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Campbell CR, Manser M, Shiratori M, Williams K, Barreiro L, Clutton-Brock T, Tung J. A female-biased gene expression signature of dominance in cooperatively breeding meerkats. Mol Ecol 2024:e17467. [PMID: 39021304 DOI: 10.1111/mec.17467] [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: 04/27/2024] [Accepted: 07/03/2024] [Indexed: 07/20/2024]
Abstract
Dominance is a primary determinant of social dynamics and resource access in social animals. Recent studies show that dominance is also reflected in the gene regulatory profiles of peripheral immune cells. However, the strength and direction of this relationship differs across the species and sex combinations investigated, potentially due to variation in the predictors and energetic consequences of dominance status. Here, we investigated the association between social status and gene expression in the blood of wild meerkats (Suricata suricatta; n = 113 individuals), including in response to lipopolysaccharide, Gardiquimod (an agonist of TLR7, which detects single-stranded RNA in vivo) and glucocorticoid stimulation. Meerkats are cooperatively breeding social carnivores in which breeding females physically outcompete other females to suppress reproduction, resulting in high reproductive skew. They therefore present an opportunity to disentangle the effects of social dominance from those of sex per se. We identify a sex-specific signature of dominance, including 1045 differentially expressed genes in females but none in males. Dominant females exhibit elevated activity in innate immune pathways and a larger fold-change response to LPS challenge. Based on these results and a preliminary comparison to other mammals, we speculate that the gene regulatory signature of social status in the immune system depends on the determinants and energetic costs of social dominance, such that it is most pronounced in hierarchies where physical competition is important and reproductive skew is large. Such a pattern has the potential to mediate life history trade-offs between investment in reproduction versus somatic maintenance.
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Affiliation(s)
- C Ryan Campbell
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Marta Manser
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kalahari Research Centre, Kuruman River Reserve, Northern Cape, South Africa
- Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Mari Shiratori
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Kelly Williams
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Luis Barreiro
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Tim Clutton-Brock
- Kalahari Research Centre, Kuruman River Reserve, Northern Cape, South Africa
- Mammal Research Institute, University of Pretoria, Pretoria, South Africa
- Large Animal Research Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Department of Biology, Duke University, Durham, North Carolina, USA
- Duke Population Research Institute, Duke University, Durham, North Carolina, USA
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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2
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Liu S, Li C, Yan W, Jin S, Wang K, Wang C, Gong H, Wu H, Fu X, Deng L, Lei C, He M, Wang H, Cheng Y, Wang Q, Lin S, Huang Y, Li D, Yang X. Using Blood Transcriptome Analysis to Determine the Changes in Immunity and Metabolism of Giant Pandas with Age. Vet Sci 2022; 9:vetsci9120667. [PMID: 36548828 PMCID: PMC9784451 DOI: 10.3390/vetsci9120667] [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: 09/12/2022] [Revised: 11/18/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
A low reproductive rate coupled with human activities has endangered the giant panda, a species endemic to southwest China. Although giant pandas feed almost exclusively on bamboo, they retain carnivorous traits and suffer from carnivorous diseases. Additionally, their immune system is susceptible to aging, resulting in a reduced ability to respond to diseases. This study aimed to determine the genes and pathways expressed differentially with age in blood tissues. The differentially expressed genes in different age groups of giant pandas were identified by RNA-seq. The elderly giant pandas had many differentially expressed genes compared with the young group (3 years old), including 548 upregulated genes and 401 downregulated genes. Further, functional enrichment revealed that innate immune upregulation and adaptive immune downregulation were observed in the elderly giant pandas compared with the young giant pandas. Meanwhile, the immune genes in the elderly giant pandas changed considerably, including genes involved in innate immunity and adaptive immunity such as PLSCR1, CLEC7A, CCL5, CCR9, and EPAS1. Time series analysis found that giant pandas store glycogen by prioritizing fat metabolism at age 11, verifying changes in the immune system. The results reported in this study will provide a foundation for further research on disease prevention and the energy metabolism of giant pandas.
