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Zhang Y, Bi J, Ning Y, Feng J. Methodology Advances in Vertebrate Age Estimation. Animals (Basel) 2024; 14:343. [PMID: 38275802 PMCID: PMC10812784 DOI: 10.3390/ani14020343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/09/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Age is a core metric in vertebrate management, and the correct estimation of the age of an individual plays a principal role in comprehending animal behavior, identifying genealogical information, and assessing the potential reproductive capacity of populations. Vertebrates have a vertebral column and a distinct head containing a developed brain; they have played an important role in the study of biological evolution. However, biological age estimations constantly exhibit large deviations due to the diversity of vertebrate taxon species, sample types, and determination methods. To systematically and comprehensively understand age estimation methods in different situations, we classify the degree of damage to vertebrates during sample collection, present the sample types and their applications, list commonly applied methods, present methodological recommendations based on the combination of accuracy and implementability, and, finally, predict future methods for vertebrate age assessments, taking into account the current level of research and requirements. Through comprehensive data gathering and compilation, this work serves as an introduction and summary for those who are eager to catch up on related fields and facilitates the rapid and accurate selection of an evaluation method for researchers engaged in related research. This is essential to promote animal conservation and guide the smooth implementation of conservation management plans.
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Affiliation(s)
- Yifei Zhang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (Y.Z.); (J.B.)
- Jilin Provincial International Cooperation Key Laboratory for Biological Control of Agricultural Pests, Changchun 130118, China
| | - Jinping Bi
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (Y.Z.); (J.B.)
- Jilin Provincial International Cooperation Key Laboratory for Biological Control of Agricultural Pests, Changchun 130118, China
| | - Yao Ning
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (Y.Z.); (J.B.)
- Jilin Provincial International Cooperation Key Laboratory for Biological Control of Agricultural Pests, Changchun 130118, China
| | - Jiang Feng
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (Y.Z.); (J.B.)
- Jilin Provincial International Cooperation Key Laboratory for Biological Control of Agricultural Pests, Changchun 130118, China
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, Changchun 130024, China
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Le Clercq LS, Kotzé A, Grobler JP, Dalton DL. Biological clocks as age estimation markers in animals: a systematic review and meta-analysis. Biol Rev Camb Philos Soc 2023; 98:1972-2011. [PMID: 37356823 DOI: 10.1111/brv.12992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 06/04/2023] [Accepted: 06/08/2023] [Indexed: 06/27/2023]
Abstract
Various biological attributes associated with individual fitness in animals change predictably over the lifespan of an organism. Therefore, the study of animal ecology and the work of conservationists frequently relies upon the ability to assign animals to functionally relevant age classes to model population fitness. Several approaches have been applied to determining individual age and, while these methods have proved useful, they are not without limitations and often lack standardisation or are only applicable to specific species. For these reasons, scientists have explored the potential use of biological clocks towards creating a universal age-determination method. Two biological clocks, tooth layer annulation and otolith layering have found universal appeal. Both methods are highly invasive and most appropriate for post-mortem age-at-death estimation. More recently, attributes of cellular ageing previously explored in humans have been adapted to studying ageing in animals for the use of less-invasive molecular methods for determining age. Here, we review two such methods, assessment of methylation and telomere length, describing (i) what they are, (ii) how they change with age, and providing (iii) a summary and meta-analysis of studies that have explored their utility in animal age determination. We found that both attributes have been studied across multiple vertebrate classes, however, telomere studies were used before methylation studies and telomere length has been modelled in nearly twice as many studies. Telomere length studies included in the review often related changes to stress responses and illustrated that telomere length is sensitive to environmental and social stressors and, in the absence of repair mechanisms such as telomerase or alternative lengthening modes, lacks the ability to recover. Methylation studies, however, while also detecting sensitivity to stressors and toxins, illustrated the ability to recover from such stresses after a period of accelerated ageing, likely due to constitutive expression or reactivation of repair enzymes such as DNA methyl transferases. We also found that both studied attributes have parentally heritable features, but the mode of inheritance differs among taxa and may relate to heterogamy. Our meta-analysis included more than 40 species in common for methylation and telomere length, although both analyses included at least 60 age-estimation models. We found that methylation outperforms telomere length in terms of predictive power evidenced from effect sizes (more than double that observed for telomeres) and smaller prediction intervals. Both methods produced age correlation models using similar sample sizes and were able to classify individuals into young, middle, or old age classes with high accuracy. Our review and meta-analysis illustrate that both methods are well suited to studying age in animals and do not suffer significantly from variation due to differences in the lifespan of the species, genome size, karyotype, or tissue type but rather that quantitative method, patterns of inheritance, and environmental factors should be the main considerations. Thus, provided that complex factors affecting the measured trait can be accounted for, both methylation and telomere length are promising targets to develop as biomarkers for age determination in animals.
