Whole-genome plasma sequencing reveals focal amplifications as a driving force in metastatic prostate cancer

Nature Communications

Volumn 7, Issue , 2016, Pages

  Ulz, Peter ^a   Belic, Jelena ^a   Graf, Ricarda ^a   Auer, Martina ^a   Lafer, Ingrid ^a   Fischereder, Katja ^a   Webersinke, Gerald ^b   Pummer, Karl ^a   Augustin, Herbert ^a   Pichler, Martin ^a   Hoefler, Gerald ^a   Bauernhofer, Thomas ^a   Geigl, Jochen B ^a   Heitzer, Ellen ^a   Speicher, Michael R ^a  

^a MEDICAL UNIVERSITY OF GRAZ   (Austria)

^b Internal Medicine I: Hematology and Medical Oncology   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NEURON SPECIFIC ENOLASE; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; MYC PROTEIN; MYC PROTEIN, HUMAN; PROSTATE SPECIFIC ANTIGEN;

CANCER; DATABASE; GENETIC ANALYSIS; GENOME; PLASMA; SAMPLING; TUMOR;

ARTICLE; BLOOD ANALYSIS; CHROMOSOME 10Q; CHROMOSOME 13Q; CHROMOSOME 21Q; CHROMOSOME 5Q; CHROMOSOME 8P; CONTROLLED STUDY; GENE; GENE AMPLIFICATION; GENE DELETION; GENE FUSION; GENE IDENTIFICATION; GENE SEQUENCE; GENOME ANALYSIS; HUMAN; HUMAN CELL; HUMAN TISSUE; MAJOR CLINICAL STUDY; MALE; METASTATIC PROSTATE CANCER; PROSTATE CANCER; RYBP GENE; SHQ1 GENE; TIME; TUMOR SUPPRESSOR GENE; WHOLE GENOME PLASMA SEQUENCING; BIOPSY; BLOOD; CELL DIFFERENTIATION; CHROMOSOME ABERRATION; CLUSTER ANALYSIS; DISEASE EXACERBATION; DNA SEQUENCE; GENE DOSAGE; GENETICS; HUMAN GENOME; METASTASIS; PROSTATE TUMOR;

BIOPSY; CELL DIFFERENTIATION; CHROMOSOME ABERRATIONS; CLUSTER ANALYSIS; DISEASE PROGRESSION; DNA, NEOPLASM; GENE DELETION; GENE DOSAGE; GENOME, HUMAN; HUMANS; MALE; NEOPLASM METASTASIS; PROSTATE-SPECIFIC ANTIGEN; PROSTATIC NEOPLASMS; PROTO-ONCOGENE PROTEINS C-MYC; SEQUENCE ANALYSIS, DNA;

EID: 84975744385     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms12008     Document Type: Article

References (57)

