1
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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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2
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Harding J, Vintersten-Nagy K, Yang H, Tang JK, Shutova M, Jong ED, Lee JH, Massumi M, Oussenko T, Izadifar Z, Zhang P, Rogers IM, Wheeler MB, Lye SJ, Sung HK, Li C, Izadifar M, Nagy A. Immune-privileged tissues formed from immunologically cloaked mouse embryonic stem cells survive long term in allogeneic hosts. Nat Biomed Eng 2024; 8:427-442. [PMID: 37996616 PMCID: PMC11087263 DOI: 10.1038/s41551-023-01133-y] [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: 04/17/2023] [Accepted: 09/30/2023] [Indexed: 11/25/2023]
Abstract
The immunogenicity of transplanted allogeneic cells and tissues is a major hurdle to the advancement of cell therapies. Here we show that the overexpression of eight immunomodulatory transgenes (Pdl1, Cd200, Cd47, H2-M3, Fasl, Serpinb9, Ccl21 and Mfge8) in mouse embryonic stem cells (mESCs) is sufficient to immunologically 'cloak' the cells as well as tissues derived from them, allowing their survival for months in outbred and allogeneic inbred recipients. Overexpression of the human orthologues of these genes in human ESCs abolished the activation of allogeneic human peripheral blood mononuclear cells and their inflammatory responses. Moreover, by using the previously reported FailSafe transgene system, which transcriptionally links a gene essential for cell division with an inducible and cell-proliferation-dependent kill switch, we generated cloaked tissues from mESCs that served as immune-privileged subcutaneous sites that protected uncloaked allogeneic and xenogeneic cells from rejection in immune-competent hosts. The combination of cloaking and FailSafe technologies may allow for the generation of safe and allogeneically accepted cell lines and off-the-shelf cell products.
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Affiliation(s)
- Jeffrey Harding
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Kristina Vintersten-Nagy
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Huijuan Yang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Jean Kit Tang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Maria Shutova
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Eric D Jong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Ju Hee Lee
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Mohammad Massumi
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Tatiana Oussenko
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Zohreh Izadifar
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Puzheng Zhang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Ian M Rogers
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - Michael B Wheeler
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, Toronto, Ontario, Canada
| | - Stephen J Lye
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - Hoon-Ki Sung
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - ChengJin Li
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Mohammad Izadifar
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada.
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia.
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3
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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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4
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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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5
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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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6
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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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7
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Petrohilos C, Patchett A, Hogg CJ, Belov K, Peel E. Tasmanian devil cathelicidins exhibit anticancer activity against Devil Facial Tumour Disease (DFTD) cells. Sci Rep 2023; 13:12698. [PMID: 37542170 PMCID: PMC10403513 DOI: 10.1038/s41598-023-39901-0] [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: 05/19/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023] Open
Abstract
The Tasmanian devil (Sarcophilus harrisii) is endangered due to the spread of Devil Facial Tumour Disease (DFTD), a contagious cancer with no current treatment options. Here we test whether seven recently characterized Tasmanian devil cathelicidins are involved in cancer regulation. We measured DFTD cell viability in vitro following incubation with each of the seven peptides and describe the effect of each on gene expression in treated cells. Four cathelicidins (Saha-CATH3, 4, 5 and 6) were toxic to DFTD cells and caused general signs of cellular stress. The most toxic peptide (Saha-CATH5) also suppressed the ERBB and YAP1/TAZ signaling pathways, both of which have been identified as important drivers of cancer proliferation. Three cathelicidins induced inflammatory pathways in DFTD cells that may potentially recruit immune cells in vivo. This study suggests that devil cathelicidins have some anti-cancer and inflammatory functions and should be explored further to determine whether they have potential as treatment leads.
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Affiliation(s)
- Cleopatra Petrohilos
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide & Protein Science, The University of Sydney, Sydney, NSW, Australia
| | - Amanda Patchett
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
- Australian Research Council Centre of Excellence for Innovations in Peptide & Protein Science, The University of Sydney, Sydney, NSW, Australia.
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide & Protein Science, The University of Sydney, Sydney, NSW, Australia
| | - Emma Peel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide & Protein Science, The University of Sydney, Sydney, NSW, Australia
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8
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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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9
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Russell GG, Palmieri C, Darby J, Morris GP, Fountain-Jones NM, Pye RJ, Flies AS. Automated Analysis of PD1 and PDL1 Expression in Lymph Nodes and the Microenvironment of Transmissible Tumors in Tasmanian Devils. Immunol Invest 2023:1-20. [PMID: 37267050 DOI: 10.1080/08820139.2023.2217845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The wild Tasmanian devil (Sarcophilus harrisii) population has suffered a devastating decline due to two clonal transmissible cancers. The first devil facial tumor 1 (DFT1) was observed in 1996, followed by a second genetically distinct transmissible tumor, the devil facial tumor 2 (DFT2), in 2014. DFT1/2 frequently metastasize, with lymph nodes being common metastatic sites. MHC-I downregulation by DFT1 cells is a primary means of evading allograft immunity aimed at polymorphic MHC-I proteins. DFT2 cells constitutively express MHC-I, and MHC-I is upregulated on DFT1/2 cells by interferon gamma, suggesting other immune evasion mechanisms may contribute to overcoming allograft and anti-tumor immunity. Human clinical trials have demonstrated PD1/PDL1 blockade effectively treats patients showing increased expression of PD1 in tumor draining lymph nodes, and PDL1 on peritumoral immune cells and tumor cells. The effects of DFT1/2 on systemic immunity remain largely uncharacterized. This study applied the open-access software QuPath to develop a semiautomated pipeline for whole slide analysis of stained tissue sections to quantify PD1/PDL1 expression in devil lymph nodes. The QuPath protocol provided strong correlations to manual counting. PD-1 expression was approximately 10-fold higher than PD-L1 expression in lymph nodes and was primarily expressed in germinal centers, whereas PD-L1 expression was more widely distributed throughout the lymph nodes. The density of PD1 positive cells was increased in lymph nodes containing DFT2 metastases, compared to DFT1. This suggests PD1/PDL1 exploitation may contribute to the poorly immunogenic nature of transmissible tumors in some devils and could be targeted in therapeutic or prophylactic treatments.Abbreviations: PD1: programmed cell death protein 1; PDL1: programmed death ligand 1; DFT1: devil facial tumor 1; DFT2: devil facial tumor 2; DFTD: devil facial tumor disease; MCC: Matthew's correlation coefficient; DAB: diaminobenzidine; ROI: region of interest.
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Affiliation(s)
- Grace G Russell
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Chiara Palmieri
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Jocelyn Darby
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Gary P Morris
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Nicholas M Fountain-Jones
- School of Natural Sciences, College of Science and Engineering, University of Tasmania, Hobart, Tasmania, Australia
| | - Ruth J Pye
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Andrew S Flies
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
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10
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AbdulJabbar K, Castillo SP, Hughes K, Davidson H, Boddy AM, Abegglen LM, Minoli L, Iussich S, Murchison EP, Graham TA, Spiro S, Maley CC, Aresu L, Palmieri C, Yuan Y. Bridging clinic and wildlife care with AI-powered pan-species computational pathology. Nat Commun 2023; 14:2408. [PMID: 37100774 PMCID: PMC10133243 DOI: 10.1038/s41467-023-37879-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/04/2023] [Indexed: 04/28/2023] Open
Abstract
Cancers occur across species. Understanding what is consistent and varies across species can provide new insights into cancer initiation and evolution, with significant implications for animal welfare and wildlife conservation. We build a pan-species cancer digital pathology atlas (panspecies.ai) and conduct a pan-species study of computational comparative pathology using a supervised convolutional neural network algorithm trained on human samples. The artificial intelligence algorithm achieves high accuracy in measuring immune response through single-cell classification for two transmissible cancers (canine transmissible venereal tumour, 0.94; Tasmanian devil facial tumour disease, 0.88). In 18 other vertebrate species (mammalia = 11, reptilia = 4, aves = 2, and amphibia = 1), accuracy (range 0.57-0.94) is influenced by cell morphological similarity preserved across different taxonomic groups, tumour sites, and variations in the immune compartment. Furthermore, a spatial immune score based on artificial intelligence and spatial statistics is associated with prognosis in canine melanoma and prostate tumours. A metric, named morphospace overlap, is developed to guide veterinary pathologists towards rational deployment of this technology on new samples. This study provides the foundation and guidelines for transferring artificial intelligence technologies to veterinary pathology based on understanding of morphological conservation, which could vastly accelerate developments in veterinary medicine and comparative oncology.
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Affiliation(s)
- Khalid AbdulJabbar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Simon P Castillo
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Katherine Hughes
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Hannah Davidson
- Zoological Society of London, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Sq, London, UK
| | - Amy M Boddy
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Lisa M Abegglen
- Department of Pediatrics and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- PEEL Therapeutics, Inc., Salt Lake City, UT, USA
| | - Lucia Minoli
- Department of Veterinary Sciences, University of Turin, 10095, Grugliasco, Italy
| | - Selina Iussich
- Department of Veterinary Sciences, University of Turin, 10095, Grugliasco, Italy
| | - Elizabeth P Murchison
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Sq, London, UK
| | | | - Carlo C Maley
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Luca Aresu
- Department of Veterinary Sciences, University of Turin, 10095, Grugliasco, Italy
| | - Chiara Palmieri
- School of Veterinary Science, The University of Queensland, 4343, Gatton, QLD, Australia
| | - Yinyin Yuan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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11
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Stammnitz MR, Gori K, Kwon YM, Harry E, Martin FJ, Billis K, Cheng Y, Baez-Ortega A, Chow W, Comte S, Eggertsson H, Fox S, Hamede R, Jones M, Lazenby B, Peck S, Pye R, Quail MA, Swift K, Wang J, Wood J, Howe K, Stratton MR, Ning Z, Murchison EP. The evolution of two transmissible cancers in Tasmanian devils. Science 2023; 380:283-293. [PMID: 37079675 DOI: 10.1126/science.abq6453] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Tasmanian devils have spawned two transmissible cancer lineages, named devil facial tumor 1 (DFT1) and devil facial tumor 2 (DFT2). We investigated the genetic diversity and evolution of these clones by analyzing 78 DFT1 and 41 DFT2 genomes relative to a newly assembled, chromosome-level reference. Time-resolved phylogenetic trees reveal that DFT1 first emerged in 1986 (1982 to 1989) and DFT2 in 2011 (2009 to 2012). Subclone analysis documents transmission of heterogeneous cell populations. DFT2 has faster mutation rates than DFT1 across all variant classes, including substitutions, indels, rearrangements, transposable element insertions, and copy number alterations, and we identify a hypermutated DFT1 lineage with defective DNA mismatch repair. Several loci show plausible evidence of positive selection in DFT1 or DFT2, including loss of chromosome Y and inactivation of MGA, but none are common to both cancers. This study reveals the parallel long-term evolution of two transmissible cancers inhabiting a common niche in Tasmanian devils.
