New insights into the role of MHC diversity in devil facial tumour disease

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Lane, Amanda ^a   Cheng, Yuanyuan ^a   Wright, Belinda ^a,b   Hamede, Rodrigo ^c   Levan, Laura ^a,d   Jones, Menna ^c   Ujvari, Beata ^a   Belov, Katherine ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b MACQUARIE UNIVERSITY   (Australia)

^c UNIVERSITY OF TASMANIA   (Australia)

^d UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MICROSATELLITE DNA;

ALLELE; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; AUSTRALIA; CONTROLLED STUDY; COPY NUMBER VARIATION; DEVIL FACIAL TUMOR DISEASE; DNA SEQUENCE; FEMALE; GENE DELETION; GENE FREQUENCY; GENE LOCUS; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; MAJOR HISTOCOMPATIBILITY COMPLEX; MALE; MARSUPIAL; MICROSATELLITE MARKER; MOUSE; NEOPLASM; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; SARCOPHILUS HARRISSI; ANIMAL; ANIMAL DISEASE; CASE CONTROL STUDY; COMPARATIVE STUDY; FACE TUMOR; GENETICS; IMMUNOLOGY; MOLECULAR GENETICS;

ANIMALS; BASE SEQUENCE; CASE-CONTROL STUDIES; DNA COPY NUMBER VARIATIONS; FACIAL NEOPLASMS; GENE FREQUENCY; GENETIC VARIATION; MAJOR HISTOCOMPATIBILITY COMPLEX; MARSUPIALIA; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; TASMANIA;

EID: 84862010465     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0036955     Document Type: Article

References (52)

