A genome-wide approach to comparative oncology: High-resolution oligonucleotide aCGH of canine and human osteosarcoma pinpoints shared microaberrations

Cancer Genetics

Volumn 205, Issue 11, 2012, Pages 572-587

  Angstadt, Andrea Y ^a   Thayanithy, Venugopal ^b   Subramanian, Subbaya ^b,c   Modiano, Jaime F ^c,d   Breen, Matthew ^a,e  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

^d UNIVERSITY OF MINNESOTA   (United States)

^e UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Canine; Comparative oncology; Oligo aCGH; Osteosarcoma

Indexed keywords

CYCLIN DEPENDENT KINASE 7; CYCLIN DEPENDENT KINASE INHIBITOR 2A; CYCLIN DEPENDENT KINASE INHIBITOR 2B; TRANSCRIPTION FACTOR RUNX2;

ADAM15 GENE; ADOLESCENT; ADULT; ANIMAL TISSUE; ARRAY COMPARATIVE GENOMIC HYBRIDIZATION; ARTICLE; CDC5L GENE; CDK7 GENE; CDKN2A GENE; CDKN2B GENE; CHILD; CHROMOSOME ABERRATION; CLINICAL ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; CTC1 GENE; DNA MICROARRAY; DOG; FEMALE; GENE; GENE IDENTIFICATION; GENOMIC INSTABILITY; HUMAN; HUMAN TISSUE; MALE; MEN1 GENE; NONHUMAN; ONCOGENE MYC; OSTEOSARCOMA; PRIORITY JOURNAL; RUNX2 GENE; SCHOOL CHILD;

ADOLESCENT; ADULT; ALGORITHMS; ANIMALS; BONE NEOPLASMS; CHILD; CHROMOSOME ABERRATIONS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; DOG DISEASES; DOGS; FEMALE; GENOME, HUMAN; GENOMICS; HUMANS; MALE; OSTEOSARCOMA; SPECIES SPECIFICITY;

EID: 84869398364     PISSN: 22107762     EISSN: 22107770     Source Type: Journal    
DOI: 10.1016/j.cancergen.2012.09.005     Document Type: Article

References (70)