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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
| | - Young Mi Kwon
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Edward Harry
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Adrian Baez-Ortega
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - William Chow
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sebastien Comte
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- Vertebrate Pest Research Unit, NSW Department of Primary Industries, Orange, NSW, Australia
| | | | - Samantha Fox
- Save the Tasmanian Devil Program, Tasmanian Department of Natural Resources and Environment, Hobart, TAS, Australia
- Toledo Zoo, Toledo, OH, USA
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- CANCEV, Centre de Recherches Ecologiques et Evolutives sur le Cancer, Montpellier, France
| | - Menna Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Billie Lazenby
- Save the Tasmanian Devil Program, Tasmanian Department of Natural Resources and Environment, Hobart, TAS, Australia
| | - Sarah Peck
- Save the Tasmanian Devil Program, Tasmanian Department of Natural Resources and Environment, Hobart, TAS, Australia
| | - Ruth Pye
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Michael A Quail
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kate Swift
- Mount Pleasant Laboratories, Tasmanian Department of Natural Resources and Environment, Prospect, TAS, Australia
| | - Jinhong Wang
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jonathan Wood
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michael R Stratton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Zemin Ning
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Elizabeth P Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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12
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Kayigwe AN, M. Darby J, Lyons AB, L. Patchett A, Lisowski L, Liu GS, S. Flies A. A human adenovirus encoding IFN-γ can transduce Tasmanian devil facial tumour cells and upregulate MHC-I. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The devil facial tumour disease (DFTD) has led to a massive decline in the wild Tasmanian devil (Sarcophilus harrisii) population. The disease is caused by two independent devil facial tumours (DFT1 and DFT2). These transmissible cancers have a mortality rate of nearly 100 %. An adenoviral vector-based vaccine has been proposed as a conservation strategy for the Tasmanian devil. This study aimed to determine if a human adenovirus serotype 5 could express functional transgenes in devil cells. As DFT1 cells do not constitutively express major histocompatibility complex class I (MHC-I), we developed a replication-deficient adenoviral vector that encodes devil interferon gamma (IFN-γ) fused to a fluorescent protein reporter. Our results show that adenoviral-expressed IFN-γ was able to stimulate upregulation of beta-2 microglobulin, a component of MHC-I, on DFT1, DFT2 and devil fibroblast cell lines. This work suggests that human adenoviruses can serve as a vaccine platform for devils and potentially other marsupials.
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Affiliation(s)
- Ahab N. Kayigwe
- Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology, Bibititi and Morogoro Rd Junction, P. O. Box 2958, Dar-es-salaam, Tanzania
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Jocelyn M. Darby
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - A. Bruce Lyons
- Tasmanian School of Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Amanda L. Patchett
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Leszek Lisowski
- Military Institute of Medicine, Laboratory of Molecular Oncology and Innovative Therapies, 04-141 Warsaw, Poland
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, 3002, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Andrew S. Flies
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
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13
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Ong CEB, Cheng Y, Siddle HV, Lyons AB, Woods GM, Flies AS. Class II transactivator induces expression of MHC-I and MHC-II in transmissible Tasmanian devil facial tumours. Open Biol 2022; 12:220208. [PMID: 36259237 PMCID: PMC9579919 DOI: 10.1098/rsob.220208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
MHC-I and MHC-II molecules are critical components of antigen presentation and T cell immunity to pathogens and cancer. The two monoclonal transmissible devil facial tumours (DFT1, DFT2) exploit MHC-I pathways to overcome immunological anti-tumour and allogeneic barriers. This exploitation underpins the ongoing transmission of DFT cells across the wild Tasmanian devil population. We have previously shown that the overexpression of NLRC5 in DFT1 and DFT2 cells can regulate components of the MHC-I pathway but not MHC-II, establishing the stable upregulation of MHC-I on the cell surface. As MHC-II molecules are crucial for CD4+ T cell activation, MHC-II expression in tumour cells is beginning to gain traction in the field of immunotherapy and cancer vaccines. The overexpression of Class II transactivator in transfected DFT1 and DFT2 cells induced the transcription of several genes of the MHC-I and MHC-II pathways. This was further supported by the upregulation of MHC-I protein on DFT1 and DFT2 cells, but interestingly MHC-II protein was upregulated only in DFT1 cells. This new insight into the regulation of MHC-I and MHC-II pathways in cells that naturally overcome allogeneic barriers can inform vaccine, immunotherapy and tissue transplant strategies for human and veterinary medicine.
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Affiliation(s)
- Chrissie E. B. Ong
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart, TAS 7000, Australia
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Hannah V. Siddle
- Department of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK,Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - A. Bruce Lyons
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS 7005, Australia
| | - Gregory M. Woods
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart, TAS 7000, Australia
| | - Andrew S. Flies
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart, TAS 7000, Australia
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14
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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] [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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15
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Jacquemin V, Antoine M, Dom G, Detours V, Maenhaut C, Dumont JE. Dynamic Cancer Cell Heterogeneity: Diagnostic and Therapeutic Implications. Cancers (Basel) 2022; 14:280. [PMID: 35053446 PMCID: PMC8773841 DOI: 10.3390/cancers14020280] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
Though heterogeneity of cancers is recognized and has been much discussed in recent years, the concept often remains overlooked in different routine examinations. Indeed, in clinical or biological articles, reviews, and textbooks, cancers and cancer cells are generally presented as evolving distinct entities rather than as an independent heterogeneous cooperative cell population with its self-oriented biology. There are, therefore, conceptual gaps which can mislead the interpretations/diagnostic and therapeutic approaches. In this short review, we wish to summarize and discuss various aspects of this dynamic evolving heterogeneity and its biological, pathological, clinical, diagnostic, and therapeutic implications, using thyroid carcinoma as an illustrative example.
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Affiliation(s)
- Valerie Jacquemin
- Correspondence: (V.J.); (J.E.D.); Tel.: +32-2-555-32-26 (V.J.); +32-2-555-41-34 (J.E.D.)
| | | | | | | | | | - Jacques E. Dumont
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles, 1070 Brussels, Belgium; (M.A.); (G.D.); (V.D.); (C.M.)
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16
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Espejo C, Patchett AL, Wilson R, Lyons AB, Woods GM. Challenges of an Emerging Disease: The Evolving Approach to Diagnosing Devil Facial Tumour Disease. Pathogens 2021; 11:27. [PMID: 35055975 PMCID: PMC8780694 DOI: 10.3390/pathogens11010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/08/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
Devil Facial Tumour Disease (DFTD) is an emerging infectious disease that provides an excellent example of how diagnostic techniques improve as disease-specific knowledge is generated. DFTD manifests as tumour masses on the faces of Tasmanian devils, first noticed in 1996. As DFTD became more prevalent among devils, karyotyping of the lesions and their devil hosts demonstrated that DFTD was a transmissible cancer. The subsequent routine diagnosis relied on microscopy and histology to characterise the facial lesions as cancer cells. Combined with immunohistochemistry, these techniques characterised the devil facial tumours as sarcomas of neuroectodermal origin. More sophisticated molecular methods identified the origin of DFTD as a Schwann cell, leading to the Schwann cell-specific protein periaxin to discriminate DFTD from other facial lesions. After the discovery of a second facial cancer (DFT2), cytogenetics and the absence of periaxin expression confirmed the independence of the new cancer from DFT1 (the original DFTD). Molecular studies of the two DFTDs led to the development of a PCR assay to differentially diagnose the cancers. Proteomics and transcriptomic studies identified different cell phenotypes among the two DFTD cell lines. Phenotypic differences were also reflected in proteomics studies of extracellular vesicles (EVs), which yielded an early diagnostic marker that could detect DFTD in its latent stage from serum samples. A mesenchymal marker was also identified that could serve as a serum-based differential diagnostic. The emergence of two transmissible cancers in one species has provided an ideal opportunity to better understand transmissible cancers, demonstrating how fundamental research can be translated into applicable and routine diagnostic techniques.
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Affiliation(s)
- Camila Espejo
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia; (C.E.); (A.B.L.)
| | - Amanda L. Patchett
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia;
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7000, Australia;
| | - A. Bruce Lyons
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia; (C.E.); (A.B.L.)
| | - Gregory M. Woods
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia;
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17
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Silva RCMC, Panis C, Pires BRB. Lessons from transmissible cancers for immunotherapy and transplant. Immunol Med 2021; 45:146-161. [PMID: 34962854 DOI: 10.1080/25785826.2021.2018783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The emergence of horizontal transmission of cancer between vertebrates is an issue that interests scientists and medical society. Transmission requires: (i) a mechanism by which cancer cells can transfer to another organism and (ii) a repressed immune response on the part of the recipient. Transmissible tumors are unique models to comprehend the responses and mechanisms mediated by the major histocompatibility complex (MHC), which can be transposed for transplant biology. Here, we discuss the mechanisms involved in immune-mediated tissue rejection, making a parallel with transmissible cancers. We also discuss cellular and molecular mechanisms involved in cancer immunotherapy and anti-rejection therapies.
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Affiliation(s)
- Rafael Cardoso Maciel Costa Silva
- Laboratory of Immunoreceptors and Signaling, Instituto de Biofísica Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio De Janeiro, Brazil
| | - Carolina Panis
- Laboratory of Tumor Biology, State University of West Paraná, UNIOESTE, Francisco Beltrão, Brazil
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18
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Espejo C, Wilson R, Willms E, Ruiz-Aravena M, Pye RJ, Jones ME, Hill AF, Woods GM, Lyons AB. Extracellular vesicle proteomes of two transmissible cancers of Tasmanian devils reveal tenascin-C as a serum-based differential diagnostic biomarker. Cell Mol Life Sci 2021; 78:7537-7555. [PMID: 34655299 PMCID: PMC11073120 DOI: 10.1007/s00018-021-03955-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/26/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022]
Abstract
The iconic Tasmanian devil (Sarcophilus harrisii) is endangered due to the transmissible cancer Devil Facial Tumour Disease (DFTD), of which there are two genetically independent subtypes (DFT1 and DFT2). While DFT1 and DFT2 can be differentially diagnosed using tumour biopsies, there is an urgent need to develop less-invasive biomarkers that can detect DFTD and distinguish between subtypes. Extracellular vesicles (EVs), the nano-sized membrane-enclosed vesicles present in most biofluids, represent a valuable resource for biomarker discovery. Here, we characterized the proteome of EVs from cultured DFTD cells using data-independent acquisition-mass spectrometry and an in-house spectral library of > 1500 proteins. EVs from both DFT1 and DFT2 cell lines expressed higher levels of proteins associated with focal adhesion functions. Furthermore, hallmark proteins of epithelial-mesenchymal transition were enriched in DFT2 EVs relative to DFT1 EVs. These findings were validated in EVs derived from serum samples, revealing that the mesenchymal marker tenascin-C was also enriched in EVs derived from the serum of devils infected with DFT2 relative to those infected with DFT1 and healthy controls. This first EV-based investigation of DFTD increases our understanding of the cancers' EVs and their possible involvement in DFTD progression, such as metastasis. Finally, we demonstrated the potential of EVs to differentiate between DFT1 and DFT2, highlighting their potential use as less-invasive liquid biopsies for the Tasmanian devil.
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Affiliation(s)
- Camila Espejo
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7000, Australia.
