Whole-genome analysis informs breast cancer response to aromatase inhibition

Nature

Volumn 486, Issue 7403, 2012, Pages 353-360

  Ellis, Matthew J ^a,b   Ding, Li ^c   Shen, Dong ^c   Luo, Jingqin ^a   Suman, Vera J ^d   Wallis, John W ^c   Van Tine, Brian A ^a   Hoog, Jeremy ^a   Goiffon, Reece J ^a,c,e   Goldstein, Theodore C ^f   Ng, Sam ^f   Lin, Li ^a   Crowder, Robert ^a   Snider, Jacqueline ^a   Ballman, Karla ^d   Weber, Jason ^a,c   Chen, Ken ^g   Koboldt, Daniel C ^c   Kandoth, Cyriac ^c   Schierding, William S ^c   McMichael, Joshua F ^c   Miller, Christopher A ^c   Lu, Charles ^c   Harris, Christopher C ^c   McLellan, Michael D ^c   Wendl, Michael C ^c   Deschryver, Katherine ^a   Allred, D Craig ^a   Esserman, Laura ^h   Unzeitig, Gary ⁱ   Margenthaler, Julie ^b   Babiera, G V ^g   Marcom, P Kelly ^j   Guenther, J M ^k   Leitch, Marilyn ^l   Hunt, Kelly ^g   Olson, John ^j   Tao, Yu ^a   Maher, Christopher A ^a,c   Fulton, Lucinda L ^c   Fulton, Robert S ^c   Harrison, Michelle ^c   Oberkfell, Ben ^c   Du, Feiyu ^c   Demeter, Ryan ^c   Vickery, Tammi L ^c   Elhammali, Adnan ^a,c,e   Piwnica Worms, Helen ^c,m   McDonald, Sandra ^a,b   Watson, Mark ^a   Dooling, David J ^c   Ota, David ⁿ   Chang, Li Wei ^a   Bose, Ron ^a,b   Ley, Timothy J ^a,b,c   Piwnica Worms, David ^a,c,e   Stuart, Joshua M ^f   Wilson, Richard K ^b,c   Mardis, Elaine R ^b,c   more..

^a WASHINGTON UNIVERSITY   (United States)

^b USA   (United States)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d MAYO CLINIC   (United States)

^e WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f University of California Santa Cruz   (United States)

^g UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^h UNIVERSITY OF CALIFORNIA   (United States)

ⁱ Doctors Hospital of Laredo   (United States)

^j DUKE CANCER INSTITUTE   (United States)

^k GOOD SAMARITAN HOSPITAL   (United States)

^l UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^m HOWARD HUGHES MEDICAL INSTITUTE   (United States)

ⁿ DUKE UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ANASTROZOLE; AROMATASE INHIBITOR; DNA; ESTROGEN RECEPTOR; EXEMESTANE; LETROZOLE; MITOGEN ACTIVATED PROTEIN KINASE; MUTANT PROTEIN; PROTEIN P53; RNA; TRANSCRIPTION FACTOR GATA 3; TRANSCRIPTION FACTOR RUNX1;

CANCER; CORRELATION; GENOME; INHIBITION; MUTATION; PHENOTYPE;

ADJUVANT THERAPY; APOPTOSIS; ARTICLE; BREAST CANCER; CANCER ADJUVANT THERAPY; CANCER CHEMOTHERAPY; CLINICAL ARTICLE; COPY NUMBER VARIATION; DNA REPAIR; ENZYME ACTIVITY; ENZYME INHIBITION; FRAMESHIFT MUTATION; GENE EXPRESSION; GENE MUTATION; GENOME; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; MISSENSE MUTATION; NONSENSE MUTATION; PHASE 2 CLINICAL TRIAL (TOPIC); POINT MUTATION; PREOPERATIVE TREATMENT; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; TREATMENT RESPONSE;

ANDROSTADIENES; ANTINEOPLASTIC AGENTS; AROMATASE; AROMATASE INHIBITORS; BREAST NEOPLASMS; DNA REPAIR; EXOME; EXONS; FEMALE; GENETIC VARIATION; GENOME, HUMAN; HUMANS; MAP KINASE KINASE 4; MAP KINASE KINASE KINASE 1; MUTATION; NITRILES; RECEPTORS, ESTROGEN; TREATMENT OUTCOME; TRIAZOLES;

