Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor

Genome Research

Volumn 25, Issue 11, 2015, Pages 1646-1655

  Decker, Brennan ^a,b   Davis, Brian W ^a   Rimbault, Maud ^a   Long, Adrienne H ^c   Karlins, Eric ^a   Jagannathan, Vidhya ^d   Reiman, Rebecca ^e   Parker, Heidi G ^a   Drögemüller, Cord ^d   Corneveaux, Jason J ^e   Chapman, Erica S ^a   Trent, Jeffery M ^e   Leeb, Tosso ^d   Huentelman, Matthew J ^e   Wayne, Robert K ^f   Karyadi, Danielle M ^a   Ostrander, Elaine A ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c NATIONAL CANCER INSTITUTE   (United States)

^d UNIVERSITY OF BERN   (Switzerland)

^e TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ANTIGEN PRESENTATION; APOPTOSIS; ARTICLE; CANIDAE; CANINE TRANSMISSIBLE VENEREAL TUMOR; CARCINOGENESIS; CLONAL VARIATION; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENOME ANALYSIS; IMMUNOSURVEILLANCE; NEOPLASM; NONHUMAN; PARASITOSIS; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION; ANIMAL; CELL LINEAGE; DNA SEQUENCE; DOG; DOG DISEASES; GENETIC ASSOCIATION STUDY; GENETIC VARIATION; GENETICS; GENOME; MUTATION; TUMOR CELL LINE; VENEREAL TUMORS, VETERINARY;

ACTIN BINDING PROTEIN; AUTOANTIGEN; CASPASE RECRUITMENT DOMAIN SIGNALING PROTEIN; CELL ADHESION MOLECULE; COLLAGEN TYPE 11; DNA BINDING PROTEIN; GUANINE NUCLEOTIDE EXCHANGE FACTOR; MYOTONIC DYSTROPHY PROTEIN KINASE; PROTEOHEPARAN SULFATE;

ANIMALS; APOPTOSIS; AUTOANTIGENS; CARD SIGNALING ADAPTOR PROTEINS; CELL ADHESION MOLECULES; CELL LINE, TUMOR; CELL LINEAGE; COLLAGEN TYPE XI; DNA-BINDING PROTEINS; DOG DISEASES; DOGS; GENETIC ASSOCIATION STUDIES; GENETIC VARIATION; GENOME; GUANINE NUCLEOTIDE EXCHANGE FACTORS; HEPARAN SULFATE PROTEOGLYCANS; MICROFILAMENT PROTEINS; MUTATION; MYOTONIN-PROTEIN KINASE; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA; VENEREAL TUMORS, VETERINARY;

EID: 84946574979     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.190314.115     Document Type: Article

References (47)

