1
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Hogg CJ, Edwards RJ, Farquharson KA, Silver LW, Brandies P, Peel E, Escalona M, Jaya FR, Thavornkanlapachai R, Batley K, Bradford TM, Chang JK, Chen Z, Deshpande N, Dziminski M, Ewart KM, Griffith OW, Marin Gual L, Moon KL, Travouillon KJ, Waters P, Whittington CM, Wilkins MR, Helgen KM, Lo N, Ho SYW, Ruiz Herrera A, Paltridge R, Marshall Graves JA, Renfree M, Shapiro B, Ottewell K, Belov K. Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nat Ecol Evol 2024; 8:1311-1326. [PMID: 38945974 PMCID: PMC11239497 DOI: 10.1038/s41559-024-02436-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/03/2024] [Indexed: 07/02/2024]
Abstract
Ninu (greater bilby, Macrotis lagotis) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation (N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom-bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY1Y2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations.
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Affiliation(s)
- Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia.
| | - Richard J Edwards
- Minderoo OceanOmics Centre at UWA, Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Katherine A Farquharson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Luke W Silver
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Parice Brandies
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Emma Peel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Merly Escalona
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Frederick R Jaya
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Rujiporn Thavornkanlapachai
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kimberley Batley
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Tessa M Bradford
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - J King Chang
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | | | - Nandan Deshpande
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Ramaciotti Centre for Genomics and School of Biotechnology and Biomolecular Science, UNSW, Sydney, New South Wales, Australia
| | - Martin Dziminski
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Oliver W Griffith
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Laia Marin Gual
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Katherine L Moon
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kenny J Travouillon
- Collections and Research, Western Australian Museum, Welshpool, Western Australia, Australia
| | - Paul Waters
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Camilla M Whittington
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Ramaciotti Centre for Genomics and School of Biotechnology and Biomolecular Science, UNSW, Sydney, New South Wales, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Aurora Ruiz Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Rachel Paltridge
- Indigenous Desert Alliance, Alice Springs, Northern Territory, Australia
| | | | - Marilyn Renfree
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kym Ottewell
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
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2
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Bramwell G, DeGregori J, Thomas F, Ujvari B. Transmissible cancers, the genomes that do not melt down. Evolution 2024; 78:1205-1211. [PMID: 38656785 DOI: 10.1093/evolut/qpae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 04/08/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
Evolutionary theory predicts that the accumulation of deleterious mutations in asexually reproducing organisms should lead to genomic decay. Clonally reproducing cell lines, i.e., transmissible cancers, when cells are transmitted as allografts/xenografts, break these rules and survive for centuries and millennia. The currently known 11 transmissible cancer lineages occur in dogs (canine venereal tumour disease), in Tasmanian devils (devil facial tumor diseases, DFT1 and DFT2), and in bivalves (bivalve transmissible neoplasia). Despite the mutation loads of these cell lines being much higher than observed in human cancers, they have not been eliminated in space and time. Here, we provide potential explanations for how these fascinating cell lines may have overcome the fitness decline due to the progressive accumulation of deleterious mutations and propose that the high mutation load may carry an indirect positive fitness outcome. We offer ideas on how these host-pathogen systems could be used to answer outstanding questions in evolutionary biology. The recent studies on the evolution of these clonal pathogens reveal key mechanistic insight into transmissible cancer genomes, information that is essential for future studies investigating how these contagious cancer cell lines can repeatedly evade immune recognition, evolve, and survive in the landscape of highly diverse hosts.
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Affiliation(s)
- Georgina Bramwell
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Waurn Ponds, VIC 3216, Australia
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Frédéric Thomas
- CREEC, UMR IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France
| | - Beata Ujvari
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Waurn Ponds, VIC 3216, Australia
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3
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Sachslehner AP, Surbek M, Holthaus KB, Steinbinder J, Golabi B, Hess C, Eckhart L. The Evolution of Transglutaminases Underlies the Origin and Loss of Cornified Skin Appendages in Vertebrates. Mol Biol Evol 2024; 41:msae100. [PMID: 38781495 DOI: 10.1093/molbev/msae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/11/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024] Open
Abstract
Transglutaminases (TGMs) cross-link proteins by introducing covalent bonds between glutamine and lysine residues. These cross-links are essential for epithelial cornification which enables tetrapods to live on land. Here, we investigated which evolutionary adaptations of vertebrates were associated with specific changes in the family of TGM genes. We determined the catalog of TGMs in the main clades of vertebrates, performed a comprehensive phylogenetic analysis of TGMs, and localized the distribution of selected TGMs in tissues. Our data suggest that TGM1 is the phylogenetically oldest epithelial TGM, with orthologs being expressed in the cornified teeth of the lamprey, a basal vertebrate. Gene duplications led to the origin of TGM10 in stem vertebrates, the origin of TGM2 in jawed vertebrates, and an increasing number of epithelium-associated TGM genes in the lineage leading to terrestrial vertebrates. TGM9 is expressed in the epithelial egg tooth, and its evolutionary origin in stem amniotes coincided with the evolution of embryonic development in eggs that are surrounded by a protective shell. Conversely, viviparous mammals have lost both the epithelial egg tooth and TGM9. TGM3 and TGM6 evolved as regulators of cornification in hair follicles and underwent pseudogenization upon the evolutionary loss of hair in cetaceans. Taken together, this study reveals the gain and loss of vertebrate TGM genes in association with the evolution of cornified skin appendages and suggests an important role of TGM9 in the evolution of amniotes.
