1
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Lin TD, Rubinstein ND, Fong NL, Smith M, Craft W, Martin-McNulty B, Perry R, Delaney MA, Roy MA, Buffenstein R. Evolution of T cells in the cancer-resistant naked mole-rat. Nat Commun 2024; 15:3145. [PMID: 38605005 PMCID: PMC11009300 DOI: 10.1038/s41467-024-47264-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Naked mole-rats (NMRs) are best known for their extreme longevity and cancer resistance, suggesting that their immune system might have evolved to facilitate these phenotypes. Natural killer (NK) and T cells have evolved to detect and destroy cells infected with pathogens and to provide an early response to malignancies. While it is known that NMRs lack NK cells, likely lost during evolution, little is known about their T-cell subsets in terms of the evolution of the genes that regulate their function, their clonotypic diversity, and the thymus where they mature. Here we find, using single-cell transcriptomics, that NMRs have a large circulating population of γδT cells, which in mice and humans mostly reside in peripheral tissues and induce anti-cancer cytotoxicity. Using single-cell-T-cell-receptor sequencing, we find that a cytotoxic γδT-cell subset of NMRs harbors a dominant clonotype, and that their conventional CD8 αβT cells exhibit modest clonotypic diversity. Consistently, perinatal NMR thymuses are considerably smaller than those of mice yet follow similar involution progression. Our findings suggest that NMRs have evolved under a relaxed intracellular pathogenic selective pressure that may have allowed cancer resistance and longevity to become stronger targets of selection to which the immune system has responded by utilizing γδT cells.
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Affiliation(s)
- Tzuhua D Lin
- Calico Life Sciences LLC, South San Francisco, California, CA, USA
| | | | - Nicole L Fong
- Calico Life Sciences LLC, South San Francisco, California, CA, USA
| | - Megan Smith
- Calico Life Sciences LLC, South San Francisco, California, CA, USA
| | - Wendy Craft
- Calico Life Sciences LLC, South San Francisco, California, CA, USA
| | | | - Rebecca Perry
- Department of Biological Science, University of Illinois at Chicago, Illinois, IL, USA
| | | | - Margaret A Roy
- Calico Life Sciences LLC, South San Francisco, California, CA, USA
| | - Rochelle Buffenstein
- Calico Life Sciences LLC, South San Francisco, California, CA, USA.
- Department of Biological Science, University of Illinois at Chicago, Illinois, IL, USA.
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2
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Birkemeier M, Swindle A, Bowman J, Lynch VJ. Pervasive loss of regulated necrotic cell death genes in elephants, hyraxes, and sea cows ( Paenungualta). bioRxiv 2024:2024.04.04.588129. [PMID: 38617256 PMCID: PMC11014510 DOI: 10.1101/2024.04.04.588129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Gene loss can promote phenotypic differences between species, for example, if a gene constrains phenotypic variation in a trait, its loss allows for the evolution of a greater range of variation or even new phenotypes. Here, we explore the contribution of gene loss to the evolution of large bodies and augmented cancer resistance in elephants. We used genomes from 17 Afrotherian and Xenarthran species to identify lost genes, i.e., genes that have pseudogenized or been completely lost, and Dollo parsimony to reconstruct the evolutionary history of gene loss across species. We unexpectedly discovered a burst of gene losses in the Afrotherian stem lineage and found that the loss of genes with functions in regulated necrotic cell death modes was pervasive in elephants, hyraxes, and sea cows (Paenungulata). Among the lost genes are MLKL and RIPK3, which mediate necroptosis, and sensors that activate inflammasomes to induce pyroptosis, including AIM2, MEFV, NLRC4, NLRP1, and NLRP6. These data suggest that the mechanisms that regulate necrosis and pyroptosis are either extremely derived or potentially lost in these lineages, which may contribute to the repeated evolution of large bodies and cancer resistance in Paenungulates as well as susceptibility to pathogen infection.
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Affiliation(s)
- Meaghan Birkemeier
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
| | - Arianna Swindle
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
| | - Jacob Bowman
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
| | - Vincent J. Lynch
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
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3
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Bowman J, Lynch VJ. Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants. bioRxiv 2024:2024.02.27.582135. [PMID: 38463968 PMCID: PMC10925141 DOI: 10.1101/2024.02.27.582135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Elephants have emerged as a model system to study the evolution of body size and cancer resistance because, despite their immense size, they have a very low prevalence of cancer. Previous studies have found that duplication of tumor suppressors at least partly contributes to the evolution of anti-cancer cellular phenotypes in elephants. Still, many other mechanisms must have contributed to their augmented cancer resistance. Here, we use a suite of codon-based maximum-likelihood methods and a dataset of 13,310 protein-coding gene alignments from 261 Eutherian mammals to identify positively selected and rapidly evolving elephant genes. We found 496 genes (3.73% of alignments tested) with statistically significant evidence for positive selection and 660 genes (4.96% of alignments tested) that likely evolved rapidly in elephants. Positively selected and rapidly evolving genes are statistically enriched in gene ontology terms and biological pathways related to regulated cell death mechanisms, DNA damage repair, cell cycle regulation, epidermal growth factor receptor (EGFR) signaling, and immune functions, particularly neutrophil granules and degranulation. All of these biological factors are plausibly related to the evolution of cancer resistance. Thus, these positively selected and rapidly evolving genes are promising candidates for genes contributing to elephant-specific traits, including the evolution of molecular and cellular characteristics that enhance cancer resistance.