EID: 84862584058     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature11143     Document Type: Article

References (45)

1. Chia, Y. H., Ellis, M. J. & Ma, C. X. Neoadjuvant endocrine therapy in primary breast cancer: indications and use as a research tool. Br. J. Cancer 103, 759-764 (2010).
2. Olson, J. A. Jr et al. Improved surgicaloutcomes for breast cancer patients receiving neoadjuvant aromatase inhibitor therapy: results froma multicenter phase II trial. J. Am. Coll. Surg. 208, 906-914; discussion 915-906 (2009).
3. Ellis, M. J. et al. Randomized phase II neoadjuvant comparison between letrozole, anastrozole, and exemestane for postmenopausalwomen with estrogen receptorrich stage 2 to 3 breast cancer: clinical and biomarker outcomes and predictive value of the baseline PAM50-based intrinsic subtype-ACOSOG Z1031. J. Clin. Oncol. 29, 2342-2349 (2011).
4. Ellis, M. J. et al. Outcome prediction for estrogen receptor-positive breast cancer based on postneoadjuvant endocrine therapy tumor characteristics. J.Natl. Cancer Inst. 100, 1380-1388 (2008).
5. Chen, K. et al. BreakDancer: an algorithmfor high-resolution mapping of genomic structural variation. Nature Methods 6, 677-681 (2009).
6. Mardis, E. R. et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N. Engl. J. Med. 361, 1058-1066 (2009).
7. Ley, T. J. et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456, 66-72 (2008).
8. Totoki, Y. et al. High-resolution characterization of a hepatocellular carcinoma genome. Nature Genet. 43, 464-469 (2011).
9. Pleasance, E. D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191-196 (2010).
10. Pleasance, E. D. et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463, 184-190 (2010).
11. Lee, W. et al. Themutation spectrumrevealed by paired genomesequences froma lung cancer patient. Nature 465, 473-477 (2010).
12. Usary, J. et al. Mutation of GATA3 in human breast tumors. Oncogene 23, 7669-7678 (2004). (Pubitemid 39424925)
13. Berx, G. et al. E-cadherin is a tumour/invasion suppressor genemutated in human lobular breast cancers. EMBO J. 14, 6107-6115 (1995). (Pubitemid 26007298)
14. Samuels, Y. et al. High frequency of mutations of the PIK3CA gene in human cancers. Science 304, 554 (2004). (Pubitemid 38541907)
15. Prosser, J., Thompson, A. M., Cranston, G.& Evans, H. J. Evidence that p53 behaves as a tumour suppressor gene in sporadic breast tumours. Oncogene 5, 1573-1579 (1990).
16. T'Ang, A., Varley, J. M., Chakraborty, S., Murphree, A. L. & Fung, Y. K. Structural rearrangement of the retinoblastoma gene in human breast carcinoma. Science 242, 263-266 (1988).
17. Wang, X. X. et al. Somatic mutations of the mixed-lineage leukemia 3 (MLL3) gene in primary breast cancers. Pathol. Oncol. Res. 17, 429-433 (2011).
18. Kan, Z. et al. Diverse somaticmutation patterns and pathway alterations in human cancers. Nature 466, 869-873 (2010).
19. Spirin, K. S. et al. p27/Kip1 mutation found in breast cancer. Cancer Res. 56, 2400-2404 (1996). (Pubitemid 26154089)
20. Fanger, G. R., Johnson, N. L.&Johnson, G. L.MEK kinases are regulated by EGFand selectively interact with Rac/Cdc42. EMBO J. 16, 4961-4972 (1997). (Pubitemid 27348405)
21. Fillmore, C. M. et al. Estrogen expands breast cancer stem-like cells through paracrine FGF/Tbx3 signaling. Proc. Natl Acad. Sci. USA 107, 21737-21742 (2010).
22. Mao, S., Frank, R. C., Zhang, J., Miyazaki, Y. & Nimer, S. D. Functional and physical interactions betweenAML1 proteins and an ETS protein,MEF: implications for the pathogenesis of t(8;21)-positive leukemias. Mol. Cell. Biol. 19, 3635-3644 (1999). (Pubitemid 29193823)