1. McCallum H, Jones M, Hawkins C, Hamede R, Lachish S, et al. (2009) Transmission dynamics of Tasmanian devil facial tumor disease may lead to disease-induced extinction. Ecology 90: 3379-3392.
2. The IUCN Red List of Threatened Species. 15 Available: http://www.iucnredlist.org/apps/redlist/details/40540/0. Accessed 2012 May.
3. Pearse A-M, Swift K, (2006) Transmission of devil facial-tumour disease. Nature 439: 549.
4. Pyecroft SB, Pearse A-M, Loh R, Swift K, Belov K, et al. (2007) Towards a case definition for Devil Facial Tumour Disease: What is it? EcoHealth 4: 346-351.
5. Siddle HV, Kriess A, Eldridge MD, Noonan E, Clarke CJ, et al. (2007a) Transmission of a fatal clonal tumour by biting occurs due to depleted MHC diversity in a threatened carnivorous marsupial. Proc Natl Acad Sci 104: 16221-16226.
6. Pemberton D, Renouf D, (1993) A field study of communication and social behaviour of the Tasmanlian devil at feeding sites. Aust J Zool 41: 507-526.
7. Hamede RK, McCallum H, Jones M, (2008) Seasonal, demographic and density-related patterns of contact between Tasmanian devils (Sarcophilus harrisii): Implications for transmission of devil facial tumour disease. Austral Ecol 33: 614-622.
8. Loh R, Bergfeld J, Hayes D, O'Hara A, Pyecroft S, et al. (2006) The pathology of Devil Facial Tumour Disease (DFTD) in Tasmanian devils (Sarcophilus harrisii). Vet Pathol 43: 890-895.
9. Hawkins CE, Baars C, Hesterman H, Hocking GJ, Jones ME, et al. (2006) Emerging disease and population decline of an island endemic, the Tasmanian devil Sarcophilus harrisii. Biol Conserv 131: 307-324.
10. Lachish S, Jones M, McCallum H, (2007) The impact of disease on the survival and population growth rate of the Tasmanian devil. J Anim Ecol 76: 926-936.
11. Lachish S, McCallum H, Jones M, (2009) Demography, disease and the devil: life-history changes in a disease-affected population of Tasmanian devils (Sarcophilus harrisii). J Anim Ecol 78: 427-436.
12. Lachish S, Miller KJ, Storfer A, Goldizen AW, Jones M, et al. (2011) Evidence that disease-induced population decline changes genetic structure and alters dispersal patterns in the Tasmanian devil. Heredity 106: 172-182.
13. Jones M, Cockburn A, Hamede RK, Hawkins CE, Hesterman H, et al. (2008) Life-history change in disease-ravaged Tasmanian devil populations. Proc Natl Acad Sci 105: 1-5.
14. Murchison EP, Tovar C, Hsu A, Bender HS, Kheradpour P, et al. (2010) The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science 327: 84-87.
15. Jones ME, Paetkau D, Geffen E, Moritz C, (2004) Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore. Mol Ecol 13: 2197-2209.
16. Miller W, Hayes VM, Ratan A, Petersen, DC, Wittekindt NE, et al. (2011) Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proc Natl Acad Sci 108: 12348-53.
17. Woods GM, Kreiss A, Belov K, Siddle HV, Obendorf DL, et al. (2007) The immune response of the Tasmanian devil (Sarcophilus harrisii) and Devil Facial Tumour Disease. Ecohealth 4: 338-345.
18. Belov K, (2011) The role of the Major Histocompatibility Complex in the spread of contagious cancers. Mamm Genome 22: 83-90.
19. Kreiss A, Cheng Y, Kimble F, Wells B, Donovan S, et al. (2011) Allorecognition in the Tasmanian devil (Sarcophilus harrisii), an endangered marsupial species with limited genetic diversity. PLoS one 6: e22402.
20. Siddle HV, Marzec J, Cheng Y, Jones M, Belov K, (2010) MHC gene copy number variation in Tasmanian devils: implications for the spread of a contagious cancer. P Roy Soc B-Biol Sci 277: 2001-6.
21. Cheng Y, Stuart A, Morris K, Taylor R, Siddle H, et al. (2012) BAC-contig-based characterization of MHC Class I and Class II regions in the Tasmanian devil. BMC Genomics. 13: 87.
22. Jones M, Barmuta L, (2000) Niche differentiation among sympatric Australian dasyurid carnivores. J Mammal 81: 434-447.
23. Hamede R, Lachish S, Belov K, Woods G, Kreiss A, et al. (2012) Reduced impact of Tasmanian Devil Facial Tumour Disease at the current disease front. Conserv Biol. 26: 124-134.
24. Hamede RK, Bashford J, McCallum H, Jones M, (2009) Contact networks in a wild Tasmanian devil (Sarcophilus harrisii) population: using social network analysis to reveal seasonal variability in social behaviour and its implications for transmission of a devil facial tumour disease. Ecol Lett 12: 1147-1157.
