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Ní Leathlobhair M, Lenski RE. Population genetics of clonally transmissible cancers. Nat Ecol Evol 2022; 6:1077-1089. [PMID: 35879542 DOI: 10.1038/s41559-022-01790-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 11/08/2022]
Abstract
Populations of cancer cells are subject to the same core evolutionary processes as asexually reproducing, unicellular organisms. Transmissible cancers are particularly striking examples of these processes. These unusual cancers are clonal lineages that can spread through populations via physical transfer of living cancer cells from one host individual to another, and they have achieved long-term success in the colonization of at least eight different host species. Population genetic theory provides a useful framework for understanding the shift from a multicellular sexual animal into a unicellular asexual clone and its long-term effects on the genomes of these cancers. In this Review, we consider recent findings from transmissible cancer research with the goals of developing an evolutionarily informed perspective on transmissible cancers, examining possible implications for their long-term fate and identifying areas for future research on these exceptional lineages.
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Affiliation(s)
- Máire Ní Leathlobhair
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland.
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
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2
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Woods GM, Fox S, Flies AS, Tovar CD, Jones M, Hamede R, Pemberton D, Lyons AB, Bettiol SS. Two Decades of the Impact of Tasmanian Devil Facial Tumor Disease. Integr Comp Biol 2019; 58:1043-1054. [PMID: 30252058 DOI: 10.1093/icb/icy118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The Tasmanian devil, a marsupial carnivore, has been restricted to the island state of Tasmania since its extinction on the Australian mainland about 3000 years ago. In the past two decades, this species has experienced severe population decline due to the emergence of devil facial tumor disease (DFTD), a transmissible cancer. During these 20 years, scientists have puzzled over the immunological and evolutionary responses by the Tasmanian devil to this transmissible cancer. Targeted strategies in population management and disease control have been developed as well as comparative processes to identify variation in tumor and host genetics. A multi-disciplinary approach with multi-institutional teams has produced considerable advances over the last decade. This has led to a greater understanding of the molecular pathogenesis and genomic classification of this cancer. New and promising developments in the Tasmanian devil's story include evidence that most immunized, and some wild devils, can produce an immune response to DFTD. Furthermore, epidemiology combined with genomic studies suggest a rapid evolution to the disease and that DFTD will become an endemic disease. Since 1998 there have been more than 350 publications, distributed over 37 Web of Science categories. A unique endemic island species has become an international curiosity that is in the spotlight of integrative and comparative biology research.
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Affiliation(s)
- Gregory M Woods
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Samantha Fox
- Save the Tasmanian Devil Program, DPIPWE, GPO Box 44, Hobart, Tasmania 7001, Australia.,Toledo Zoo, 2605 Broadway, Toledo, OH 43609, USA
| | - Andrew S Flies
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Cesar D Tovar
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7005, Australia.,School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Menna Jones
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - David Pemberton
- Save the Tasmanian Devil Program, DPIPWE, GPO Box 44, Hobart, Tasmania 7001, Australia
| | - A Bruce Lyons
- School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Silvana S Bettiol
- School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Tasmania 7005, Australia
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3
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Fernández Robledo JA, Yadavalli R, Allam B, Pales Espinosa E, Gerdol M, Greco S, Stevick RJ, Gómez-Chiarri M, Zhang Y, Heil CA, Tracy AN, Bishop-Bailey D, Metzger MJ. From the raw bar to the bench: Bivalves as models for human health. Dev Comp Immunol 2019; 92:260-282. [PMID: 30503358 PMCID: PMC6511260 DOI: 10.1016/j.dci.2018.11.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/09/2018] [Accepted: 11/24/2018] [Indexed: 05/05/2023]
Abstract
Bivalves, from raw oysters to steamed clams, are popular choices among seafood lovers and once limited to the coastal areas. The rapid growth of the aquaculture industry and improvement in the preservation and transport of seafood have enabled them to be readily available anywhere in the world. Over the years, oysters, mussels, scallops, and clams have been the focus of research for improving the production, managing resources, and investigating basic biological and ecological questions. During this decade, an impressive amount of information using high-throughput genomic, transcriptomic and proteomic technologies has been produced in various classes of the Mollusca group, and it is anticipated that basic and applied research will significantly benefit from this resource. One aspect that is also taking momentum is the use of bivalves as a model system for human health. In this review, we highlight some of the aspects of the biology of bivalves that have direct implications in human health including the shell formation, stem cells and cell differentiation, the ability to fight opportunistic and specific pathogens in the absence of adaptive immunity, as source of alternative drugs, mucosal immunity and, microbiome turnover, toxicology, and cancer research. There is still a long way to go; however, the next time you order a dozen oysters at your favorite raw bar, think about a tasty model organism that will not only please your palate but also help unlock multiple aspects of molluscan biology and improve human health.