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Eduard Willms
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Manuel Ruiz-Aravena
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7001, Australia
| | - Ruth J Pye
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7000, Australia
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7001, Australia
| | - Andrew F Hill
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Gregory M Woods
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7000, Australia
| | - A Bruce Lyons
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7000, Australia
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19
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Owen RS, Ramarathinam SH, Bailey A, Gastaldello A, Hussey K, Skipp PJ, Purcell AW, Siddle HV. The differentiation state of the Schwann cell progenitor drives phenotypic variation between two contagious cancers. PLoS Pathog 2021; 17:e1010033. [PMID: 34780568 PMCID: PMC8629380 DOI: 10.1371/journal.ppat.1010033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/29/2021] [Accepted: 10/13/2021] [Indexed: 01/04/2023] Open
Abstract
Contagious cancers are a rare pathogenic phenomenon in which cancer cells gain the ability to spread between genetically distinct hosts. Nine examples have been identified across marine bivalves, dogs and Tasmanian devils, but the Tasmanian devil is the only mammalian species known to have given rise to two distinct lineages of contagious cancer, termed Devil Facial Tumour 1 (DFT1) and 2 (DFT2). Remarkably, DFT1 and DFT2 arose independently from the same cell type, a Schwann cell, and while their ultra-structural features are highly similar they exhibit variation in their mutational signatures and infection dynamics. As such, DFT1 and DFT2 provide a unique framework for investigating how a common progenitor cell can give rise to distinct contagious cancers. Using a proteomics approach, we show that DFT1 and DFT2 are derived from Schwann cells in different differentiation states, with DFT2 carrying a molecular signature of a less well differentiated Schwann cell. Under inflammatory signals DFT1 and DFT2 have different gene expression profiles, most notably involving Schwann cell markers of differentiation, reflecting the influence of their distinct origins. Further, DFT2 cells express immune cell markers typically expressed during nerve repair, consistent with an ability to manipulate their extracellular environment, facilitating the cell’s ability to transmit between individuals. The emergence of two contagious cancers in the Tasmanian devil suggests that the inherent plasticity of Schwann cells confers a vulnerability to the formation of contagious cancers. Cancer can be an infectious pathogen, with nine known cases, infecting bivalves, dogs and two independent tumours circulating in the endangered Tasmanian devil. These cancers, known as Devil Facial Tumour 1 (DFT1) and Devil Facial Tumour 2 (DFT2), spread through the wild population much like parasites, moving between genetically distinct hosts during social biting behaviours and persisting in the population. As DFT1 and DFT2 are independent contagious cancers that arose from the same cell type, a Schwann cell, they provide a unique model system for studying the emergence of phenotypic variation in cancers derived from a single progenitor cell. In this study, we have shown that these two remarkably similar tumours have emerged from Schwann cells in different differentiation states. The differentiation state of the progenitor has altered the characteristics of each tumour, resulting in different responses to external signals. This work demonstrates that the cellular origin of infection can direct the phenotype of a contagious cancer and how it responds to signals from the host environment. Further, the plasticity of Schwann cells may make these cells more prone to forming contagious cancers, raising the possibility that further parasitic cancers could emerge from this cell type.
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Affiliation(s)
- Rachel S. Owen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Sri H. Ramarathinam
- Department of Biochemistry and Molecular Biology and the Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Alistair Bailey
- Centre for Cancer Immunology, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Annalisa Gastaldello
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Kathryn Hussey
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Paul J. Skipp
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology and the Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Hannah V. Siddle
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- * E-mail:
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20
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Between the Devil and the Deep Blue Sea: Non-Coding RNAs Associated with Transmissible Cancers in Tasmanian Devil, Domestic Dog and Bivalves. Noncoding RNA 2021; 7:ncrna7040072. [PMID: 34842768 PMCID: PMC8628904 DOI: 10.3390/ncrna7040072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 12/20/2022] Open
Abstract
Currently there are nine known examples of transmissible cancers in nature. They have been observed in domestic dog, Tasmanian devil, and six bivalve species. These tumours can overcome host immune defences and spread to other members of the same species. Non-coding RNAs (ncRNAs) are known to play roles in tumorigenesis and immune system evasion. Despite their potential importance in transmissible cancers, there have been no studies on ncRNA function in this context to date. Here, we present possible applications of the CRISPR/Cas system to study the RNA biology of transmissible cancers. Specifically, we explore how ncRNAs may play a role in the immortality and immune evasion ability of these tumours.
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21
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Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection. BMC Genomics 2021; 22:698. [PMID: 34579650 PMCID: PMC8477496 DOI: 10.1186/s12864-021-07994-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/08/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Transmissible cancers lie at the intersection of oncology and infectious disease, two traditionally divergent fields for which gene expression studies are particularly useful for identifying the molecular basis of phenotypic variation. In oncology, transcriptomics studies, which characterize the expression of thousands of genes, have identified processes leading to heterogeneity in cancer phenotypes and individual prognoses. More generally, transcriptomics studies of infectious diseases characterize interactions between host, pathogen, and environment to better predict population-level outcomes. Tasmanian devils have been impacted dramatically by a transmissible cancer (devil facial tumor disease; DFTD) that has led to widespread population declines. Despite initial predictions of extinction, populations have persisted at low levels, due in part to heterogeneity in host responses, particularly between sexes. However, the processes underlying this variation remain unknown. RESULTS We sequenced transcriptomes from healthy and DFTD-infected devils, as well as DFTD tumors, to characterize host responses to DFTD infection, identify differing host-tumor molecular interactions between sexes, and investigate the extent to which tumor gene expression varies among host populations. We found minimal variation in gene expression of devil lip tissues, either with respect to DFTD infection status or sex. However, 4088 genes were differentially expressed in tumors among our sampling localities. Pathways that were up- or downregulated in DFTD tumors relative to normal tissues exhibited the same patterns of expression with greater intensity in tumors from localities that experienced DFTD for longer. No mRNA sequence variants were associated with expression variation. CONCLUSIONS Expression variation among localities may reflect morphological differences in tumors that alter ratios of normal-to-tumor cells within biopsies. Phenotypic variation in tumors may arise from environmental variation or differences in host immune response that were undetectable in lip biopsies, potentially reflecting variation in host-tumor coevolutionary relationships among sites that differ in the time since DFTD arrival.
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22
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Stahlke AR, Epstein B, Barbosa S, Margres MJ, Patton AH, Hendricks SA, Veillet A, Fraik AK, Schönfeld B, McCallum HI, Hamede R, Jones ME, Storfer A, Hohenlohe PA. Contemporary and historical selection in Tasmanian devils ( Sarcophilus harrisii) support novel, polygenic response to transmissible cancer. Proc Biol Sci 2021; 288:20210577. [PMID: 34034517 PMCID: PMC8150010 DOI: 10.1098/rspb.2021.0577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022] Open
Abstract
Tasmanian devils (Sarcophilus harrisii) are evolving in response to a unique transmissible cancer, devil facial tumour disease (DFTD), first described in 1996. Persistence of wild populations and the recent emergence of a second independently evolved transmissible cancer suggest that transmissible cancers may be a recurrent feature in devils. Here, we compared signatures of selection across temporal scales to determine whether genes or gene pathways under contemporary selection (six to eight generations) have also been subject to historical selection (65-85 Myr). First, we used targeted sequencing, RAD-capture, in approximately 2500 devils in six populations to identify genomic regions subject to rapid evolution. We documented genome-wide contemporary evolution, including 186 candidate genes related to cell cycling and immune response. Then we used a molecular evolution approach to identify historical positive selection in devils compared to other marsupials and found evidence of selection in 1773 genes. However, we found limited overlap across time scales, with only 16 shared candidate genes, and no overlap in enriched functional gene sets. Our results are consistent with a novel, multi-locus evolutionary response of devils to DFTD. Our results can inform conservation by identifying high priority targets for genetic monitoring and guiding maintenance of adaptive potential in managed populations.
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Affiliation(s)
- Amanda R. Stahlke
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844, USA
| | - Brendan Epstein
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Soraia Barbosa
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844, USA
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Mark J. Margres
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Austin H. Patton
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Sarah A. Hendricks
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844, USA
| | - Anne Veillet
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844, USA
| | - Alexandra K. Fraik
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Barbara Schönfeld
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Hamish I. McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844, USA
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23
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Kattner P, Zeiler K, Herbener VJ, Ferla-Brühl KL, Kassubek R, Grunert M, Burster T, Brühl O, Weber AS, Strobel H, Karpel-Massler G, Ott S, Hagedorn A, Tews D, Schulz A, Prasad V, Siegelin MD, Nonnenmacher L, Fischer-Posovszky P, Halatsch ME, Debatin KM, Westhoff MA. What Animal Cancers teach us about Human Biology. Theranostics 2021; 11:6682-6702. [PMID: 34093847 PMCID: PMC8171098 DOI: 10.7150/thno.56623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/09/2021] [Indexed: 12/30/2022] Open
Abstract
Cancers in animals present a large, underutilized reservoir of biomedical information with critical implication for human oncology and medicine in general. Discussing two distinct areas of tumour biology in non-human hosts, we highlight the importance of these findings for our current understanding of cancer, before proposing a coordinated strategy to harvest biomedical information from non-human resources and translate it into a clinical setting. First, infectious cancers that can be transmitted as allografts between individual hosts, have been identified in four distinct, unrelated groups, dogs, Tasmanian devils, Syrian hamsters and, surprisingly, marine bivalves. These malignancies might hold the key to improving our understanding of the interaction between tumour cell and immune system and, thus, allow us to devise novel treatment strategies that enhance anti-cancer immunosurveillance, as well as suggesting more effective organ and stem cell transplantation strategies. The existence of these malignancies also highlights the need for increased scrutiny when considering the existence of infectious cancers in humans. Second, it has long been understood that no linear relationship exists between the number of cells within an organism and the cancer incidence rate. To resolve what is known as Peto's Paradox, additional anticancer strategies within different species have to be postulated. These naturally occurring idiosyncrasies to avoid carcinogenesis represent novel potential therapeutic strategies.
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Affiliation(s)
- Patricia Kattner
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Katharina Zeiler
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
- Department of Neurosurgery, University Medical Center Ulm, Ulm, Germany
| | - Verena J. Herbener
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | | | | | - Michael Grunert
- Department of Nuclear Medicine, German Armed Forces Hospital of Ulm, Ulm, Germany
- Department of Nuclear Medicine, University Medical Center Ulm, Ulm, Germany
| | - Timo Burster
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan Republic
| | - Oliver Brühl
- Laboratorio Analisi Sicilia Catania, Lentini; SR, Italy
| | - Anna Sarah Weber
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Hannah Strobel
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Georg Karpel-Massler
- Department of Neurosurgery, University Medical Center Ulm, Ulm, Germany
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Sibylle Ott
- Animal Research Center, University of Ulm, Ulm, Germany
| | | | - Daniel Tews
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University Medical Center, Ulm, Germany
| | - Ansgar Schulz
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Vikas Prasad
- Department of Nuclear Medicine, University Medical Center Ulm, Ulm, Germany
| | - Markus D. Siegelin
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Lisa Nonnenmacher
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Pamela Fischer-Posovszky
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University Medical Center, Ulm, Germany
| | | | - Klaus-Michael Debatin
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Mike-Andrew Westhoff
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
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24
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Ong CEB, Patchett AL, Darby JM, Chen J, Liu GS, Lyons AB, Woods GM, Flies AS. NLRC5 regulates expression of MHC-I and provides a target for anti-tumor immunity in transmissible cancers. J Cancer Res Clin Oncol 2021; 147:1973-1991. [PMID: 33797607 PMCID: PMC8017436 DOI: 10.1007/s00432-021-03601-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022]
Abstract
Purpose Downregulation of MHC class I (MHC-I) is a common immune evasion strategy of many cancers. Similarly, two allogeneic clonal transmissible cancers have killed thousands of wild Tasmanian devils (Sarcophilus harrisii) and also modulate MHC-I expression to evade anti-cancer and allograft responses. IFNG treatment restores MHC-I expression on devil facial tumor (DFT) cells but is insufficient to control tumor growth. Transcriptional co-activator NLRC5 is a master regulator of MHC-I in humans and mice but its role in transmissible cancers remains unknown. In this study, we explored the regulation and role of MHC-I in these unique genetically mis-matched tumors. Methods We used transcriptome and flow cytometric analyses to determine how MHC-I shapes allogeneic and anti-tumor responses. Cell lines that overexpress NLRC5 to drive antigen presentation, and B2M-knockout cell lines incapable of presenting antigen on MHC-I were used to probe the role of MHC-I in rare cases of tumor regressions. Results Transcriptomic results suggest that NLRC5 plays a major role in MHC-I regulation in devils. NLRC5 was shown to drive the expression of many components of the antigen presentation pathway but did not upregulate PDL1. Serum from devils with tumor regressions showed strong binding to IFNG-treated and NLRC5 cell lines; antibody binding to IFNG-treated and NRLC5 transgenic tumor cells was diminished or absent following B2M knockout. Conclusion MHC-I could be identified as a target for anti-tumor and allogeneic immunity. Consequently, NLRC5 could be a promising target for immunotherapy and vaccines to protect devils from transmissible cancers and inform development of transplant and cancer therapies for humans. Supplementary Information The online version contains supplementary material available at 10.1007/s00432-021-03601-x.
