Prediction of central nervous system embryonal tumour outcome based on gene expression (original) (raw)

References

1. Rorke, L. B. The cerebellar medulloblastoma and its relationship to primitive neuroectodermal tumors. J. Neuropathol. Exp. Neurol. 42, 1–15 (1983).
   Article CAS Google Scholar
2. Kadin, M. E., Rubenstein, L. J. & Nelson, J. S. Neonatal cerebellar medulloblastoma originating from the fetal external granular layer. J. Neuropath. Exp. Neurol. 29, 583–600 (1970).
   Article CAS Google Scholar
3. Packer, R. J. et al. Treatment of children with medulloblastomas with reduced-dose craniospinal radiation therapy and adjuvant chemotherapy: a children's cancer group study. J. Clin. Oncol. 17, 2127–2136 (1999).
   Article CAS Google Scholar
4. Mardia, K. V., Kent, J. T. & Bibby, J. M. Multivariate Analysis (Academic, London, 1979).
   MATH Google Scholar
5. 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 ADS CAS Google Scholar
6. Golub, T. R. et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531–537 (1999).
   Article CAS Google Scholar
7. Aruga, J. et al. A novel zinc finger protein, Zic, is involved in neurogenesis, especially in the cell lineage of cerebellar granule cells. J. Neurochem. 63, 1880–1890 (1994).
   Article CAS Google Scholar
8. Yokota, N. et al. Predominant expression of human Zic in cerebellar granule cell lineage and medulloblastoma. Cancer Res. 56, 377–383 (1996).
   CAS Google Scholar
9. Rorke, L. B., Packer, R. J. & Biegel, J. A. Central nervous system atypical teratoid/rhabdoid tumors of infancy and childhood: definition of an entity. J. Neurosurg. 85, 56–65 (1996).
   Article CAS Google Scholar
10. Biegel, J. A. et al. Germ-line and acquired mutations of INI1 in atypical teratoid and rhabdoid tumors. Cancer Res. 59, 74–79 (1999).
    CAS Google Scholar
11. Versteege, I. et al. Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer. Nature 394, 203–206 (1998).
    Article ADS CAS Google Scholar
12. Hahn, H. et al. Mutations of the human homolog of Drosophila patched in the nevoid basal cell carcinoma syndrome. Cell 85, 841–851 (1996).
    Article CAS Google Scholar
13. Johnson, R. L. et al. Human homolog of patched, a candidate gene for the basal cell nevus syndrome. Science 272, 1668–1671 (1996).
    Article ADS CAS Google Scholar
14. Pietsch, T. et al. Medulloblastomas of the desmoplastic variant carry mutations of the human homologue of Drosophila patched. Cancer Res. 57, 2085–2088 (1997).
    CAS Google Scholar
15. Raffel, C. et al. Sporadic medulloblastomas contain PTCH mutations. Cancer Res. 57, 842–845 (1997).
    CAS Google Scholar
16. Xie, J. et al. Mutations of the PATCHED gene in several types of sporadic extracutaneous tumors. Cancer Res. 57, 2369–2372 (1997).
    CAS Google Scholar
17. Wechsler-Reya, R. J. & Scott, M. P. Control of neuronal precursor proliferation in the cerebellum by Sonic Hedgehog. Neuron 22, 103–114 (1999).
    Article CAS Google Scholar
18. Wetmore, C., Eberhart, D. E. & Curran, T. The normal patched allele is expressed in medulloblastomas from mice with heterozygous germ-line mutation of patched. Cancer Res. 60, 2239–2246 (2000).
    CAS Google Scholar
19. Giangaspero, F. et al. in World Health Organization Histological Classification of Tumours of the Nervous System (eds Kleihues, P. & Cavenee, W. K.) 129–137 (International Agency for Research on Cancer, Lyon, 2000).
    Google Scholar
20. Murone, M., Rosenthal, A. & deSauvage, F. J. Sonic hedgehog signaling by the patched-smoothened receptor complex. Curr. Biol. 28, 76–84 (1999).
    Article Google Scholar
21. Hahn, H. et al. Patched target IGF2 is indispensable for the formation of medulloblastoma and rhabdomyosarcoma. J. Biol. Chem. 275, 28341–28344 (2000).
    Article CAS Google Scholar
22. Segal, R. A., Goumnerova, L. C., Kwon, Y. K., Stiles, C. D. & Pomeroy, S. L. Expression of the neurotrophin receptor TRKC is linked to a favorable outcome in medulloblastoma. Proc. Natl Acad. Sci. USA 91, 12867–12871 (1994).
    Article ADS CAS Google Scholar
23. Kim, J. Y. H. et al. Activation of neurotrophin-3 receptor TRKC induces apoptosis in medulloblastomas. Cancer Res. 59, 711–719 (1999).
    CAS Google Scholar
24. 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
25. Tamayo, P. et al. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA 96, 2907–2912 (1999).
    Article ADS CAS Google Scholar
26. Dasarathy, V. B. (ed). Nearest Neighbor (NN) Norms: NN Pattern Classification Techniques (IEEE Computer Society Press, Los Alamitos, California, 1991).
    Google Scholar
27. Slonim, D. K. et al. in Proc. 4th Annu. Int. Conf. Computational Mol. Biol. 263–272 (ACM Press, New York, 2000).
    Google Scholar
28. Mukherjee, S. et al. Support vector machine classification of microarray data. CBCL paper 182/AI memo 1676 (Massachusetts Institute of Technology, Cambridge, Massachusetts, 1999); also at http://www.ai.mit.edu/projects/cbcl/publications/ps/cancer.ps.
29. Brown, M. P. S. et al. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl Acad. Sci. USA 97, 262–267 (2000).
    Article ADS CAS Google Scholar
30. Califano, et al. in Proc. 8th Int. Conf. Intel. Syst. Mol. Biol. (eds Bourne, P. et al.) 75–85 (AAAI Press, Menlo Park, CA, 2000.
    Google Scholar