1. Paoloni M., Khanna C. Translation of new cancer treatments from pet dogs to humans. Nat Rev Cancer 2008, 8:147-156.
2. Khanna C., Lindblad-Toh K., Vail D., et al. The dog as a cancer model. Nat Biotechnol 2006, 24:1065-1066.
3. Breen M., Hitte C., Lorentzen T.D., et al. An integrated 4249 marker FISH/RH map of the canine genome. BMC Genomics 2004, 5:65.
4. Breen M., Jouquand S., Renier C., et al. Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes. Genome Res 2001, 11:1784-1795.
5. Breen M., Langford C.F., Carter N.P., et al. FISH mapping and identification of canine chromosomes. J Hered 1999, 90:27-30.
6. Kirkness E.F., Bafna V., Halpern A.L., et al. The dog genome: survey sequencing and comparative analysis. Science 2003, 301:1898-1903.
7. Lindblad-Toh K., Wade C.M., Mikkelsen T.S., et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 2005, 438:803-819.
8. Thomas R., Duke S.E., Karlsson E.K., et al. A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis. Cytogenet Genome Res 2008, 122:110-121.
9. Thomas R., Scott A., Langford C.F., et al. Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors. Genome Res 2005, 15:1831-1837.
10. Lander E.S., Linton L.M., Birren B., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
11. Sadikovic B., Yoshimoto M., Chilton-MacNeill S., et al. Identification of interactive networks of gene expression associated with osteosarcoma oncogenesis by integrated molecular profiling. Hum Mol Genet 2009, 18:1962-1975.
12. Selvarajah S., Yoshimoto M., Ludkovski O., et al. Genomic signatures of chromosomal instability and osteosarcoma progression detected by high resolution array CGH and interphase FISH. Cytogenet Genome Res 2008, 122:5-15.
13. Squire J.A., Pei J., Marrano P., et al. High-resolution mapping of amplifications and deletions in pediatric osteosarcoma by use of CGH analysis of cDNA microarrays. Genes Chromosomes Cancer 2003, 38:215-225.
14. Zielenska M., Bayani J., Pandita A., et al. Comparative genomic hybridization analysis identifies gains of 1p35 approximately p36 and chromosome 19 in osteosarcoma. Cancer Genet Cytogenet 2001, 130:14-21.
15. Withrow S.J., Powers B.E., Straw R.C., et al. Comparative aspects of osteosarcoma. Dog versus man. Clin Orthop Relat Res 1991, 270:159-168.
16. Fossey S.L., Liao A.T., McCleese J.K., et al. Characterization of STAT3 activation and expression in canine and human osteosarcoma. BMC Cancer 2009, 9:81.
17. Gokgoz N., Wunder J.S., Mousses S., et al. Comparison of p53 mutations in patients with localized osteosarcoma and metastatic osteosarcoma. Cancer 2001, 92:2181-2189.
18. Paoloni M., Davis S., Lana S., et al. Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression. BMC Genomics 2009, 10:625.
19. Scott M.C., Sarver A.L., Gavin K.J., et al. Molecular subtypes of osteosarcoma identified by reducing tumor heterogeneity through an interspecies comparative approach. Bone 2011, 49:356-367.
20. Batanian J.R., Cavalli L.R., Aldosari N.M., et al. Evaluation of paediatric osteosarcomas by classic cytogenetic and CGH analyses. Mol Pathol 2002, 55:389-393.
21. Lim G., Karaskova J., Beheshti B., et al. An integrated mBAND and submegabase resolution tiling set (SMRT) CGH array analysis of focal amplification, microdeletions, and ladder structures consistent with breakage-fusion-bridge cycle events in osteosarcoma. Genes Chromosomes Cancer 2005, 42:392-403.
22. Lim G., Karaskova J., Vukovic B., et al. Combined spectral karyotyping, multicolor banding, and microarray comparative genomic hybridization analysis provides a detailed characterization of complex structural chromosomal rearrangements associated with gene amplification in the osteosarcoma cell line MG-63. Cancer Genet Cytogenet 2004, 153:158-164.
23. Sadikovic B., Thorner P., Chilton-Macneill S., et al. Expression analysis of genes associated with human osteosarcoma tumors shows correlation of RUNX2 overexpression with poor response to chemotherapy. BMC Cancer 2010, 10:202.
24. Sandberg A.A., Bridge J.A. Updates on the cytogenetics and molecular genetics of bone and soft tissue tumors: osteosarcoma and related tumors. Cancer Genet Cytogenet 2003, 145:1-30.