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Affiliation(s)
- Louis-Stéphane Le Clercq
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Antoinette Kotzé
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Desiré Lee Dalton
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BA, UK
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Hibernation slows epigenetic ageing in yellow-bellied marmots. Nat Ecol Evol 2022; 6:418-426. [PMID: 35256811 PMCID: PMC8986532 DOI: 10.1038/s41559-022-01679-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 01/20/2022] [Indexed: 01/02/2023]
Abstract
Species that hibernate generally live longer than would be expected based solely on their body size. Hibernation is characterized by long periods of metabolic suppression (torpor) interspersed by short periods of increased metabolism (arousal). The torpor–arousal cycles occur multiple times during hibernation, and it has been suggested that processes controlling the transition between torpor and arousal states cause ageing suppression. Metabolic rate is also a known correlate of longevity; we thus proposed the ‘hibernation–ageing hypothesis’ whereby ageing is suspended during hibernation. We tested this hypothesis in a well-studied population of yellow-bellied marmots (Marmota flaviventer), which spend 7–8 months per year hibernating. We used two approaches to estimate epigenetic age: the epigenetic clock and the epigenetic pacemaker. Variation in epigenetic age of 149 samples collected throughout the life of 73 females was modelled using generalized additive mixed models (GAMM), where season (cyclic cubic spline) and chronological age (cubic spline) were fixed effects. As expected, the GAMM using epigenetic ages calculated from the epigenetic pacemaker was better able to detect nonlinear patterns in epigenetic ageing over time. We observed a logarithmic curve of epigenetic age with time, where the epigenetic age increased at a higher rate until females reached sexual maturity (two years old). With respect to circannual patterns, the epigenetic age increased during the active season and essentially stalled during the hibernation period. Taken together, our results are consistent with the hibernation–ageing hypothesis and may explain the enhanced longevity in hibernators. Species that hibernate generally have longer lifespans than expected based on their body size. The authors show epigenetic ageing patterns from a natural population of hibernating yellow-bellied marmots consistent with the hypothesis that ageing is suspended during hibernation.
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Bors EK, Baker CS, Wade PR, O'Neill KB, Shelden KEW, Thompson MJ, Fei Z, Jarman S, Horvath S. An epigenetic clock to estimate the age of living beluga whales. Evol Appl 2021; 14:1263-1273. [PMID: 34025766 PMCID: PMC8127720 DOI: 10.1111/eva.13195] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/20/2022] Open
Abstract
DNA methylation data facilitate the development of accurate molecular estimators of chronological age or "epigenetic clocks." We present a robust epigenetic clock for the beluga whale, Delphinapterus leucas, developed for an endangered population in Cook Inlet, Alaska, USA. We used a custom methylation array to measure methylation levels at 37,491 cytosine-guanine sites (CpGs) from skin samples of dead whales (n = 67) whose chronological ages were estimated based on tooth growth layer groups. Using these calibration data, a penalized regression model selected 23 CpGs, providing an R 2 = 0.92 for the training data; and an R 2 = 0.74 and median absolute age error = 2.9 years for the leave one out cross-validation. We applied the epigenetic clock to an independent dataset of 38 skin samples collected with a biopsy dart from living whales between 2016 and 2018. Age estimates ranged from 11 to 27 years. We also report sex correlations in CpG data and describe an approach of identifying the sex of an animal using DNA methylation. The epigenetic estimators of age and sex presented here have broad applications for conservation and management of Cook Inlet beluga whales and potentially other cetaceans.
