Translating insights from the cancer genome into clinical practice (original) (raw)
Hanahan, D. & Weinberg, R. A. The hallmarks of cancer. Cell100, 57–70 (2000). CASPubMed Google Scholar
Collins, F. S. & Barker, A. D. Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies. Sci. Am.296, 50–57 (2007). CASPubMed Google Scholar
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). ArticleCASPubMed Google Scholar
Paez, J. G. et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science304, 1497–1500 (2004). ArticleADSCASPubMed Google Scholar
Pao, W. et al. EGF receptor gene mutations are common in lung cancers from 'never smokers' and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc. Natl Acad. Sci. USA101, 13306–13311 (2004). References 3–5 show that a subset of patients with lung cancer haveEGFRmutations and are responsive to an EGFR-specific tyrosine kinase inhibitor, a finding based on prospective analyses of retrospective data. ADSCASPubMedPubMed Central Google Scholar
Druker, B. J. et al. Efficacy and safety of a specific inhibitor of the BCR–ABL tyrosine kinase in chronic myeloid leukemia. N. Engl. J. Med.344, 1031–1037 (2001). This paper provides the first proof of concept of targeted therapy: chronic myeloid leukaemia harbouringBCR–ABLwas shown to be sensitive to treatment with a BCR–ABL-specific tyrosine-kinase inhibitor, imatinib mesylate. CASPubMed Google Scholar
Pegram, M. & Slamon, D. Biological rationale for HER2/neu (c-erbB2) as a target for monoclonal antibody therapy. Semin. Oncol.27, 13–19 (2000). CASPubMed Google Scholar
Malkin, D. et al. Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms. Science250, 1233–1238 (1990). ADSCASPubMed Google Scholar
Futreal, P. A. et al. BRCA1 mutations in primary breast and ovarian carcinomas. Science266, 120–122 (1994). ADSCASPubMed Google Scholar
Miki, Y. et al. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1 . Science266, 66–71 (1994). ADSCASPubMed Google Scholar
Wooster, R. et al. Identification of the breast cancer susceptibility gene BRCA2 . Nature378, 789–792 (1995). ADSCASPubMed Google Scholar
Marra, G. & Boland, C. R. Hereditary nonpolyposis colorectal cancer: the syndrome, the genes, and historical perspectives. J. Natl Cancer Inst.87, 1114–1125 (1995). CASPubMed Google Scholar
Gruis, N. A. et al. Homozygotes for CDKN2 (p16) germline mutation in Dutch familial melanoma kindreds. Nature Genet.10, 351–3 (1995). CASPubMed Google Scholar
Nowell, P. C. Discovery of the Philadelphia chromosome: a personal perspective. J. Clin. Invest.117, 2033–2035 (2007). CASPubMedPubMed Central Google Scholar
Nardi, V., Azam, M. & Daley, G. Q. Mechanisms and implications of imatinib resistance mutations in BCR–ABL. Curr. Opin. Hematol.11, 35–43 (2004). CASPubMed Google Scholar
Quintas-Cardama, A., Kantarjian, H. & Cortes, J. Flying under the radar: the new wave of BCR–ABL inhibitors. Nature Rev. Drug Discov.6, 834–848 (2007). CAS Google Scholar
Demetri, G. D. Targeting c-kit mutations in solid tumors: scientific rationale and novel therapeutic options. Semin. Oncol.28, 19–26 (2001). CASPubMed Google Scholar
Curtin, J. A., Busam, K., Pinkel, D. & Bastian, B. C. Somatic activation of KIT in distinct subtypes of melanoma. J. Clin. Oncol.24, 4340–4346 (2006). CASPubMed Google Scholar
Hodi, F. et al. A major response to Imatinib mesylate in KIT mutated melanoma. J. Clin. Orthod. (in the press).