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Affiliation(s)
| | - Marta Surbek
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Julia Steinbinder
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Bahar Golabi
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Claudia Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
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4
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Hartley GA, Frankenberg SR, Robinson NM, MacDonald AJ, Hamede RK, Burridge CP, Jones ME, Faulkner T, Shute H, Rose K, Brewster R, O'Neill RJ, Renfree MB, Pask AJ, Feigin CY. Genome of the endangered eastern quoll (Dasyurus viverrinus) reveals signatures of historical decline and pelage color evolution. Commun Biol 2024; 7:636. [PMID: 38796620 PMCID: PMC11128018 DOI: 10.1038/s42003-024-06251-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/26/2024] [Indexed: 05/28/2024] Open
Abstract
The eastern quoll (Dasyurus viverrinus) is an endangered marsupial native to Australia. Since the extirpation of its mainland populations in the 20th century, wild eastern quolls have been restricted to two islands at the southern end of their historical range. Eastern quolls are the subject of captive breeding programs and attempts have been made to re-establish a population in mainland Australia. However, few resources currently exist to guide the genetic management of this species. Here, we generated a reference genome for the eastern quoll with gene annotations supported by multi-tissue transcriptomes. Our assembly is among the most complete marsupial genomes currently available. Using this assembly, we infer the species' demographic history, identifying potential evidence of a long-term decline beginning in the late Pleistocene. Finally, we identify a deletion at the ASIP locus that likely underpins pelage color differences between the eastern quoll and the closely related Tasmanian devil (Sarcophilus harrisii).
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Affiliation(s)
- Gabrielle A Hartley
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
| | | | - Natasha M Robinson
- Fenner School of Environment & Society, Australian National University, Canberra, ACT, 2601, Australia
| | - Anna J MacDonald
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, TAS, 7050, Australia
| | - Rodrigo K Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia
| | | | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Tim Faulkner
- Australian Reptile Park & Aussie Ark, Somersby, NSW, 2250, Australia
| | - Hayley Shute
- Australian Reptile Park & Aussie Ark, Somersby, NSW, 2250, Australia
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, NSW, 2088, Australia
| | - Rob Brewster
- WWF-Australia, PO Box 528, Sydney, NSW, 2001, Australia
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Andrew J Pask
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Sciences, Museums Victoria, Carlton, VIC, 3053, Australia
| | - Charles Y Feigin
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
- Department of Environment and Genetics, La Trobe University, Bundoora, VIC, 3086, Australia.
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5
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Hogg CJ. Translating genomic advances into biodiversity conservation. Nat Rev Genet 2024; 25:362-373. [PMID: 38012268 DOI: 10.1038/s41576-023-00671-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 11/29/2023]
Abstract
A key action of the new Global Biodiversity Framework is the maintenance of genetic diversity in all species to safeguard their adaptive potential. To achieve this goal, a translational mindset, which aims to convert results of basic research into direct practical benefits, needs to be applied to biodiversity conservation. Despite much discussion on the value of genomics to conservation, a disconnect between those generating genomic resources and those applying it to biodiversity management remains. As global efforts to generate reference genomes for non-model species increase, investment into practical biodiversity applications is critically important. Applications such as understanding population and multispecies diversity and longitudinal monitoring need support alongside education for policymakers on integrating the data into evidence-based decisions. Without such investment, the opportunity to revolutionize global biodiversity conservation using genomics will not be fully realized.
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Affiliation(s)
- Carolyn J Hogg
- School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
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6
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Chaganti T, Tsai CY, Juang YP, Abdelalim M, Cernak T. Medicinal Chemistry Gone Wild. J Med Chem 2024. [PMID: 38662285 DOI: 10.1021/acs.jmedchem.3c02334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Earth is currently experiencing a mass extinction event. The flora and fauna of our planet are experiencing mass die-offs from a multitude of factors, with wildlife disease emerging as one parameter where medicinal chemists are equipped to intervene. While contemporary medicinal chemistry focuses on human health, many traditional pharmaceutical companies have historic roots in human health, animal health, and plant health. This trifecta of health sciences perfectly maps to the current field of One Health, which recognizes that optimal health outcomes can only be achieved through the health of humans, plants, animals, and their shared environments. This Perspective imagines a world where state-of-the-art medicinal chemistry tactics are used to prevent the extinction of endangered species and points to preliminary work in the emerging area of conservation medicine.