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Affiliation(s)
- Song Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Caiwu Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Wenjun Yan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Senlong Jin
- Sichuan Wolong National Nature Reserve Administration, Wenchuan 623006, China
| | - Kailu Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Chengdong Wang
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Huiling Gong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Honglin Wu
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Xue Fu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Linhua Deng
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Changwei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Ming He
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Hongning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Yanxi Cheng
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Qian Wang
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Shanshan Lin
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Yan Huang
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Desheng Li
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
- Correspondence: (D.L.); (X.Y.)
| | - Xin Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
- Correspondence: (D.L.); (X.Y.)
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3
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Luo J, Zhang L, Shen F, Luo L, Chen L, Fan Z, Hou R, Yue B, Zhang X. Blood transcriptome analysis revealing aging gene expression profiles in red panda. PeerJ 2022; 10:e13743. [PMID: 35898935 PMCID: PMC9310792 DOI: 10.7717/peerj.13743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/27/2022] [Indexed: 01/17/2023] Open
Abstract
The red panda is an endangered forest species distributed on the edge of the Qinghai Tibet Plateau. The species has been conserved in ex-situ in many countries and its survival is threatened by many diseases. Its immune system is vulnerable to age-associated alterations, which accumulate and result in a progressive deterioration that leads to an increased incidence of diseases. We identified 2,219 differentially expressed genes (DEGs) between geriatric (11-16 years) and adult individuals (4-8 years), and 1690 DEGs between adults and juveniles (1 year). The gene expression and functional annotation results showed that the innate immunity of red pandas increases significantly in geriatric individuals, whereas its change remains unclear when comparing adults and juveniles. We found that the adaptive immunity of red pandas first increased and then decreased with age. We identified CXCR3, BLNK, and CCR4 as the hub genes in the age-related protein-protein interaction network, which showed their central role in age-related immune changes. Many DNA repair genes were down-regulated in geriatric red pandas, suggesting that the DNA repair ability of the blood tissue in geriatric red pandas is significantly reduced. The significantly up-regulated TLR5 in geriatric individuals also suggests the possibility of enhancing the vaccination immune response by incorporating flagellin, which could be used to address decreased vaccine responses caused by age-related declines in immune system function. This work provides an insight into gene expression changes associated with aging and paves the way for effective disease prevention and treatment strategies for red pandas in the future.
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Affiliation(s)
- Jing Luo
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Liang Zhang
- Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan, China
| | - Fujun Shen
- Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan, China
| | - Li Luo
- Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan, China
| | - Lei Chen
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Zhenxin Fan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Rong Hou
- Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan, China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
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4
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Johnston RA, Rheinwald JG, vonHoldt BM, Stahler DR, Lowry W, Tung J, Wayne RK. K Locus Effects in Gray Wolves: Experimental Assessment of TLR3 Signaling and the Gene Expression Response to Canine Distemper Virus. J Hered 2021; 112:458-468. [PMID: 34132805 PMCID: PMC8567826 DOI: 10.1093/jhered/esab029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/04/2021] [Accepted: 05/06/2021] [Indexed: 12/21/2022] Open
Abstract
In North American gray wolves, black coat color is dominantly inherited via a 3 base pair coding deletion in the canine beta defensin 3 (CBD103) gene. This 3 base pair deletion, called the KB allele, was introduced through hybridization with dogs and subsequently underwent a selective sweep that increased its frequency in wild wolves. Despite apparent positive selection, KBB wolves have lower fitness than wolves with the KyB genotype, even though the 2 genotypes show no observable differences in black coat color. Thus, the KB allele is thought to have pleiotropic effects on as-yet unknown phenotypes. Given the role of skin-expressed CBD103 in innate immunity, we hypothesized that the KB allele influences the keratinocyte gene expression response to TLR3 pathway stimulation and/or infection by canine distemper virus (CDV). To test this hypothesis, we developed a panel of primary epidermal keratinocyte cell cultures from 24 wild North American gray wolves of both Kyy and KyB genotypes. In addition, we generated an immortalized Kyy line and used CRISPR/Cas9 editing to produce a KyB line on the same genetic background. We assessed the transcriptome-wide responses of wolf keratinocytes to the TLR3 agonist polyinosinic:polycytidylic acid (polyI:C), and to live CDV. K locus genotype did not predict the transcriptional response to either challenge, suggesting that variation in the gene expression response does not explain pleiotropic effects of the KB allele on fitness. This study supports the feasibility of using cell culture methods to investigate the phenotypic effects of naturally occurring genetic variation in wild mammals.