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Affiliation(s)
- Jacob Bowman
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, 14260, USA
| | - Vincent J. Lynch
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, 14260, USA
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4
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Shi M, Chen F, Sahu SK, Wang Q, Yang S, Wang Z, Chen J, Liu H, Hou Z, Fang SG, Lan T. Haplotype-resolved chromosome-scale genomes of the Asian and African Savannah Elephants. Sci Data 2024; 11:63. [PMID: 38212399 PMCID: PMC10784532 DOI: 10.1038/s41597-023-02729-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/07/2023] [Indexed: 01/13/2024] Open
Abstract
The Proboscidea, which includes modern elephants, were once the largest terrestrial animals among extant species. They suffered mass extinction during the Ice Age. As a unique branch on the evolutionary tree, the Proboscidea are of great significance for the study of living animals. In this study, we generate chromosome-scale and haplotype-resolved genome assemblies for two extant Proboscidea species (Asian Elephant, Elephas maximus and African Savannah Elephant, Loxodonta africana) using Pacbio, Hi-C, and DNBSEQ technologies. The assembled genome sizes of the Asian and African Savannah Elephant are 3.38 Gb and 3.31 Gb, with scaffold N50 values of 130 Mb and 122 Mb, respectively. Using Hi-C technology ~97% of the scaffolds are anchored to 29 pseudochromosomes. Additionally, we identify ~9 Mb Y-linked sequences for each species. The high-quality genome assemblies in this study provide a valuable resource for future research on ecology, evolution, biology and conservation of Proboscidea species.
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Affiliation(s)
- Minhui Shi
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Chen
- Southwest Survey and Planning Institute of National Forestry and Grassland Administration, Kunming, 650031, China
- Asian Elephant Research Center of National Forestry and Grassland Administration, Kunming, 650031, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Shangchen Yang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhihong Wang
- Southwest Survey and Planning Institute of National Forestry and Grassland Administration, Kunming, 650031, China
- Asian Elephant Research Center of National Forestry and Grassland Administration, Kunming, 650031, China
| | - Jin Chen
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
- China National GeneBank, BGI Research, Shenzhen, 518083, China
| | - Huan Liu
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Zhijun Hou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Tianming Lan
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China.
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China.
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5
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Arai K, Qi H, Inoue-Murayama M. Age estimation of captive Asian elephants (Elephas maximus) based on DNA methylation: An exploratory analysis using methylation-sensitive high-resolution melting (MS-HRM). PLoS One 2023; 18:e0294994. [PMID: 38079426 PMCID: PMC10712859 DOI: 10.1371/journal.pone.0294994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Age is an important parameter for bettering the understanding of biodemographic trends-development, survival, reproduction and environmental effects-critical for conservation. However, current age estimation methods are challenging to apply to many species, and no standardised technique has been adopted yet. This study examined the potential use of methylation-sensitive high-resolution melting (MS-HRM), a labour-, time-, and cost-effective method to estimate chronological age from DNA methylation in Asian elephants (Elephas maximus). The objective of this study was to investigate the accuracy and validation of MS-HRM use for age determination in long-lived species, such as Asian elephants. The average lifespan of Asian elephants is between 50-70 years but some have been known to survive for more than 80 years. DNA was extracted from 53 blood samples of captive Asian elephants across 11 zoos in Japan, with known ages ranging from a few months to 65 years. Methylation rates of two candidate age-related epigenetic genes, RALYL and TET2, were significantly correlated with chronological age. Finally, we established a linear, unisex age estimation model with a mean absolute error (MAE) of 7.36 years. This exploratory study suggests an avenue to further explore MS-HRM as an alternative method to estimate the chronological age of Asian elephants.
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Affiliation(s)
- Kana Arai
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, Japan
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6
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Abstract
Sir Richard Peto is well known for proposing puzzling paradoxes in cancer biology-some more well-known than others. In a 1984 piece, Peto proposed that after decades of molecular biology in cancer research, we are still ignorant of the biology underpinning cancer. Cancer is a product of somatic mutations. How do these mutations arise and what are the mechanisms? As an epidemiologist, Peto asked if we really need to understand mechanisms in order to prevent cancer? Four decades after Peto's proposed ignorance in cancer research, we can simply ask, are we still ignorant? Did the great pursuit to uncover mechanisms of cancer eclipse our understanding of causes and preventions? Or can we get closer to treating and preventing cancer by understanding the underlying mechanisms that make us most vulnerable to this disease?
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Affiliation(s)
- Amy M Boddy
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA.
- Arizona Cancer and Evolution Center, Arizona State University, Tempe, AZ, USA.