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Affiliation(s)
- Tesko Chaganti
- Canton High School, Canton, Michigan 48187, United States
| | - Chun-Yi Tsai
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yu-Pu Juang
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mohamed Abdelalim
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tim Cernak
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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7
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Stammnitz MR, Gori K, Murchison EP. No evidence that a transmissible cancer has shifted from emergence to endemism in Tasmanian devils. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231875. [PMID: 38633353 PMCID: PMC11022658 DOI: 10.1098/rsos.231875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 04/19/2024]
Abstract
Tasmanian devils are endangered by a transmissible cancer known as Tasmanian devil facial tumour 1 (DFT1). A 2020 study by Patton et al. (Science 370, eabb9772 (doi:10.1126/science.abb9772)) used genome data from DFT1 tumours to produce a dated phylogenetic tree for this transmissible cancer lineage, and thence, using phylodynamics models, to estimate its epidemiological parameters and predict its future trajectory. It concluded that the effective reproduction number for DFT1 had declined to a value of one, and that the disease had shifted from emergence to endemism. We show that the study is based on erroneous mutation calls and flawed methodology, and that its conclusions cannot be substantiated.
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Affiliation(s)
- Maximilian R. Stammnitz
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Kevin Gori
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Elizabeth P. Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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8
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Gallinson DG, Kozakiewicz CP, Rautsaw RM, Beer MA, Ruiz-Aravena M, Comte S, Hamilton DG, Kerlin DH, McCallum HI, Hamede R, Jones ME, Storfer A, McMinds R, Margres MJ. Intergenomic signatures of coevolution between Tasmanian devils and an infectious cancer. Proc Natl Acad Sci U S A 2024; 121:e2307780121. [PMID: 38466855 PMCID: PMC10962979 DOI: 10.1073/pnas.2307780121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/17/2024] [Indexed: 03/13/2024] Open
Abstract
Coevolution is common and frequently governs host-pathogen interaction outcomes. Phenotypes underlying these interactions often manifest as the combined products of the genomes of interacting species, yet traditional quantitative trait mapping approaches ignore these intergenomic interactions. Devil facial tumor disease (DFTD), an infectious cancer afflicting Tasmanian devils (Sarcophilus harrisii), has decimated devil populations due to universal host susceptibility and a fatality rate approaching 100%. Here, we used a recently developed joint genome-wide association study (i.e., co-GWAS) approach, 15 y of mark-recapture data, and 960 genomes to identify intergenomic signatures of coevolution between devils and DFTD. Using a traditional GWA approach, we found that both devil and DFTD genomes explained a substantial proportion of variance in how quickly susceptible devils became infected, although genomic architectures differed across devils and DFTD; the devil genome had fewer loci of large effect whereas the DFTD genome had a more polygenic architecture. Using a co-GWA approach, devil-DFTD intergenomic interactions explained ~3× more variation in how quickly susceptible devils became infected than either genome alone, and the top genotype-by-genotype interactions were significantly enriched for cancer genes and signatures of selection. A devil regulatory mutation was associated with differential expression of a candidate cancer gene and showed putative allele matching effects with two DFTD coding sequence variants. Our results highlight the need to account for intergenomic interactions when investigating host-pathogen (co)evolution and emphasize the importance of such interactions when considering devil management strategies.
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Affiliation(s)
- Dylan G. Gallinson
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
- College of Public Health, University of South Florida, Tampa, FL33620
| | - Christopher P. Kozakiewicz
- School of Biological Sciences, Washington State University, Pullman, WA99163
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI49060
| | - Rhett M. Rautsaw
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
- School of Biological Sciences, Washington State University, Pullman, WA99163
| | - Marc A. Beer
- School of Biological Sciences, Washington State University, Pullman, WA99163
| | - Manuel Ruiz-Aravena
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY14853
| | - Sebastien Comte
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
- New South Wales Department of Primary Industries, Vertebrate Pest Research Unit, Orange, NSW2800, Australia
| | - David G. Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
| | - Douglas H. Kerlin
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD4111, Australia
| | - Hamish I. McCallum
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD4111, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
- CANECEV Centre de Recherches Ecologiques et Evolutives sur le Cancer, Montpellier34394, France
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA99163
| | - Ryan McMinds
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
- College of Public Health, University of South Florida, Tampa, FL33620
| | - Mark J. Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
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9
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Raven N, Klaassen M, Madsen T, Jones M, Hamilton DG, Ruiz-Aravena M, Thomas F, Hamede RK, Ujvari B. Complex associations between cancer progression and immune gene expression reveals early influence of transmissible cancer on Tasmanian devils. Front Immunol 2024; 15:1286352. [PMID: 38515744 PMCID: PMC10954821 DOI: 10.3389/fimmu.2024.1286352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/29/2024] [Indexed: 03/23/2024] Open
Abstract
The world's largest extant carnivorous marsupial, the Tasmanian devil, is challenged by Devil Facial Tumor Disease (DFTD), a fatal, clonally transmitted cancer. In two decades, DFTD has spread across 95% of the species distributional range. A previous study has shown that factors such as season, geographic location, and infection with DFTD can impact the expression of immune genes in Tasmanian devils. To date, no study has investigated within-individual immune gene expression changes prior to and throughout the course of DFTD infection. To explore possible changes in immune response, we investigated four locations across Tasmania that differed in DFTD exposure history, ranging between 2 and >30 years. Our study demonstrated considerable complexity in the immune responses to DFTD. The same factors (sex, age, season, location and DFTD infection) affected immune gene expression both across and within devils, although seasonal and location specific variations were diminished in DFTD affected devils. We also found that expression of both adaptive and innate immune genes starts to alter early in DFTD infection and continues to change as DFTD progresses. A novel finding was that the lower expression of immune genes MHC-II, NKG2D and CD8 may predict susceptibility to earlier DFTD infection. A case study of a single devil with regressed tumor showed opposite/contrasting immune gene expression patterns compared to the general trends observed across devils with DFTD infection. Our study highlights the complexity of DFTD's interactions with the host immune system and the need for long-term studies to fully understand how DFTD alters the evolutionary trajectory of devil immunity.