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Affiliation(s)
- Chrissie E B Ong
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia
| | - Amanda L Patchett
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia
| | - Jocelyn M Darby
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia
| | - Jinying Chen
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia.,Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, Australia
| | - A Bruce Lyons
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Gregory M Woods
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia
| | - Andrew S Flies
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia.
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25
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Patchett AL, Tovar C, Blackburn NB, Woods GM, Lyons AB. Mesenchymal plasticity of devil facial tumour cells during in vivo vaccine and immunotherapy trials. Immunol Cell Biol 2021; 99:711-723. [PMID: 33667023 DOI: 10.1111/imcb.12451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/12/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022]
Abstract
Immune evasion is critical to the growth and survival of cancer cells. This is especially pertinent to transmissible cancers, which evade immune detection across genetically diverse hosts. The Tasmanian devil (Sarcophilus harrisii) is threatened by the emergence of Devil Facial Tumour Disease (DFTD), comprising two transmissible cancers (DFT1 and DFT2). The development of effective prophylactic vaccines and therapies against DFTD has been restricted by an incomplete understanding of how allogeneic DFT1 and DFT2 cells maintain immune evasion upon activation of tumour-specific immune responses. In this study, we used RNA sequencing to examine tumours from three experimental DFT1 cases. Two devils received a vaccine prior to inoculation with live DFT1 cells, providing an opportunity to explore changes to DFT1 cancers under immune pressure. Analysis of DFT1 in the non-immunised devil revealed a 'myelinating Schwann cell' phenotype, reflecting both natural DFT1 cancers and the DFT1 cell line used for the experimental challenge. Comparatively, immunised devils exhibited a 'dedifferentiated mesenchymal' DFT1 phenotype. A third 'immune-enriched' phenotype, characterised by increased PDL1 and CTLA-4 expression, was detected in a DFT1 tumour that arose after immunotherapy. In response to immune pressure, mesenchymal plasticity and upregulation of immune checkpoint molecules are used by human cancers to evade immune responses. Similar mechanisms are associated with immune evasion by DFTD cancers, providing novel insights that will inform modification of DFTD vaccines. As DFT1 and DFT2 are clonal cancers transmitted across genetically distinct hosts, the Tasmanian devil provides a 'natural' disease model for more broadly exploring these immune evasion mechanisms in cancer.
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Affiliation(s)
- Amanda L Patchett
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Cesar Tovar
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Nicholas B Blackburn
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Gregory M Woods
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - A Bruce Lyons
- School of Medicine, University of Tasmania, Hobart, TAS, Australia
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26
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Ikonomopoulou MP, Lopez-Mancheño Y, Novelle MG, Martinez-Uña M, Gangoda L, Pal M, Costa-Machado LF, Fernandez-Marcos PJ, Ramm GA, Fernandez-Rojo MA. LXR stimulates a metabolic switch and reveals cholesterol homeostasis as a statin target in Tasmanian devil facial tumor disease. Cell Rep 2021; 34:108851. [PMID: 33730574 DOI: 10.1016/j.celrep.2021.108851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 11/02/2020] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Devil facial tumor disease (DFTD) and its lack of available therapies are propelling the Tasmanian devil population toward extinction. This study demonstrates that cholesterol homeostasis and carbohydrate energy metabolism sustain the proliferation of DFTD cells in a cell-type-dependent manner. In addition, we show that the liver-X nuclear receptor-β (LXRβ), a major cholesterol cellular sensor, and its natural ligand 24S-hydroxycholesterol promote the proliferation of DFTD cells via a metabolic switch toward aerobic glycolysis. As a proof of concept of the role of cholesterol homeostasis on DFTD proliferation, we show that atorvastatin, an FDA-approved statin-drug subtype used against human cardiovascular diseases that inhibits cholesterol synthesis, shuts down DFTD energy metabolism and prevents tumor growth in an in vivo DFTD-xenograft model. In conclusion, we show that intervention against cholesterol homeostasis and carbohydrate-dependent energy metabolism by atorvastatin constitutes a feasible biochemical treatment against DFTD, which may assist in the conservation of the Tasmanian devil.
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Affiliation(s)
- Maria P Ikonomopoulou
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; The University of Queensland, Brisbane, QLD, Australia; Translational Venomics Laboratory, Madrid Institute for Advanced Studies (IMDEA) Food, Madrid 28049, Spain.
| | - Yaiza Lopez-Mancheño
- Hepatic Regenerative Medicine Laboratory, Madrid Institute for Advanced Studies (IMDEA) Food, Madrid 28049, Spain
| | - Marta G Novelle
- Hepatic Regenerative Medicine Laboratory, Madrid Institute for Advanced Studies (IMDEA) Food, Madrid 28049, Spain
| | - Maite Martinez-Uña
- Hepatic Regenerative Medicine Laboratory, Madrid Institute for Advanced Studies (IMDEA) Food, Madrid 28049, Spain
| | - Lahiru Gangoda
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Melbourne, VIC 3052, Australia
| | - Martin Pal
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Melbourne, VIC 3052, Australia
| | - Luis Filipe Costa-Machado
- Metabolic Syndrome Laboratory, Madrid Institute for Advanced Studies (IMDEA) Food, Madrid 28049, Spain
| | | | - Grant A Ramm
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; The University of Queensland, Brisbane, QLD, Australia
| | - Manuel Alejandro Fernandez-Rojo
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; The University of Queensland, Brisbane, QLD, Australia; Hepatic Regenerative Medicine Laboratory, Madrid Institute for Advanced Studies (IMDEA) Food, Madrid 28049, Spain.
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27
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Yetsko K, Farrell JA, Blackburn NB, Whitmore L, Stammnitz MR, Whilde J, Eastman CB, Ramia DR, Thomas R, Krstic A, Linser P, Creer S, Carvalho G, Devlin MA, Nahvi N, Leandro AC, deMaar TW, Burkhalter B, Murchison EP, Schnitzler C, Duffy DJ. Molecular characterization of a marine turtle tumor epizootic, profiling external, internal and postsurgical regrowth tumors. Commun Biol 2021; 4:152. [PMID: 33526843 PMCID: PMC7851172 DOI: 10.1038/s42003-021-01656-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/31/2020] [Indexed: 01/30/2023] Open
Abstract
Sea turtle populations are under threat from an epizootic tumor disease (animal epidemic) known as fibropapillomatosis. Fibropapillomatosis continues to spread geographically, with prevalence of the disease also growing at many longer-affected sites globally. However, we do not yet understand the precise environmental, mutational and viral events driving fibropapillomatosis tumor formation and progression.Here we perform transcriptomic and immunohistochemical profiling of five fibropapillomatosis tumor types: external new, established and postsurgical regrowth tumors, and internal lung and kidney tumors. We reveal that internal tumors are molecularly distinct from the more common external tumors. However, they have a small number of conserved potentially therapeutically targetable molecular vulnerabilities in common, such as the MAPK, Wnt, TGFβ and TNF oncogenic signaling pathways. These conserved oncogenic drivers recapitulate remarkably well the core pan-cancer drivers responsible for human cancers. Fibropapillomatosis has been considered benign, but metastatic-related transcriptional signatures are strongly activated in kidney and established external tumors. Tumors in turtles with poor outcomes (died/euthanized) have genes associated with apoptosis and immune function suppressed, with these genes providing putative predictive biomarkers.Together, these results offer an improved understanding of fibropapillomatosis tumorigenesis and provide insights into the origins, inter-tumor relationships, and therapeutic treatment for this wildlife epizootic.
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Affiliation(s)
- Kelsey Yetsko
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Jessica A Farrell
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Nicholas B Blackburn
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, USA
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Liam Whitmore
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
- Department of Biological Sciences, School of Natural Sciences, Faculty of Science and Engineering, University of Limerick, Limerick, Ireland
| | - Maximilian R Stammnitz
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Jenny Whilde
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Catherine B Eastman
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Devon Rollinson Ramia
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Rachel Thomas
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Aleksandar Krstic
- Systems Biology Ireland & Precision Oncology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Paul Linser
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | | | - Nina Nahvi
- Sea Turtle Inc., South Padre Island, TX, USA
| | - Ana Cristina Leandro
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | | | - Brooke Burkhalter
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Elizabeth P Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Christine Schnitzler
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - David J Duffy
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
- Department of Biological Sciences, School of Natural Sciences, Faculty of Science and Engineering, University of Limerick, Limerick, Ireland.
- Systems Biology Ireland & Precision Oncology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland.
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
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28
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Höffken V, Hermann A, Pavenstädt H, Kremerskothen J. WWC Proteins: Important Regulators of Hippo Signaling in Cancer. Cancers (Basel) 2021; 13:cancers13020306. [PMID: 33467643 PMCID: PMC7829927 DOI: 10.3390/cancers13020306] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 12/22/2022] Open
Abstract
Simple Summary The conserved Hippo pathway regulates cell proliferation and apoptosis via a complex interplay of transcriptional activities, post-translational protein modifications, specific protein–protein interactions and cellular transport processes. Deregulating this highly balanced system can lead to hyperproliferation, organ overgrowth and cancer. Although WWC proteins are known as components of the Hippo signaling pathway, their association with tumorigenesis is often neglected. This review aims to summarize the current knowledge on WWC proteins and their contribution to Hippo signaling in the context of cancer. Abstract The Hippo signaling pathway is known to regulate cell differentiation, proliferation and apoptosis. Whereas activation of the Hippo signaling pathway leads to phosphorylation and cytoplasmic retention of the transcriptional coactivator YAP, decreased Hippo signaling results in nuclear import of YAP and subsequent transcription of pro-proliferative genes. Hence, a dynamic and precise regulation of the Hippo signaling pathway is crucial for organ size control and the prevention of tumor formation. The transcriptional activity of YAP is controlled by a growing number of upstream regulators including the family of WWC proteins. WWC1, WWC2 and WWC3 represent cytosolic scaffolding proteins involved in intracellular transport processes and different signal transduction pathways. Earlier in vitro experiments demonstrated that WWC proteins positively regulate the Hippo pathway via the activation of large tumor suppressor kinases 1/2 (LATS1/2) kinases and the subsequent cytoplasmic accumulation of phosphorylated YAP. Later, reduced WWC expression and subsequent high YAP activity were shown to correlate with the progression of human cancer in different organs. Although the function of WWC proteins as upstream regulators of Hippo signaling was confirmed in various studies, their important role as tumor modulators is often overlooked. This review has been designed to provide an update on the published data linking WWC1, WWC2 and WWC3 to cancer, with a focus on Hippo pathway-dependent mechanisms.