Rowley, J. D. The role of chromosome translocations in leukemogenesis. Semin. Hematol.36, 59–72 (1999). CASPubMed Google Scholar
Tomlins, S. A. et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science310, 644–648 (2005). ADSCASPubMed Google Scholar
Bradford, T. J., Tomlins, S. A., Wang, X. & Chinnaiyan, A. M. Molecular markers of prostate cancer. Urol. Oncol.24, 538–551 (2006). CASPubMed Google Scholar
Volik, S. et al. End-sequence profiling: sequence-based analysis of aberrant genomes. Proc. Natl Acad. Sci. USA100, 7696–7701 (2003). ADSPubMedPubMed Central Google Scholar
Bignell, G. R. et al. Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res.17, 1296–1303 (2007). CASPubMedPubMed Central Google Scholar
Campbell, P. J. et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nature Genet. (in the press).
Schechter, A. L. et al. The neu oncogene: an _erb-B_-related gene encoding a 185,000-M r tumour antigen. Nature312, 513–516 (1984). ADSCASPubMed Google Scholar
King, C. R., Kraus, M. H. & Aaronson, S. A. Amplification of a novel v-_erbB_-related gene in a human mammary carcinoma. Science229, 974–976 (1985). ADSCASPubMed Google Scholar
Semba, K., Kamata, N., Toyoshima, K. & Yamamoto, T. A v-_erbB_-related protooncogene, c-erbB-2, is distinct from the c-erbB-1/epidermal growth factor-receptor gene and is amplified in a human salivary gland adenocarcinoma. Proc. Natl Acad. Sci. USA82, 6497–6501 (1985). ADSCASPubMedPubMed Central Google Scholar
Coussens, L. et al. Tyrosine kinase receptor with extensive homology to EGF receptor shares chromosomal location with neu oncogene. Science230, 1132–1139 (1985). ADSCASPubMed Google Scholar
Slamon, D. J. et al. Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science235, 177–182 (1987). This study correlatedERBB2amplification with outcome for individuals with breast cancer. ADSCASPubMed Google Scholar
Kallioniemi, A. et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science258, 818–821 (1992). ADSCASPubMed Google Scholar
Cameron, D. et al. A phase III randomized comparison of lapatinib plus capecitabine versus capecitabine alone in women with advanced breast cancer that has progressed on trastuzumab: updated efficacy and biomarker analyses. Breast Cancer Res. Treat. doi:10.1007/s10549-007-9885-0 (in the press).
Davies, H. et al. Mutations of the BRAF gene in human cancer. Nature417, 949–954 (2002). ADSCASPubMed Google Scholar
Samuels, Y. et al. High frequency of mutations of the PIK3CA gene in human cancers. Science304, 554 (2004). CASPubMed Google Scholar
Carpten, J. D. et al. A transforming mutation in the pleckstrin homology domain of AKT1 in cancer. Nature448, 439–444 (2007). ADSCASPubMed Google Scholar
Stephens, P. et al. Lung cancer: intragenic ERBB2 kinase mutations in tumours. Nature431, 525–526 (2004). ADSCASPubMed Google Scholar
Sharma, S. V., Bell, D. W., Settleman, J. & Haber, D. A. Epidermal growth factor receptor mutations in lung cancer. Nature Rev. Cancer7, 169–181 (2007). CAS Google Scholar
Blackhall, F., Ranson, M. & Thatcher, N. Where next for gefitinib in patients with lung cancer? Lancet Oncol.7, 499–507 (2006). CASPubMed Google Scholar
Farmer, H. et al. Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature434, 917–921 (2005). ADSCASPubMed Google Scholar
Wood, L. D. et al. The genomic landscapes of human breast and colorectal cancers. Science318, 1108–1113 (2007). References 40 and 41 report on large-scale sequencing studies aimed at identifying somatic mutations in human cancers. ADSCASPubMed Google Scholar
Sharpless, N. E. INK4a/ARF: a multifunctional tumor suppressor locus. Mutat. Res.576, 22–38 (2005). CASPubMed Google Scholar
Shayesteh, L. et al. PIK3CA is implicated as an oncogene in ovarian cancer. Nature Genet.21, 99–102 (1999). CASPubMed Google Scholar
Horvitz, H. R., Shaham, S. & Hengartner, M. O. The genetics of programmed cell death in the nematode Caenorhabditis elegans . Cold Spring Harb. Symp. Quant. Biol.59, 377–385 (1994). CASPubMed Google Scholar
