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Molecular portraits and the family tree of cancer

Abstract

The twenty-first century heralds a new era for the biological sciences and medicine. The tools of our time are allowing us to analyze complex genomes more comprehensively than ever before. A principal technology contributing to this explosion of information is the DNA microarray, which enables us to study genome-wide expression patterns in complex biological systems. Although the potential of microarrays is yet to be fully realized, these tools have shown great promise in deciphering complex diseases such as cancer. The early results are painting a detailed portrait of cancer that illustrates the individuality of each tumor and allows familial relationships to be recognized through the identification of cell types sharing common expression patterns.

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Figure 1

Bob Crimi

Figure 2: Classification of histologically similar CNS tumors.
Figure 3: Combined hierarchical cluster analysis of breast and lung carcinomas.

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References

  1. Perou, C.M. et al. Molecular portraits of human breast tumours. Nature 406, 747–752 (2000).

    Article  CAS  Google Scholar 

  2. Sørlie, T. et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl Acad. Sci. USA 98, 10869–10874 (2001).

    Article  Google Scholar 

  3. van 't Veer, L.J. et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530–536 (2002).

    Article  CAS  Google Scholar 

  4. West, M. et al. Predicting the clinical status of human breast cancer by using gene expression profiles. Proc. Natl Acad. Sci. USA 98, 11462–11467 (2001).

    Article  CAS  Google Scholar 

  5. Hedenfalk, I. et al. Gene-expression profiles in hereditary breast cancer. N. Engl. J. Med. 344, 539–548 (2001).

    Article  CAS  Google Scholar 

  6. Gruvberger, S. et al. Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res. 61, 5979–5984 (2001).

    CAS  Google Scholar 

  7. MacDonald, T.J. et al. Expression profiling of medulloblastoma: PDGFRA and the RAS/MAPK pathway as therapeutic targets for metastatic disease. Nature Genet. 29, 143–152 (2001).

    Article  CAS  Google Scholar 

  8. Pomeroy, S.L. et al. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415, 436–442 (2002).

    Article  CAS  Google Scholar 

  9. Jazaeri, A.A. et al. Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers. J. Natl Cancer Inst. 94, 990–1000 (2002).

    Article  CAS  Google Scholar 

  10. Welsh, J.B. et al. Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc. Natl Acad. Sci. USA 98, 1176–1181 (2001).

    Article  CAS  Google Scholar 

  11. Wang, K. et al. Monitoring gene expression profile changes in ovarian carcinomas using cDNA microarray. Gene 229, 101–108 (1999).

    Article  CAS  Google Scholar 

  12. Beer, D.G. et al. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nature Med. 8, 816–824 (2002).

    Article  CAS  Google Scholar 

  13. Garber, M.E. et al. Diversity of gene expression in adenocarcinoma of the lung. Proc. Natl Acad. Sci. USA 98, 13784–13789 (2001).

    Article  CAS  Google Scholar 

  14. Bhattacharjee, A. et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc. Natl Acad. Sci. USA 98, 13790–13795 (2001).

    Article  CAS  Google Scholar 

  15. Zou, T.T. et al. Application of cDNA microarrays to generate a molecular taxonomy capable of distinguishing between colon cancer and normal colon. Oncogene 21, 4855–4862 (2002).

    Article  CAS  Google Scholar 

  16. Lin, Y.M. et al. Molecular diagnosis of colorectal tumors by expression profiles of 50 genes expressed differentially in adenomas and carcinomas. Oncogene 21, 4120–4128 (2002).

    Article  CAS  Google Scholar 

  17. Alon, U. et al. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl Acad. Sci. USA 96, 6745–6750 (1999).

    Article  CAS  Google Scholar 

  18. Takahashi, M. et al. Gene expression profiling of clear cell renal cell carcinoma: gene identification and prognostic classification. Proc. Natl Acad. Sci. USA 98, 9754–9759 (2001).

    Article  CAS  Google Scholar 

  19. Singh, D. et al. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 1, 203–209 (2002).

    Article  CAS  Google Scholar 

  20. LaTulippe, E. et al. Comprehensive gene expression analysis of prostate cancer reveals distinct transcriptional programs associated with metastatic disease. Cancer Res. 62, 4499–4506 (2002).

    CAS  Google Scholar 

  21. Welsh, J.B. et al. Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Res. 61, 5974–5978 (2001).

    CAS  Google Scholar 

  22. Dhanasekaran, S.M. et al. Delineation of prognostic biomarkers in prostate cancer. Nature 412, 822–826 (2001).

    Article  CAS  Google Scholar 

  23. Hippo, Y. et al. Global gene expression analysis of gastric cancer by oligonucleotide microarrays. Cancer Res. 62, 233–240 (2002).

    CAS  Google Scholar 

  24. Yeoh, E.J. et al. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell 1, 133–143 (2002).

    Article  CAS  Google Scholar 

  25. Hofmann, W.K. et al. Relation between resistance of Philadelphia-chromosome-positive acute lymphoblastic leukaemia to the tyrosine kinase inhibitor STI571 and gene-expression profiles: a gene-expression study. Lancet 359, 481–486 (2002).