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Affiliation(s)
- Nynke Raven
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, Geelong, VIC, Australia
| | - Marcel Klaassen
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, Geelong, VIC, Australia
| | - Thomas Madsen
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, Geelong, VIC, Australia
| | - Menna Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - David G. Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Manuel Ruiz-Aravena
- Mississippi State University, Forest & Wildlife Research Center (FWRC)-Wildlife, Fisheries & Aquaculture, Starkville, MS, United States
| | - Frederic Thomas
- CREEC/CANECEV, CREES-MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
| | - Rodrigo K. Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Beata Ujvari
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, Geelong, VIC, Australia
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10
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Gérard A, Owen RS, Dujon AM, Roche B, Hamede R, Thomas F, Ujvari B, Siddle HV. In vitro competition between two transmissible cancers and potential implications for their host, the Tasmanian devil. Evol Appl 2024; 17:e13670. [PMID: 38468711 PMCID: PMC10925828 DOI: 10.1111/eva.13670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/02/2024] [Accepted: 02/09/2024] [Indexed: 03/13/2024] Open
Abstract
Since the emergence of a transmissible cancer, devil facial tumour disease (DFT1), in the 1980s, wild Tasmanian devil populations have been in decline. In 2016, a second, independently evolved transmissible cancer (DFT2) was discovered raising concerns for survival of the host species. Here, we applied experimental and modelling frameworks to examine competition dynamics between the two transmissible cancers in vitro. Using representative cell lines for DFT1 and DFT2, we have found that in monoculture, DFT2 grows twice as fast as DFT1 but reaches lower maximum cell densities. Using co-cultures, we demonstrate that DFT2 outcompetes DFT1: the number of DFT1 cells decreasing over time, never reaching exponential growth. This phenomenon could not be replicated when cells were grown separated by a semi-permeable membrane, consistent with exertion of mechanical stress on DFT1 cells by DFT2. A logistic model and a Lotka-Volterra competition model were used to interrogate monoculture and co-culture growth curves, respectively, suggesting DFT2 is a better competitor than DFT1, but also showing that competition outcomes might depend on the initial number of cells, at least in the laboratory. We provide theories how the in vitro results could be translated to observations in the wild and propose that these results may indicate that although DFT2 is currently in a smaller geographic area than DFT1, it could have the potential to outcompete DFT1. Furthermore, we provide a framework for improving the parameterization of epidemiological models applied to these cancer lineages, which will inform future disease management.
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Affiliation(s)
- Anne‐Lise Gérard
- School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
- CREEC/MIVEGEC, CNRS, IRDUniversité de MontpellierMontpellierFrance
| | - Rachel S. Owen
- School of Biological SciencesUniversity of SouthamptonSouthamptonUK
- Institute for Life SciencesUniversity of SouthamptonSouthamptonUK
- The Roslin InstituteThe University of EdinburghEdinburghUK
| | - Antoine M. Dujon
- School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
| | - Benjamin Roche
- CREEC/MIVEGEC, CNRS, IRDUniversité de MontpellierMontpellierFrance
| | - Rodrigo Hamede
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Frédéric Thomas
- CREEC/MIVEGEC, CNRS, IRDUniversité de MontpellierMontpellierFrance
| | - Beata Ujvari
- School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
| | - Hannah V. Siddle
- School of Biological SciencesUniversity of SouthamptonSouthamptonUK
- Institute for Life SciencesUniversity of SouthamptonSouthamptonUK
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11
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The devil is in the detail. Nat Ecol Evol 2024; 8:177-178. [PMID: 38337065 DOI: 10.1038/s41559-024-02340-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
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12
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Beer MA, Proft KM, Veillet A, Kozakiewicz CP, Hamilton DG, Hamede R, McCallum H, Hohenlohe PA, Burridge CP, Margres MJ, Jones ME, Storfer A. Disease-driven top predator decline affects mesopredator population genomic structure. Nat Ecol Evol 2024; 8:293-303. [PMID: 38191839 DOI: 10.1038/s41559-023-02265-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/02/2023] [Indexed: 01/10/2024]
Abstract
Top predator declines are pervasive and often have dramatic effects on ecological communities via changes in food web dynamics, but their evolutionary consequences are virtually unknown. Tasmania's top terrestrial predator, the Tasmanian devil, is declining due to a lethal transmissible cancer. Spotted-tailed quolls benefit via mesopredator release, and they alter their behaviour and resource use concomitant with devil declines and increased disease duration. Here, using a landscape community genomics framework to identify environmental drivers of population genomic structure and signatures of selection, we show that these biotic factors are consistently among the top variables explaining genomic structure of the quoll. Landscape resistance negatively correlates with devil density, suggesting that devil declines will increase quoll genetic subdivision over time, despite no change in quoll densities detected by camera trap studies. Devil density also contributes to signatures of selection in the quoll genome, including genes associated with muscle development and locomotion. Our results provide some of the first evidence of the evolutionary impacts of competition between a top predator and a mesopredator species in the context of a trophic cascade. As top predator declines are increasing globally, our framework can serve as a model for future studies of evolutionary impacts of altered ecological interactions.