1. Abyzov A, Urban AE, Snyder M, Gerstein M. 2011. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 21: 974-984.
2. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SAJR, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Børresen-Dale AL, et al. 2013. Signatures of mutational processes in human cancer. Nature 500: 415-421.
3. Axelsson E, Ratnakumar A, Arendt ML, Maqbool K, Webster MT, Perloski M, Liberg O, Arnemo JM, Hedhammar A, Lindblad-Toh K. 2013. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 495: 360-364.
4. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, et al. 2011. The variant call format and VCFtools. Bioinformatics 27: 2156-2158.
5. Darmon AJ, NicholsonDW, Bleackley RC. 1995. Activation of the apoptotic protease CPP32 by cytotoxic T-cell-derived granzyme B. Nature 377: 446-448.
6. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491-498.
7. Enari M, Talanian RV, WongWW, Nagata S. 1996. Sequential activation of ICE-like and CPP32-like proteases during Fas-mediated apoptosis. Nature 380: 723-726.
8. Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, et al. 2014. Ensembl 2014. Nucleic Acids Res 42: D749-D755.
9. Imai Y, Kimura T, Murakami A, Yajima N, Sakamaki K, Yonehara S. 1999. The CED-4-homologous protein FLASH is involved in Fas-mediated activation of caspase-8 during apoptosis. Nature 398: 777-785.
10. Katzir N, Arman E, Cohen D, Givol D, Rechavi G. 1987. Common origin of transmissible venereal tumors (TVT) in dogs. Oncogene 1: 445-448.
11. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. 2009. Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639-1645.
12. Kumar A, White TA, MacKenzie AP, Clegg N, Lee C, Dumpit RF, Coleman I, Ng SB, Salipante SJ, Rieder MJ, et al. 2011. Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers. Proc Natl Acad Sci 108: 17087-17092.
13. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25: 1754-1760.
14. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
15. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. 2010. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26: 2069-2070.
16. Meredith RW, Janečka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, Goodbla A, Eizirik E, Simão TLL, Stadler T, et al. 2011. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction onmammal diversification. Science 334: 521-524.
17. Motyka B, Korbutt G, Pinkoski MJ, Heibein JA, Caputo A, Hobman M, Barry M, Shostak I, Sawchuk T, Holmes CF, et al. 2000. Mannose 6-phosphate/insulin-like growth factor II receptor is a death receptor for granzyme B during cytotoxic T cell-induced apoptosis. Cell 103: 491-500.
18. Muller HJ. 1964. The relation of recombination to mutational advance. Mutat Res 106: 2-9.
19. Murchison EP, Wedge DC, Alexandrov LB, Fu B, Martincorena I, Ning Z, Tubio JMC, Werner EI, Allen J, De Nardi AB, et al. 2014. Transmissible dog cancer genome reveals the origin and history of an ancient cell lineage. Science 343: 437-440.
20. Murgia C, Pritchard JK, Kim SY, Fassati A, Weiss RA. 2006. Clonal origin and evolution of a transmissible cancer. Cell 126: 477-487.
21. Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426.
22. Ng PC, Henikoff S. 2001. Predicting deleterious amino acid substitutions. Genome Res 11: 863-874.
23. Ostrow SL, Barshir R, DeGregori J, Yeger-Lotem E, Hershberg R. 2014. Cancer evolution is associated with pervasive positive selection on globally expressed genes. PLoS Genet 10: e1004239.
24. Patterson N, Price AL, Reich D. 2006. Population structure and eigenanalysis. PLoS Genet 2: e190.
25. Posada D. 2006. ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Res 34: W700-W703.
26. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. Principal components analysis corrects for stratification in genome- wide association studies. Nat Genet 38: 904-909.
27. Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. 2012. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28: i333-i339.
28. Rebbeck CA, Leroi AM, Burt A. 2011. Mitochondrial capture by a transmissible cancer. Science 331: 303.
29. Saric T, Chang SC, Hattori A, York IA, Markant S, Rock KL, Tsujimoto M, Goldberg AL. 2002. An IFN-γ-induced aminopeptidase in the ER, ERAP1, trims precursors to MHC class I-presented peptides. Nat Immunol 3: 1169-1176.
30. Shankaran V, Ikeda H, Bruce AT, White JM, Swanson PE, Old LJ, Schreiber RD. 2001. IFNγ and lymphocytes prevent primary tumour development and shape tumour immunogenicity. Nature 410: 1107-1111.
31. Sherry ST. 2001. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29: 308-311.
32. Siddle HV, Kreiss A, Tovar C, Yuen CK, Cheng Y, Belov K, Swift K, PearseAM, Hamede R, Jones ME, et al. 2013. Reversible epigenetic down-regulation of MHC molecules by devil facial tumour disease illustrates immune escape by a contagious cancer. Proc Natl Acad Sci 110: 5103-5108.
33. Spies T, Cerundolo V, Colonna M, Cresswell P, Townsend A, DeMars R. 1992. Presentation of viral antigen by MHC class I molecules is dependent on a putative peptide transporter heterodimer. Nature 355: 644-646.
34. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313.
35. Stamatakis A, Aberer AJ. 2013. Novel parallelization schemes for large-scale likelihood-based phylogenetic inference. In 2013 IEEE 27th international symposium on parallel and distributed processing (IPDPS), pp. 1195-1204, IEEE, Piscataway, NJ.
36. Strakova A, Murchison EP. 2014. The changing global distribution and prevalence of canine transmissible venereal tumour. BMC Vet Res 10: 168.
37. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. 2005. Gene set enrichment analysis: a knowledge-based approach for interpreting genome- wide expression profiles. Proc Natl Acad Sci 102: 15545-15550.
38. Thomas R, Rebbeck C, Leroi AM, Burt A, Breen M. 2009. Extensive conservation of genomic imbalances in canine transmissible venereal tumors (CTVT) detected by microarray-based CGH analysis. Chromosome Res 17: 927-934.
39. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, Levy- Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, et al. 2013. From fastQ data to high-confidence variant cells: the Genome Analysis Toolkit Best Practices pipeline. Curr Protoc Bioinformatics 11: 11.10.1-11.10.33.
40. Van Kaer L, Ashton-Rickardt PG, Ploegh HL, Tonegawa S. 1992. TAP1 mutant mice are deficient in antigen presentation, surface class I molecules, and CD4-8+ T cells. Cell 71: 1205-1214.
41. Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Rosengren Pielberg G, Sigurdsson S, Fall T, Seppälä EH, Hansen MS, Lawley CT, et al. 2011. Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genet 7: e1002316.
42. Wijayawardena BK, Minchella DJ, DeWoody JA. 2013. Hosts, parasites, and horizontal gene transfer. Trends Parasitol 29: 329-338.
43. Yang TJ. 1988. Immunobiology of a spontaneously regressive tumor, the canine transmissible venereal sarcoma (review). Anticancer Res 8: 93-95.
44. Yang Z, Nielsen R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol 46: 409-418.
45. Yang Z, Yoder AD. 1999. Estimation of the transition/transversion rate bias and species sampling. J Mol Evol 48: 274-283.
46. York IA, Chang SC, Saric T, Keys JA, Favreau JM, Goldberg AL, Rock KL. 2002. The ER aminopeptidase ERAP1 enhances or limits antigen presentation by trimming epitopes to 8-9 residues. Nat Immunol 3: 1177-1184.
47. Zhao H, Thienpont B, Yesilyurt BT, Moisse M, Reumers J, Coenegrachts L, Sagaert X, Schrauwen S, Smeets D, Matthijs G, et al. 2014. Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks. Elife 3: e02725.