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Affiliation(s)
- Rachel A Johnston
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - James G Rheinwald
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, USA
| | - William Lowry
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Biology, Duke University, Durham, NC, USA
- Duke Population Research Institute, Duke University, Durham, NC, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
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5
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Yin D, Lin D, Guo H, Gu H, Ying C, Zhang Y, Zhang J, Liu K, Tang W. Integrated analysis of blood mRNAs and microRNAs reveals immune changes with age in the Yangtze finless porpoise (Neophocaena asiaeorientalis). Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110635. [PMID: 34119650 DOI: 10.1016/j.cbpb.2021.110635] [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: 03/10/2021] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022]
Abstract
Populations of Yangtze finless porpoises (YFPs) have rapidly declined in recent decades, raising the specter of extinction. In order to protect YFPs, a greater understanding of their biology is needed, including studying how their immune functioning changes with age. Here, we systematically studied the hematologic and biochemical parameters, as well as mRNAs and miRNAs profiles of old, adult, and young YFPs. The lymphocyte (LYMPH), neutrophils (NEUT) and eosinophils (EOS) counts in old YFPs were lower than those in young or adult YFPs. When comparing old to adult YFPs, the latter showed higher expression of genes associated with the innate and adaptive immune systems, including complement components, major histocompatibility complex, interleukins, TNF receptors, and chemokines/cytokines. When comparing old to young YFPs, the most striking difference was in higher toll-like receptor signaling in the latter. When comparing adult to young YFPs, the former exhibited higher expression of genes related to adaptive immunity and the FoxO signaling pathway, but lower expression of genes associated with the PI3K-Akt signaling pathway. Negative miRNA-mRNA interactions were predicted in comparisons of the old and adult (326), old and young (316), adult and young (211) groups. Overall, these results delineate a progression from early innate immune function dominance to adaptive immune function enhancement (young to adult) and deterioration (adult to old), and the changes in miRNAs profile correlate with the effects of age on immune functions. This study is the first to observe the changes of immune function of Yangtze finless porpoise with age using transcriptome method, and the study's findings are of great significance for protecting this endangered species.
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Affiliation(s)
- Denghua Yin
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China; Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi 214081, China
| | - Danqing Lin
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi 214081, China
| | - Hongyi Guo
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Hailong Gu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Congping Ying
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi 214081, China
| | - Ya Zhang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Jialu Zhang
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi 214081, China
| | - Kai Liu
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi 214081, China.
| | - Wenqiao Tang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China.
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6
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Wang J, Lan Y, He L, Tang R, Li Y, Huang Y, Liang S, Gao Z, Price M, Yue B, He M, Guo T, Fan Z. Sex-specific gene expression in the blood of four primates. Genomics 2021; 113:2605-2613. [PMID: 34116169 DOI: 10.1016/j.ygeno.2021.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/03/2021] [Accepted: 06/06/2021] [Indexed: 10/21/2022]
Abstract
Blood is an important non-reproductive tissue, but little is known about the sex-specific gene expressions in the blood. Therefore, we investigated sex-specific gene expression differences in the blood tissues of four primates, rhesus macaques (Macaca mulatta), Tibetan macaques (M. thibetana), yellow baboons (Papio cynocephalus), and humans. We identified seven sex-specific differentially expressed genes (SDEGs) in each non-human primate and 31 SDEGs in humans. The four primates had only one common SDEG, MAP7D2. In humans, immune-related SDEGs were identified as up-regulated, but also down-regulated in females. We also found that most of the X-Y gene pairs had similar expression levels between species, except pair EIF1AY/EIF1AX. The expression level of X-Y gene pairs of rhesus and Tibetan macaques showed no significant differential expression levels, while humans had six significant XY-biased and three XX-biased X-Y gene pairs. Our observed sex differences in blood should increase understanding of sex differences in primate blood tissue.