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Affiliation(s)
- Marc A Beer
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Kirstin M Proft
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Anne Veillet
- Hilo Core Genomics Facility, University of Hawaii at Hilo, Hilo, HI, USA
| | - Christopher P Kozakiewicz
- Department of Integrative Biology, Michigan State University, W.K. Kellogg Biological Station, Hickory Corners, MI, USA
| | - David G Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le Cancer, Montpellier, France
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | | | - Mark J Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, USA.
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13
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Steinbinder J, Sachslehner AP, Holthaus KB, Eckhart L. Comparative genomics of monotremes provides insights into the early evolution of mammalian epidermal differentiation genes. Sci Rep 2024; 14:1437. [PMID: 38228724 PMCID: PMC10791643 DOI: 10.1038/s41598-024-51926-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/11/2024] [Indexed: 01/18/2024] Open
Abstract
The function of the skin as a barrier against the environment depends on the differentiation of epidermal keratinocytes into highly resilient corneocytes that form the outermost skin layer. Many genes encoding structural components of corneocytes are clustered in the epidermal differentiation complex (EDC), which has been described in placental and marsupial mammals as well as non-mammalian tetrapods. Here, we analyzed the genomes of the platypus (Ornithorhynchus anatinus) and the echidna (Tachyglossus aculeatus) to determine the gene composition of the EDC in the basal clade of mammals, the monotremes. We report that mammal-specific subfamilies of EDC genes encoding small proline-rich proteins (SPRRs) and late cornified envelope proteins as well as single-copy EDC genes such as involucrin are conserved in monotremes, suggesting that they have originated in stem mammals. Monotremes have at least one gene homologous to the group of filaggrin (FLG), FLG2 and hornerin (HRNR) in placental mammals, but no clear one-to-one pairwise ortholog of either FLG, FLG2 or HRNR. Caspase-14, a keratinocyte differentiation-associated protease implicated in the processing of filaggrin, is encoded by at least 3 gene copies in the echidna. Our results reveal evolutionarily conserved and clade-specific features of the genetic regulation of epidermal differentiation in monotremes.
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Affiliation(s)
- Julia Steinbinder
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | | | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, Vienna, Austria.
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14
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Vittoria MA, Quinton RJ, Ganem NJ. Whole-genome doubling in tissues and tumors. Trends Genet 2023; 39:954-967. [PMID: 37714734 PMCID: PMC10840902 DOI: 10.1016/j.tig.2023.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/17/2023]
Abstract
The overwhelming majority of proliferating somatic human cells are diploid, and this genomic state is typically maintained across successive cell divisions. However, failures in cell division can induce a whole-genome doubling (WGD) event, in which diploid cells transition to a tetraploid state. While some WGDs are developmentally programmed to produce nonproliferative tetraploid cells with specific cellular functions, unscheduled WGDs can be catastrophic: erroneously arising tetraploid cells are ill-equipped to cope with their doubled cellular and chromosomal content and quickly become genomically unstable and tumorigenic. Deciphering the genetics that underlie the genesis, physiology, and evolution of whole-genome doubled (WGD+) cells may therefore reveal therapeutic avenues to selectively eliminate pathological WGD+ cells.
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Affiliation(s)
- Marc A Vittoria
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Ryan J Quinton
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Neil J Ganem
- Department of Medicine, Division of Hematology and Oncology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; Department of Pharmacology, Physiology, and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA.
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15
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Morrissey KA, Stammnitz MR, Murchison E, Miller RD. Comparative genomics of the T cell receptor μ locus in marsupials and monotremes. Immunogenetics 2023; 75:507-515. [PMID: 37747540 PMCID: PMC7615758 DOI: 10.1007/s00251-023-01320-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/17/2023] [Indexed: 09/26/2023]
Abstract
T cells are a primary component of the vertebrate adaptive immune system. There are three mammalian T cell lineages based on their T cell receptors (TCR). The αβ T cells and γδ T cells are ancient and found broadly in vertebrates. The more recently discovered γμ T cells are uniquely mammalian and only found in marsupials and monotremes. In this study, we compare the TCRμ locus (TRM) across the genomes of two marsupials, the gray short-tailed opossum and Tasmanian devil, and one monotreme, the platypus. These analyses revealed lineage-specific duplications, common to all non-eutherian mammals described. There is conserved synteny in the TRM loci of both marsupials but not in the monotreme. Our results are consistent with an ancestral cluster organization which was present in the last common mammalian ancestor which underwent lineage-specific duplications and divergence among the non-eutherian mammals.
