Abstract
Cancer cells have diverse biological capabilities that are conferred by numerous genetic aberrations and epigenetic modifications. Today's powerful technologies are enabling these changes to the genome to be catalogued in detail. Tomorrow is likely to bring a complete atlas of the reversible and irreversible alterations that occur in individual cancers. The challenge now is to work out which molecular abnormalities contribute to cancer and which are simply 'noise' at the genomic and epigenomic levels. Distinguishing between these will aid in understanding how the aberrations in a cancer cell collaborate to drive pathophysiology. Past successes in converting information from genomic discoveries into clinical tools provide valuable lessons to guide the translation of emerging insights from the genome into clinical end points that can affect the practice of cancer medicine.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 51 print issues and online access
$199.00 per year
only $3.90 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Hanahan, D. & Weinberg, R. A. The hallmarks of cancer. Cell 100, 57–70 (2000).
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).
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).
Paez, J. G. et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science 304, 1497–1500 (2004).
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. USA 101, 13306–13311 (2004). References 3–5 show that a subset of patients with lung cancer have EGFR mutations and are responsive to an EGFR-specific tyrosine kinase inhibitor, a finding based on prospective analyses of retrospective data.
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 harbouring BCR–ABL was shown to be sensitive to treatment with a BCR–ABL-specific tyrosine-kinase inhibitor, imatinib mesylate.
Pegram, M. & Slamon, D. Biological rationale for HER2/neu (c-erbB2) as a target for monoclonal antibody therapy. Semin. Oncol. 27, 13–19 (2000).
Malkin, D. et al. Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms. Science 250, 1233–1238 (1990).
Futreal, P. A. et al. BRCA1 mutations in primary breast and ovarian carcinomas. Science 266, 120–122 (1994).
Miki, Y. et al. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1 . Science 266, 66–71 (1994).
Wooster, R. et al. Identification of the breast cancer susceptibility gene BRCA2 . Nature 378, 789–792 (1995).
Marra, G. & Boland, C. R. Hereditary nonpolyposis colorectal cancer: the syndrome, the genes, and historical perspectives. J. Natl Cancer Inst. 87, 1114–1125 (1995).
Gruis, N. A. et al. Homozygotes for CDKN2 (p16) germline mutation in Dutch familial melanoma kindreds. Nature Genet. 10, 351–3 (1995).
Nowell, P. C. Discovery of the Philadelphia chromosome: a personal perspective. J. Clin. Invest. 117, 2033–2035 (2007).
Nardi, V., Azam, M. & Daley, G. Q. Mechanisms and implications of imatinib resistance mutations in BCR–ABL. Curr. Opin. Hematol. 11, 35–43 (2004).
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).
Demetri, G. D. Targeting c-kit mutations in solid tumors: scientific rationale and novel therapeutic options. Semin. Oncol. 28, 19–26 (2001).
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).
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).
Tomlins, S. A. et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310, 644–648 (2005).
Bradford, T. J., Tomlins, S. A., Wang, X. & Chinnaiyan, A. M. Molecular markers of prostate cancer. Urol. Oncol. 24, 538–551 (2006).
Volik, S. et al. End-sequence profiling: sequence-based analysis of aberrant genomes. Proc. Natl Acad. Sci. USA 100, 7696–7701 (2003).
Bignell, G. R. et al. Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res. 17, 1296–1303 (2007).
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. Nature 312, 513–516 (1984).
King, C. R., Kraus, M. H. & Aaronson, S. A. Amplification of a novel v-erbB-related gene in a human mammary carcinoma. Science 229, 974–976 (1985).
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. USA 82, 6497–6501 (1985).
Coussens, L. et al. Tyrosine kinase receptor with extensive homology to EGF receptor shares chromosomal location with neu oncogene. Science 230, 1132–1139 (1985).
Slamon, D. J. et al. Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 235, 177–182 (1987). This study correlated ERBB2 amplification with outcome for individuals with breast cancer.
Kallioniemi, A. et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258, 818–821 (1992).