Download references

Acknowledgements

We thank members of the Whitehead/MIT Center for Genome Research, Program in Cancer Genomics, and J. Volpe for discussions and comments on the manuscript. This work was supported in part by Millennium Pharmaceuticals, Affymetrix and Bristol-Myers Squibb (E.S.L.); NIH grants (S.L.P. and T.C.); NIH-supported Mental Retardation Research Center (S.L.P.) and Cancer Center Support CORE (T.C.); the American Lebanese Syrian Associated Charities (ALSAC); and the Kyle Mullarkey Medulloblastoma Research Fund. We acknowledge the Cooperative Human Tissue Network and the Children's Oncology Group for contributing tumour samples.

Author information

Authors and Affiliations

1. Division of Neuroscience, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA,
   Scott L. Pomeroy, Lisa M. Sturla & John Y. H. Kim
2. Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
   Margaret E. McLaughlin
3. Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
   Liliana C. Goumnerova & Peter M. Black
4. Department of Medicine, Children's Hospital, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
   Todd R. Golub
5. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
   John Y. H. Kim & Todd R. Golub
6. Department of Pathology and Neurosurgical Service, Massachusetts General Hospital, Harvard Medical School, Boston, 02115, Massachusetts, USA
   David N. Louis
7. Whitehead Institute/MIT Center for Genome Research, AI Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
   Pablo Tamayo, Michelle Gaasenbeek, Michael Angelo, Jill P. Mesirov, Eric S. Lander & Todd R. Golub
8. McGovern Institute, Center for Biological and Computational Learning, AI Lab, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA
   Tomaso Poggio, Shayan Mukherjee & Ryan Rifkin
9. Division of Pediatric Oncology, Baylor College of Medicine, Houston, 77030, Texas, USA
   Ching Lau
10. Beth Israel Medical Center, New York, 10128, USA
    Jeffrey C. Allen
11. Department of Pathology, New York University School of Medicine, New York, 10016, USA
    David Zagzag
12. Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, Washington, USA
    James M. Olson
13. Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, 38105, Tennessee, USA
    Tom Curran & Cynthia Wetmore
14. Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, 19104, Pennsylvania, USA
    Jaclyn A. Biegel
15. Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA
    Eric S. Lander
16. IBM Watson Research Center, Yorktown Heights, 10598, New York, USA
    Andrea Califano & Gustavo Stolovitzky

Authors

1. Scott L. Pomeroy
   You can also search for this author inPubMed Google Scholar
2. Pablo Tamayo
   You can also search for this author inPubMed Google Scholar
3. Michelle Gaasenbeek
   You can also search for this author inPubMed Google Scholar
4. Lisa M. Sturla
   You can also search for this author inPubMed Google Scholar
5. Michael Angelo
   You can also search for this author inPubMed Google Scholar
6. Margaret E. McLaughlin
   You can also search for this author inPubMed Google Scholar
7. John Y. H. Kim
   You can also search for this author inPubMed Google Scholar
8. Liliana C. Goumnerova
   You can also search for this author inPubMed Google Scholar
9. Peter M. Black
   You can also search for this author inPubMed Google Scholar
10. Ching Lau
    You can also search for this author inPubMed Google Scholar
11. Jeffrey C. Allen
    You can also search for this author inPubMed Google Scholar
12. David Zagzag
    You can also search for this author inPubMed Google Scholar
13. James M. Olson
    You can also search for this author inPubMed Google Scholar
14. Tom Curran
    You can also search for this author inPubMed Google Scholar
15. Cynthia Wetmore
    You can also search for this author inPubMed Google Scholar
16. Jaclyn A. Biegel
    You can also search for this author inPubMed Google Scholar
17. Tomaso Poggio
    You can also search for this author inPubMed Google Scholar
18. Shayan Mukherjee
    You can also search for this author inPubMed Google Scholar
19. Ryan Rifkin
    You can also search for this author inPubMed Google Scholar
20. Andrea Califano
    You can also search for this author inPubMed Google Scholar
21. Gustavo Stolovitzky
    You can also search for this author inPubMed Google Scholar
22. David N. Louis
    You can also search for this author inPubMed Google Scholar
23. Jill P. Mesirov
    You can also search for this author inPubMed Google Scholar
24. Eric S. Lander
    You can also search for this author inPubMed Google Scholar
25. Todd R. Golub
    You can also search for this author inPubMed Google Scholar

Corresponding authors

Correspondence toScott L. Pomeroy or Todd R. Golub.

Ethics declarations

Competing interests

We received research funding from Affymetrix (manufacturer of the microarrays used in this study) but do not have a financial (ownership) interest in the company.

Supplementary information

Rights and permissions

About this article

Cite this article

Pomeroy, S., Tamayo, P., Gaasenbeek, M. et al. Prediction of central nervous system embryonal tumour outcome based on gene expression.Nature 415, 436–442 (2002). https://doi.org/10.1038/415436a

Download citation

• Received: 18 July 2001
• Accepted: 13 November 2001
• Issue Date: 24 January 2002
• DOI: https://doi.org/10.1038/415436a