Nurse, P., Masui, Y. & Hartwell, L. Understanding the cell cycle. Nature Med.4, 1103–1106 (1998). CASPubMed Google Scholar
Schreiber-Agus, N. et al. Drosophila Myc is oncogenic in mammalian cells and plays a role in the diminutive phenotype. Proc. Natl Acad. Sci. USA94, 1235–1240 (1997). ADSCASPubMedPubMed Central Google Scholar
Kim, M. et al. Comparative oncogenomics identifies NEDD9 as a melanoma metastasis gene. Cell125, 1269–1281 (2006). CASPubMed Google Scholar
Zender, L. et al. Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach. Cell125, 1253–1267 (2006). References 47 and 48 show the power of cross-species integration of cancer genome data for oncogene discovery. CASPubMedPubMed Central Google Scholar
Maser, R. S. et al. Chromosomally unstable mouse tumours have genomic alterations similar to diverse human cancers. Nature447, 966–971 (2007). This paper compares the genomes of mouse tumour cells with genetically engineered chromosomal instability to the genomes of various human cancers and shows that there is a significant non-random number of syntenic events, proving that mouse and human cells can experience common biological processes driven by orthologous genetic events during transformation. ADSCASPubMedPubMed Central Google Scholar
Sweet-Cordero, A. et al. An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nature Genet.37, 48–55 (2005). CASPubMed Google Scholar
Chin, L., Garraway, L. A. & Fisher, D. E. Malignant melanoma: genetics and therapeutics in the genomic era. Genes Dev.20, 2149–2182 (2006). CASPubMed Google Scholar
Hodgson, J. G. et al. Copy number aberrations in mouse breast tumors reveal loci and genes important in tumorigenic receptor tyrosine kinase signaling. Cancer Res.65, 9695–9704 (2005). CASPubMed Google Scholar
Artandi, S. E. & DePinho, R. A. Mice without telomerase: what can they teach us about human cancer? Nature Med.6, 852–855 (2000). CASPubMed Google Scholar
Artandi, S. E. et al. Telomere dysfunction promotes non-reciprocal translocations and epithelial cancers in mice. Nature406, 641–645 (2000). ADSCASPubMed Google Scholar
Maser, R. S. et al. DNA-dependent protein kinase catalytic subunit is not required for dysfunctional telomere fusion and checkpoint response in the telomerase-deficient mouse. Mol. Cell. Biol.27, 2253–2265 (2007). CASPubMed Google Scholar
O'Hagan, R. C. et al. Telomere dysfunction provokes regional amplification and deletion in cancer genomes. Cancer Cell2, 149–155 (2002). CASPubMed Google Scholar
Palomero, T. et al. Mutational loss of PTEN induces resistance to NOTCH1 inhibition in T-cell leukemia. Nature Med.13, 1203–1210 (2007). CASPubMed Google Scholar
Ewart-Toland, A. et al. Identification of Stk6/STK15 as a candidate low-penetrance tumor-susceptibility gene in mouse and human. Nature Genet.34, 403–412 (2003). CASPubMed Google Scholar
Ewart-Toland, A. et al. Aurora-A/STK15 T+91A is a general low penetrance cancer susceptibility gene: a meta-analysis of multiple cancer types. Carcinogenesis26, 1368–1373 (2005). CASPubMed Google Scholar
Uren, A. G., Kool, J., Berns, A. & van Lohuizen, M. Retroviral insertional mutagenesis: past, present and future. Oncogene24, 7656–7672 (2005). CASPubMed Google Scholar
Sharpless, N. E. & Depinho, R. A. The mighty mouse: genetically engineered mouse models in cancer drug development. Nature Rev. Drug Discov.5, 741–754 (2006). CAS Google Scholar
Westbrook, T. F. et al. A genetic screen for candidate tumor suppressors identifies REST. Cell121, 837–848 (2005). CASPubMed Google Scholar
Boehm, J. S. et al. Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell129, 1065–1079 (2007). References 63 and 64 integrate hits from forward genetic screening, using RNAi, with genomic profiles of human cancers to find previously unidentified oncogenes. CASPubMed Google Scholar