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Affiliation(s)
| | | | - Bassem Allam
- Stony Brook University, School of Marine and Atmospheric Sciences, Stony Brook, NY, 11794, USA
| | | | - Marco Gerdol
- University of Trieste, Department of Life Sciences, 34127, Trieste, Italy
| | - Samuele Greco
- University of Trieste, Department of Life Sciences, 34127, Trieste, Italy
| | - Rebecca J Stevick
- University of Rhode Island, Graduate School of Oceanography, Narragansett, RI, 02882, USA
| | - Marta Gómez-Chiarri
- University of Rhode Island, Department of Fisheries, Animal and Veterinary Science, Kingston, RI, 02881, USA
| | - Ying Zhang
- University of Rhode Island, Department of Cell and Molecular Biology, Kingston, RI, 02881, USA
| | - Cynthia A Heil
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Adrienne N Tracy
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA; Colby College, Waterville, 4,000 Mayflower Hill Dr, ME, 04901, USA
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Abstract
Making my career in Australia exposed me to the tyranny of distance, but it gave me opportunities to study our unique native fauna. Distantly related animal species present genetic variation that we can use to explore the most fundamental biological structures and processes. I have compared chromosomes and genomes of kangaroos and platypus, tiger snakes and emus, devils (Tasmanian) and dragons (lizards). I particularly love the challenges posed by sex chromosomes, which, apart from determining sex, provide stunning examples of epigenetic control and break all the evolutionary rules that we currently understand. Here I describe some of those amazing animals and the insights on genome structure, function, and evolution they have afforded us. I also describe my sometimes-random walk in science and the factors and people who influenced my direction. Being a woman in science is still not easy, and I hope others will find encouragement and empathy in my story.
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Affiliation(s)
- Jennifer A. Marshall Graves
- School of Life Science, La Trobe University, Melbourne, Victoria 3086, Australia
- Australia Institute of Applied Ecology, University of Canberra, ACT 2617, Australia
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Whilde J, Martindale MQ, Duffy DJ. Precision wildlife medicine: applications of the human-centred precision medicine revolution to species conservation. Glob Chang Biol 2017; 23:1792-1805. [PMID: 27809394 DOI: 10.1111/gcb.13548] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 09/21/2016] [Indexed: 06/06/2023]
Abstract
The current species extinction crisis is being exacerbated by an increased rate of emergence of epizootic disease. Human-induced factors including habitat degradation, loss of biodiversity and wildlife population reductions resulting in reduced genetic variation are accelerating disease emergence. Novel, efficient and effective approaches are required to combat these epizootic events. Here, we present the case for the application of human precision medicine approaches to wildlife medicine in order to enhance species conservation efforts. We consider how the precision medicine revolution, coupled with the advances made in genomics, may provide a powerful and feasible approach to identifying and treating wildlife diseases in a targeted, effective and streamlined manner. A number of case studies of threatened species are presented which demonstrate the applicability of precision medicine to wildlife conservation, including sea turtles, amphibians and Tasmanian devils. These examples show how species conservation could be improved by using precision medicine techniques to determine novel treatments and management strategies for the specific medical conditions hampering efforts to restore population levels. Additionally, a precision medicine approach to wildlife health has in turn the potential to provide deeper insights into human health and the possibility of stemming and alleviating the impacts of zoonotic diseases. The integration of the currently emerging Precision Medicine Initiative with the concepts of EcoHealth (aiming for sustainable health of people, animals and ecosystems through transdisciplinary action research) and One Health (recognizing the intimate connection of humans, animal and ecosystem health and addressing a wide range of risks at the animal-human-ecosystem interface through a coordinated, collaborative, interdisciplinary approach) has great potential to deliver a deeper and broader interdisciplinary-based understanding of both wildlife and human diseases.
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Affiliation(s)
- Jenny Whilde
- The Whitney Laboratory for Marine Bioscience & Sea Turtle Hospital, University of Florida, 9505 Ocean Shore Blvd., St. Augustine, FL, 32080-8610, USA
| | - Mark Q Martindale
- The Whitney Laboratory for Marine Bioscience & Sea Turtle Hospital, University of Florida, 9505 Ocean Shore Blvd., St. Augustine, FL, 32080-8610, USA
| | - David J Duffy
- The Whitney Laboratory for Marine Bioscience & Sea Turtle Hospital, University of Florida, 9505 Ocean Shore Blvd., St. Augustine, FL, 32080-8610, USA
- Systems Biology Ireland, Science Link Building, University College Dublin, Belfield, Dublin 4, Ireland
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Irizarry KJ, Bryant D, Kalish J, Eng C, Schmidt PL, Barrett G, Barr MC. Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species. Int J Genomics 2016; 2016:2374610. [PMID: 27376076 DOI: 10.1155/2016/2374610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 12/31/2022] Open
Abstract
Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs) that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management.