23. Stender, J. D. et al. Genome-wide analysis of estrogen receptor a DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptormediated transcriptional activation. Mol. Cell. Biol. 30, 3943-3955 (2010).
24. Papaemmanuil, E. et al. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N. Engl. J. Med. 365, 1384-1395 (2011).
25. Wang, L. et al. SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N. Engl. J. Med. 365, 2497-2506 (2011).
26. Chen, Z. et al. The May-Hegglin anomaly gene MYH9 is a negative regulator of platelet biogenesis modulated by the Rho-ROCK pathway. Blood 110, 171-179 (2007). (Pubitemid 47026832)
27. Lamant, L. et al. Non-muscle myosin heavy chain (MYH9): a new partner fused to ALK in anaplastic large cell lymphoma. Genes Chromosom. Cancer 37, 427-432 (2003). (Pubitemid 36775787)
28. Wilund, K. R. et al. Molecular mechanisms of autosomal recessive hypercholesterolemia. Hum. Mol. Genet. 11, 3019-3030 (2002). (Pubitemid 35414815)
29. Dellê, H. et al. Antifibrotic effect of tamoxifen in a model of progressive renal disease. J. Am. Soc. Nephrol. 23, 37-48 (2012).
30. Tararuk, T. et al. JNK1 phosphorylation of SCG10 determines microtubule dynamics and axodendritic length. J. Cell Biol. 173, 265-277 (2006).
31. Westerlund, N. et al.PhosphorylationofSCG10/stathmin- 2determinesmultipolar stage exit and neuronal migration rate. Nature Neurosci. 14, 305-313 (2011).
32. Tripathi, V. et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing bymodulatingSRsplicing factor phosphorylation.Mol. Cell39, 925-938 (2010).
33. Rajaram, V., Knezevich, S., Bove, K. E., Perry, A. & Pfeifer, J. D. DNA sequence of the translocation breakpoints in undifferentiated embryonal sarcoma arising in mesenchymal hamartoma of the liver harboring the t(11;19)(q11;q13.4) translocation. Genes Chromosom. Cancer 46, 508-513 (2007). (Pubitemid 46449254)
34. Xu, C., Yang, M., Tian, J., Wang, X. & Li, Z. MALAT-1: a long non-coding RNA and its important 39 end functional motif in colorectal cancer metastasis. Int. J. Oncol. 39, 169-175 (2011).
35. Wendl, M. C. et al. PathScan: a tool for discerningmutational significance in groups of putative cancer genes. Bioinformatics 27, 1595-1602 (2011).
36. Vaske, C. J. et al. Inference of patient-specific pathway activities from multidimensional cancer genomics data using PARADIGM. Bioinformatics 26, i237-i245 (2010).
37. Lynch, T. J. et al. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N. Engl. J. Med. 350, 2129-2139 (2004). (Pubitemid 38637993)
38. Johnson, G. L. & Lapadat, R. Mitogen-activated protein kinase pathways mediated by ERK, JNK, and p38 protein kinases. Science 298, 1911-1912 (2002). (Pubitemid 35425238)
39. Widmann, C., Johnson, N. L., Gardner, A. M., Smith, R. J. & Johnson, G. L. Potentiation of apoptosis by low dose stress stimuli in cells expressing activated MEK kinase 1. Oncogene 15, 2439-2447 (1997). (Pubitemid 27503530)
40. Wagner, E. F. & Nebreda, A. R. Signal integration by JNK and p38 MAPK pathways in cancer development. Nature Rev. Cancer 9, 537-549 (2009).
41. Ellis, M. J. et al. Phosphatidyl-inositol-3-kinase alpha catalytic subunit mutation and response to neoadjuvant endocrine therapy for estrogen receptor positive breast cancer. Breast Cancer Res. Treat. 119, 379-390 (2010).
42. Prat, A. & Perou, C. M. Mammary development meets cancer genomics. Nature Med. 15, 842-844 (2009).
43. Larson, D. E. et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics 28, 311-317 (2011).
44. Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).
45. Dees, N. et al. MuSiC: Identifying mutational significance in cancer genomes. Genome Res. (in the press).