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7
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Huang Z, Jiang C, Gu J, Uvizl M, Power S, Douglas D, Kacprzyk J. Duplications of Human Longevity-Associated Genes Across Placental Mammals. Genome Biol Evol 2023; 15:evad186. [PMID: 37831410 PMCID: PMC10588791 DOI: 10.1093/gbe/evad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/31/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023] Open
Abstract
Natural selection has shaped a wide range of lifespans across mammals, with a few long-lived species showing negligible signs of ageing. Approaches used to elucidate the genetic mechanisms underlying mammalian longevity usually involve phylogenetic selection tests on candidate genes, detections of convergent amino acid changes in long-lived lineages, analyses of differential gene expression between age cohorts or species, and measurements of age-related epigenetic changes. However, the link between gene duplication and evolution of mammalian longevity has not been widely investigated. Here, we explored the association between gene duplication and mammalian lifespan by analyzing 287 human longevity-associated genes across 37 placental mammals. We estimated that the expansion rate of these genes is eight times higher than their contraction rate across these 37 species. Using phylogenetic approaches, we identified 43 genes whose duplication levels are significantly correlated with longevity quotients (False Discovery Rate (FDR) < 0.05). In particular, the strong correlation observed for four genes (CREBBP, PIK3R1, HELLS, FOXM1) appears to be driven mainly by their high duplication levels in two ageing extremists, the naked mole rat (Heterocephalus glaber) and the greater mouse-eared bat (Myotis myotis). Further sequence and expression analyses suggest that the gene PIK3R1 may have undergone a convergent duplication event, whereby the similar region of its coding sequence was independently duplicated multiple times in both of these long-lived species. Collectively, this study identified several candidate genes whose duplications may underlie the extreme longevity in mammals, and highlighted the potential role of gene duplication in the evolution of mammalian long lifespans.
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Affiliation(s)
- Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Chongyi Jiang
- Institute of Ecology and Evolution, Friedrich Schiller University, Jena, Germany
| | - Jiayun Gu
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Marek Uvizl
- Department of Zoology, National Museum, Prague, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Sarahjane Power
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Declan Douglas
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Joanna Kacprzyk
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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8
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Li X, Wang P, Pan Q, Liu G, Liu W, Omotoso O, Du J, Li Z, Yu Y, Huang Y, Zhu P, Li M, Zhou X. Chromosome-level Asian elephant genome assembly and comparative genomics of long-lived mammals reveal the common substitutions for cancer resistance. Aging Cell 2023; 22:e13917. [PMID: 37395176 PMCID: PMC10497851 DOI: 10.1111/acel.13917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/17/2023] [Accepted: 05/25/2023] [Indexed: 07/04/2023] Open
Abstract
The naked mole rat (Heterocephalus glaber), bats (e.g., genus Myotis), and elephants (family Elephantidae) are known as long-lived mammals and are assumed to be excellent cancer antagonists. However, whether there are common genetic changes underpinning cancer resistance in these long-lived species is yet to be fully established. Here, we newly generated a high-quality chromosome-level Asian elephant (Elephas maximus) genome and identified that the expanded gene families in elephants are involved in Ras-associated and base excision repair pathways. Moreover, we performed comparative genomic analyses of 12 mammals and examined genes with signatures of positive selection in elephants, naked mole rat, and greater horseshoe bat. Residues at positively selected sites of CDR2L and ALDH6A1 in these long-lived mammals enhanced the inhibition of tumor cell migration compared to those in short-lived relatives. Overall, our study provides a new genome resource and a preliminary survey of common genetic changes in long-lived mammals.
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Affiliation(s)
- Xuanjing Li
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Pengcheng Wang
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Qi Pan
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
| | - Weiqiang Liu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Olatunde Omotoso
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zihao Li
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yang Yu
- Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Yun Huang
- Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
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9
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Prado NA, Armstrong EE, Brown JL, Goldenberg SZ, Leimgruber P, Pearson VR, Maldonado JE, Campana MG. Genomic resources for Asian (Elephas maximus) and African savannah elephant (Loxodonta africana) conservation and health research. J Hered 2023; 114:529-538. [PMID: 37246890 DOI: 10.1093/jhered/esad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/26/2023] [Indexed: 05/30/2023] Open
Abstract
We provide novel genomic resources to help understand the genomic traits involved in elephant health and to aid conservation efforts. We sequence 11 elephant genomes (5 African savannah, 6 Asian) from North American zoos, including 9 de novo assemblies. We estimate elephant germline mutation rates and reconstruct demographic histories. Finally, we provide an in-solution capture assay to genotype Asian elephants. This assay is suitable for analyzing degraded museum and noninvasive samples, such as feces and hair. The elephant genomic resources we present here should allow for more detailed and uniform studies in the future to aid elephant conservation efforts and disease research.
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Affiliation(s)
- Natalia A Prado
- Biology Department, College of Arts and Sciences, Adelphi University, Garden City, NY, United States
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Endocrinology Research Laboratory, Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Ellie E Armstrong
- Department of Biology, Stanford University, Stanford, CA, United States
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Janine L Brown
- Endocrinology Research Laboratory, Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Shifra Z Goldenberg
- Conservation Ecology Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
| | - Peter Leimgruber
- Conservation Ecology Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Virginia R Pearson
- Glenn Rall Laboratory, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
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10
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Díez-Del-Molino D, Dehasque M, Chacón-Duque JC, Pečnerová P, Tikhonov A, Protopopov A, Plotnikov V, Kanellidou F, Nikolskiy P, Mortensen P, Danilov GK, Vartanyan S, Gilbert MTP, Lister AM, Heintzman PD, van der Valk T, Dalén L. Genomics of adaptive evolution in the woolly mammoth. Curr Biol 2023; 33:1753-1764.e4. [PMID: 37030294 DOI: 10.1016/j.cub.2023.03.084] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/24/2023] [Accepted: 03/29/2023] [Indexed: 04/10/2023]
Abstract
Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.