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Affiliation(s)
- K A Morrissey
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico Albuquerque, Albuquerque, NM, USA
| | - M R Stammnitz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - E Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - R D Miller
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico Albuquerque, Albuquerque, NM, USA.
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16
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Hart SFM, Yonemitsu MA, Giersch RM, Garrett FES, Beal BF, Arriagada G, Davis BW, Ostrander EA, Goff SP, Metzger MJ. Centuries of genome instability and evolution in soft-shell clam, Mya arenaria, bivalve transmissible neoplasia. NATURE CANCER 2023; 4:1561-1574. [PMID: 37783804 PMCID: PMC10663159 DOI: 10.1038/s43018-023-00643-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 08/29/2023] [Indexed: 10/04/2023]
Abstract
Transmissible cancers are infectious parasitic clones that metastasize to new hosts, living past the death of the founder animal in which the cancer initiated. We investigated the evolutionary history of a cancer lineage that has spread though the soft-shell clam (Mya arenaria) population by assembling a chromosome-scale soft-shell clam reference genome and characterizing somatic mutations in transmissible cancer. We observe high mutation density, widespread copy-number gain, structural rearrangement, loss of heterozygosity, variable telomere lengths, mitochondrial genome expansion and transposable element activity, all indicative of an unstable cancer genome. We also discover a previously unreported mutational signature associated with overexpression of an error-prone polymerase and use this to estimate the lineage to be >200 years old. Our study reveals the ability for an invertebrate cancer lineage to survive for centuries while its genome continues to structurally mutate, likely contributing to the evolution of this lineage as a parasitic cancer.
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Affiliation(s)
- Samuel F M Hart
- Pacific Northwest Research Institute, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Marisa A Yonemitsu
- Pacific Northwest Research Institute, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | | | | | - Brian F Beal
- Division of Environmental and Biological Sciences, University of Maine at Machias, Machias, ME, USA
- Downeast Institute, Beals, ME, USA
| | - Gloria Arriagada
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Santiago, Chile
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University School of Veterinary Medicine, College Station, TX, USA
- Department of Small Animal Clinical Sciences, Texas A&M University School of Veterinary Medicine, College Station, TX, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Michael J Metzger
- Pacific Northwest Research Institute, Seattle, WA, USA.
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
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17
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Fulda FC. Agential autonomy and biological individuality. Evol Dev 2023; 25:353-370. [PMID: 37317487 DOI: 10.1111/ede.12450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/26/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023]
Abstract
What is a biological individual? How are biological individuals individuated? How can we tell how many individuals there are in a given assemblage of biological entities? The individuation and differentiation of biological individuals are central to the scientific understanding of living beings. I propose a novel criterion of biological individuality according to which biological individuals are autonomous agents. First, I articulate an ecological-dynamical account of natural agency according to which, agency is the gross dynamical capacity of a goal-directed system to bias its repertoire to respond to its conditions as affordances. Then, I argue that agents or agential dynamical systems can be agentially dependent on, or agentially autonomous from, other agents and that this agential dependence/autonomy can be symmetrical or asymmetrical, strong or weak. Biological individuals, I propose, are all and only those agential dynamical systems that are strongly agentially autonomous. So, to determine how many individuals there are in a given multiagent aggregate, such as multicellular organism, a colony, symbiosis, or a swarm, we first have to identify how many agential dynamical systems there are, and then what their relations of agential dependence/autonomy are. I argue that this criterion is adequate to the extent that it vindicates the paradigmatic cases, and explains why the paradigmatic cases are paradigmatic, and why the problematic cases are problematic. Finally, I argue for the importance of distinguishing between agential and causal dependence and show the relevance of agential autonomy for understanding the explanatory structure of evolutionary developmental biology.