1. Barbieri, C. E. & Tomlins, S. A. The prostate cancer genome: perspectives and potential. Urol. Oncol. 32, 53.e15-53.e22 (2014).
2. Baca, S. C. et al. Punctuated evolution of prostate cancer genomes. Cell 153, 666-677 (2013).
3. Barbieri, C. E. et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat. Genet. 44, 685-689 (2012).
4. Berger, M. F. et al. The genomic complexity of primary human prostate cancer. Nature 470, 214-220 (2011).
5. Grasso, C. S. et al. The mutational landscape of lethal castration-resistant prostate cancer. Nature 487, 239-243 (2012).
6. Gundem, G. et al. The evolutionary history of lethal metastatic prostate cancer. Nature 520, 353-357 (2015).
7. Hong, M. K. et al. Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer. Nat. Commun. 6, 6605 (2015).
8. Robinson, D. et al. Integrative clinical genomics of advanced prostate cancer. Cell 161, 1215-1228 (2015).
9. Taylor, B. S. et al. Integrative genomic profiling of human prostate cancer. Cancer Cell 18, 11-22 (2010).
10. Heitzer, E. et al. Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing. Genome Med. 5, 30 (2013).
11. Mohan, S. et al. Changes in colorectal carcinoma genomes under anti-EGFR therapy identified by whole-genome plasma DNA sequencing. PLoS Genet. 10, e1004271 (2014).
12. Heidary, M. et al. The dynamic range of circulating tumor DNA in metastatic breast cancer. Breast Cancer Res. 16, 421 (2014).
13. Heitzer, E., Auer, M., Ulz, P., Geigl, J. B. & Speicher, M. R. Circulating tumor cells and DNA as liquid biopsies. Genome Med. 5, 73 (2013).
14. Heitzer, E., Ulz, P. & Geigl, J. B. Circulating tumor DNA as a liquid biopsy for cancer. Clin. Chem. 61, 112-123 (2015).
15. Mermel, C. H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).
16. Robbins, C. M. et al. Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors. Genome Res. 21, 47-55 (2011).
17. Tomlins, S. A. et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310, 644-648 (2005).
18. Attard, G. et al. Prostate cancer. Lancet 387, 70-82 (2016).
19. Romanel, A. et al. Plasma AR and abiraterone-resistant prostate cancer. Sci. Transl. Med. 7, 312re10 (2015).
20. Azad, A. A. et al. Androgen receptor gene aberrations in circulating cell-free dna: biomarkers of therapeutic resistance in castration-resistant prostate cancer. Clin. Cancer Res. 21, 2315-2324 (2015).
21. Carreira, S. et al. Tumor clone dynamics in lethal prostate cancer. Sci. Transl. Med. 6, 254ra125 (2014).
22. Shen, M. M. & Abate-Shen, C. Molecular genetics of prostate cancer: new prospects for old challenges. Genes Dev. 24, 1967-2000 (2010).
23. Visakorpi, T. et al. In vivo amplification of the androgen receptor gene and progression of human prostate cancer. Nat. Genet. 9, 401-406 (1995).
24. Santarius, T., Shipley, J., Brewer, D., Stratton, M. R. & Cooper, C. S. A census of amplified and overexpressed human cancer genes. Nat. Rev. Cancer 10, 59-64 (2010).
25. Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899-905 (2010).
26. Zack, T. I. et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45, 1134-1140 (2013).
27. Ulz, P., Heitzer, E. & Speicher, M. R. Co-occurrence of MYC amplification and TP53 mutations in human cancer. Nat. Genet. 48, 104-106 (2016).
28. Bernard, D., Pourtier-Manzanedo, A., Gil, J. & Beach, D. H. Myc confers androgen-independent prostate cancer cell growth. J. Clin. Invest. 112, 1724-1731 (2003).
29. Malik, R. et al. Targeting the MLL complex in castration-resistant prostate cancer. Nat. Med. 21, 344-352 (2015).
30. Luo, J. H. et al. Transcriptomic and genomic analysis of human hepatocellular carcinomas and hepatoblastomas. Hepatology 44, 1012-1024 (2006).
31. Zou, X. et al. Downregulation of developmentally regulated endothelial cell locus-1 inhibits the growth of colon cancer. J. Biomed. Sci. 16, 33 (2009).
32. Schilsky, R. L. Implementing personalized cancer care. Nat. Rev. Clin. Oncol. 11, 432-438 (2014).
33. Sun, Y. et al. Histone methyltransferase SETDB1 is required for prostate cancer cell proliferation, migration and invasion. Asian J. Androl. 16, 319-324 (2014).
34. Beltran, H. et al. Challenges in recognizing treatment-related neuroendocrine prostate cancer. J. Clin. Oncol. 30, e386-e389 (2012).
35. Mosquera, J. M. et al. Concurrent AURKA and MYCN gene amplifications are harbingers of lethal treatment-related neuroendocrine prostate cancer. Neoplasia 15, 1-10 (2013).
36. Lallous, N. et al. Functional analysis of androgen receptor mutations that confer anti-androgen resistance identified in circulating cell-free DNA from prostate cancer patients. Genome Biol. 17, 10 (2016).
37. Bettegowda, C. et al. Detection of circulating tumor DNA in early-and latestage human malignancies. Sci. Transl. Med. 6, 224ra24 (2014).
38. Dawson, S. J. et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N. Engl. J. Med. 368, 1199-1209 (2013).
39. Forshew, T. et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci. Transl. Med. 4, 136ra68 (2012).
40. Leary, R. J. et al. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci. Transl. Med. 4, 162ra154 (2012).
41. Murtaza, M. et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 497, 108-112 (2013).
42. Aryee, M. J. et al. DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Sci. Transl. Med. 5, 169ra10 (2013).
43. Liu, W. et al. Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer. Nat. Med. 15, 559-565 (2009).
44. Rubin, M. A., Maher, C. A. & Chinnaiyan, A. M. Common gene rearrangements in prostate cancer. J. Clin. Oncol. 29, 3659-3668 (2011).
45. Arora, V. K. et al. Glucocorticoid receptor confers resistance to antiandrogens by bypassing androgen receptor blockade. Cell 155, 1309-1322 (2013).
46. Asangani, I. A. et al. Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer. Nature 510, 278-282 (2014).
47. Manning, G., Whyte, D. B., Martinez, R., Hunter, T. & Sudarsanam, S. The protein kinase complement of the human genome. Science 298, 1912-1934 (2002).
48. Rick, F. G., Block, N. L. & Schally, A. V. An update on the use of degarelix in the treatment of advanced hormone-dependent prostate cancer. Onco Targets Ther. 6, 391-402 (2013).
49. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
50. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
51. Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).
52. Baslan, T. et al. Genome-wide copy number analysis of single cells. Nat. Protoc. 7, 1024-1041 (2012).
53. Lai, W., Choudhary, V. & Park, P. J. CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms. Bioinformatics 24, 1014-1015 (2008).
54. Cazier, J. B., Holmes, C. C. & Broxholme, J. GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples. Bioinformatics 28, 2981-2982 (2012).
55. Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).
56. van Bokhoven, A. et al. Molecular characterization of human prostate carcinoma cell lines. Prostate 57, 205-225 (2003).
57. Hay, C. W. & McEwan, I. J. The impact of point mutations in the human androgen receptor: classification of mutations on the basis of transcriptional activity. PLoS ONE 7, e32514 (2012).