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Affiliation(s)
- Jiao Wang
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Yue Lan
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Lewei He
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Ruixiang Tang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Yuhui Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu 610052, Sichuan, China
| | - Yuan Huang
- Medical Laboratory Department of West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Shan Liang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu 610052, Sichuan, China
| | - Zhan Gao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu 610052, Sichuan, China
| | - Megan Price
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Miao He
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu 610052, Sichuan, China.
| | - Tao Guo
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
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7
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Yan CC, Zhang XS, Zhou L, Yang Q, Zhou M, Zhang LW, Xing JC, Yan ZF, Price M, Li J, Yue BS, Fan ZX. Effects of aging on gene expression in blood of captive Tibetan macaques ( Macaca thibetana) and comparisons with expression in humans. Zool Res 2021; 41:557-563. [PMID: 32746507 PMCID: PMC7475009 DOI: 10.24272/j.issn.2095-8137.2020.092] [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] [Indexed: 12/15/2022] Open
Abstract
Changes in gene expression occur as animals, including primates, age. Macaques have long been used as a model species for primate evolution and biomedical studies. Here, to study gene expression in Tibetan macaques (Macaca thibetana, TMs) and its differences to humans, we applied RNA-Seq to obtain the blood transcriptomes of 24 TMs. In total, 2 523 age-associated differentially expressed genes (DEGs) were identified. Several pathways and processes that regulate aging, including the FoxO signaling pathway, autophagy, and platelet activation, were significantly enriched in the up-regulated DEGs. Two significantly age-related modules were identified by weighted gene co-expression network analysis (WGCNA). The TMs and humans shared 279 common DEGs, including 111 up-regulated and 141 down-regulated genes with advancing age in the same expression direction. However, 27 age-related DEGs presented the opposite expression direction in TMs as that in humans. For example, INPPL1, with inhibitory effects on the B cell receptor signaling pathway, was up-regulated in humans but down-regulated in TMs. In general, our study suggests that aging is a critical factor affecting gene expression in the captive TM population. The similarities and differences in gene expression patterns between TMs and humans could provide new insights into primate evolution and benefit TM model development.
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Affiliation(s)
- Chao-Chao Yan
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Xin-Shang Zhang
- Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan 610212, China
| | - Liang Zhou
- Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan 610212, China
| | - Qiao Yang
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Min Zhou
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Lin-Wan Zhang
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Jin-Chuan Xing
- Department of Genetics, Rutgers, State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Zhi-Feng Yan
- Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan 610212, China
| | - Megan Price
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Jing Li
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Bi-Song Yue
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Zhen-Xin Fan
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China. E-mail:
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8
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Zhou M, Zhang L, Yang Q, Yan C, Jiang P, Lan Y, Wang J, Tang R, He M, Lei G, Sun P, Su N, Price M, Li J, Lin F, Yue B, Fan Z. Age-related gene expression and DNA methylation changes in rhesus macaque. Genomics 2020; 112:5147-5156. [DOI: 10.1016/j.ygeno.2020.09.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/23/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023]
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9
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Meitern R, Fort J, Giraudeau M, Rattiste K, Sild E, Sepp T. Age-dependent expression of cancer-related genes in a long-lived seabird. Evol Appl 2020; 13:1708-1718. [PMID: 32821278 PMCID: PMC7428815 DOI: 10.1111/eva.13024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/21/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022] Open
Abstract