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. Nature 417, 949–954 (2002).
Samuels, Y. et al. High frequency of mutations of the PIK3CA gene in human cancers. Science 304, 554 (2004).
Carpten, J. D. et al. A transforming mutation in the pleckstrin homology domain of AKT1 in cancer. Nature 448, 439–444 (2007).
Stephens, P. et al. Lung cancer: intragenic ERBB2 kinase mutations in tumours. Nature 431, 525–526 (2004).
Sharma, S. V., Bell, D. W., Settleman, J. & Haber, D. A. Epidermal growth factor receptor mutations in lung cancer. Nature Rev. Cancer 7, 169–181 (2007).
Blackhall, F., Ranson, M. & Thatcher, N. Where next for gefitinib in patients with lung cancer? Lancet Oncol. 7, 499–507 (2006).
Farmer, H. et al. Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature 434, 917–921 (2005).
Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153–158 (2007).
Wood, L. D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108–1113 (2007). References 40 and 41 report on large-scale sequencing studies aimed at identifying somatic mutations in human cancers.
Sharpless, N. E. INK4a/ARF: a multifunctional tumor suppressor locus. Mutat. Res. 576, 22–38 (2005).
Shayesteh, L. et al. PIK3CA is implicated as an oncogene in ovarian cancer. Nature Genet. 21, 99–102 (1999).
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).
Nurse, P., Masui, Y. & Hartwell, L. Understanding the cell cycle. Nature Med. 4, 1103–1106 (1998).
Schreiber-Agus, N. et al. Drosophila Myc is oncogenic in mammalian cells and plays a role in the diminutive phenotype. Proc. Natl Acad. Sci. USA 94, 1235–1240 (1997).
Kim, M. et al. Comparative oncogenomics identifies NEDD9 as a melanoma metastasis gene. Cell 125, 1269–1281 (2006).
Zender, L. et al. Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach. Cell 125, 1253–1267 (2006). References 47 and 48 show the power of cross-species integration of cancer genome data for oncogene discovery.
Maser, R. S. et al. Chromosomally unstable mouse tumours have genomic alterations similar to diverse human cancers. Nature 447, 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.
Sweet-Cordero, A. et al. An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nature Genet. 37, 48–55 (2005).
O'Neil, J. et al. Activating Notch1 mutations in mouse models of T-ALL. Blood 107, 781–785 (2006).
Chin, L., Garraway, L. A. & Fisher, D. E. Malignant melanoma: genetics and therapeutics in the genomic era. Genes Dev. 20, 2149–2182 (2006).
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).
Artandi, S. E. & DePinho, R. A. Mice without telomerase: what can they teach us about human cancer? Nature Med. 6, 852–855 (2000).
Artandi, S. E. et al. Telomere dysfunction promotes non-reciprocal translocations and epithelial cancers in mice. Nature 406, 641–645 (2000).
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).
O'Hagan, R. C. et al. Telomere dysfunction provokes regional amplification and deletion in cancer genomes. Cancer Cell 2, 149–155 (2002).
Palomero, T. et al. Mutational loss of PTEN induces resistance to NOTCH1 inhibition in T-cell leukemia. Nature Med. 13, 1203–1210 (2007).
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).
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. Carcinogenesis 26, 1368–1373 (2005).
Uren, A. G., Kool, J., Berns, A. & van Lohuizen, M. Retroviral insertional mutagenesis: past, present and future. Oncogene 24, 7656–7672 (2005).
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).
Westbrook, T. F. et al. A genetic screen for candidate tumor suppressors identifies REST. Cell 121, 837–848 (2005).
Boehm, J. S. et al. Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell 129, 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.
Berns, K. et al. A functional genetic approach identifies the PI3K pathway as a major determinant of trastuzumasb resistance in breast cancer. Cancer Cell 12, 395–402 (2007).
Staunton, J. E. et al. Chemosensitivity prediction by transcriptional profiling. Proc. Natl Acad. Sci. USA 98, 10787–10792 (2001).