25. Schwaiger FW, Buitkamp J, Weyers E, Epplen JT, (1993) Typing of artiodactyl Mhc-Drb genes with the help of intronic simple repeated Dna-sequences. Mol Ecol 2: 55-59.
26. Aguilar A, Roemer G, Debenham S, Binns M, Garcelon D, et al. (2004) High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal. Proc Natl Acad Sci 101: 3490-3494.
27. Doxiadis GGM, de Groot N, Claas FHJ, Doxiadis IIN, van Rood JJ, et al. (2007) A highly divergent microsatellite facilitating fast and accurate DRB haplotyping in humans and rhesus macaques. Proc Natl Acad Sci 104: 8907-8912.
28. Prasad VK, Yang SY, (1996) Allele assignment for HLA-A,-B, and -C genes to the Tenth International Histocompatibility Workshop cell lines. Tissue Antigens 47: 538-546.
29. Santamaria P, Lindstrom AL, Boyce-Jacino MT, Myster SH, Barbosa JJ, et al. (1993) HLA class I sequence-based typing. Hum Immunol 37: 39-50.
30. Cheng Y, Belov K, (2011) Isolation and characterisation of 11 MHC-linked microsatellite loci in the Tasmanian devil (Sarcophilus harrisii). Conserv Genet Res DOI 10.1007/s12686-011-9575-4.
31. Piertney SB, Oliver MK, (2006) The evolutionary ecology of the major histocompatibility complex (MHC), Heredity 96: 7-21.
32. Paddle R, (2012) The thylacine's last straw: epidemic disease in a recent mammalian extinction. Australian Zoologist 35: to be published March/April 2012.
33. Cheng Y, Sanderson C, Jones M, Belov K, (2012) Low MHC Class II diversity in the Tasmanian devil (Sarcophilus harrisii). Immunogenetics, in press (PMID. 22460528).
34. Lai CH, Chou CY, Ch'ang LY, Liu CS, Lin WC, (2000) Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. Genome Res 10: 703-713.
35. Lamarca V, Sanz-Clemente A, Perez-Pe R, Martinez-Lorenzo MJ, Halaihel N, et al. (2007) Two isoforms of PSAP/MTCH1 share two proapoptotic domains and multiple internal signals for import into the mitochondrial outer membrane. Am J Physiol Cell Physiol 293: C1347-C1361.
36. Xu X, Shi YC, Gao W, Mao G, Zhao G, et al. (2002) The novel presenilin-1-associated protein is a proapoptotic mitochondrial protein. J Biol Chem 277: 48913-22.
37. Meijer D, Jansen MPHM, Look MP, Ruigrok-Ritstier K, van Staveren IL, et al. (2009) TSC22D1 and PSAP predict clinical outcome of tamoxifen treatment in patients with recurrent breast cancer. Breast Cancer Res Treat 113: 253-260.
38. Pasteris NG, Gorski JL, (1999) Isolation, characterization, and mapping of the mouse and human Fgd2 genes, faciogenital dysplasia (Fgd1: Aaeskog syndrome) gene homologues. Genomics pp. 57-66.
39. Huber C, Martensson A, Bokoch GM, Nemazee D, Gavin AL, (2008) FGD2, a CDC42-specific exchange factor expressed y antigen-presenting cells, localizes to early endosomes and active membrane ruffles. J Biol Chem 283: 34002-34012.
40. Truett GE, Heeger P, Mynatt RL, Truett AA, Walker JA, et al. (2000) Preparation of the PCR-quality mouse genomic DNA with hot sodium hydroxide and Tris (HotSHOT). Biotechniques 29: 52-54.
41. Siddle HV, Sanderson C, Belov K, (2007b) Characterization of major histocompatibility complex Class I and Class II genes from the Tasmanian devil (Sarcophilus harrisii). Immunogenetics 59: 753-760.
42. Hall TA, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acid S 41: 95-98.
43. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
44. Siddle HV, Deakin JE, Coggill P, Hart E, Cheng Y, et al. (2009) MHC-linked and un-linked class I genes in the wallaby. BMC Genomics 10: 310.
45. Jones ME, Paetkau D, Geffen E, Moritz C, (2003) Microsatellites for the Tasmanian devil (Sarcophilus laniarius). Mol Ecol Notes 3: 277-279.
46. Excoffier L, Laval G, Schneider S, (2005) Arelequin (version 3.0): An integrated software package for population genetic data analysis. Evol Bioinform Online 1: 47-50.
47. Goudet F, (1995) FSTAT (version 1.2): A computer program to calculate F-statistics. J Hered 86: 485-486.
48. Guo S, Thompson E, (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48: 361-372.
49. Peakall R, Smouse PE, (2006) GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6: 288-295.
50. Rice WR, (1989) Analyzing tables of statistical tests. Evolution 43: 223-225.
51. Manly BFJ, (1997) Randomization, Bootstrap and Monte Carlo Methods in Biology, 2nd edition. Taylor and Francis Inc., London.
52. Hood GM, (2008) PopTools version 3.2. Available:http://www.poptools.org/.