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Affiliation(s)
- David Díez-Del-Molino
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden.
| | - Marianne Dehasque
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Patrícia Pečnerová
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alexei Tikhonov
- Zoological Institute of the Russian Academy of Sciences, 190121 Saint Petersburg, Russia
| | | | | | - Foteini Kanellidou
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Facility, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Pavel Nikolskiy
- Geological Institute, Russian Academy of Sciences, 119017 Moscow, Russia
| | - Peter Mortensen
- Department of Zoology, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | - Gleb K Danilov
- Peter the Great Museum of Anthropology and Ethnography, Kunstkamera, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A. Shilo, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), 685000 Magadan, Russia
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark; University Museum NTNU, 7012 Trondheim, Norway
| | | | - Peter D Heintzman
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Geological Sciences, Stockholm University, 11418 Stockholm, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Science for Life Laboratory, 17165 Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden.
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11
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Preston AJ, Rogers A, Sharp M, Mitchell G, Toruno C, Barney BB, Donovan LN, Bly J, Kennington R, Payne E, Iovino A, Furukawa G, Robinson R, Shamloo B, Buccilli M, Anders R, Eckstein S, Fedak EA, Wright T, Maley CC, Kiso WK, Schmitt D, Malkin D, Schiffman JD, Abegglen LM. Elephant TP53-RETROGENE 9 induces transcription-independent apoptosis at the mitochondria. Cell Death Discov 2023; 9:66. [PMID: 36797268 PMCID: PMC9935553 DOI: 10.1038/s41420-023-01348-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 01/24/2023] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Approximately 20 TP53 retrogenes exist in the African and Asian elephant genomes (Loxodonta Africana, Elephas Maximus) in addition to a conserved TP53 gene that encodes a full-length protein. Elephant TP53-RETROGENE 9 (TP53-R9) encodes a p53 protein (p53-R9) that is truncated in the middle of the canonical DNA binding domain. This C-terminally truncated p53 retrogene protein lacks the nuclear localization signals and oligomerization domain of its full-length counterpart. When expressed in human osteosarcoma cells (U2OS), p53-R9 binds to Tid1, the chaperone protein responsible for mitochondrial translocation of human p53 in response to cellular stress. Tid1 expression is required for p53-R9-induced apoptosis. At the mitochondria, p53-R9 binds to the pro-apoptotic BCL-2 family member Bax, which leads to caspase activation, cytochrome c release, and cell death. Our data show, for the first time, that expression of this truncated elephant p53 retrogene protein induces apoptosis in human cancer cells. Understanding the molecular mechanism by which the additional elephant TP53 retrogenes function may provide evolutionary insight that can be utilized for the development of therapeutics to treat human cancers.
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Affiliation(s)
- Aidan J Preston
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Aaron Rogers
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Miranda Sharp
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Gareth Mitchell
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Cristhian Toruno
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Brayden B Barney
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | | | - Journey Bly
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Ryan Kennington
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Emily Payne
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Anthony Iovino
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Gabriela Furukawa
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | | | | | - Matthew Buccilli
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Rachel Anders
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Sarah Eckstein
- Duke Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Elizabeth A Fedak
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Mathematics, University of Utah, Salt Lake City, UT, USA
| | - Tanner Wright
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carlo C Maley
- Biodesign Institute, School of Life Sciences, and Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ, USA
| | | | - Dennis Schmitt
- Department of Animal Science, William H. Darr College of Agriculture, Missouri State University, Springfield, MO, USA
| | - David Malkin
- Division of Haematology/Oncology, The Hospital for Sick Children; Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Joshua D Schiffman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
- Peel Therapeutics, Salt Lake City, UT, USA
| | - Lisa M Abegglen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA.
- Peel Therapeutics, Salt Lake City, UT, USA.
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12
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Abstract
Naked mole-rats (NMRs, Heterocephalus glaber) are the longest-lived rodents with a maximum life span exceeding 37 years. They exhibit a delayed aging phenotype and resistance to age-related functional decline/diseases. Specifically, they do not display increased mortality with age, maintain several physiological functions until nearly the end of their lifetime, and rarely develop cancer and Alzheimer's disease. NMRs live in a hypoxic environment in underground colonies in East Africa and are highly tolerant of hypoxia. These unique characteristics of NMRs have attracted considerable interest from zoological and biomedical researchers. This review summarizes previous studies of the ecology, hypoxia tolerance, longevity/delayed aging, and cancer resistance of NMRs and discusses possible mechanisms contributing to their healthy aging. In addition, we discuss current issues and future perspectives to fully elucidate the mechanisms underlying delayed aging and resistance to age-related diseases in NMRs.
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Affiliation(s)
- Kaori Oka
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; , ,
| | - Masanori Yamakawa
- Department of Evolutionary Studies of Biosystems, Sokendai (The Graduate University for Advanced Studies), Kanagawa, Japan; ,
| | - Yoshimi Kawamura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; , ,
| | - Nobuyuki Kutsukake
- Department of Evolutionary Studies of Biosystems, Sokendai (The Graduate University for Advanced Studies), Kanagawa, Japan; , .,Research Center for Integrative Evolutionary Science, Sokendai (The Graduate University for Advanced Studies), Kanagawa, Japan
| | - Kyoko Miura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; , , .,Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
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13
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Zhang X, Fang B, Huang YF. Transcription factor binding sites are frequently under accelerated evolution in primates. Nat Commun 2023; 14:783. [PMID: 36774380 PMCID: PMC9922303 DOI: 10.1038/s41467-023-36421-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 01/31/2023] [Indexed: 02/13/2023] Open
Abstract
Recent comparative genomic studies have identified many human accelerated elements (HARs) with elevated substitution rates in the human lineage. However, it remains unknown to what extent transcription factor binding sites (TFBSs) are under accelerated evolution in humans and other primates. Here, we introduce two pooling-based phylogenetic methods with dramatically enhanced sensitivity to examine accelerated evolution in TFBSs. Using these new methods, we show that more than 6000 TFBSs annotated in the human genome have experienced accelerated evolution in Hominini, apes, and Old World monkeys. Although these TFBSs individually show relatively weak signals of accelerated evolution, they collectively are more abundant than HARs. Also, we show that accelerated evolution in Pol III binding sites may be driven by lineage-specific positive selection, whereas accelerated evolution in other TFBSs might be driven by nonadaptive evolutionary forces. Finally, the accelerated TFBSs are enriched around developmental genes, suggesting that accelerated evolution in TFBSs may drive the divergence of developmental processes between primates.