Berns, K. et al. A functional genetic approach identifies the PI3K pathway as a major determinant of trastuzumasb resistance in breast cancer. Cancer Cell12, 395–402 (2007). CASPubMed Google Scholar
Staunton, J. E. et al. Chemosensitivity prediction by transcriptional profiling. Proc. Natl Acad. Sci. USA98, 10787–10792 (2001). ADSCASPubMedPubMed Central Google Scholar
Bild, A. H. et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature439, 353–357 (2006). ADSCASPubMed Google Scholar
Konecny, G. E. et al. Activity of the dual kinase inhibitor lapatinib (GW572016) against HER-2-overexpressing and trastuzumab-treated breast cancer cells. Cancer Res.66, 1630–1639 (2006). CASPubMed Google Scholar
Hieronymus, H. et al. Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators. Cancer Cell10, 321–330 (2006). CASPubMed Google Scholar
Wei, G. et al. Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance. Cancer Cell10, 331–342 (2006). CASPubMed Google Scholar
Neve, R. M. et al. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell10, 515–527 (2006). This study shows that the cancer genomes of a panel of human cancer cell lines reflect the genomic diversity of human cancers. CASPubMedPubMed Central Google Scholar
Wong, K. K. HKI-272 in non small cell lung cancer. Clin. Cancer Res.13, s4593–s4596 (2007). PubMed Google Scholar
Scappini, B. et al. Changes associated with the development of resistance to imatinib (STI571) in two leukemia cell lines expressing p210 Bcr/Abl protein. Cancer100, 1459–1471 (2004). CASPubMed Google Scholar
Furnari, F. B. et al. Malignant astrocytic glioma: genetics, biology, and paths to treatment. Genes Dev.21, 2683–2710 (2007). CASPubMed Google Scholar
Mellinghoff, I. K. et al. Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N. Engl. J. Med.353, 2012–2024 (2005). CASPubMed Google Scholar
Stommel, J. M. et al. Coactivation of receptor tyrosine kinases affects the response of tumor cells to targeted therapies. Science318, 287–290 (2007). ADSCASPubMed Google Scholar
Greshock, J. et al. A comparison of DNA copy number profiling platforms. Cancer Res.67, 10173–10180 (2007). CASPubMed Google Scholar
Korbel, J. O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science318, 420–426 (2007). ADSCASPubMedPubMed Central Google Scholar
Drmanac, R. et al. DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing. Science260, 1649–1652 (1993). ADSCASPubMed Google Scholar
Sanger, F. & Coulson, A. R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol.94, 441–448 (1975). CASPubMed Google Scholar
Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science309, 1728–1732 (2005). ADSCASPubMed Google Scholar
Porreca, G. J. et al. Multiplex amplification of large sets of human exons. Nature Methods4, 931–936 (2007). CASPubMed Google Scholar
Costello, J. F. et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nature Genet.24, 132–138 (2000). CASPubMed Google Scholar
Dai, Z. et al. An _Asc_I boundary library for the studies of genetic and epigenetic alterations in CpG islands. Genome Res.12, 1591–1598 (2002). CASPubMedPubMed Central Google Scholar
Plass, C. et al. An arrayed human not I-_Eco_RV boundary library as a tool for RLGS spot analysis. DNA Res.4, 253–255 (1997). CASPubMed Google Scholar
van Steensel, B. & Henikoff, S. Epigenomic profiling using microarrays. Biotechniques35, 346–350, 352–354, 356–357 (2003). CASPubMed Google Scholar
Meissner, A. et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res.33, 5868–5877 (2005). CASPubMedPubMed Central Google Scholar
Hu, M. et al. Distinct epigenetic changes in the stromal cells of breast cancers. Nature Genet.37, 899–905 (2005). CASPubMed Google Scholar
Leary, R. J., Cummins, J., Wang, T. L. & Velculescu, V. E. Digital karyotyping. Nature Protoc.2, 1973–1986 (2007). CAS Google Scholar
Collas, P. & Dahl, J. A. Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation. Front. Biosci.13, 929–943 (2008). CASPubMed Google Scholar