Studies of model animals like mice and rats have led to great advances in our understanding of the process of tumorigenesis, but this line of study has less to offer for understanding the mechanisms of cancer resistance. Increasing the diversity of nonmodel species from the perspective of molecular mechanisms of natural cancer resistance can lead to new insights into the evolution of protective mechanisms against neoplastic processes and to a wider understanding of natural cancer defense mechanisms. Such knowledge could then eventually be harnessed for the development of human cancer therapies. We suggest here that seabirds are promising, albeit currently completely ignored candidates for studying cancer defense mechanisms, as they have a longer maximum life span than expected from their body size and rates of energy metabolism and may have thus evolved mechanisms to limit neoplasia progression, especially at older ages. We here apply a novel, intraspecific approach of comparing old and young seabirds for improving our understanding of aging and neoplastic processes in natural settings. We used the long-lived common gulls (Larus canus) for studying the age-related pattern of expression of cancer-related genes, based on transcriptome analysis and databases of orthologues of human cancer genes. The analysis of differently expressed cancer-related genes between young and old gulls indicated that similarly to humans, age is potentially affecting cancer risk in this species. Out of eleven differentially expressed cancer-related genes between the groups, three were likely artifactually linked to cancer. The remaining eight were downregulated in old gulls compared to young ones. The downregulation of five of them could be interpreted as a mechanism suppressing neoplasia risk and three as increasing the risk. Based on these results, we suggest that old gulls differ from young ones both from the aspect of cancer susceptibility and tumor suppression at the genetic level.
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Affiliation(s)
- Richard Meitern
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Jérôme Fort
- Littoral Environnement et Sociétés (LIENSs)UMR 7266 CNRS‐La Rochelle UniversitéLa RochelleFrance
| | | | - Kalev Rattiste
- Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartuEstonia
| | - Elin Sild
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Tuul Sepp
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
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10
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Guerrero TP, Fickel J, Benhaiem S, Weyrich A. Epigenomics and gene regulation in mammalian social systems. Curr Zool 2020; 66:307-319. [PMID: 32440291 PMCID: PMC7233906 DOI: 10.1093/cz/zoaa005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 02/12/2020] [Indexed: 12/19/2022] Open
Abstract
Social epigenomics is a new field of research that studies how the social environment shapes the epigenome and how in turn the epigenome modulates behavior. We focus on describing known gene-environment interactions (GEIs) and epigenetic mechanisms in different mammalian social systems. To illustrate how epigenetic mechanisms integrate GEIs, we highlight examples where epigenetic mechanisms are associated with social behaviors and with their maintenance through neuroendocrine, locomotor, and metabolic responses. We discuss future research trajectories and open questions for the emerging field of social epigenomics in nonmodel and naturally occurring social systems. Finally, we outline the technological advances that aid the study of epigenetic mechanisms in the establishment of GEIs and vice versa.
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Affiliation(s)
- Tania P Guerrero
- Department Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
- Faculty of Environment and Natural Resources, Albert Ludwig University of Freiburg, Tennenbacher Str. 4, Freiburg, D-79085, Germany
| | - Jörns Fickel
- Department Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
| | - Sarah Benhaiem
- Department Ecological Dynamics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
| | - Alexandra Weyrich
- Department Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
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11
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Du L, Liu Q, Shen F, Fan Z, Hou R, Yue B, Zhang X. Transcriptome analysis reveals immune-related gene expression changes with age in giant panda ( Ailuropoda melanoleuca) blood. Aging (Albany NY) 2020; 11:249-262. [PMID: 30641486 PMCID: PMC6339791 DOI: 10.18632/aging.101747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/26/2018] [Indexed: 12/24/2022]
Abstract
The giant panda (Ailuropoda melanoleuca), an endangered species endemic to western China, has long been threatened with extinction that is exacerbated by highly contagious and fatal diseases. Aging is the most well-defined risk factor for diseases and is associated with a decline in immune function leading to increased susceptibility to infection and reduced response to vaccination. Therefore, this study aimed to determine which genes and pathways show differential expression with age in blood tissues. We obtained 210 differentially expressed genes by RNA-seq, including 146 up-regulated and 64 down-regulated genes in old pandas (18-21yrs) compared to young pandas (2-6yrs). We identified ISG15, STAT1, IRF7 and DDX58 as the hub genes in the protein-protein interaction network. All of these genes were up-regulated with age and played important roles in response to pathogen invasion. Functional enrichment analysis indicated that up-regulated genes were mainly involved in innate immune response, while the down-regulated genes were mainly related to B cell activation. These may suggest that the innate immunity is relatively well preserved to compensate for the decline in the adaptive immune function. In conclusion, our findings will provide a foundation for future studies on the molecular mechanisms underlying immune changes associated with ageing.