Bild, A. H. et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 439, 353–357 (2006).
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).
Hieronymus, H. et al. Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators. Cancer Cell 10, 321–330 (2006).
Wei, G. et al. Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance. Cancer Cell 10, 331–342 (2006).
Neve, R. M. et al. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 10, 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.
Wong, K. K. HKI-272 in non small cell lung cancer. Clin. Cancer Res. 13, s4593–s4596 (2007).
Scappini, B. et al. Changes associated with the development of resistance to imatinib (STI571) in two leukemia cell lines expressing p210 Bcr/Abl protein. Cancer 100, 1459–1471 (2004).
Furnari, F. B. et al. Malignant astrocytic glioma: genetics, biology, and paths to treatment. Genes Dev. 21, 2683–2710 (2007).
Mellinghoff, I. K. et al. Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N. Engl. J. Med. 353, 2012–2024 (2005).
Stommel, J. M. et al. Coactivation of receptor tyrosine kinases affects the response of tumor cells to targeted therapies. Science 318, 287–290 (2007).
Greshock, J. et al. A comparison of DNA copy number profiling platforms. Cancer Res. 67, 10173–10180 (2007).
Korbel, J. O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420–426 (2007).
Drmanac, R. et al. DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing. Science 260, 1649–1652 (1993).
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).
Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005).
Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728–1732 (2005).
Porreca, G. J. et al. Multiplex amplification of large sets of human exons. Nature Methods 4, 931–936 (2007).
Costello, J. F. et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nature Genet. 24, 132–138 (2000).
Dai, Z. et al. An AscI boundary library for the studies of genetic and epigenetic alterations in CpG islands. Genome Res. 12, 1591–1598 (2002).
Plass, C. et al. An arrayed human not I-EcoRV boundary library as a tool for RLGS spot analysis. DNA Res. 4, 253–255 (1997).
van Steensel, B. & Henikoff, S. Epigenomic profiling using microarrays. Biotechniques 35, 346–350, 352–354, 356–357 (2003).
Meissner, A. et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 33, 5868–5877 (2005).
Hu, M. et al. Distinct epigenetic changes in the stromal cells of breast cancers. Nature Genet. 37, 899–905 (2005).
Leary, R. J., Cummins, J., Wang, T. L. & Velculescu, V. E. Digital karyotyping. Nature Protoc. 2, 1973–1986 (2007).
Collas, P. & Dahl, J. A. Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation. Front. Biosci. 13, 929–943 (2008).
Acknowledgements
We thank R. DePinho, A. Futreal, P. Mischel, A. Kimmelman, K.-K. Wong, W. Hahn and K. Polyak for discussions and critical reading of the manuscript. This work was supported in part by the US Department of Energy, the Office of Science, the Office of Biological and Environmental Research, the National Institutes of Health and the National Cancer Institute.
Author information
Authors and Affiliations
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Additional information
Reprints and permissions information is available at http://npg.nature.com/reprints.
Correspondence should be addressed to L.C. (lynda_chin@dfci.harvard.edu).
Rights and permissions
About this article
Cite this article
Chin, L., Gray, J. Translating insights from the cancer genome into clinical practice. Nature 452, 553–563 (2008). https://doi.org/10.1038/nature06914
Published:
Issue Date:
DOI: https://doi.org/10.1038/nature06914
This article is cited by
-
Surface-enhanced Raman scattering (SERS)–based immunosystem for ultrasensitive detection of the 90K biomarker
Analytical and Bioanalytical Chemistry (2020)
-
The novel TP53 3′-end methylation pattern associated with its expression would be a potential biomarker for breast cancer detection
Breast Cancer Research and Treatment (2020)
-
Between Minimal and Greater Than Minimal Risk: How Research Participants and Oncologists Assess Data-Sharing and the Risk of Re-identification in Genomic Research
Philosophy & Technology (2019)
-
Clinical significance of APOB inactivation in hepatocellular carcinoma
Experimental & Molecular Medicine (2018)
Comments
By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.