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29
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Pye R, Darby J, Flies AS, Fox S, Carver S, Elmer J, Swift K, Hogg C, Pemberton D, Woods G, Lyons AB. Post-release immune responses of Tasmanian devils vaccinated with an experimental devil facial tumour disease vaccine. WILDLIFE RESEARCH 2021. [DOI: 10.1071/wr20210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Abstract
ContextDisease is increasingly becoming a driver of wildlife population declines and an extinction risk. Vaccines are one of the most successful health interventions in human history, but few have been tested for mitigating wildlife disease. The transmissible cancer, devil facial tumour disease (DFTD), triggered the Tasmanian devil’s (Sarcophilus harrisii) inclusion on the international endangered species list. In 2016, 33 devils from a DFTD-free insurance population were given an experimental DFTD vaccination before their wild release on the Tasmanian northern coast.
AimTo determine the efficacy of the vaccination protocol and the longevity of the induced responses.
MethodSix trapping trips took place over the 2.5 years following release, and both vaccinated and incumbent devils had blood samples and tumour biopsies collected.
Key resultsIn all, 8 of the 33 vaccinated devils were re-trapped, and six of those developed DFTD within the monitoring period. Despite the lack of protection provided by the vaccine, we observed signs of immune activation not usually found in unvaccinated devils. First, sera collected from the eight devils showed that anti-DFTD antibodies persisted for up to 2 years post-vaccination. Second, tumour-infiltrating lymphocytes were found in three of four biopsies collected from vaccinated devils, which contrasts with the ‘immune deserts’ typical of DFTs; only 1 of the 20 incumbent devils with DFTD had a tumour biopsy exhibiting immune-cell infiltrate. Third, immunohistochemical analysis of the vaccinated devils’ tumour biopsies identified the functional immune molecules associated with antigen-presenting cells (MHC-II) and T-cells (CD3), and the immune checkpoint molecule PD-1, all being associated with anti-tumour immunity in other species.
ConclusionsThese results correlate with our previous study on captive devils in which a prophylactic vaccine primed the devil immune system and, following DFTD challenge and tumour growth, immunotherapy induced complete tumour regressions. The field trial results presented here provide further evidence that the devil immune system can be primed to recognise DFTD cells, but additional immune manipulation could be needed for complete protection or induction of tumour regressions.
ImplicationsA protective DFTD vaccine would provide a valuable management approach for conservation of the Tasmanian devil.
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30
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Simberloff D. Maintenance management and eradication of established aquatic invaders. HYDROBIOLOGIA 2021; 848:2399-2420. [PMID: 32836349 PMCID: PMC7407435 DOI: 10.1007/s10750-020-04352-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/01/2020] [Accepted: 07/08/2020] [Indexed: 05/04/2023]
Abstract
Although freshwater invasions have not been targeted for maintenance management or eradication as often as terrestrial invasions have, attempts to do so are frequent. Failures as well as successes abound, but several methods have been improved and new approaches are on the horizon. Many freshwater fish and plant invaders have been eliminated, especially by chemical and physical methods for fishes and herbicides for plants. Efforts to maintain invasive freshwater fishes at low levels have sometimes succeeded, although continuing the effort has proven challenging. By contrast, successful maintenance management of invasive freshwater plants is uncommon, although populations of several species have been managed by biological control. Invasive crayfish populations have rarely been controlled for long. Marine invasions have proven far less tractable than those in fresh water, with a few striking eradications of species detected before they had spread widely, and no marine invasions have been substantially managed for long at low levels. The rapid development of technologies based on genetics has engendered excitement about possibly eradicating or controlling terrestrial invaders, and such technologies may also prove useful for certain aquatic invaders. Methods of particular interest, alone or in various combinations, are gene-silencing, RNA-guided gene drives, and the use of transgenes.
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Affiliation(s)
- Daniel Simberloff
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996 USA
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Ohmer MEB, Costantini D, Czirják GÁ, Downs CJ, Ferguson LV, Flies A, Franklin CE, Kayigwe AN, Knutie S, Richards-Zawacki CL, Cramp RL. Applied ecoimmunology: using immunological tools to improve conservation efforts in a changing world. CONSERVATION PHYSIOLOGY 2021; 9:coab074. [PMID: 34512994 PMCID: PMC8422949 DOI: 10.1093/conphys/coab074] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/27/2021] [Accepted: 08/09/2021] [Indexed: 05/11/2023]
Abstract
Ecoimmunology is a rapidly developing field that explores how the environment shapes immune function, which in turn influences host-parasite relationships and disease outcomes. Host immune defence is a key fitness determinant because it underlies the capacity of animals to resist or tolerate potential infections. Importantly, immune function can be suppressed, depressed, reconfigured or stimulated by exposure to rapidly changing environmental drivers like temperature, pollutants and food availability. Thus, hosts may experience trade-offs resulting from altered investment in immune function under environmental stressors. As such, approaches in ecoimmunology can provide powerful tools to assist in the conservation of wildlife. Here, we provide case studies that explore the diverse ways that ecoimmunology can inform and advance conservation efforts, from understanding how Galapagos finches will fare with introduced parasites, to using methods from human oncology to design vaccines against a transmissible cancer in Tasmanian devils. In addition, we discuss the future of ecoimmunology and present 10 questions that can help guide this emerging field to better inform conservation decisions and biodiversity protection. From better linking changes in immune function to disease outcomes under different environmental conditions, to understanding how individual variation contributes to disease dynamics in wild populations, there is immense potential for ecoimmunology to inform the conservation of imperilled hosts in the face of new and re-emerging pathogens, in addition to improving the detection and management of emerging potential zoonoses.
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Affiliation(s)
- Michel E B Ohmer
- Living Earth Collaborative, Washington University in St. Louis, MO 63130, USA
| | - David Costantini
- Unité Physiologie Moléculaire et Adaptation (PhyMA), Muséum National d’Histoire Naturelle, CNRS, 57 Rue Cuvier, CP32, 75005, Paris, France
| | - Gábor Á Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
| | - Cynthia J Downs
- Department of Environmental Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Laura V Ferguson
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Andy Flies
- Menzies Institute for Medical Research, University of Tasmania, Tasmania 7001, Australia
| | - Craig E Franklin
- School of Biological Sciences, The University of Queensland, Queensland 4072, Australia
| | - Ahab N Kayigwe
- Menzies Institute for Medical Research, University of Tasmania, Tasmania 7001, Australia
| | - Sarah Knutie
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06268, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06268, USA
| | | | - Rebecca L Cramp
- School of Biological Sciences, The University of Queensland, Queensland 4072, Australia
- Corresponding author: School of Biological Sciences, The University of Queensland, Queensland 4072, Australia.
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32
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Gerdol M, Moreira R, Cruz F, Gómez-Garrido J, Vlasova A, Rosani U, Venier P, Naranjo-Ortiz MA, Murgarella M, Greco S, Balseiro P, Corvelo A, Frias L, Gut M, Gabaldón T, Pallavicini A, Canchaya C, Novoa B, Alioto TS, Posada D, Figueras A. Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel. Genome Biol 2020; 21:275. [PMID: 33168033 PMCID: PMC7653742 DOI: 10.1186/s13059-020-02180-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/15/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other bivalves. Although these traits have been recently linked with the maintenance of a high genetic variation within natural populations, the factors underlying the evolutionary success of this species remain unclear. RESULTS Here, after the assembly of a 1.28-Gb reference genome and the resequencing of 14 individuals from two independent populations, we reveal a complex pan-genomic architecture in M. galloprovincialis, with a core set of 45,000 genes plus a strikingly high number of dispensable genes (20,000) subject to presence-absence variation, which may be entirely missing in several individuals. We show that dispensable genes are associated with hemizygous genomic regions affected by structural variants, which overall account for nearly 580 Mb of DNA sequence not included in the reference genome assembly. As such, this is the first study to report the widespread occurrence of gene presence-absence variation at a whole-genome scale in the animal kingdom. CONCLUSIONS Dispensable genes usually belong to young and recently expanded gene families enriched in survival functions, which might be the key to explain the resilience and invasiveness of this species. This unique pan-genome architecture is characterized by dispensable genes in accessory genomic regions that exceed by orders of magnitude those observed in other metazoans, including humans, and closely mirror the open pan-genomes found in prokaryotes and in a few non-metazoan eukaryotes.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, Università degli Studi di Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Rebeca Moreira
- Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Jessica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Anna Vlasova
- CRG - Centre for Genomic Regulation, Doctor Aiguader, 88, 08003 Barcelona, Spain
| | - Umberto Rosani
- Department of Biology, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Paola Venier
- Department of Biology, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Miguel A. Naranjo-Ortiz
- CRG - Centre for Genomic Regulation, Doctor Aiguader, 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Maria Murgarella
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Samuele Greco
- Department of Life Sciences, Università degli Studi di Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Pablo Balseiro
- Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
- Norce Norwegian Research Centre AS, Bergen, Norway
| | - André Corvelo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- New York Genome Center, New York, NY 10013 USA
| | - Leonor Frias
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Toni Gabaldón
- CRG - Centre for Genomic Regulation, Doctor Aiguader, 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Current address: Barelona Supercomputing Centre (BSC-CNS) and Institute for Research in Biomedicine (IRB), 08034 Barcelona, Spain
| | - Alberto Pallavicini
- Department of Life Sciences, Università degli Studi di Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
- Anton Dohrn Zoological Station, 80121 Villa Comunale, Naples, Italy
| | - Carlos Canchaya
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute, 36310 Vigo, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
| | - Tyler S. Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute, 36310 Vigo, Spain
| | - Antonio Figueras
- Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
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Kwon YM, Gori K, Park N, Potts N, Swift K, Wang J, Stammnitz MR, Cannell N, Baez-Ortega A, Comte S, Fox S, Harmsen C, Huxtable S, Jones M, Kreiss A, Lawrence C, Lazenby B, Peck S, Pye R, Woods G, Zimmermann M, Wedge DC, Pemberton D, Stratton MR, Hamede R, Murchison EP. Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils. PLoS Biol 2020; 18:e3000926. [PMID: 33232318 PMCID: PMC7685465 DOI: 10.1371/journal.pbio.3000926] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/19/2020] [Indexed: 12/17/2022] Open
Abstract
Devil facial tumour 1 (DFT1) is a transmissible cancer clone endangering the Tasmanian devil. The expansion of DFT1 across Tasmania has been documented, but little is known of its evolutionary history. We analysed genomes of 648 DFT1 tumours collected throughout the disease range between 2003 and 2018. DFT1 diverged early into five clades, three spreading widely and two failing to persist. One clade has replaced others at several sites, and rates of DFT1 coinfection are high. DFT1 gradually accumulates copy number variants (CNVs), and its telomere lengths are short but constant. Recurrent CNVs reveal genes under positive selection, sites of genome instability, and repeated loss of a small derived chromosome. Cultured DFT1 cell lines have increased CNV frequency and undergo highly reproducible convergent evolution. Overall, DFT1 is a remarkably stable lineage whose genome illustrates how cancer cells adapt to diverse environments and persist in a parasitic niche.
