Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity

Nature

Volumn 543, Issue 7643, 2017, Pages 122-125

  Turner, Kristen M ^a   Deshpande, Viraj ^b   Beyter, Doruk ^b   Koga, Tomoyuki ^a   Rusert, Jessica ^c   Lee, Catherine ^c   Li, Bin ^a   Arden, Karen ^a   Ren, Bing ^a   Nathanson, David A ^d   Kornblum, Harley I ^d,e   Taylor, Michael D ^f   Kaushal, Sharmeela ^g   Cavenee, Webster K ^a   Wechsler Reya, Robert ^c   Furnari, Frank B ^a   Vandenberg, Scott R ^h   Rao, P Nagesh ^d   Wahl, Geoffrey M ⁱ   Bafna, Vineet ^b   Mischel, Paul S ^a,g   more..

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c BURNHAM INSTITUTE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f HOSPITAL FOR SICK CHILDREN   (Canada)

^g UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^h UNIVERSITY OF CALIFORNIA   (United States)

ⁱ SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; EXTRACHROMOSOMAL DNA; MYC PROTEIN; MESSENGER RNA; RNA;

CANCER; CHROMOSOME; DNA; GENETIC ANALYSIS; GENOME; TUMOR;

ARTICLE; CANCER GROWTH; CELL DIVISION; CONTROLLED STUDY; GENE AMPLIFICATION; GENETIC HETEROGENEITY; HUMAN; HUMAN CELL; MATHEMATICAL MODEL; MITOTIC RECOMBINATION; ONCOGENE; PREDICTIVE VALUE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; WHOLE GENOME SEQUENCING; BIOLOGICAL MODEL; CHROMOSOME ANALYSIS; CLASSIFICATION; COPY NUMBER VARIATION; DNA MUTATIONAL ANALYSIS; GENETICS; HUMAN CHROMOSOME; HUMAN GENOME; METAPHASE; MOLECULAR EVOLUTION; NEOPLASM; REPRODUCIBILITY; SOFTWARE;

CHROMOSOMES, HUMAN; CYTOGENETIC ANALYSIS; DNA COPY NUMBER VARIATIONS; DNA MUTATIONAL ANALYSIS; EVOLUTION, MOLECULAR; GENE AMPLIFICATION; GENETIC HETEROGENEITY; GENOME, HUMAN; HUMANS; METAPHASE; MODELS, GENETIC; NEOPLASMS; ONCOGENES; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; RNA, NEOPLASM; SOFTWARE;

EID: 85014518333     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature21356     Document Type: Article

References (36)

