Development of an integrated genomic classifier for a novel agent in colorectal cancer

Approach to individualized therapy in early development

Todd M. Pitts, Aik-Choon Tan, Gillian N. Kulikowski, John J. Tentler, Amy M. Brown, Sara A. Flanigan, Stephen Leong, Christopher D. Coldren, Fred R. Hirsch, Marileila Varella-Garcia, Christopher Korch, S. Gail Eckhardt

Research output: Contribution to journalArticle

66 Citations (Scopus)

Abstract

Background: A plethora of agents is in early stages of development for colorectal cancer (CRC), including those that target the insulin-like growth factor I receptor (IGFIR) pathway. In the current environment of numerous cancer targets, it is imperative that patient selection strategies be developed with the intent of preliminary testing in the latter stages of phase I trials. The goal of this study was to develop and characterize predictive biomarkers for an IGFIR tyrosine kinase inhibitor, OSI-906, that could be applied in CRC-specific studies of this agent. Methods: Twenty-seven CRC cell lines were exposed to OSI-906 and classified according to IC50 value as sensitive (≤1.5 μmol/L) or resistant (>5 μmol/L). Cell lines were subjected to immunoblotting and immunohistochemistry for effector proteins, IGFIR copy number by fluorescence in situ hybridization, KRAS/BRAF/phosphoinositide 3-kinase mutation status, and baseline gene array analysis. The most sensitive and resistant cell lines were used for gene array and pathway analyses, along with shRNA knockdown of highly ranked genes. The resulting integrated genomic classifier was then tested against eight human CRC explants in vivo. Results: Baseline gene array data from cell lines and xenografts were used to develop a k-top scoring pair (k-TSP) classifier, which, in combination with IGFIR fluorescence in situ hybridization and KRAS mutational status, was able to predict with 100% accuracy a test set of patient-derived CRC xenografts. Conclusions: These results indicate that an integrated approach to the development of individualized therapy is feasible and should be applied early in the development of novel agents, ideally in conjunction with late-stage phase I trials.

Original languageEnglish
Pages (from-to)3193-3204
Number of pages12
JournalClinical Cancer Research
Volume16
Issue number12
DOIs
Publication statusPublished - 2010 Jun 15
Externally publishedYes

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IGF Type 1 Receptor
Colorectal Neoplasms
Cell Line
Fluorescence In Situ Hybridization
Heterografts
Genes
Therapeutics
1-Phosphatidylinositol 4-Kinase
Immunoblotting
Protein-Tyrosine Kinases
Patient Selection
Small Interfering RNA
Inhibitory Concentration 50
Biomarkers
Immunohistochemistry
Mutation
Neoplasms
Proteins
3-(8-amino-1-(2-phenylquinolin-7-yl)imidazo(1,5-a)pyrazin-3-yl)-1-methylcyclobutanol

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Pitts, T. M., Tan, A-C., Kulikowski, G. N., Tentler, J. J., Brown, A. M., Flanigan, S. A., ... Eckhardt, S. G. (2010). Development of an integrated genomic classifier for a novel agent in colorectal cancer: Approach to individualized therapy in early development. Clinical Cancer Research, 16(12), 3193-3204. https://doi.org/10.1158/1078-0432.CCR-09-3191

Development of an integrated genomic classifier for a novel agent in colorectal cancer : Approach to individualized therapy in early development. / Pitts, Todd M.; Tan, Aik-Choon; Kulikowski, Gillian N.; Tentler, John J.; Brown, Amy M.; Flanigan, Sara A.; Leong, Stephen; Coldren, Christopher D.; Hirsch, Fred R.; Varella-Garcia, Marileila; Korch, Christopher; Eckhardt, S. Gail.

In: Clinical Cancer Research, Vol. 16, No. 12, 15.06.2010, p. 3193-3204.

Research output: Contribution to journalArticle

Pitts, TM, Tan, A-C, Kulikowski, GN, Tentler, JJ, Brown, AM, Flanigan, SA, Leong, S, Coldren, CD, Hirsch, FR, Varella-Garcia, M, Korch, C & Eckhardt, SG 2010, 'Development of an integrated genomic classifier for a novel agent in colorectal cancer: Approach to individualized therapy in early development', Clinical Cancer Research, vol. 16, no. 12, pp. 3193-3204. https://doi.org/10.1158/1078-0432.CCR-09-3191
Pitts, Todd M. ; Tan, Aik-Choon ; Kulikowski, Gillian N. ; Tentler, John J. ; Brown, Amy M. ; Flanigan, Sara A. ; Leong, Stephen ; Coldren, Christopher D. ; Hirsch, Fred R. ; Varella-Garcia, Marileila ; Korch, Christopher ; Eckhardt, S. Gail. / Development of an integrated genomic classifier for a novel agent in colorectal cancer : Approach to individualized therapy in early development. In: Clinical Cancer Research. 2010 ; Vol. 16, No. 12. pp. 3193-3204.
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AU - Tentler, John J.

AU - Brown, Amy M.

AU - Flanigan, Sara A.

AU - Leong, Stephen

AU - Coldren, Christopher D.

AU - Hirsch, Fred R.

AU - Varella-Garcia, Marileila

AU - Korch, Christopher

AU - Eckhardt, S. Gail

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