25. Selvarajah S., Yoshimoto M., Maire G., et al. Identification of cryptic microaberrations in osteosarcoma by high-definition oligonucleotide array comparative genomic hybridization. Cancer Genet Cytogenet 2007, 179:52-61.
26. Angstadt A.Y., Motsinger-Reif A., Thomas R., et al. Characterization of canine osteosarcoma by array comparative genomic hybridization and qRT-PCR: signatures of genomic imbalance in canine osteosarcoma parallels the human counterpart. Genes Chromosomes Cancer 2011, 50:859-874.
27. Selvarajah G.T., Kirpensteijn J., van Wolferen M.E., et al. Gene expression profiling of canine osteosarcoma reveals genes associated with short and long survival times. Mol Cancer 2009, 8:72.
28. Thomas R., Wang H.J., Tsai P.C., et al. Influence of genetic background on tumor karyotypes: evidence for breed-associated cytogenetic aberrations in canine appendicular osteosarcoma. Chromosome Res 2009, 17:365-377.
29. Ferracini R., Angelini P., Cagliero E., et al. MET oncogene aberrant expression in canine osteosarcoma. J Orthop Res 2000, 18:253-256.
30. Flint A.F., U'Ren L., Legare M.E., et al. Overexpression of the erbB-2 proto-oncogene in canine osteosarcoma cell lines and tumors. Vet Pathol 2004, 41:291-296.
31. Kirpensteijn J., Kik M., Teske E., et al. TP53 gene mutations in canine osteosarcoma. Vet Surg 2008, 37:454-460.
32. Levine R.A., Fleischli M.A. Inactivation of p53 and retinoblastoma family pathways in canine osteosarcoma cell lines. Vet Pathol 2000, 37:54-61.
33. Levine R.A., Forest T., Smith C. Tumor suppressor PTEN is mutated in canine osteosarcoma cell lines and tumors. Vet Pathol 2002, 39:372-378.
34. Mendoza S., Konishi T., Dernell W.S., et al. Status of the p53, Rb and MDM2 genes in canine osteosarcoma. Anticancer Res 1998, 18:4449-4453.
35. McCleese J.K., Bear M.D., Fossey S.L., et al. The novel HSP90 inhibitor STA-1474 exhibits biologic activity against osteosarcoma cell lines. Int J Cancer 2009, 125:2792-2801.
36. Wittenburg L.A., Bisson L., Rose B.J., et al. The histone deacetylase inhibitor valproic acid sensitizes human and canine osteosarcoma to doxorubicin. Cancer Chemother Pharmacol 2010, 67:83-92.
37. Kirpensteijn J., Kik M., Rutteman G.R., et al. Prognostic significance of a new histologic grading system for canine osteosarcoma. Vet Pathol 2002, 39:240-246.
38. Seiser E.L., Thomas R., Richards K.L., et al. Reading between the lines: molecular characterization of five widely used canine lymphoid tumour cell lines. Vet Comp Oncol 2011.
39. Bayani J., Zielenska M., Pandita A., et al. Spectral karyotyping identifies recurrent complex rearrangements of chromosomes 8, 17, and 20 in osteosarcomas. Genes Chromosomes Cancer 2003, 36:7-16.
40. Forus A., Weghuis D.O., Smeets D., et al. Comparative genomic hybridization analysis of human sarcomas: II. Identification of novel amplicons at 6p and 17p in osteosarcomas. Genes Chromosomes Cancer 1995, 14:15-21.
41. Simons A., Janssen I.M., Suijkerbuijk R.F., et al. Isolation of osteosarcoma-associated amplified DNA sequences using representational difference analysis. Genes Chromosomes Cancer 1997, 20:196-200.
42. Tarkkanen M., Bohling T., Gamberi G., et al. Comparative genomic hybridization of low-grade central osteosarcoma. Mod Pathol 1998, 11:421-426.
43. Tarkkanen M., Elomaa I., Blomqvist C., et al. DNA sequence copy number increase at 8q: a potential new prognostic marker in high-grade osteosarcoma. Int J Cancer 1999, 84:114-121.
44. Tarkkanen M., Karhu R., Kallioniemi A., et al. Gains and losses of DNA sequences in osteosarcomas by comparative genomic hybridization. Cancer Res 1995, 55:1334-1338.
45. Derrien T., Andre C., Galibert F., et al. AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps. Bioinformatics 2007, 23:498-499.
46. Berriz G.F., Beaver J.E., Cenik C., et al. Next generation software for functional trend analysis. Bioinformatics 2009, 25:3043-3044.
47. Berriz G.F., King O.D., Bryant B., et al. Characterizing gene sets with FuncAssociate. Bioinformatics 2003, 19:2502-2504.