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Affiliation(s)
- Xinru Zhang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA. .,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA. .,Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Bohao Fang
- Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, Boston, MA, 02135, USA
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA. .,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
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14
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Abstract
Cancer, a disease due to uncontrolled cell proliferation is as ancient as multicellular organisms. A 255-million-years-old fossilized forerunner mammal gorgonopsian is probably the oldest evidence of cancer, to date. Cancer seems to have evolved by adapting to the microenvironment occupied by immune sentinel, modulating the cellular behavior from cytotoxic to regulatory, acquiring resistance to chemotherapy and surviving hypoxia. The interaction of genes with environmental carcinogens is central to cancer onset, seen as a spectrum of cancer susceptibility among human population. Cancer occurs in life forms other than human also, although their exposure to environmental carcinogens can be different. Role of genetic etiology in cancer in multiple species can be interesting with regard to not only cancer susceptibility, but also genetic conservation and adaptation in speciation. The widely used model organisms for cancer research are mouse and rat which are short-lived and reproduce rapidly. Research in these cancer prone animal models has been valuable as these have led to cancer therapy. However, another rewarding area of cancer research can be the cancer-resistant animal species. The Peto's paradox and G-value paradox are evident when natural cancer resistance is observed in large mammals, like elephant and whale, small rodents viz. Naked Mole Rat and Blind Mole Rat, and Bat. The cancer resistance remains to be explored in other small or large and long-living animals like giraffe, camel, rhinoceros, water buffalo, Indian bison, Shire horse, polar bear, manatee, elephant seal, walrus, hippopotamus, turtle and tortoise, sloth, and squirrel. Indeed, understanding the molecular mechanisms of avoiding neoplastic transformation across various life forms can be potentially having translational value for human cancer management. Adapted and Modified from (Hanahan and Weinberg 2011).
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15
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Willey C, Korstanje R. Sequencing and assembling bear genomes: the bare necessities. Front Zool 2022; 19:30. [PMID: 36451195 PMCID: PMC9710173 DOI: 10.1186/s12983-022-00475-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Unique genetic adaptations are present in bears of every species across the world. From (nearly) shutting down important organs during hibernation to preventing harm from lifestyles that could easily cause metabolic diseases in humans, bears may hold the answer to various human ailments. However, only a few of these unique traits are currently being investigated at the molecular level, partly because of the lack of necessary tools. One of these tools is well-annotated genome assemblies from the different, extant bear species. These reference genomes are needed to allow us to identify differences in genetic variants, isoforms, gene expression, and genomic features such as transposons and identify those that are associated with biomedical-relevant traits. In this review we assess the current state of the genome assemblies of the eight different bear species, discuss current gaps, and the future benefits these reference genomes may have in informing human biomedical applications, while at the same time improving bear conservation efforts.
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Affiliation(s)
- Courtney Willey
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Ron Korstanje
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory, Bar Harbor, ME 04609 USA
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16
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Abegglen LM, Harrison TM, Moresco A, Fowles JS, Troan BV, Kiso WK, Schmitt D, Boddy AM, Schiffman JD. Of Elephants and Other Mammals: A Comparative Review of Reproductive Tumors and Potential Impact on Conservation. Animals (Basel) 2022; 12:2005. [PMID: 35953994 PMCID: PMC9367617 DOI: 10.3390/ani12152005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/13/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022] Open
Abstract
Reproductive tumors can impact conception, pregnancy, and birth in mammals. These impacts are well documented in humans, while data in other mammals are limited. An urgent need exists to understand the reproductive impact of these lesions in endangered species, because some endangered species have a documented high prevalence of reproductive tumors. This article documents that the prevalence of both benign and malignant neoplasia differs between African and Asian elephants, with Asian elephants more frequently diagnosed and negatively affected by both. The prevalence of these tumors across mammalian species is compared, and impact plus treatment options in human medicine are reviewed to inform decision making in elephants. Evidence suggests that reproductive tumors can negatively impact elephant conservation. Future studies that document reproductive outcomes, including the success of various treatment approaches in elephants with tumors will benefit conservation efforts.