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Affiliation(s)
| | - C. Scott Baker
- Marine Mammal InstituteOregon State UniversityNewportORUSA
| | - Paul R. Wade
- Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanographic and Atmospheric AdministrationSeattleWAUSA
| | | | - Kim E. W. Shelden
- Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanographic and Atmospheric AdministrationSeattleWAUSA
| | - Michael J. Thompson
- Molecular, Cell and Developmental BiologyUniversity of California Los AngelesLos AngelesCAUSA
| | - Zhe Fei
- Department of BiostatisticsSchool of Public HealthUniversity of California‐Los AngelesLos AngelesCAUSA
| | - Simon Jarman
- School of Biological SciencesUniversity of Western AustraliaPerthWAAustralia
| | - Steve Horvath
- Department of BiostatisticsSchool of Public HealthUniversity of California‐Los AngelesLos AngelesCAUSA
- Department of Human GeneticsGonda Research CenterDavid Geffen School of MedicineLos AngelesCAUSA
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Liu YR, Ba F, Cheng LJ, Li X, Zhang SW, Zhang SC. Efficacy of Sox10 Promoter Methylation in the Diagnosis of Intestinal Neuronal Dysplasia From the Peripheral Blood. Clin Transl Gastroenterol 2019; 10:e00093. [PMID: 31789936 PMCID: PMC6970557 DOI: 10.14309/ctg.0000000000000093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 09/19/2019] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Intestinal neuronal dysplasia (IND) is a common malformation of the enteric nervous system. Diagnosis requires a full-thickness colonic specimen and an experienced pathologist, emphasizing the need for noninvasive analytical methods. Recently, the methylation level of the Sox10 promoter has been found to be critical for enteric nervous system development. However, whether it can be used for diagnostic purposes in IND is unclear. METHODS Blood and colon specimens were collected from 32 patients with IND, 60 patients with Hirschsprung disease (HD), and 60 controls. Sox10 promoter methylation in the blood and the Sox10 expression level in the colon were determined, and their correlation was analyzed. The diagnostic efficacy of blood Sox10 promoter methylation was analyzed by receiver operating characteristic curve. RESULTS The blood level of Sox10 promoter methylation at the 32nd locus was 100% (90%-100%; 95% confidence interval [CI], 92.29%-96.37%) in control, 90% (80%-90%; 95% CI, 82.84%-87.83%) in HD, and 60% (50%-80%; 95% CI, 57.12%-69.76%) in IND specimens. Sox10 promoter methylation in the peripheral blood was negatively correlated with Sox10 expression in the colon, which was low in control, moderate in HD, and high in IND specimens (r = -0.89). The area under the curve of Sox10 promoter methylation in the diagnosis of IND was 0.94 (95% CI, 0.874-1.000, P = 0.000), with a cutoff value of 85% (sensitivity, 90.6%; specificity, 95.0%). By applying a cutoff value of 65%, promoter methylation was more indicative of IND than HD. DISCUSSION The analysis of Sox10 promoter methylation in the peripheral blood can be used as a noninvasive method for IND diagnosis.
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Affiliation(s)
- Yu-Rong Liu
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Fang Ba
- Department of Rehabilitation, Shengjing Hospital of China Medical University, Shenyang, China
| | - Lan-Jie Cheng
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xu Li
- Department of Pediatric Surgery, Capital Institute of Pediatrics of Capital Medical University, Beijing, China
| | - Shi-Wei Zhang
- Department of Pediatric Surgery, Harbin Children's Hospital, Harbin, China
| | - Shu-Cheng Zhang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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Epiphanio TMF, Fernandes NCCDA, de Oliveira TF, Lopes PA, Réssio RA, Gonçalves S, Scattone NV, Tedardi MV, Kulikowski LD, Damasceno J, Loureiro APDM, Dagli MLZ. Global DNA methylation of peripheral blood leukocytes from dogs bearing multicentric non-Hodgkin lymphomas and healthy dogs: A comparative study. PLoS One 2019; 14:e0211898. [PMID: 30908498 PMCID: PMC6433272 DOI: 10.1371/journal.pone.0211898] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 01/22/2019] [Indexed: 12/31/2022] Open
Abstract
Non-Hodgkin lymphomas are among the most common types of tumors in dogs, and they are currently accepted as comparative models of the disease in humans. Aberrant patterns of DNA methylation seem to play a key role in the development of hematopoietic neoplasms in humans, constitute a special mechanism of transcriptional control, and may be influenced by genetic and environmental factors. Blood leukocyte DNA global methylation has been poorly investigated in dogs. The aim of this study is to examine whether peripheral blood global DNA methylation is associated with canine multicentric lymphomas. Peripheral venous blood samples from ten healthy dogs and nine dogs bearing multicentric lymphomas were collected, and the buffy coat was separated. Global DNA methylation was analyzed by High Performance Liquid Chromatography (HPLC) and immunocytochemistry (ICC). In both analyses, leukocytes from dogs with lymphoma presented lower global DNA methylation than in healthy dogs (HPLC: p = 0.027/ 5MeCyt immunoreactivity scores: p = 0.015). Moderate correlation was observed between the results obtained by HPLC and ICC (correlation coefficient = 0.50). For the identification of differently methylated genes between both groups, the Infinium Human Methylation (HM) EPIC BeadChip (850K) was used. Of the 853,307 CpGs investigated in the microarray, there were 34,574 probes hybridized in the canine samples. From this total, significant difference was observed in the methylation level of 8433 regions, and through the homologous and orthologous similarities 525 differently methylated genes were identified between the two groups. This study is pioneer in suggesting that dogs bearing non-Hodgkin lymphoma presented DNA global hypomethylation of circulating leukocytes compared with healthy dogs. Although canine samples were used in an assay developed specifically for human DNA, it was possible to identify differently methylated genes and our results reiterate the importance of the use of peripheral blood leukocytes in cancer research and possible new biomarkers targets.