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Grueber CE, Peel E, Gooley R, Belov K. Genomic insights into a contagious cancer in Tasmanian devils. Trends Genet 2015; 31:528-35. [DOI: 10.1016/j.tig.2015.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/03/2015] [Accepted: 05/04/2015] [Indexed: 02/08/2023]
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Abstract
Genomic approaches are gathering momentum in biology and emerging opportunities lie in the creative use of comparative molecular methods for revealing the processes that influence diversity of wildlife. However, few comparative genomic studies are performed with explicit and specific objectives to aid conservation of wild populations. Here I provide a brief overview of comparative genomic approaches that offer specific benefits to biodiversity conservation. Because conservation examples are few, I draw on research from other areas to demonstrate how comparing genomic data across taxa may be used to inform the characterisation of conservation units and studies of hybridisation, as well as studies that provide conservation outcomes from a better understanding of the drivers of divergence. A comparative approach can also provide valuable insight into the threatening processes that impact rare species, such as emerging diseases and their management in conservation. In addition to these opportunities, I note areas where additional research is warranted. Overall, comparing and contrasting the genomic composition of threatened and other species provide several useful tools for helping to preserve the molecular biodiversity of the global ecosystem.
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Gallus S, Hallström BM, Kumar V, Dodt WG, Janke A, Schumann GG, Nilsson MA. Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil. Mol Biol Evol 2015; 32:1268-83. [PMID: 25633377 PMCID: PMC4408412 DOI: 10.1093/molbev/msv017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The largest living carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii), is the sole survivor of a lineage originating about 12 Ma. We set out to investigate the spectrum of transposable elements found in the Tasmanian devil genome, the first high-coverage genome of an Australian marsupial. Marsupial genomes have been shown to have the highest amount of transposable elements among vertebrates. We analyzed the horizontally transmitted DNA transposons OC1 and hAT-1_MEu in the Tasmanian devil genome. OC1 is present in all carnivorous marsupials, while having a very limited distribution among the remaining Australian marsupial orders. In contrast, hAT-1_MEu is present in all Australian marsupial orders, and has so far only been identified in a few placental mammals. We screened 158 introns for phylogenetically informative retrotransposons in the order Dasyuromorphia, and found that the youngest SINE (Short INterspersed Element), WSINE1, is no longer active in the subfamily Dasyuridae. The lack of detectable WSINE1 activity in this group may be due to a retrotransposon inactivation event approximately 30 Ma. We found that the Tasmanian devil genome contains a relatively low number of continuous full-length LINE-1 (Long INterspersed Element 1, L1) retrotransposons compared with the opossum genome. Furthermore, all L1 elements in the Tasmanian devil appeared to be nonfunctional. Hidden Markov Model approaches suggested that other potential sources of functional reverse transcriptase are absent from the genome. We discuss the issues associated with assembling long, highly similar L1 copies from short read Illumina data and describe how assembly artifacts can potentially lead to erroneous conclusions.
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Affiliation(s)
- Susanne Gallus
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Björn M Hallström
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Vikas Kumar
- LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - William G Dodt
- LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Qld, Australia
| | - Axel Janke
- LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Maria A Nilsson
- LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
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Abstract
The emergence of a fatal transmissible cancer known as devil facial tumor disease (DFTD) is threatening the iconic Tasmanian devil with extinction in the wild within the next few decades. Since the first report of the disease in 1996, DFTD has spread to over 85% of the devils' distribution and dramatically reduced devil numbers. Research into DFTD has focused on gaining a deeper understanding of the disease on multiple levels, including an accurate assessment of the tissue origin of the tumor, elucidation of how the tumor evades immune detection, and determination of how the tumor is transmitted between individuals and how it is evolving as it spreads through the population. Knowledge gained from these studies has important implications for DFTD management and devil conservation.
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Affiliation(s)
- Hannah S Bender
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
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Affiliation(s)
- Jennifer A. Marshall Graves
- La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne 3186, Australia
- Research School of Biology, Australian National University, Canberra 2060, Australia;
- Department of Zoology, University of Melbourne, Melbourne 3010, Australia
| | - Marilyn B. Renfree
- Department of Zoology, University of Melbourne, Melbourne 3010, Australia
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Deakin JE. Marsupial genome sequences: providing insight into evolution and disease. Scientifica (Cairo) 2012; 2012:543176. [PMID: 24278712 PMCID: PMC3820666 DOI: 10.6064/2012/543176] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 09/26/2012] [Indexed: 05/08/2023]
Abstract
Marsupials (metatherians), with their position in vertebrate phylogeny and their unique biological features, have been studied for many years by a dedicated group of researchers, but it has only been since the sequencing of the first marsupial genome that their value has been more widely recognised. We now have genome sequences for three distantly related marsupial species (the grey short-tailed opossum, the tammar wallaby, and Tasmanian devil), with the promise of many more genomes to be sequenced in the near future, making this a particularly exciting time in marsupial genomics. The emergence of a transmissible cancer, which is obliterating the Tasmanian devil population, has increased the importance of obtaining and analysing marsupial genome sequence for understanding such diseases as well as for conservation efforts. In addition, these genome sequences have facilitated studies aimed at answering questions regarding gene and genome evolution and provided insight into the evolution of epigenetic mechanisms. Here I highlight the major advances in our understanding of evolution and disease, facilitated by marsupial genome projects, and speculate on the future contributions to be made by such sequences.
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Affiliation(s)
- Janine E. Deakin
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
- *Janine E. Deakin:
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