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Affiliation(s)
- Fermin C Fulda
- Institute for the History and Philosophy of Science and Technology, Faculty of Arts & Science, University of Toronto, Toronto, Ontario, Canada
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18
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Schönbichler A, Bergthaler A. A deep dive into transmissible cancer evolution in bivalve mollusks. NATURE CANCER 2023; 4:1528-1530. [PMID: 37993693 DOI: 10.1038/s43018-023-00655-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
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19
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Bruzos AL, Santamarina M, García-Souto D, Díaz S, Rocha S, Zamora J, Lee Y, Viña-Feás A, Quail MA, Otero I, Pequeño-Valtierra A, Temes J, Rodriguez-Castro J, Aramburu L, Vidal-Capón A, Villanueva A, Costas D, Rodríguez R, Prieto T, Tomás L, Alvariño P, Alonso J, Cao A, Iglesias D, Carballal MJ, Amaral AM, Balseiro P, Calado R, El Khalfi B, Izagirre U, de Montaudouin X, Pade NG, Probert I, Ricardo F, Ruiz P, Skazina M, Smolarz K, Pasantes JJ, Villalba A, Ning Z, Ju YS, Posada D, Demeulemeester J, Baez-Ortega A, Tubio JMC. Somatic evolution of marine transmissible leukemias in the common cockle, Cerastoderma edule. NATURE CANCER 2023; 4:1575-1591. [PMID: 37783803 DOI: 10.1038/s43018-023-00641-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/23/2023] [Indexed: 10/04/2023]
Abstract
Transmissible cancers are malignant cell lineages that spread clonally between individuals. Several such cancers, termed bivalve transmissible neoplasia (BTN), induce leukemia-like disease in marine bivalves. This is the case of BTN lineages affecting the common cockle, Cerastoderma edule, which inhabits the Atlantic coasts of Europe and northwest Africa. To investigate the evolution of cockle BTN, we collected 6,854 cockles, diagnosed 390 BTN tumors, generated a reference genome and assessed genomic variation across 61 tumors. Our analyses confirmed the existence of two BTN lineages with hemocytic origins. Mitochondrial variation revealed mitochondrial capture and host co-infection events. Mutational analyses identified lineage-specific signatures, one of which likely reflects DNA alkylation. Cytogenetic and copy number analyses uncovered pervasive genomic instability, with whole-genome duplication, oncogene amplification and alkylation-repair suppression as likely drivers. Satellite DNA distributions suggested ancient clonal origins. Our study illuminates long-term cancer evolution under the sea and reveals tolerance of extreme instability in neoplastic genomes.
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Affiliation(s)
- Alicia L Bruzos
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Martín Santamarina
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Daniel García-Souto
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Wellcome Sanger Institute, Hinxton, UK
| | - Seila Díaz
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- ECOMARE, Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Sara Rocha
- CINBIO, Universidade de Vigo, Vigo, Spain
| | - Jorge Zamora
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Yunah Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Alejandro Viña-Feás
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | | | - Iago Otero
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Ana Pequeño-Valtierra
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Javier Temes
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Jorge Rodriguez-Castro
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Leyre Aramburu
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - André Vidal-Capón
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Vigo, Spain
| | - Antonio Villanueva
- Centro de Investigación Mariña (CIM-ECIMAT), Universidade de Vigo, Vigo, Spain
| | - Damián Costas
- Centro de Investigación Mariña (CIM-ECIMAT), Universidade de Vigo, Vigo, Spain
| | - Rosana Rodríguez
- Centro de Investigación Mariña (CIM-ECIMAT), Universidade de Vigo, Vigo, Spain
| | - Tamara Prieto
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- New York Genome Center, New York, NY, USA
| | - Laura Tomás
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Pilar Alvariño
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Juana Alonso
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Asunción Cao
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
| | - David Iglesias
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
| | - María J Carballal
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
| | - Ana M Amaral
- Centro de Ciencias do Mar do Algarve (CCMAR), Universidade do Algarve, Faro, Portugal
| | - Pablo Balseiro
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- NORCE AS, Bergen, Norway
| | - Ricardo Calado
- ECOMARE, Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Bouchra El Khalfi
- Laboratory of Physiopathology, Molecular Genetics & Biotechnology, Faculty of Sciences Ain Chock, Health and Biotechnology Research Centre, Hassan II University of Casablanca, Casablanca, Morocco
| | - Urtzi Izagirre
- Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plenzia-Bitzkaia, Spain
- Cell Biology in Environmental Toxicology Research Group, University of the Basque Country (UPV/EHU), Leioa-Bizkaia, Spain
| | | | - Nicolas G Pade
- European Marine Biology Resources Centre (EMBRC-ERIC), Paris, France
| | - Ian Probert
- FR2424 Station Biologique de Roscoff, Sorbonne University/CNRS, Roscoff, France
| | - Fernando Ricardo
- ECOMARE, Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Pamela Ruiz
- Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plenzia-Bitzkaia, Spain
- Cell Biology in Environmental Toxicology Research Group, University of the Basque Country (UPV/EHU), Leioa-Bizkaia, Spain
| | - Maria Skazina
- Department of Applied Ecology, St Petersburg State University, St Petersburg, Russia
| | - Katarzyna Smolarz
- Department of Marine Ecosystem Functioning, University of Gdańsk, Gdynia, Poland
| | - Juan J Pasantes
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Vigo, Spain
- Centro de Investigación Mariña (CIM-ECIMAT), Universidade de Vigo, Vigo, Spain
| | - Antonio Villalba
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plenzia-Bitzkaia, Spain
- Department of Life Sciences, Universidad de Alcalá, Alcalá de Henares, Spain
| | | | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - David Posada
- CINBIO, Universidade de Vigo, Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Jonas Demeulemeester
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- The Francis Crick Institute, London, UK
| | - Adrian Baez-Ortega
- Wellcome Sanger Institute, Hinxton, UK.