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Affiliation(s)
- Young Mi Kwon
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Kevin Gori
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Naomi Park
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Nicole Potts
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Kate Swift
- Mount Pleasant Laboratories, Tasmanian Department of Primary Industries, Parks, Water and the Environment (DPIPWE), Prospect, Tasmania, Australia
| | - Jinhong Wang
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Maximilian R. Stammnitz
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Naomi Cannell
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Adrian Baez-Ortega
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sebastien Comte
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- Vertebrate Pest Research Unit, NSW Department of Primary Industries, Orange, New South Wales, Australia
| | - Samantha Fox
- Tasmanian Department of Primary Industries, Parks, Water and the Environment (DPIPWE), Save the Tasmanian Devil Program, Hobart, Tasmania, Australia
- Toledo Zoo, Toledo, Ohio, United States of America
| | - Colette Harmsen
- Mount Pleasant Laboratories, Tasmanian Department of Primary Industries, Parks, Water and the Environment (DPIPWE), Prospect, Tasmania, Australia
| | - Stewart Huxtable
- Tasmanian Department of Primary Industries, Parks, Water and the Environment (DPIPWE), Save the Tasmanian Devil Program, Hobart, Tasmania, Australia
| | - Menna Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Alexandre Kreiss
- Menzies Institute, University of Tasmania, Hobart, Tasmania, Australia
| | - Clare Lawrence
- Tasmanian Department of Primary Industries, Parks, Water and the Environment (DPIPWE), Save the Tasmanian Devil Program, Hobart, Tasmania, Australia
| | - Billie Lazenby
- Tasmanian Department of Primary Industries, Parks, Water and the Environment (DPIPWE), Save the Tasmanian Devil Program, Hobart, Tasmania, Australia
| | - Sarah Peck
- Tasmanian Department of Primary Industries, Parks, Water and the Environment (DPIPWE), Save the Tasmanian Devil Program, Hobart, Tasmania, Australia
| | - Ruth Pye
- Menzies Institute, University of Tasmania, Hobart, Tasmania, Australia
| | - Gregory Woods
- Menzies Institute, University of Tasmania, Hobart, Tasmania, Australia
| | - Mona Zimmermann
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - David C. Wedge
- Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - David Pemberton
- Tasmanian Department of Primary Industries, Parks, Water and the Environment (DPIPWE), Save the Tasmanian Devil Program, 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
| | - Elizabeth P. Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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Deakin JE, Potter S. Marsupial chromosomics: bridging the gap between genomes and chromosomes. Reprod Fertil Dev 2020; 31:1189-1202. [PMID: 30630589 DOI: 10.1071/rd18201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 12/05/2018] [Indexed: 12/12/2022] Open
Abstract
Marsupials have unique features that make them particularly interesting to study, and sequencing of marsupial genomes is helping to understand their evolution. A decade ago, it was a huge feat to sequence the first marsupial genome. Now, the advances in sequencing technology have made the sequencing of many more marsupial genomes possible. However, the DNA sequence is only one component of the structures it is packaged into: chromosomes. Knowing the arrangement of the DNA sequence on each chromosome is essential for a genome assembly to be used to its full potential. The importance of combining sequence information with cytogenetics has previously been demonstrated for rapidly evolving regions of the genome, such as the sex chromosomes, as well as for reconstructing the ancestral marsupial karyotype and understanding the chromosome rearrangements involved in the Tasmanian devil facial tumour disease. Despite the recent advances in sequencing technology assisting in genome assembly, physical anchoring of the sequence to chromosomes is required to achieve a chromosome-level assembly. Once chromosome-level assemblies are achieved for more marsupials, we will be able to investigate changes in the packaging and interactions between chromosomes to gain an understanding of the role genome architecture has played during marsupial evolution.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Sally Potter
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
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Kozakiewicz CP, Ricci L, Patton AH, Stahlke AR, Hendricks SA, Margres MJ, Ruiz-Aravena M, Hamilton DG, Hamede R, McCallum H, Jones ME, Hohenlohe PA, Storfer A. Comparative landscape genetics reveals differential effects of environment on host and pathogen genetic structure in Tasmanian devils (Sarcophilus harrisii) and their transmissible tumour. Mol Ecol 2020; 29:3217-3233. [PMID: 32682353 PMCID: PMC9805799 DOI: 10.1111/mec.15558] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 06/24/2020] [Accepted: 07/08/2020] [Indexed: 01/03/2023]
Abstract
Genetic structure in host species is often used to predict disease spread. However, host and pathogen genetic variation may be incongruent. Understanding landscape factors that have either concordant or divergent influence on host and pathogen genetic structure is crucial for wildlife disease management. Devil facial tumour disease (DFTD) was first observed in 1996 and has spread throughout almost the entire Tasmanian devil geographic range, causing dramatic population declines. Whereas DFTD is predominantly spread via biting among adults, devils typically disperse as juveniles, which experience low DFTD prevalence. Thus, we predicted little association between devil and tumour population structure and that environmental factors influencing gene flow differ between devils and tumours. We employed a comparative landscape genetics framework to test the influence of environmental factors on patterns of isolation by resistance (IBR) and isolation by environment (IBE) in devils and DFTD. Although we found evidence for broad-scale costructuring between devils and tumours, we found no relationship between host and tumour individual genetic distances. Further, the factors driving the spatial distribution of genetic variation differed for each. Devils exhibited a strong IBR pattern driven by major roads, with no evidence of IBE. By contrast, tumours showed little evidence for IBR and a weak IBE pattern with respect to elevation in one of two tumour clusters we identify herein. Our results warrant caution when inferring pathogen spread using host population genetic structure and suggest that reliance on environmental barriers to host connectivity may be ineffective for managing the spread of wildlife diseases. Our findings demonstrate the utility of comparative landscape genetics for identifying differential factors driving host dispersal and pathogen transmission.
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Affiliation(s)
| | - Lauren Ricci
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Austin H. Patton
- School of Biological Sciences, Washington State University, Pullman, Washington, USA,Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Amanda R. Stahlke
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - Sarah A. Hendricks
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - Mark J. Margres
- School of Biological Sciences, Washington State University, Pullman, Washington, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Manuel Ruiz-Aravena
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia,Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - 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
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, USA,corresponding author: Andrew Storfer, School of Biological Sciences, Washington State University, Pullman, WA, USA.
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36
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Boddy AM, Harrison TM, Abegglen LM. Comparative Oncology: New Insights into an Ancient Disease. iScience 2020; 23:101373. [PMID: 32738614 PMCID: PMC7394918 DOI: 10.1016/j.isci.2020.101373] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/30/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer has deep evolutionary roots and is an important source of selective pressure in organismal evolution. Yet, we find a great deal of variation in cancer vulnerabilities across the tree of life. Comparative oncology offers insights into why some species vary in their susceptibility to cancer and the mechanisms responsible for the diversity of cancer defenses. Here we provide an overview for why cancer persists across the tree of life. We then summarize current data on cancer in mammals, reptiles, and birds in comparison with commonly reported human cancers. We report on both novel and shared mechanisms of cancer protection in animals. Cross-discipline collaborations, including zoological and aquarium institutions, wildlife and evolutionary biologists, veterinarians, medical doctors, cancer biologists, and oncologists, will be essential for progress in the field of comparative oncology. Improving medical treatment of humans and animals with cancer is the ultimate promise of comparative oncology.
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Affiliation(s)
- Amy M Boddy
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Tara M Harrison
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Lisa M Abegglen
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
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Hamede R, Owen R, Siddle H, Peck S, Jones M, Dujon AM, Giraudeau M, Roche B, Ujvari B, Thomas F. The ecology and evolution of wildlife cancers: Applications for management and conservation. Evol Appl 2020; 13:1719-1732. [PMID: 32821279 PMCID: PMC7428810 DOI: 10.1111/eva.12948] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/23/2020] [Accepted: 02/28/2020] [Indexed: 02/06/2023] Open
Abstract
Ecological and evolutionary concepts have been widely adopted to understand host-pathogen dynamics, and more recently, integrated into wildlife disease management. Cancer is a ubiquitous disease that affects most metazoan species; however, the role of oncogenic phenomena in eco-evolutionary processes and its implications for wildlife management and conservation remains undeveloped. Despite the pervasive nature of cancer across taxa, our ability to detect its occurrence, progression and prevalence in wildlife populations is constrained due to logistic and diagnostic limitations, which suggests that most cancers in the wild are unreported and understudied. Nevertheless, an increasing number of virus-associated and directly transmissible cancers in terrestrial and aquatic environments have been detected. Furthermore, anthropogenic activities and sudden environmental changes are increasingly associated with cancer incidence in wildlife. This highlights the need to upscale surveillance efforts, collection of critical data and developing novel approaches for studying the emergence and evolution of cancers in the wild. Here, we discuss the relevance of malignant cells as important agents of selection and offer a holistic framework to understand the interplay of ecological, epidemiological and evolutionary dynamics of cancer in wildlife. We use a directly transmissible cancer (devil facial tumour disease) as a model system to reveal the potential evolutionary dynamics and broader ecological effects of cancer epidemics in wildlife. We provide further examples of tumour-host interactions and trade-offs that may lead to changes in life histories, and epidemiological and population dynamics. Within this framework, we explore immunological strategies at the individual level as well as transgenerational adaptations at the population level. Then, we highlight the need to integrate multiple disciplines to undertake comparative cancer research at the human-domestic-wildlife interface and their environments. Finally, we suggest strategies for screening cancer incidence in wildlife and discuss how to integrate ecological and evolutionary concepts in the management of current and future cancer epizootics.
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Affiliation(s)
- Rodrigo Hamede
- School of Natural SciencesUniversity of TasmaniaHobartTas.Australia
- Centre for Integrative EcologySchool of Life and Environmental SciencesDeakin UniversityVic.Australia
| | - Rachel Owen
- Centre for Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Hannah Siddle
- Centre for Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Sarah Peck
- Wildlife Veterinarian, Veterinary Register of TasmaniaSouth HobartTas.Australia
| | - Menna Jones
- School of Natural SciencesUniversity of TasmaniaHobartTas.Australia
| | - Antoine M. Dujon
- Centre for Integrative EcologySchool of Life and Environmental SciencesDeakin UniversityVic.Australia
| | - Mathieu Giraudeau
- Centre de Recherches Ecologiques et Evolutives sur le Cancer/Centre de Recherches en Ecologie et Evolution de la SantéUnité Mixte de RecherchesInstitut de Recherches pour le Développement 224‐Centre National de la Recherche Scientifique 5290‐Université de MontpellierMontpellierFrance
| | - Benjamin Roche
- Centre de Recherches Ecologiques et Evolutives sur le Cancer/Centre de Recherches en Ecologie et Evolution de la SantéUnité Mixte de RecherchesInstitut de Recherches pour le Développement 224‐Centre National de la Recherche Scientifique 5290‐Université de MontpellierMontpellierFrance
| | - Beata Ujvari
- School of Natural SciencesUniversity of TasmaniaHobartTas.Australia
- Centre for Integrative EcologySchool of Life and Environmental SciencesDeakin UniversityVic.Australia
| | - Frédéric Thomas
- Centre de Recherches Ecologiques et Evolutives sur le Cancer/Centre de Recherches en Ecologie et Evolution de la SantéUnité Mixte de RecherchesInstitut de Recherches pour le Développement 224‐Centre National de la Recherche Scientifique 5290‐Université de MontpellierMontpellierFrance
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Dujon AM, Gatenby RA, Bramwell G, MacDonald N, Dohrmann E, Raven N, Schultz A, Hamede R, Gérard AL, Giraudeau M, Thomas F, Ujvari B. Transmissible Cancers in an Evolutionary Perspective. iScience 2020; 23:101269. [PMID: 32592998 PMCID: PMC7327844 DOI: 10.1016/j.isci.2020.101269] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/02/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023] Open
Abstract
Inter-individual transmission of cancer cells represents an intriguing and unexplored host-pathogen system, with significant ecological and evolutionary ramifications. The pathogen consists of clonal malignant cell lines that spread horizontally as allografts and/or xenografts. Although only nine transmissible cancer lineages in eight host species from both terrestrial and marine environments have been investigated, they exhibit evolutionary dynamics that may provide novel insights into tumor-host interactions particularly in the formation of metastases. Here we present an overview of known transmissible cancers, discuss the necessary and sufficient conditions for cancer transmission, and provide a comprehensive review on the evolutionary dynamics between transmissible cancers and their hosts.