1. Vogelstein, B. et al. Cancer genome landscapes. Science 339, 1546-1558 (2013).
2. Stark, G. R., Debatisse, M., Giulotto, E. & Wahl, G. M. Recent progress in understanding mechanisms of mammalian DNA amplification. Cell 57, 901-908 (1989).
3. Schimke, R. T. Gene amplification in cultured animal cells. Cell 37, 705-713 (1984).
4. Fan, Y. et al. Frequency of double minute chromosomes and combined cytogenetic abnormalities and their characteristics. J. Appl. Genet. 52, 53-59 (2011).
5. Nowell, P. C. The clonal evolution of tumor cell populations. Science 194, 23-28 (1976).
6. McGranahan, N. & Swanton, C. Biological and therapeutic impact of intratumor heterogeneity in cancer evolution. Cancer Cell 27, 15-26 (2015).
7. Marusyk, A., Almendro, V. & Polyak, K. Intra-tumour heterogeneity: A looking glass for cancer Nat. Rev. Cancer 12, 323-334 (2012).
8. Yates, L. R. & Campbell, P. J. Evolution of the cancer genome. Nat. Rev. Genet. 13, 795-806 (2012).
9. Greaves, M. & Maley, C. C. Clonal evolution in cancer. Nature 481, 306-313 (2012).
10. Andor, N. et al. Pan-cancer analysis of the extent and consequences of intratumor heterogeneity. Nat. Med. 22, 105-113 (2016).
11. Gillies, R. J., Verduzco, D. & Gatenby, R. A. Evolutionary dynamics of carcinogenesis and why targeted therapy does not work. Nat. Rev. Cancer 12, 487-493 (2012).
12. Von Hoff, D. D., Needham-VanDevanter, D. R., Yucel, J., Windle, B. E. & Wahl, G. M. Amplified human MYC oncogenes localized to replicating submicroscopic circular DNA molecules. Proc. Natl Acad. Sci. USA 85, 4804-4808 (1988).
13. Garsed, D. W. et al. The architecture and evolution of cancer neochromosomes. Cancer Cell 26, 653-667 (2014).
14. Carroll, S. M. et al. Double minute chromosomes can be produced from precursors derived from a chromosomal deletion. Mol. Cell. Biol. 8, 1525-1533 (1988).
15. Windle, B., Draper, B. W., Yin, Y. X., O'Gorman, S. & Wahl, G. M. A central role for chromosome breakage in gene amplification, deletion formation, and amplicon integration. Genes Dev. 5, 160-174 (1991).
16. Kanda, T., Otter, M. & Wahl, G. M. Mitotic segregation of viral and cellular acentric extrachromosomal molecules by chromosome tethering. J. Cell Sci. 114, 49-58 (2001).
17. Mitelman, F., Johansson, B. & Mertens, F. Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer. http://cgap. nci. nih. gov/Chromosomes/ Mitelman (2016).
18. Sanborn, J. Z. et al. Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. Cancer Res. 73, 6036-6045 (2013).
19. Almendro, V. et al. Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. Cell Reports 6, 514-527 (2014).
20. Zack, T. I. et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45, 1134-1140 (2013).
21. Nathanson, D. A. et al. Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science 343, 72-76 (2014).
22. Storlazzi, C. T. et al. Gene amplification as double minutes or homogeneously staining regions in solid tumors: origin and structure. Genome Res. 20, 1198-1206 (2010).
23. Bozic, I. et al. Accumulation of driver and passenger mutations during tumor progression. Proc. Natl Acad. Sci. USA 107, 18545-18550 (2010).
24. Li, X. et al. Temporal and spatial evolution of somatic chromosomal alterations: A case-cohort study of Barrett's esophagus. Cancer Prev. Res. 7, 114-127 (2014).
25. Mishra, S. & Whetstine, J. R. Different facets of copy number changes: permanent, transient, and adaptive. Mol. Cell. Biol. 36, 1050-1063 (2016).
26. Schimke, R. T., Kaufman, R. J., Alt, F. W. & Kellems, R. F. Gene amplification and drug resistance in cultured murine cells. Science 202, 1051-1055 (1978).
27. Nikolaev, S. et al. Extrachromosomal driver mutations in glioblastoma and low-grade glioma. Nat. Commun. 5, 5690 (2014).
28. Biedler, J. L., Schrecker, A. W. & Hutchison, D. J. Selection of chromosomal variant in amethopterin-resistant sublines of leukemia L1210 with increased levels of dihydrofolate reductase. J. Natl. Cancer Inst. 31, 575-601 (1963).
29. Lee, P. M. Bayesian statistics: An introduction. 4th edn (John Wiley & Sons, 2012).
30. Motl, J. Bradley local image thresholding. https://www. mathworks. com/ matlabcentral/fileexchange/40854 (2015).
31. Bradley, D. & Roth, G. Adaptive thresholding using the integral image. J. Graphics Tools 12, 13-21 (2007).
32. Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
33. Kent, W. J. et al. The human genome browser at UCSC. Genome Res 12, 996-1006 (2002).
34. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
35. Miller, C. A., Hampton, O., Coarfa, C. & Milosavljevic, A. ReadDepth: A parallel R package for detecting copy number alterations from short sequencing reads. PLoS One 6, e16327 (2011).
36. Pavlova, N. N. & Thompson, C. B. The emerging hallmarks of cancer metabolism. Cell Metab. 23, 27-47 (2016).