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Affiliation(s)
- Lisa M. Abegglen
- Department of Pediatrics & Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ 85281, USA
- Exotic Species Cancer Research Alliance, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607, USA
| | - Tara M. Harrison
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ 85281, USA
- Exotic Species Cancer Research Alliance, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607, USA
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607, USA
| | - Anneke Moresco
- Exotic Species Cancer Research Alliance, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607, USA
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607, USA
- Reproductive Health Surveillance Program, Morrison, CO 80465, USA
| | - Jared S. Fowles
- Department of Pediatrics & Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Brigid V. Troan
- Exotic Species Cancer Research Alliance, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607, USA
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607, USA
| | - Wendy K. Kiso
- White Oak Conservation Foundation, Yulee, FL 32097, USA
| | - Dennis Schmitt
- Department of Animal Science, William H. Darr College of Agriculture, Missouri State University, Springfield, MO 65809, USA
| | - Amy M. Boddy
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ 85281, USA
- Exotic Species Cancer Research Alliance, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607, USA
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Joshua D. Schiffman
- Department of Pediatrics & Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ 85281, USA
- Exotic Species Cancer Research Alliance, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607, USA
- Peel Therapeutics, Inc., Salt Lake City, UT 84108, USA
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17
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van der Valk T, Dehasque M, Chacón-Duque JC, Oskolkov N, Vartanyan S, Heintzman PD, Pečnerová P, Díez-del-Molino D, Dalén L. Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome. iScience 2022; 25:104826. [PMID: 35992080 PMCID: PMC9382235 DOI: 10.1016/j.isci.2022.104826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/02/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
Woolly mammoths had a set of adaptations that enabled them to thrive in the Arctic environment. Many mammoth-specific single nucleotide polymorphisms (SNPs) responsible for unique mammoth traits have been previously identified from ancient genomes. However, a multitude of other genetic variants likely contributed to woolly mammoth evolution. In this study, we sequenced two woolly mammoth genomes and combined these with previously sequenced mammoth and elephant genomes to conduct a survey of mammoth-specific deletions and indels. We find that deletions are highly enriched in non-coding regions, suggesting selection against structural variants that affect protein sequences. Nonetheless, at least 87 woolly mammoth genes contain deletions or indels that modify the coding sequence, including genes involved in skeletal morphology and hair growth. These results suggest that deletions and indels contributed to the unique phenotypic adaptations of the woolly mammoth, and were potentially critical to surviving in its natural environment. Two new high-quality woolly mammoth genomes have been generated A new method was used to identify deletions and insertions in woolly mammoths At least 87 genes have been affected by deletions or indels in the mammoth lineage Genes involved in skeletal morphology and hair growth are affected by deletions
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18
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Rajbhandari RM, de la Fuente J, Karmacharya D, Mathema S, Maharjan B, Dixit SM, Shrestha N, Queirós J, Gortázar C, Alves PC. Understanding Mycobacterium tuberculosis complex in elephants through a One Health approach: a systematic review. BMC Vet Res 2022; 18:262. [PMID: 35794608 PMCID: PMC9258206 DOI: 10.1186/s12917-022-03356-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 06/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Mycobacterium tuberculosis complex (MTC) that causes the chronic infectious disease- tuberculosis (TB), often presents with a complicated epidemiological pattern where the transmission chain may include humans, domestic animals and wildlife, including elephants. TB has been reported globally in both captive and wild elephants. The One Health approach might be the most effective way of understanding the shared MTC infection dynamics in captive and wild animals like Asian elephants. This systematic review accumulates evidence on occurrence, transmission pathways, and preventive measures of TB in elephants from a One Health perspective. Results The prevalence of TB reported in elephant populations ranges from 0 to 23.33% and high prevalence’s are reported for elephants that are in close proximity to infected humans. The risk of elephant to human infection transmission increased significantly with exposure duration and contact with infected elephants. Some studies described the plausible TB transmission to captive elephants from other animals (wild and domestic), suggesting inter- and intra-species transmission. The results of this systematic review based on 27 relevant published works, suggest three overarching interrelated transmission pathways for M. tuberculosis infections in Asian elephants- i) humans and elephants, ii) other animals (wild or domestic) and elephants and iii) unclear sources of infection. Conclusions The progress made with new TB diagnostic tools provides multiple methods to choose from. However, lack of harmonization of TB testing in elephants and their human contacts remains a challenge to prevent TB in those animals. Routine TB screening among elephants and caretakers by setting up an occupational health program for early diagnosis of infection through combined efforts of public health, veterinary medicine, and occupational health experts is suggested. This implies the need for a One Health approach to elephant TB control. This review reveals the need for more research on Mycobacterium tuberculosis complex transmission pathways at the human-animal interface.
