of genetic variants on aging and health related traits. Data and methods: We used EMMAX software with modified correction for population stratification to perform genome wide association studies (GWAS) of female lifespan from the original FHS cohort. The male data from the original FHS cohort and male and female data combined from the offspring FHS cohort were used to confirm findings. We evaluated pleiotropic effects of selected genetic variants as well as gene-smoking interactions on health and aging related traits. Then we reviewed current knowledge on functional properties of genes related to detected variants. Results: The eight SNPs with genome-wide significant variants were negatively associated with lifespan in both males and females. After additional QC, two of these variants were selected for further analyses of their associations with major diseases (cancer and CHD) and physiological aging changes. Gene-smoking interactions contributed to these effects. Genes closest to detected variants appear to be involved in similar biological processes and health disorders, as those found in other studies of aging and longevity e.g., in cancer and neurodegeneration. Conclusions: The impact of genes on longevity may involve trade-off-like effects on different health traits. Genes that influence lifespan represent various molecular functions but may be involved in similar biological processes and health disorders, which could contribute to genetic heterogeneity of longevity and the lack of replication in genetic association studies.
Collapse
Affiliation(s)
- Anatoliy I Yashin
- Biodemography of Aging Research Unit, Center for Population Health and Aging, Social Science Research Institute, Duke University Durham, NC, USA
| | - Deqing Wu
- Biodemography of Aging Research Unit, Center for Population Health and Aging, Social Science Research Institute, Duke University Durham, NC, USA
| | - Liubov S Arbeeva
- Biodemography of Aging Research Unit, Center for Population Health and Aging, Social Science Research Institute, Duke University Durham, NC, USA
| | - Konstantin G Arbeev
- Biodemography of Aging Research Unit, Center for Population Health and Aging, Social Science Research Institute, Duke University Durham, NC, USA
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Center for Population Health and Aging, Social Science Research Institute, Duke University Durham, NC, USA
| | - Igor Akushevich
- Biodemography of Aging Research Unit, Center for Population Health and Aging, Social Science Research Institute, Duke University Durham, NC, USA
| | - Mikhail Kovtun
- Biodemography of Aging Research Unit, Center for Population Health and Aging, Social Science Research Institute, Duke University Durham, NC, USA ; Integrative Genomic Analysis Shared Resource, Duke Center for Genomic and Computational Biology, Duke University Durham, NC, USA
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Center for Population Health and Aging, Social Science Research Institute, Duke University Durham, NC, USA
| | - Eric Stallard
- Biodemography of Aging Research Unit, Center for Population Health and Aging, Social Science Research Institute, Duke University Durham, NC, USA
| | - Miaozhu Li
- Biodemography of Aging Research Unit, Center for Population Health and Aging, Social Science Research Institute, Duke University Durham, NC, USA
| | - Svetlana V Ukraintseva
- Biodemography of Aging Research Unit, Center for Population Health and Aging, Social Science Research Institute, Duke University Durham, NC, USA
| |
Collapse
|
20
|
Eriksson CJP. Genetic–Epidemiological Evidence for the Role of Acetaldehyde in Cancers Related to Alcohol Drinking. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 815:41-58. [DOI: 10.1007/978-3-319-09614-8_3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
21
|
Polymorphisms in the RANK/RANKL genes and their effect on bone specific prognosis in breast cancer patients. BIOMED RESEARCH INTERNATIONAL 2014; 2014:842452. [PMID: 24729980 PMCID: PMC3963378 DOI: 10.1155/2014/842452] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 01/30/2014] [Indexed: 01/06/2023]
Abstract
The receptor activator of NF-κB (RANK) pathway is involved in bone health as well as breast cancer (BC) pathogenesis and progression. Whereas the therapeutic implication of this pathway is established for the treatment of osteoporosis and bone metastases, the application in adjuvant BC is currently investigated. As genetic variants in this pathway have been described to influence bone health, aim of this study was the prognostic relevance of genetic variants in RANK and RANKL. Single nucleotide polymorphisms in RANK(L) (rs1054016/rs1805034/rs35211496) were genotyped and analyzed with regard to bone metastasis-free survival (BMFS), disease-free survival, and overall survival for a retrospective cohort of 1251 patients. Cox proportional hazard models were built to examine the prognostic influence in addition to commonly established prognostic factors. The SNP rs1054016 seems to influence BMFS. Patients with two minor alleles had a more favorable prognosis than patients with at least one common allele (HR 0.37 (95% CI: 0.17, 0.84)), whereas other outcome parameters remained unaffected. rs1805034 and rs35211496 had no prognostic relevance. The effect of rs1054016(RANKL) adds to the evidence that the RANK pathway plays a role in BC pathogenesis and progression with respect to BMFS, emphasizing the connection between BC and bone health.