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Affiliation(s)
- Lianming Du
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China.,Institute for Advanced Study, Chengdu University, Chengdu 610106, China
| | - Qin Liu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China.,College of Life Sciences and Food Engineering, Yibin University, Yibin 644000, China
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Zhenxin Fan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
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12
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Affiliation(s)
- Jean‐Michel Gaillard
- Laboratoire de Biométrie et Biologie Evolutive UMR5558 CNRS Université Lyon 1 University of Lyon Villeurbanne France
| | - Jean‐François Lemaître
- Laboratoire de Biométrie et Biologie Evolutive UMR5558 CNRS Université Lyon 1 University of Lyon Villeurbanne France
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13
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Longitudinal comparative transcriptomics reveals unique mechanisms underlying extended healthspan in bats. Nat Ecol Evol 2019; 3:1110-1120. [DOI: 10.1038/s41559-019-0913-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/01/2019] [Indexed: 12/22/2022]
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14
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15
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Simons ND, Eick GN, Ruiz-Lopez MJ, Hyeroba D, Omeja PA, Weny G, Zheng H, Shankar A, Frost SDW, Jones JH, Chapman CA, Switzer WM, Goldberg TL, Sterner KN, Ting N. Genome-Wide Patterns of Gene Expression in a Wild Primate Indicate Species-Specific Mechanisms Associated with Tolerance to Natural Simian Immunodeficiency Virus Infection. Genome Biol Evol 2019; 11:1630-1643. [PMID: 31106820 PMCID: PMC6561381 DOI: 10.1093/gbe/evz099] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2019] [Indexed: 12/12/2022] Open
Abstract
Over 40 species of nonhuman primates host simian immunodeficiency viruses (SIVs). In natural hosts, infection is generally assumed to be nonpathogenic due to a long coevolutionary history between host and virus, although pathogenicity is difficult to study in wild nonhuman primates. We used whole-blood RNA-seq and SIV prevalence from 29 wild Ugandan red colobus (Piliocolobus tephrosceles) to assess the effects of SIV infection on host gene expression in wild, naturally SIV-infected primates. We found no evidence for chronic immune activation in infected individuals, suggesting that SIV is not immunocompromising in this species, in contrast to human immunodeficiency virus in humans. Notably, an immunosuppressive gene, CD101, was upregulated in infected individuals. This gene has not been previously described in the context of nonpathogenic SIV infection. This expands the known variation associated with SIV infection in natural hosts and may suggest a novel mechanism for tolerance of SIV infection in the Ugandan red colobus.