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19
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Padariya M, Jooste ML, Hupp T, Fåhraeus R, Vojtesek B, Vollrath F, Kalathiya U, Karakostis K. The Elephant evolved p53 isoforms that escape mdm2-mediated repression and cancer. Mol Biol Evol 2022; 39:6632613. [PMID: 35792674 PMCID: PMC9279639 DOI: 10.1093/molbev/msac149] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The p53 tumor suppressor is a transcription factor with roles in cell development, apoptosis, oncogenesis, aging, and homeostasis in response to stresses and infections. p53 is tightly regulated by the MDM2 E3 ubiquitin ligase. The p53–MDM2 pathway has coevolved, with MDM2 remaining largely conserved, whereas the TP53 gene morphed into various isoforms. Studies on prevertebrate ancestral homologs revealed the transition from an environmentally induced mechanism activating p53 to a tightly regulated system involving cell signaling. The evolution of this mechanism depends on structural changes in the interacting protein motifs. Elephants such as Loxodonta africana constitute ideal models to investigate this coevolution as they are large and long-living as well as having 20 copies of TP53 isoformic sequences expressing a variety of BOX-I MDM2-binding motifs. Collectively, these isoforms would enhance sensitivity to cellular stresses, such as DNA damage, presumably accounting for strong cancer defenses and other adaptations favoring healthy aging. Here we investigate the molecular evolution of the p53–MDM2 system by combining in silico modeling and in vitro assays to explore structural and functional aspects of p53 isoforms retaining the MDM2 interaction, whereas forming distinct pools of cell signaling. The methodology used demonstrates, for the first time that in silico docking simulations can be used to explore functional aspects of elephant p53 isoforms. Our observations elucidate structural and mechanistic aspects of p53 regulation, facilitate understanding of complex cell signaling, and suggest testable hypotheses of p53 evolution referencing Peto’s Paradox.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk , ul. Kładki 24, 80-822 Gdansk , Poland
| | - Mia-Lyn Jooste
- Institute of Genetics and Cancer, University of Edinburgh , Edinburgh EH4 2XR, UK
| | - Ted Hupp
- Institute of Genetics and Cancer, University of Edinburgh , Edinburgh EH4 2XR, UK
| | - Robin Fåhraeus
- International Centre for Cancer Vaccine Science, University of Gdansk , ul. Kładki 24, 80-822 Gdansk , Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire , Université Paris 7, Hôpital St. Louis, F-75010 Paris , France
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute , 65653 Brno , Czech Republic
- Department of Medical Biosciences, Umeå University , 90185 Umeå , Sweden
| | - Borek Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute , 65653 Brno , Czech Republic
| | - Fritz Vollrath
- Department of Zoology, Zoology Research and Administration Building, University of Oxford , Oxford, UK
- Save the Elephants Marula Manor , Marula Lane, Karen P.O. Box 54667. Nairobi 00200. Kenya Office: +254 720 441 178
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk , ul. Kładki 24, 80-822 Gdansk , Poland
| | - Konstantinos Karakostis
- Inserm UMRS1131, Institut de Génétique Moléculaire , Université Paris 7, Hôpital St. Louis, F-75010 Paris , France
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona , 08193 Bellaterra (Barcelona) , Spain
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20
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Nunney L. Cancer suppression and the evolution of multiple retrogene copies of TP53 in elephants: a re‐evaluation. Evol Appl 2022; 15:891-901. [PMID: 35603034 PMCID: PMC9108310 DOI: 10.1111/eva.13383] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/27/2022] [Accepted: 04/02/2022] [Indexed: 11/28/2022] Open
Abstract
Evolving to become bigger and/or longer lived should increase cancer susceptibility, but this predicted increase is not observed, a contradiction named Peto's paradox. A solution is that cancer suppression evolves to minimize cancer susceptibility, and the discovery of 19 retrogene (RTG) copies of the tumor suppressor gene TP53 in the African elephant (Loxodonta africana) is increasingly cited as a classic example of such adaptive suppression. However, classic examples need rigorous evaluation and an alternative hypothesis is that the RTGs spread by genetic drift. This study shows that before its duplication, the ancestral elephant RTG was already truncated from 390 amino acids to 157 by a frameshift mutation, and that 14 of the 19 copies are now truncated to ≤88 amino acids. There was no compelling evidence of either positive or negative selection acting on these 88 codons, and the pattern of RTG accumulation fits a neutral model with a duplication rate of ~10−6 per generation. It is concluded that there is no evidence supporting the hypothesis that the 19 elephant RTGs spread to fixation by selection; instead, the evidence indicates that these RTGs accumulated primarily by segmental duplication and drift. It is shown that the evolutionary multistage model of carcinogenesis (EMMC) predicts the recruitment of 1–2 independently acting tumor suppressor genes to suppress the increased cancer risk in elephants, so it is possible that one or a few RTGs may have been favored by selection resulting in the known enhanced sensitivity of elephant cells to DNA damage. However, the analysis does not provide any support for either a direct (via conserved TP53 activity) or indirect (via supporting canonical TP53 function) role of the RTGs sequences, so that the presence of multiple copies of TP53 retrogenes in elephants needs to be further justified before being used as a classic example of tumor suppression in large‐bodied animals.
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Affiliation(s)
- Leonard Nunney
- Department of Evolution, Ecology, and Organismal Biology University of California Riverside 900 University Avenue Riverside CA 92521 USA
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21
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Nery MF, Rennó M, Picorelli A, Ramos E. A phylogenetic review of cancer resistance highlights evolutionary solutions to Peto’s Paradox. Genet Mol Biol 2022; 45:e20220133. [DOI: 10.1590/1678-4685-gmb-2022-0133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/03/2022] [Indexed: 12/12/2022] Open
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22
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Vincze O, Colchero F, Lemaître JF, Conde DA, Pavard S, Bieuville M, Urrutia AO, Ujvari B, Boddy AM, Maley CC, Thomas F, Giraudeau M. Cancer risk across mammals. Nature 2022; 601:263-267. [PMID: 34937938 PMCID: PMC8755536 DOI: 10.1038/s41586-021-04224-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 11/09/2021] [Indexed: 12/13/2022]
Abstract
Cancer is a ubiquitous disease of metazoans, predicted to disproportionately affect larger, long-lived organisms owing to their greater number of cell divisions, and thus increased probability of somatic mutations1,2. While elevated cancer risk with larger body size and/or longevity has been documented within species3-5, Peto's paradox indicates the apparent lack of such an association among taxa6. Yet, unequivocal empirical evidence for Peto's paradox is lacking, stemming from the difficulty of estimating cancer risk in non-model species. Here we build and analyse a database on cancer-related mortality using data on adult zoo mammals (110,148 individuals, 191 species) and map age-controlled cancer mortality to the mammalian tree of life. We demonstrate the universality and high frequency of oncogenic phenomena in mammals and reveal substantial differences in cancer mortality across major mammalian orders. We show that the phylogenetic distribution of cancer mortality is associated with diet, with carnivorous mammals (especially mammal-consuming ones) facing the highest cancer-related mortality. Moreover, we provide unequivocal evidence for the body size and longevity components of Peto's paradox by showing that cancer mortality risk is largely independent of both body mass and adult life expectancy across species. These results highlight the key role of life-history evolution in shaping cancer resistance and provide major advancements in the quest for natural anticancer defences.