Collapse
|
22
|
Chen CH, Ferreira JCB, Gross ER, Mochly-Rosen D. Targeting aldehyde dehydrogenase 2: new therapeutic opportunities. Physiol Rev 2014; 94:1-34. [PMID: 24382882 DOI: 10.1152/physrev.00017.2013] [Citation(s) in RCA: 421] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A family of detoxifying enzymes called aldehyde dehydrogenases (ALDHs) has been a subject of recent interest, as its role in detoxifying aldehydes that accumulate through metabolism and to which we are exposed from the environment has been elucidated. Although the human genome has 19 ALDH genes, one ALDH emerges as a particularly important enzyme in a variety of human pathologies. This ALDH, ALDH2, is located in the mitochondrial matrix with much known about its role in ethanol metabolism. Less known is a new body of research to be discussed in this review, suggesting that ALDH2 dysfunction may contribute to a variety of human diseases including cardiovascular diseases, diabetes, neurodegenerative diseases, stroke, and cancer. Recent studies suggest that ALDH2 dysfunction is also associated with Fanconi anemia, pain, osteoporosis, and the process of aging. Furthermore, an ALDH2 inactivating mutation (termed ALDH2*2) is the most common single point mutation in humans, and epidemiological studies suggest a correlation between this inactivating mutation and increased propensity for common human pathologies. These data together with studies in animal models and the use of new pharmacological tools that activate ALDH2 depict a new picture related to ALDH2 as a critical health-promoting enzyme.
Collapse
|
23
|
Jacobson PA, Schladt D, Israni A, Oetting WS, Lin YC, Leduc R, Guan W, Lamba V, Matas AJ. Genetic and clinical determinants of early, acute calcineurin inhibitor-related nephrotoxicity: results from a kidney transplant consortium. Transplantation 2012; 93:624-31. [PMID: 22334041 DOI: 10.1097/tp.0b013e3182461288] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Calcineurin inhibitor (CNI)-related acute nephrotoxicity is a common complication of transplantation. Clinical factors and elevated CNI levels are associated with nephrotoxicity; however, they do not fully explain the risk. Genetic factors may also predispose individuals to nephrotoxicity. METHODS We enrolled 945 kidney recipients into a multicenter, prospective study. DNA was genotyped for 2724 single-nucleotide polymorphisms (SNPs) using a customized chip. Cox models, unadjusted and adjusted for clinical factors, examined the association between SNPs and time to early CNI-related acute nephrotoxicity in the first 6 months posttransplant. RESULTS Cyclosporine was associated with a 1.49 hazard (95% confidence interval, 1.04-2.14) of acute nephrotoxicity relative to tacrolimus. Acute nephrotoxicity occurred in 22.6% of cyclosporine and 19.8% of tacrolimus recipients. The median (interquartile range) daily dose and trough concentration at time of nephrotoxicity were 400 mg (400-500 mg) and 228 ng/mL (190-272 ng/mL) in the cyclosporine group, and 6 mg (4-8 mg) and 12.6 ng/mL (10.2-15.9 ng/mL) in the tacrolimus group, respectively. In single-SNP adjusted analysis, nine SNPs in the XPC, CYP2C9, PAX4, MTRR, and GAN genes were associated with cyclosporine nephrotoxicity. In a multi-SNP analysis, SNPs from the same genes remained significant after adjusting for the clinical factors, showing that the SNPs are jointly and independently predictive of cyclosporine nephrotoxicity. No SNPs were associated with tacrolimus nephrotoxicity. CONCLUSION We identified SNPs that were potentially associated with early, acute cyclosporine-related nephrotoxicity. Identifying risk SNPs before transplantation provides an opportunity for personalization of immunosuppression by identifying those who may benefit from CNI-avoidance or minimization, or assist in selecting CNI type. These SNPs require independent validation.
Collapse
Affiliation(s)
- Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Iliadi KG, Knight D, Boulianne GL. Healthy aging - insights from Drosophila. Front Physiol 2012; 3:106. [PMID: 22529821 PMCID: PMC3328947 DOI: 10.3389/fphys.2012.00106] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 04/03/2012] [Indexed: 11/13/2022] Open
Abstract
Human life expectancy has nearly doubled in the past century due, in part, to social and economic development, and a wide range of new medical technologies and treatments. As the number of elderly increase it becomes of vital importance to understand what factors contribute to healthy aging. Human longevity is a complex process that is affected by both environmental and genetic factors and interactions between them. Unfortunately, it is currently difficult to identify the role of genetic components in human longevity. In contrast, model organisms such as C. elegans, Drosophila, and rodents have facilitated the search for specific genes that affect lifespan. Experimental evidence obtained from studies in model organisms suggests that mutations in a single gene may increase longevity and delay the onset of age-related symptoms including motor impairments, sexual and reproductive and immune dysfunction, cardiovascular disease, and cognitive decline. Furthermore, the high degree of conservation between diverse species in the genes and pathways that regulate longevity suggests that work in model organisms can both expand our theoretical knowledge of aging and perhaps provide new therapeutic targets for the treatment of age-related disorders.
Collapse
Affiliation(s)
- Konstantin G Iliadi
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Toronto, ON, Canada
| | | | | |
Collapse
|
25
|
|