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Affiliation(s)
- Antoine M Dujon
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic 3216, Australia
| | - Robert A Gatenby
- Department of Radiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Georgina Bramwell
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic 3216, Australia
| | - Nick MacDonald
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic 3216, Australia
| | - Erin Dohrmann
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic 3216, Australia
| | - Nynke Raven
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic 3216, Australia
| | - Aaron Schultz
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic 3216, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Anne-Lise Gérard
- CREEC, UMR IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
| | - Mathieu Giraudeau
- CREEC, UMR IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
| | - Frédéric Thomas
- CREEC, UMR IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
| | - Beata Ujvari
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic 3216, Australia; School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia.
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Patchett AL, Flies AS, Lyons AB, Woods GM. Curse of the devil: molecular insights into the emergence of transmissible cancers in the Tasmanian devil (Sarcophilus harrisii). Cell Mol Life Sci 2020; 77:2507-2525. [PMID: 31900624 PMCID: PMC11104928 DOI: 10.1007/s00018-019-03435-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022]
Abstract
The Tasmanian devil (Sarcophilus harrisii) is the only mammalian species known to be affected by multiple transmissible cancers. Devil facial tumours 1 and 2 (DFT1 and DFT2) are independent neoplastic cell lineages that produce large, disfiguring cancers known as devil facial tumour disease (DFTD). The long-term persistence of wild Tasmanian devils is threatened due to the ability of DFTD cells to propagate as contagious allografts and the high mortality rate of DFTD. Recent studies have demonstrated that both DFT1 and DFT2 cancers originated from founder cells of the Schwann cell lineage, an uncommon origin of malignant cancer in humans. This unprecedented finding has revealed a potential predisposition of Tasmanian devils to transmissible cancers of the Schwann cell lineage. In this review, we compare the molecular nature of human Schwann cells and nerve sheath tumours with DFT1 and DFT2 to gain insights into the emergence of transmissible cancers in the Tasmanian devil. We discuss a potential mechanism, whereby Schwann cell plasticity and frequent wounding in Tasmanian devils combine with an inherent cancer predisposition and low genetic diversity to give rise to transmissible Schwann cell cancers in devils on rare occasions.
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Affiliation(s)
- Amanda L Patchett
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Andrew S Flies
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - A Bruce Lyons
- School of Medicine, University of Tasmania, Hobart, TAS, 7000, Australia
| | - Gregory M Woods
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
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40
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Flies AS, Darby JM, Lennard PR, Murphy PR, Ong CEB, Pinfold TL, De Luca A, Lyons AB, Woods GM, Patchett AL. A novel system to map protein interactions reveals evolutionarily conserved immune evasion pathways on transmissible cancers. SCIENCE ADVANCES 2020; 6:6/27/eaba5031. [PMID: 32937435 PMCID: PMC7458443 DOI: 10.1126/sciadv.aba5031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/20/2020] [Indexed: 05/02/2023]
Abstract
Around 40% of humans and Tasmanian devils (Sarcophilus harrisii) develop cancer in their lifetime, compared to less than 10% for most species. In addition, devils are affected by two of the three known transmissible cancers in mammals. Immune checkpoint immunotherapy has transformed human medicine, but a lack of species-specific reagents has limited checkpoint immunology in most species. We developed a cut-and-paste reagent development system and used the fluorescent fusion protein system to show that immune checkpoint interactions are conserved across 160,000,000 years of evolution, CD200 is highly expressed on transmissible tumor cells, and coexpression of CD200R1 can block CD200 surface expression. The system's versatility across species was demonstrated by fusing a fluorescent reporter to a camelid-derived nanobody that binds human programmed death ligand 1. The evolutionarily conserved pathways suggest that naturally occurring cancers in devils and other species can be used to advance our understanding of cancer and immunological tolerance.
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Affiliation(s)
- Andrew S Flies
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia.
| | - Jocelyn M Darby
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia
| | - Patrick R Lennard
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia
- The Roslin Institute and Royal School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Peter R Murphy
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Chrissie E B Ong
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia
| | - Terry L Pinfold
- School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia
| | - Alana De Luca
- School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia
| | - A Bruce Lyons
- School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia
| | - Gregory M Woods
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia
| | - Amanda L Patchett
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia
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41
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Spontaneous Tumor Regression in Tasmanian Devils Associated with RASL11A Activation. Genetics 2020; 215:1143-1152. [PMID: 32554701 DOI: 10.1534/genetics.120.303428] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/12/2020] [Indexed: 12/30/2022] Open
Abstract
Spontaneous tumor regression has been documented in a small proportion of human cancer patients, but the specific mechanisms underlying tumor regression without treatment are not well understood. Tasmanian devils are threatened with extinction from a transmissible cancer due to universal susceptibility and a near 100% case fatality rate. In over 10,000 cases, <20 instances of natural tumor regression have been detected. Previous work in this system has focused on Tasmanian devil genetic variation associated with the regression phenotype. Here, we used comparative and functional genomics to identify tumor genetic variation associated with tumor regression. We show that a single point mutation in the 5' untranslated region of the putative tumor suppressor RASL11A significantly contributes to tumor regression. RASL11A was expressed in regressed tumors but silenced in wild-type, nonregressed tumors, consistent with RASL11A downregulation in human cancers. Induced RASL11A expression significantly reduced tumor cell proliferation in vitro The RAS pathway is frequently altered in human cancers, and RASL11A activation may provide a therapeutic treatment option for Tasmanian devils as well as a general mechanism for tumor inhibition.
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42
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Fraik AK, Margres MJ, Epstein B, Barbosa S, Jones M, Hendricks S, Schönfeld B, Stahlke AR, Veillet A, Hamede R, McCallum H, Lopez-Contreras E, Kallinen SJ, Hohenlohe PA, Kelley JL, Storfer A. Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations. Evolution 2020; 74:1392-1408. [PMID: 32445281 DOI: 10.1111/evo.14023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 05/14/2020] [Indexed: 12/11/2022]
Abstract
Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors (i.e., disease). The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species' extinction, suggesting possible adaptation to DFTD. Here, we test the extent to which spatial variation and genetic diversity are associated with the abiotic environment (i.e., climatic variables, elevation, vegetation cover) and/or DFTD. We employ genetic-environment association analyses using 6886 SNPs from 3287 individuals sampled pre- and post-disease arrival across the devil's geographic range. Pre-disease, we find significant correlations of allele frequencies with environmental variables, including 365 unique loci linked to 71 genes, suggesting local adaptation to abiotic environment. The majority of candidate loci detected pre-DFTD are not detected post-DFTD arrival. Several post-DFTD candidate loci are associated with disease prevalence and were in linkage disequilibrium with genes involved in tumor suppression and immune response. Loss of apparent signal of abiotic local adaptation post-disease suggests swamping by strong selection resulting from the rapid onset of DFTD.
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Affiliation(s)
- Alexandra K Fraik
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Mark J Margres
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Brendan Epstein
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164.,Plant Biology, University of Minnesota, Minneapolis, Minnesota, 55455
| | - Soraia Barbosa
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Menna Jones
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Sarah Hendricks
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Barbara Schönfeld
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Amanda R Stahlke
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Anne Veillet
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Rodrigo Hamede
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Hamish McCallum
- School of Environment, Griffith University Nathan, Nathan, QLD, 4111, Australia
| | - Elisa Lopez-Contreras
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Samantha J Kallinen
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
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43
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Boddy AM, Abegglen LM, Pessier AP, Aktipis A, Schiffman JD, Maley CC, Witte C. Lifetime cancer prevalence and life history traits in mammals. EVOLUTION MEDICINE AND PUBLIC HEALTH 2020; 2020:187-195. [PMID: 33209304 PMCID: PMC7652303 DOI: 10.1093/emph/eoaa015] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/19/2020] [Indexed: 12/12/2022]
Abstract
Background Cancer is a common diagnosis in many mammalian species, yet they vary in their vulnerability to cancer. The factors driving this variation are unknown, but life history theory offers potential explanations to why cancer defense mechanisms are not equal across species. Methodology Here we report the prevalence of neoplasia and malignancy in 37 mammalian species, representing 11 mammalian orders, using 42 years of well curated necropsy data from the San Diego Zoo and San Diego Zoo Safari Park. We collected data on life history components of these species and tested for associations between life history traits and both neoplasia and malignancy, while controlling for phylogenetic history. Results These results support Peto's paradox, in that we find no association between lifespan and/or body mass and the prevalence of neoplasia or malignancy. However, a positive relationship exists between litter size and prevalence of malignancy (P = 0.005, Adj. R2 = 0.212), suggesting that a species' life history strategy may influence cancer vulnerabilities. Lastly, we tested for the relationship between placental invasiveness and malignancy. We find no evidence for an association between placental depth and malignancy prevalence (P = 0.618, Adj. R2 = 0.068). Conclusions Life history theory offers a powerful framework to understand variation in cancer defenses across the tree of life. These findings provide insight into the relationship between life history traits and cancer vulnerabilities, which suggest a trade-off between reproduction and cancer defenses. Lay summary Why are some mammals more vulnerable to cancer than others? We test whether life history trade-offs may explain this variation in cancer risk. Bigger, longer-lived animals do not develop more cancer compared to smaller, shorter-lived animals. However, we find a positive association between litter size and cancer prevalence in mammals.