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Affiliation(s)
- Orsolya Vincze
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France.
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS-La Rochelle Université, La Rochelle, France.
- Institute of Aquatic Ecology, Centre for Ecological Research, Debrecen, Hungary.
- Evolutionary Ecology Group, Hungarian Department of Biology and Ecology, Babeş-Bolyai University, Cluj-Napoca, Romania.
| | - Fernando Colchero
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
- Interdisciplinary Centre on Population Dynamics, University of Southern Denmark, Odense, Denmark
- Species360 Conservation Science Alliance, Bloomington, MN, USA
| | - Jean-Francois Lemaître
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1; CNRS,UMR5558, Villeurbanne, France
| | - Dalia A Conde
- Interdisciplinary Centre on Population Dynamics, University of Southern Denmark, Odense, Denmark
- Species360 Conservation Science Alliance, Bloomington, MN, USA
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Samuel Pavard
- Eco-Anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université de Paris, Musée de l'Homme, Paris, France
| | - Margaux Bieuville
- Eco-Anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université de Paris, Musée de l'Homme, Paris, France
| | - Araxi O Urrutia
- Instituto de Ecologia, UNAM, Mexico City, Mexico
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Amy M Boddy
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Carlo C Maley
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Frédéric Thomas
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France
| | - Mathieu Giraudeau
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS-La Rochelle Université, La Rochelle, France
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23
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Filice DCS. CANCER AND EVOLUTION: A STORY OF CHEATERS AND REBELS. Evolution 2021; 75:2317-2320. [PMID: 37139875 DOI: 10.1111/evo.14311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022]
Affiliation(s)
- David C. S. Filice
- Lyman Briggs College Michigan State University East Lansing Michigan 48825
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24
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Chusyd DE, Ackermans NL, Austad SN, Hof PR, Mielke MM, Sherwood CC, Allison DB. Aging: What We Can Learn From Elephants. Front Aging 2021; 2:726714. [PMID: 35822016 PMCID: PMC9261397 DOI: 10.3389/fragi.2021.726714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/03/2021] [Indexed: 11/13/2022]
Abstract
Elephants are large-brained, social mammals with a long lifespan. Studies of elephants can provide insight into the aging process, which may be relevant to understanding diseases that affect elderly humans because of their shared characteristics that have arisen through independent evolution. Elephants become sexually mature at 12 to 14 years of age and are known to live into, and past, their 7th decade of life. Because of their relatively long lifespans, elephants may have evolved mechanisms to counter age-associated morbidities, such as cancer and cognitive decline. Elephants rely heavily on their memory, and engage in multiple levels of competitive and collaborative relationships because they live in a fission-fusion system. Female matrilineal relatives and dependent offspring form tight family units led by an older-aged matriarch, who serves as the primary repository for social and ecological knowledge in the herd. Similar to humans, elephants demonstrate a dependence on social bonds, memory, and cognition to navigate their environment, behaviors that might be associated with specializations of brain anatomy. Compared with other mammals, the elephant hippocampus is proportionally smaller, whereas the temporal lobe is disproportionately large and expands laterally. The elephant cerebellum is also relatively enlarged, and the cerebral cortex is highly convoluted with numerous gyral folds, more than in humans. Last, an interesting characteristic unique to elephants is the presence of at least 20 copies of the TP53 tumor suppressor gene. Humans have only a single copy. TP53 encodes for the p53 protein, which is known to orchestrate cellular response to DNA damage. The effects of these multiple copies of TP53 are still being investigated, but it may be to protect elephants against multiple age-related diseases. For these reasons, among others, studies of elephants would be highly informative for aging research. Elephants present an underappreciated opportunity to explore further common principles of aging in a large-brained mammal with extended longevity. Such research can contribute to contextualizing our knowledge of age-associated morbidities in humans.
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Affiliation(s)
- Daniella E. Chusyd
- Department of Epidemiology and Biostatistics, Indiana University-Bloomington, Bloomington, IN, United States
- *Correspondence: Daniella E. Chusyd,
| | - Nicole L. Ackermans
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Center for Anatomy and Functional Morphology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Steven N. Austad
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Nathan Shock Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Patrick R. Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Michelle M. Mielke
- Division of Epidemiology, Department of Quantitative Health Sciences and Department of Neurology, Mayo Clinic, Rochester, MN, United States
| | - Chet C. Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, DC, United States
| | - David B. Allison
- Department of Epidemiology and Biostatistics, Indiana University-Bloomington, Bloomington, IN, United States
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