- Magdalene College, University of Cambridge, Cambridge, UK.
| | - Jose M C Tubio
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain.
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Mármol-Sánchez E, Fromm B, Oskolkov N, Pochon Z, Kalogeropoulos P, Eriksson E, Biryukova I, Sekar V, Ersmark E, Andersson B, Dalén L, Friedländer MR. Historical RNA expression profiles from the extinct Tasmanian tiger. Genome Res 2023; 33:1299-1316. [PMID: 37463752 PMCID: PMC10552650 DOI: 10.1101/gr.277663.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden;
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
| | - Bastian Fromm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, 9006 Tromsø, Norway
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 223 62 Lund, Sweden
| | - Zoé Pochon
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
| | - Panagiotis Kalogeropoulos
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Eli Eriksson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Inna Biryukova
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Vaishnovi Sekar
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology (CMB), Karolinska Institute, 171 77 Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden;
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Marc R Friedländer
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden;
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21
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Fonti N, Parisi F, Mancianti F, Freer G, Poli A. Cancerogenic parasites in veterinary medicine: a narrative literature review. Infect Agent Cancer 2023; 18:45. [PMID: 37496079 PMCID: PMC10373346 DOI: 10.1186/s13027-023-00522-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
Parasite infection is one of the many environmental factors that can significantly contribute to carcinogenesis and is already known to be associated with a variety of malignancies in both human and veterinary medicine. However, the actual number of cancerogenic parasites and their relationship to tumor development is far from being fully understood, especially in veterinary medicine. Thus, the aim of this review is to investigate parasite-related cancers in domestic and wild animals and their burden in veterinary oncology. Spontaneous neoplasia with ascertained or putative parasite etiology in domestic and wild animals will be reviewed, and the multifarious mechanisms of protozoan and metazoan cancer induction will be discussed.
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Affiliation(s)
- Niccolò Fonti
- Dipartimento di Scienze veterinarie, Università di Pisa, Viale delle Piagge, 2, 56124, Pisa, Italy.
| | - Francesca Parisi
- Dipartimento di Scienze veterinarie, Università di Pisa, Viale delle Piagge, 2, 56124, Pisa, Italy
| | - Francesca Mancianti
- Dipartimento di Scienze veterinarie, Università di Pisa, Viale delle Piagge, 2, 56124, Pisa, Italy
| | - Giulia Freer
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Via Savi, 10, 56126, Pisa, Italy
| | - Alessandro Poli
- Dipartimento di Scienze veterinarie, Università di Pisa, Viale delle Piagge, 2, 56124, Pisa, Italy
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22
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Hamede R, Fountain‐Jones NM, Arce F, Jones M, Storfer A, Hohenlohe PA, McCallum H, Roche B, Ujvari B, Thomas F. The tumour is in the detail: Local phylogenetic, population and epidemiological dynamics of a transmissible cancer in Tasmanian devils. Evol Appl 2023; 16:1316-1327. [PMID: 37492149 PMCID: PMC10363845 DOI: 10.1111/eva.13569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/27/2023] Open
Abstract
Infectious diseases are a major threat for biodiversity conservation and can exert strong influence on wildlife population dynamics. Understanding the mechanisms driving infection rates and epidemic outcomes requires empirical data on the evolutionary trajectory of pathogens and host selective processes. Phylodynamics is a robust framework to understand the interaction of pathogen evolutionary processes with epidemiological dynamics, providing a powerful tool to evaluate disease control strategies. Tasmanian devils have been threatened by a fatal transmissible cancer, devil facial tumour disease (DFTD), for more than two decades. Here we employ a phylodynamic approach using tumour mitochondrial genomes to assess the role of tumour genetic diversity in epidemiological and population dynamics in a devil population subject to 12 years of intensive monitoring, since the beginning of the epidemic outbreak. DFTD molecular clock estimates of disease introduction mirrored observed estimates in the field, and DFTD genetic diversity was positively correlated with estimates of devil population size. However, prevalence and force of infection were the lowest when devil population size and tumour genetic diversity was the highest. This could be due to either differential virulence or transmissibility in tumour lineages or the development of host defence strategies against infection. Our results support the view that evolutionary processes and epidemiological trade-offs can drive host-pathogen coexistence, even when disease-induced mortality is extremely high. We highlight the importance of integrating pathogen and population evolutionary interactions to better understand long-term epidemic dynamics and evaluating disease control strategies.
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Affiliation(s)
- Rodrigo Hamede
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
| | | | - Fernando Arce
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Menna Jones
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Andrew Storfer
- School of Biological SciencesWashington State UniversityPullmanWashingtonUSA
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdahoUSA
| | - Hamish McCallum
- Centre for Planetary Health and Food SecurityGriffith University, Nathan CampusNathanQueenslandAustralia
| | - Benjamin Roche
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
| | - Beata Ujvari
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
| | - Frédéric Thomas
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
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23
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Conroy G. Tasmanian devils' contagious cancers sequenced for first time. Nature 2023:10.1038/d41586-023-01349-7. [PMID: 37081271 DOI: 10.1038/d41586-023-01349-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
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