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Affiliation(s)
| | | | - Tiago Franco de Oliveira
- Department of Pharmacoscience, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Priscila Assis Lopes
- Veterinary Laboratory, Veterinary Image Institute, IVI, São Paulo, São Paulo, Brazil
| | | | - Simone Gonçalves
- Veterinary Hemotherapy Center, Hemovet, São Paulo, São Paulo, Brazil
| | - Náyra Villar Scattone
- Laboratory of Experimental and Comparative Oncology, Department of Pathology, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Marcello Vannucci Tedardi
- Laboratory of Experimental and Comparative Oncology, Department of Pathology, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Jullian Damasceno
- Cytogenomic Laboratory, Department of Pathology, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Ana Paula de Melo Loureiro
- Department of Clinical and Toxicological Analysis, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Maria Lucia Zaidan Dagli
- Laboratory of Experimental and Comparative Oncology, Department of Pathology, University of São Paulo, São Paulo, São Paulo, Brazil
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Ito H, Udono T, Hirata S, Inoue-Murayama M. Estimation of chimpanzee age based on DNA methylation. Sci Rep 2018; 8:9998. [PMID: 29968770 PMCID: PMC6030051 DOI: 10.1038/s41598-018-28318-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/19/2018] [Indexed: 01/05/2023] Open
Abstract
In wild animal conservation, knowing the age of an individual animal is extremely beneficial. However, estimating the age is difficult for many species. Recently, epigenetics-based methods of estimating age have been reported. These studies were predominantly on humans with few reports on other animals, especially wild animals. In the present study, a chimpanzee (Pan troglodytes) age prediction model was developed based on the ELOVL2, CCDC102B, and ZNF423 genes that may also have application in human age prediction. Pyrosequencing was used to measure methylation in 20 chimpanzee blood samples and correlation between age and methylation status was calculated. Age and methylation of sites in ELOVL2 and CCDC102B were significantly correlated and an age prediction model was created using these genes. In the regression equation using only ELOVL2, the highest correlation coefficient was 0.741, with a mean absolute deviation (MAD) of 5.41, compared with the combination of ELOVL2 and CCDC102B, where the highest correlation coefficient was 0.742 and the MAD was 5.41. Although larger MADs were observed in chimpanzees than in humans based on these genes, the results indicate the feasibility of estimating chimpanzee age using DNA methylation, and can have implications in understanding the ecology of chimpanzees and chimpanzee conservation.
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Affiliation(s)
- Hideyuki Ito
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,Kyoto City Zoo, Kyoto, Japan
| | | | - Satoshi Hirata
- Wildlife Research Center, Kyoto University, Kyoto, Japan
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De Paoli-Iseppi R, Deagle BE, McMahon CR, Hindell MA, Dickinson JL, Jarman SN. Measuring Animal Age with DNA Methylation: From Humans to Wild Animals. Front Genet 2017; 8:106. [PMID: 28878806 PMCID: PMC5572392 DOI: 10.3389/fgene.2017.00106] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/02/2017] [Indexed: 01/19/2023] Open
Abstract
DNA methylation (DNAm) is a key mechanism for regulating gene expression in animals and levels are known to change with age. Recent studies have used DNAm changes as a biomarker to estimate chronological age in humans and these techniques are now also being applied to domestic and wild animals. Animal age is widely used to track ongoing changes in ecosystems, however chronological age information is often unavailable for wild animals. An ability to estimate age would lead to improved monitoring of (i) population trends and status and (ii) demographic properties such as age structure and reproductive performance. Recent studies have revealed new examples of DNAm age association in several new species increasing the potential for developing DNAm age biomarkers for a broad range of wild animals. Emerging technologies for measuring DNAm will also enhance our ability to study age-related DNAm changes and to develop new molecular age biomarkers.
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Affiliation(s)
- Ricardo De Paoli-Iseppi
- Institute for Marine and Antarctic Studies, University of TasmaniaHobart, TAS, Australia.,Australian Antarctic DivisionHobart, TAS, Australia
| | | | | | - Mark A Hindell
- Institute for Marine and Antarctic Studies, University of TasmaniaHobart, TAS, Australia
| | - Joanne L Dickinson
- Cancer, Genetics and Immunology Group, Menzies Institute for Medical ResearchHobart, TAS, Australia
| | - Simon N Jarman
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin UniversityPerth, WA, Australia.,CSIRO Indian Ocean Marine Research Centre, University of Western AustraliaPerth, WA, Australia
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