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Affiliation(s)
| | - Geeta N Eick
- Department of Anthropology, University of Oregon
| | | | - David Hyeroba
- College of Veterinary Medicine, Animal Resources, and Bio-Security, Makerere University, Kampala, Uganda
| | - Patrick A Omeja
- Makerere University Biological Field Station, Fort Portal, Uganda
| | - Geoffrey Weny
- Makerere University Biological Field Station, Fort Portal, Uganda
| | - HaoQiang Zheng
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Anupama Shankar
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - James H Jones
- Department of Earth System Science, Woods Institute for the Environment, Stanford University
| | - Colin A Chapman
- Makerere University Biological Field Station, Fort Portal, Uganda
- Department of Anthropology, McGill School of Environment, McGill University, Montreal, Quebec, Canada
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison
- Global Health Institute, University of Wisconsin-Madison
| | | | - Nelson Ting
- Department of Anthropology, University of Oregon
- Institute of Ecology and Evolution, University of Oregon
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16
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Snyder-Mackler N, Lea AJ. Functional genomic insights into the environmental determinants of mammalian fitness. Curr Opin Genet Dev 2018; 53:105-112. [PMID: 30142491 PMCID: PMC6296864 DOI: 10.1016/j.gde.2018.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 07/17/2018] [Accepted: 08/02/2018] [Indexed: 01/05/2023]
Abstract
Both the social and physical environment shape health, reproduction, and survival across many species, and identifying how these effects manifest at the molecular level has long been a priority in medicine and evolutionary biology. The recent rise of functional genomics has enabled researchers to gain new insights into how environmental inputs shape variation in gene regulation, and consequently, downstream organism-level traits. Here, we discuss recent work on this topic, as well as key knowledge gaps. Research in this area spans a wide range of taxa, but we focus our review on mammalian species because of their close evolutionary proximity to humans and because of their relevance for understanding human health. Improving our understanding of how the environment and the genome are connected promises to shed new light on the mechanisms underlying environmentally-induced disease in humans, as well as the evolution of environmental sensitivity more generally.
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Affiliation(s)
- Noah Snyder-Mackler
- Department of Psychology, University of Washington, Seattle, WA 98195, USA; Center for Studies in Demography and Ecology, University of Washington, Seattle, WA 98195, USA; Washington National Primate Research Center, Seattle, WA 98195, USA.
| | - Amanda J Lea
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Ecology and Evolutionary, Princeton University, Princeton, NJ 08544, USA.
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17
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vonHoldt BM, Ji SS, Aardema ML, Stahler DR, Udell MAR, Sinsheimer JS. Activity of Genes with Functions in Human Williams-Beuren Syndrome Is Impacted by Mobile Element Insertions in the Gray Wolf Genome. Genome Biol Evol 2018; 10:1546-1553. [PMID: 29860323 PMCID: PMC6007319 DOI: 10.1093/gbe/evy112] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2018] [Indexed: 12/13/2022] Open
Abstract
In canines, transposon dynamics have been associated with a hyper-social behavioral syndrome, although the functional mechanism has yet to be described. We investigate the epigenetic and transcriptional consequences of these behavior-associated mobile element insertions (MEIs) in dogs and Yellowstone gray wolves. We posit that the transposons themselves may not be the causative feature; rather, their transcriptional regulation may exert the functional impact. We survey four outlier transposons associated with hyper-sociability, with the expectation that they are targeted for epigenetic silencing. We predict hyper-methylation of MEIs, suggestive that the epigenetic silencing of and not the MEIs themselves may be driving dysregulation of nearby genes. We found that transposon-derived sequences are significantly hyper-methylated, regardless of their copy number or species. Further, we have assessed transcriptome sequence data and found evidence that MEIs impact the expression levels of six genes (WBSCR17, LIMK1, GTF2I, WBSCR27, BAZ1B, and BCL7B), all of which have known roles in human Williams-Beuren syndrome due to changes in copy number, typically hemizygosity. Although further evidence is needed, our results suggest that a few insertions alter local expression at multiple genes, likely through a cis-regulatory mechanism that excludes proximal methylation.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, New Jersey
| | - Sarah S Ji
- Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, California
| | - Matthew L Aardema
- Department of Biology, Montclair State University, New Jersey
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming
| | - Monique A R Udell
- Department of Animal & Rangeland Sciences, Oregon State University, Oregon
| | - Janet S Sinsheimer
- Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, California
- Departments of Human Genetics and Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, California
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18