    Article  CAS  Google Scholar 

  26. Ferrando, A.A. et al. Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell 1, 75–87 (2002).

    Article  CAS  Google Scholar 

  27. Shipp, M.A. et al. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nature Med. 8, 68–74 (2002).

    Article  CAS  Google Scholar 

  28. Rosenwald, A. et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N. Engl. J. Med. 346, 1937–1947 (2002).

    Article  Google Scholar 

  29. Alizadeh, A.A. et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503–511 (2000).

    Article  CAS  Google Scholar 

  30. Hanahan, D. & Weinberg, R.A. The hallmarks of cancer. Cell 100, 57–70 (2000).

    Article  CAS  Google Scholar 

  31. Ross, D.T. et al. Systematic variation in gene expression patterns in human cancer cell lines. Nature Genet. 24, 227–235 (2000).

    Article  CAS  Google Scholar 

  32. Slonim, D.K. From patterns to pathways: gene expression data analysis comes of age. Nature Genet. 32, 502–508 (2002).

    Article  CAS  Google Scholar 

  33. Churchill, G.A. Fundamentals of experimental design for cDNA microarrays. Nature Genet. 32, 490–495 (2002).

    Article  CAS  Google Scholar 

  34. Ramaswamy, S. et al. Multiclass cancer diagnosis using tumor gene expression signatures. Proc. Natl Acad. Sci. USA 98, 15149–15154 (2001).

    Article  CAS  Google Scholar 

  35. Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95, 14863–14868 (1998).

    Article  CAS  Google Scholar 

  36. Tusher, V., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116–5121 (2001).

    Article  CAS  Google Scholar 

  37. Tibshirani, R., Hastie, T., Narasimhan, B. & Chu, G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc. Natl Acad. Sci. USA 99, 6567–6572 (2002).

    Article  CAS  Google Scholar 

  38. Chen, X. et al. Gene expression patterns in human liver cancers. Mol. Biol. Cell 13, 1929–1939 (2002).

    Article  CAS  Google Scholar 

  39. Nielsen, T.O. et al. Molecular characterisation of soft tissue tumours: a gene expression study. Lancet 359, 1301–1307 (2002).

    Article  CAS  Google Scholar 

  40. Wigle, D.A. et al. Molecular profiling of non-small cell lung cancer and correlation with disease-free survival. Cancer Res. 62, 3005–3008 (2002).

    CAS  Google Scholar 

  41. Bernards, R. & Weinberg, R.A. A progression puzzle. Nature 418, 823 (2002).

  42. Fisher, B. et al. A randomized clinical trial evaluating tamoxifen in the treatment of patients with node-negative breast cancer who have estrogen-receptor-positive tumors. N. Engl. J. Med. 320, 479–484 (1989).

    Article  CAS  Google Scholar 

  43. Druker, B.J. et al. Activity of a specific inhibitor of the BCR-ABL tyrosine kinase in the blast crisis of chronic myeloid leukemia and acute lymphoblastic leukemia with the Philadelphia chromosome. N. Engl. J. Med. 344, 1038–1042 (2001).

    Article  CAS  Google Scholar 

  44. Dematteo, R.P., Heinrich, M.C., El-Rifai, W.M. & Demetri, G. Clinical management of gastrointestinal stromal tumors: before and after STI-571. Hum. Pathol. 33, 466–477 (2002).

    Article  CAS  Google Scholar 

  45. Su, A.I. et al. Molecular classification of human carcinomas by use of gene expression signatures. Cancer Res. 61, 7388–7393 (2001).

    CAS  Google Scholar 

  46. Hsiao, L.L. et al. A compendium of gene expression in normal human tissues. Physiol. Genom. 7, 97–104 (2001).

    Article  CAS  Google Scholar 

  47. Perou, C.M. et al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc. Natl Acad. Sci. USA 96, 9212–9217 (1999).

    Article  CAS  Google Scholar 

  48. Rickman, D.S. et al. Distinctive molecular profiles of high-grade and low-grade gliomas based on oligonucleotide microarray analysis. Cancer Res. 61, 6885–6891 (2001).

    CAS  Google Scholar 

  49. Whitfield, M.L. et al. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol. Biol. Cell 13, 1977–2000 (2002).

    Article  CAS  Google Scholar 

  50. Levsky, J.M., Shenoy, S.M., Pezo, R.C. & Singer, R.H. Single-cell gene expression profiling. Science 297, 836–840 (2002).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank J. Parker for comments and apologize to the researchers whose work was not discussed owing to length considerations. This work was supported by grants from the National Cancer Institute and the National Institute of Environmental Health Sciences.

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Correspondence to Charles M. Perou.

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Chung, C., Bernard, P. & Perou, C. Molecular portraits and the family tree of cancer. Nat Genet 32 (Suppl 4), 533–540 (2002). https://doi.org/10.1038/ng1038

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