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Affiliation(s)
- Amy M Boddy
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Lisa M Abegglen
- Department of Pediatrics and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Allan P Pessier
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA
| | - Athena Aktipis
- Department of Psychology, Arizona State University, Tempe, AZ.,Arizona Cancer Evolution Center, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Joshua D Schiffman
- Department of Pediatrics and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Carlo C Maley
- Arizona Cancer Evolution Center, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Carmel Witte
- Institute for Conservation Research, San Diego Zoo Global, CA, USA
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44
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Patchett AL, Coorens THH, Darby J, Wilson R, McKay MJ, Kamath KS, Rubin A, Wakefield M, Mcintosh L, Mangiola S, Pye RJ, Flies AS, Corcoran LM, Lyons AB, Woods GM, Murchison EP, Papenfuss AT, Tovar C. Two of a kind: transmissible Schwann cell cancers in the endangered Tasmanian devil (Sarcophilus harrisii). Cell Mol Life Sci 2020; 77:1847-1858. [PMID: 31375869 PMCID: PMC11104932 DOI: 10.1007/s00018-019-03259-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 01/01/2023]
Abstract
Devil facial tumour disease (DFTD) comprises two genetically distinct transmissible cancers (DFT1 and DFT2) endangering the survival of the Tasmanian devil (Sarcophilus harrisii) in the wild. DFT1 first arose from a cell of the Schwann cell lineage; however, the tissue-of-origin of the recently discovered DFT2 cancer is unknown. In this study, we compared the transcriptome and proteome of DFT2 tumours to DFT1 and normal Tasmanian devil tissues to determine the tissue-of-origin of the DFT2 cancer. Our findings demonstrate that DFT2 expresses a range of Schwann cell markers and exhibits expression patterns consistent with a similar origin to the DFT1 cancer. Furthermore, DFT2 cells express genes associated with the repair response to peripheral nerve damage. These findings suggest that devils may be predisposed to transmissible cancers of Schwann cell origin. The combined effect of factors such as frequent nerve damage from biting, Schwann cell plasticity and low genetic diversity may allow these cancers to develop on rare occasions. The emergence of two independent transmissible cancers from the same tissue in the Tasmanian devil presents an unprecedented opportunity to gain insight into cancer development, evolution and immune evasion in mammalian species.
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Affiliation(s)
- Amanda L Patchett
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
| | - Tim H H Coorens
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Jocelyn Darby
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS, 7001, Australia
| | - Matthew J McKay
- Australian Proteome Analysis Facility, Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Karthik S Kamath
- Australian Proteome Analysis Facility, Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Alan Rubin
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3000, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Matthew Wakefield
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3000, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Lachlan Mcintosh
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3000, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Stefano Mangiola
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3000, Australia
- Department of Surgery, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Ruth J Pye
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Andrew S Flies
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Lynn M Corcoran
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3000, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - A Bruce Lyons
- School of Medicine, University of Tasmania, Hobart, TAS, 7000, Australia
| | - Gregory M Woods
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | | | - Anthony T Papenfuss
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3000, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3000, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Cesar Tovar
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
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45
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Comparative Cytogenetic Mapping and Telomere Analysis Provide Evolutionary Predictions for Devil Facial Tumour 2. Genes (Basel) 2020; 11:genes11050480. [PMID: 32354058 PMCID: PMC7290341 DOI: 10.3390/genes11050480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/06/2020] [Accepted: 04/26/2020] [Indexed: 01/20/2023] Open
Abstract
The emergence of a second transmissible tumour in the Tasmanian devil population, devil facial tumour 2 (DFT2), has prompted questions on the origin and evolution of these transmissible tumours. We used a combination of cytogenetic mapping and telomere length measurements to predict the evolutionary trajectory of chromosome rearrangements in DFT2. Gene mapping by fluorescence in situ hybridization (FISH) provided insight into the chromosome rearrangements in DFT2 and identified the evolution of two distinct DFT2 lineages. A comparison of devil facial tumour 1 (DFT1) and DFT2 chromosome rearrangements indicated that both started with the fusion of a chromosome, with potentially critically short telomeres, to chromosome 1 to form dicentric chromosomes. In DFT1, the dicentric chromosome resulted in breakage–fusion–bridge cycles leading to highly rearranged chromosomes. In contrast, the silencing of a centromere on the dicentric chromosome in DFT2 stabilized the chromosome, resulting in a less rearranged karyotype than DFT1. DFT2 retains a bimodal distribution of telomere length dimorphism observed on Tasmanian devil chromosomes, a feature lost in DFT1. Using long term cell culture, we observed homogenization of telomere length over time. We predict a similar homogenization of telomere lengths occurred in DFT1, and that DFT2 is unlikely to undergo further substantial rearrangements due to maintained telomere length.
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46
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Woods GM, Lyons AB, Bettiol SS. A Devil of a Transmissible Cancer. Trop Med Infect Dis 2020; 5:tropicalmed5020050. [PMID: 32244613 PMCID: PMC7345153 DOI: 10.3390/tropicalmed5020050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/25/2022] Open
Abstract
Devil facial tumor disease (DFTD) encompasses two independent transmissible cancers that have killed the majority of Tasmanian devils. The cancer cells are derived from Schwann cells and are spread between devils during biting, a common behavior during the mating season. The Centers for Disease Control and Prevention (CDC) defines a parasite as "An organism that lives on or in a host organism and gets its food from, or at, the expense of its host." Most cancers, including DFTD, live within a host organism and derive resources from its host, and consequently have parasitic-like features. Devil facial tumor disease is a transmissible cancer and, therefore, DFTD shares one additional feature common to most parasites. Through direct contact between devils, DFTD has spread throughout the devil population. However, unlike many parasites, the DFTD cancer cells have a simple lifecycle and do not have either independent, vector-borne, or quiescent phases. To facilitate a description of devil facial tumor disease, this review uses life cycles of parasites as an analogy.
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Affiliation(s)
- Gregory M. Woods
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia
- Correspondence:
| | - A. Bruce Lyons
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia; (A.B.L.); (S.S.B.)
| | - Silvana S. Bettiol
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia; (A.B.L.); (S.S.B.)
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47
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Dujon AM, Schofield G, Bramwell G, Raven N, Hamede R, Thomas F, Ujvari B. Global meta‐analysis of over 50 years of multidisciplinary and international collaborations on transmissible cancers. Evol Appl 2020. [DOI: 10.1111/eva.12938] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Antoine M. Dujon
- School of Life and Environmental Sciences Centre for Integrative Ecology Deakin University Victoria Australia
- CREEC/MIVEGEC UMR IRD/CNRS/UM 5290 Montpellier Cedex 5 France
| | - Gail Schofield
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - Georgina Bramwell
- School of Life and Environmental Sciences Centre for Integrative Ecology Deakin University Victoria Australia
| | - Nynke Raven
- School of Life and Environmental Sciences Centre for Integrative Ecology Deakin University Victoria Australia
| | - Rodrigo Hamede
- School of Natural Sciences University of Tasmania Hobart Tasmania Australia
| | - Frédéric Thomas
- CREEC/MIVEGEC UMR IRD/CNRS/UM 5290 Montpellier Cedex 5 France
| | - Beata Ujvari
- School of Life and Environmental Sciences Centre for Integrative Ecology Deakin University Victoria Australia
- School of Natural Sciences University of Tasmania Hobart Tasmania Australia
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48
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Affiliation(s)
- Amanda Patchett
- Menzies Institute for Medical Research, Hobart, Tasmania 7000, Australia
| | - Gregory Woods
- Menzies Institute for Medical Research, Hobart, Tasmania 7000, Australia.
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49
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Patton AH, Margres MJ, Stahlke AR, Hendricks S, Lewallen K, Hamede RK, Ruiz-Aravena M, Ryder O, McCallum HI, Jones ME, Hohenlohe PA, Storfer A. Contemporary Demographic Reconstruction Methods Are Robust to Genome Assembly Quality: A Case Study in Tasmanian Devils. Mol Biol Evol 2020; 36:2906-2921. [PMID: 31424552 PMCID: PMC6878949 DOI: 10.1093/molbev/msz191] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Reconstructing species’ demographic histories is a central focus of molecular ecology and evolution. Recently, an expanding suite of methods leveraging either the sequentially Markovian coalescent (SMC) or the site-frequency spectrum has been developed to reconstruct population size histories from genomic sequence data. However, few studies have investigated the robustness of these methods to genome assemblies of varying quality. In this study, we first present an improved genome assembly for the Tasmanian devil using the Chicago library method. Compared with the original reference genome, our new assembly reduces the number of scaffolds (from 35,975 to 10,010) and increases the scaffold N90 (from 0.101 to 2.164 Mb). Second, we assess the performance of four contemporary genomic methods for inferring population size history (PSMC, MSMC, SMC++, Stairway Plot), using the two devil genome assemblies as well as simulated, artificially fragmented genomes that approximate the hypothesized demographic history of Tasmanian devils. We demonstrate that each method is robust to assembly quality, producing similar estimates of Ne when simulated genomes were fragmented into up to 5,000 scaffolds. Overall, methods reliant on the SMC are most reliable between ∼300 generations before present (gbp) and 100 kgbp, whereas methods exclusively reliant on the site-frequency spectrum are most reliable between the present and 30 gbp. Our results suggest that when used in concert, genomic methods for reconstructing species’ effective population size histories 1) can be applied to nonmodel organisms without highly contiguous reference genomes, and 2) are capable of detecting independently documented effects of historical geological events.
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Affiliation(s)
- Austin H Patton
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Mark J Margres
- School of Biological Sciences, Washington State University, Pullman, WA.,Department of Organismic and Evolutionary Biology, Harvard University, MA
| | - Amanda R Stahlke
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Sarah Hendricks
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Kevin Lewallen
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Rodrigo K Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | | | - Oliver Ryder
- Institute for Conservation Research, San Diego, CA
| | | | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA
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50
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Flies AS, Flies EJ, Fox S, Gilbert A, Johnson SR, Liu GS, Lyons AB, Patchett AL, Pemberton D, Pye RJ. An oral bait vaccination approach for the Tasmanian devil facial tumor diseases. Expert Rev Vaccines 2020; 19:1-10. [PMID: 31971036 DOI: 10.1080/14760584.2020.1711058] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Introduction: The Tasmanian devil (Sarcophilus harrisii) is the largest extant carnivorous marsupial. Since 1996, its population has declined by 77% primarily due to a clonal transmissible tumor, known as devil facial tumor (DFT1) disease. In 2014, a second transmissible devil facial tumor (DFT2) was discovered. DFT1 and DFT2 are nearly 100% fatal.Areas covered: We review DFT control approaches and propose a rabies-style oral bait vaccine (OBV) platform for DFTs. This approach has an extensive safety record and was a primary tool in large-scale rabies virus elimination from wild carnivores across diverse landscapes. Like rabies virus, DFTs are transmitted by oral contact, so immunizing the oral cavity and stimulating resident memory cells could be advantageous. Additionally, exposing infected devils that already have tumors to OBVs could serve as an oncolytic virus immunotherapy. The primary challenges may be identifying appropriate DFT-specific antigens and optimization of field delivery methods.Expert opinion: DFT2 is currently found on a peninsula in southern Tasmania, so an OBV that could eliminate DFT2 should be the priority for this vaccine approach. Translation of an OBV approach to control DFTs will be challenging, but the approach is feasible for combatting ongoing and future disease threats.
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Affiliation(s)
- Andrew S Flies
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Australia
| | - Emily J Flies
- School of Natural Sciences, College of Sciences and Engineering, University of Tasmania, Sandy Bay, Australia
| | - Samantha Fox
- Save the Tasmanian Devil Program, DPIPWE, Hobart, Australia.,Toledo Zoo, Toledo, OH, USA
| | - Amy Gilbert
- National Wildlife Research Center, USDA, APHIS, Wildlife Services, Fort Collins, CO, USA
| | - Shylo R Johnson
- National Wildlife Research Center, USDA, APHIS, Wildlife Services, Fort Collins, CO, USA
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, Australia
| | - A Bruce Lyons
- School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Australia
| | - Amanda L Patchett
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Australia
| | | | - Ruth J Pye
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Australia
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