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Lea AJ, Tung J, Archie EA, Alberts SC. Developmental plasticity: Bridging research in evolution and human health. Evol Med Public Health 2018; 2017:162-175. [PMID: 29424834 PMCID: PMC5798083 DOI: 10.1093/emph/eox019] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/19/2017] [Indexed: 02/06/2023] Open
Abstract
Early life experiences can have profound and persistent effects on traits expressed throughout the life course, with consequences for later life behavior, disease risk, and mortality rates. The shaping of later life traits by early life environments, known as 'developmental plasticity', has been well-documented in humans and non-human animals, and has consequently captured the attention of both evolutionary biologists and researchers studying human health. Importantly, the parallel significance of developmental plasticity across multiple fields presents a timely opportunity to build a comprehensive understanding of this phenomenon. We aim to facilitate this goal by highlighting key outstanding questions shared by both evolutionary and health researchers, and by identifying theory and empirical work from both research traditions that is designed to address these questions. Specifically, we focus on: (i) evolutionary explanations for developmental plasticity, (ii) the genetics of developmental plasticity and (iii) the molecular mechanisms that mediate developmental plasticity. In each section, we emphasize the conceptual gains in human health and evolutionary biology that would follow from filling current knowledge gaps using interdisciplinary approaches. We encourage researchers interested in developmental plasticity to evaluate their own work in light of research from diverse fields, with the ultimate goal of establishing a cross-disciplinary understanding of developmental plasticity.
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Affiliation(s)
- Amanda J Lea
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
- Duke University Population Research Institute, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Elizabeth A Archie
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
- Duke University Population Research Institute, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
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19
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Lea AJ, Vilgalys TP, Durst PAP, Tung J. Maximizing ecological and evolutionary insight in bisulfite sequencing data sets. Nat Ecol Evol 2017; 1:1074-1083. [PMID: 29046582 PMCID: PMC5656403 DOI: 10.1038/s41559-017-0229-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 05/31/2017] [Indexed: 12/12/2022]
Abstract
Genome-scale bisulfite sequencing approaches have opened the door to ecological and evolutionary studies of DNA methylation in many organisms. These approaches can be powerful. However, they introduce new methodological and statistical considerations, some of which are particularly relevant to non-model systems. Here, we highlight how these considerations influence a study's power to link methylation variation with a predictor variable of interest. Relative to current practice, we argue that sample sizes will need to increase to provide robust insights. We also provide recommendations for overcoming common challenges and an R Shiny app to aid in study design.
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Affiliation(s)
- Amanda J Lea
- Department of Biology, Duke University, Durham, NC, 27708, USA.
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Washington Road, Princeton University, Princeton, NJ, 08540, USA.
| | - Tauras P Vilgalys
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA
| | - Paul A P Durst
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC, 27708, USA.
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA.
- Institute of Primate Research, National Museums of Kenya, Nairobi, 00502, Kenya.
- Duke University Population Research Institute, Duke University, Durham, NC, 27708, USA.
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20
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Freedman AH, Lohmueller KE, Wayne RK. Evolutionary History, Selective Sweeps, and Deleterious Variation in the Dog. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032155] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The dog is our oldest domesticate and has experienced a wide variety of demographic histories, including a bottleneck associated with domestication and individual bottlenecks associated with the formation of modern breeds. Admixture with gray wolves, and among dog breeds and populations, has also occurred throughout its history. Likewise, the intensity and focus of selection have varied, from an initial focus on traits enhancing cohabitation with humans, to more directed selection on specific phenotypic characteristics and behaviors. In this review, we summarize and synthesize genetic findings from genome-wide and complete genome studies that document the genomic consequences of demography and selection, including the effects on adaptive and deleterious variation. Consistent with the evolutionary history of the dog, signals of natural and artificial selection are evident in the dog genome. However, conclusions from studies of positive selection are fraught with the problem of false positives given that demographic history is often not taken into account.
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Affiliation(s)
- Adam H. Freedman
- Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, Massachusetts 02138
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095
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