48. Gordon I., Paoloni M., Mazcko C., et al. The Comparative Oncology Trials Consortium: using spontaneously occurring cancers in dogs to inform the cancer drug development pathway. PLoS Med 2009, 6:e1000161.
49. Tang J., Le S., Sun L., et al. Copy number abnormalities in sporadic canine colorectal cancers. Genome Res 2010, 20:341-350.
50. Zhang J., Chen X., Kent M.S., et al. Establishment of a dog model for the p53 family pathway and identification of a novel isoform of p21 cyclin-dependent kinase inhibitor. Mol Cancer Res 2009, 7:67-78.
51. Lu X.Y., Lu Y., Zhao Y.J., et al. Cell cycle regulator gene CDC5L, a potential target for 6p12-p21 amplicon in osteosarcoma. Mol Cancer Res 2008, 6:937-946.
52. de Nigris F., Botti C., Rossiello R., et al. Cooperation between Myc and YY1 provides novel silencing transcriptional targets of alpha3beta1-integrin in tumour cells. Oncogene 2007, 26:382-394.
53. Gamberi G., Benassi M.S., Bohling T., et al. C-myc and c-fos in human osteosarcoma: prognostic value of mRNA and protein expression. Oncology 1998, 55:556-563.
54. Thayanithy V., Sarver A.L., Kartha R.V., et al. Perturbation of 14q32 miRNAs-cMYC gene network in osteosarcoma. Bone 2012, 50:171-181.
55. Duffy M.J., Mullooly M., O'Donovan N., et al. The ADAMs family of proteases: new biomarkers and therapeutic targets for cancer?. Clin Proteomics 2011, 8:9.
56. Najy A.J., Day K.C., Day M.L. The ectodomain shedding of E-cadherin by ADAM15 supports ErbB receptor activation. J Biol Chem 2008, 283:18393-18401.
57. Chen L.Y., Redon S., Lingner J. The human CST complex is a terminator of telomerase activity. Nature 2012, 488:540-544.
58. Stewart J.A., Wang F., Chaiken M.F., et al. Human CST promotes telomere duplex replication and general replication restart after fork stalling. EMBO J 2012, 31:3537-3549.
59. Mirabello L., Richards E.G., Duong L.M., et al. Telomere length and variation in telomere biology genes in individuals with osteosarcoma. Int J Mol Epidemiol Genet 2011, 2:19-29.
60. Nasir L., Devlin P., McKevitt T., et al. Telomere lengths and telomerase activity in dog tissues: a potential model system to study human telomere and telomerase biology. Neoplasia 2001, 3:351-359.
61. Shay J.W. Telomerase in human development and cancer. J Cell Physiol 1997, 173:266-270.
62. Mohseny A.B., Szuhai K., Romeo S., et al. Osteosarcoma originates from mesenchymal stem cells in consequence of aneuploidization and genomic loss of Cdkn2. J Pathol 2009, 219:294-305.
63. Tsuchiya T., Sekine K., Hinohara S., et al. Analysis of the p16INK4, p14ARF, p15, TP53, and MDM2 genes and their prognostic implications in osteosarcoma and Ewing sarcoma. Cancer Genet Cytogenet 2000, 120:91-98.
64. Barry K.H., Koutros S., Andreotti G., et al. Genetic variation in nucleotide excision repair pathway genes, pesticide exposure and prostate cancer risk. Carcinogenesis 2012, 33:331-337.
65. Wesierska-Gadek J., Kramer M.P. The impact of multi-targeted cyclin-dependent kinase inhibition in breast cancer cells: clinical implications. Expert Opin Investig Drugs 2011, 20:1611-1628.
66. Ma H., Chen J., Pan S., et al. Potentially functional polymorphisms in cell cycle genes and the survival of non-small cell lung cancer in a Chinese population. Lung Cancer 2011, 73:32-37.
67. Cai D., Byth K.F., Shapiro G.I. AZ703, an imidazo[1,2-a]pyridine inhibitor of cyclin-dependent kinases 1 and 2, induces E2F-1-dependent apoptosis enhanced by depletion of cyclin-dependent kinase 9. Cancer Res 2006, 66:435-444.
68. Iurisci I., Filipski E., Reinhardt J., et al. Improved tumor control through circadian clock induction by Seliciclib, a cyclin-dependent kinase inhibitor. Cancer Res 2006, 66:10720-10728.
69. Scrace S.F., Kierstan P., Borgognoni J., et al. Transient treatment with CDK inhibitors eliminates proliferative potential even when their abilities to evoke apoptosis and DNA damage are blocked. Cell Cycle 2008, 7:3898-3907.
70. Trowbridge J.M., Rogatsky I., Garabedian M.J. Regulation of estrogen receptor transcriptional enhancement by the cyclin A/Cdk2 complex. Proc Natl Acad Sci U S A 1997, 94:10132-10137.