Oncogenic pathway signatures in human cancers as a guide to targeted therapies

Andrea H. Bild, Guang Yao, Jeffrey T. Chang, Quanli Wang, Anil Potti, Dawn Chasse, Mary Beth Joshi, David Harpole, Johnathan M. Lancaster, Andrew Berchuck, John A. Olson, Jeffrey R. Marks, Holly K. Dressman, Mike West, Joseph R. Nevins

Research output: Contribution to journalArticle

1442 Citations (Scopus)

Abstract

The development of an oncogenic state is a complex process involving the accumulation of multiple independent mutations that lead to deregulation of cell signalling pathways central to the control of cell growth and cell fate 1-3. The ability to define cancer subtypes, recurrence of disease and response to specific therapies using DNA microarray-based gene expression signatures has been demonstrated in multiple studies4. Various studies have also demonstrated the potential for using gene expression profiles for the analysis of oncogenic pathways5-11. Here we show that gene expression signatures can be identified that reflect the activation status of several oncogenic pathways. When evaluated in several large collections of human cancers, these gene expression signatures identify patterns of pathway deregulation in tumours and clinically relevant associations with disease outcomes. Combining signature-based predictions across several pathways identifies coordinated patterns of pathway deregulation that distinguish between specific cancers and tumour subtypes. Clustering tumours based on pathway signatures further defines prognosis in respective patient subsets, demonstrating that patterns of oncogenic pathway deregulation underlie the development of the oncogenic phenotype and reflect the biology and outcome of specific cancers. Predictions of pathway deregulation in cancer cell lines are also shown to predict the sensitivity to therapeutic agents that target components of the pathway. Linking pathway deregulation with sensitivity to therapeutics that target components of the pathway provides an opportunity to make use of these oncogenic pathway signatures to guide the use of targeted therapeutics.

Original languageEnglish (US)
Pages (from-to)353-357
Number of pages5
JournalNature
Volume439
Issue number7074
DOIs
StatePublished - Jan 19 2006
Externally publishedYes

Fingerprint

Transcriptome
Neoplasms
Therapeutics
Neoplasm Genes
Therapeutic Uses
Oligonucleotide Array Sequence Analysis
Cluster Analysis
Phenotype
Recurrence
Cell Line
Mutation
Growth

ASJC Scopus subject areas

  • General

Cite this

Bild, A. H., Yao, G., Chang, J. T., Wang, Q., Potti, A., Chasse, D., ... Nevins, J. R. (2006). Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature, 439(7074), 353-357. https://doi.org/10.1038/nature04296

Oncogenic pathway signatures in human cancers as a guide to targeted therapies. / Bild, Andrea H.; Yao, Guang; Chang, Jeffrey T.; Wang, Quanli; Potti, Anil; Chasse, Dawn; Joshi, Mary Beth; Harpole, David; Lancaster, Johnathan M.; Berchuck, Andrew; Olson, John A.; Marks, Jeffrey R.; Dressman, Holly K.; West, Mike; Nevins, Joseph R.

In: Nature, Vol. 439, No. 7074, 19.01.2006, p. 353-357.

Research output: Contribution to journalArticle

Bild, AH, Yao, G, Chang, JT, Wang, Q, Potti, A, Chasse, D, Joshi, MB, Harpole, D, Lancaster, JM, Berchuck, A, Olson, JA, Marks, JR, Dressman, HK, West, M & Nevins, JR 2006, 'Oncogenic pathway signatures in human cancers as a guide to targeted therapies', Nature, vol. 439, no. 7074, pp. 353-357. https://doi.org/10.1038/nature04296
Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature. 2006 Jan 19;439(7074):353-357. https://doi.org/10.1038/nature04296
Bild, Andrea H. ; Yao, Guang ; Chang, Jeffrey T. ; Wang, Quanli ; Potti, Anil ; Chasse, Dawn ; Joshi, Mary Beth ; Harpole, David ; Lancaster, Johnathan M. ; Berchuck, Andrew ; Olson, John A. ; Marks, Jeffrey R. ; Dressman, Holly K. ; West, Mike ; Nevins, Joseph R. / Oncogenic pathway signatures in human cancers as a guide to targeted therapies. In: Nature. 2006 ; Vol. 439, No. 7074. pp. 353-357.
@article{3e1a83044f7c4a1db5b92d41af783395,
title = "Oncogenic pathway signatures in human cancers as a guide to targeted therapies",
abstract = "The development of an oncogenic state is a complex process involving the accumulation of multiple independent mutations that lead to deregulation of cell signalling pathways central to the control of cell growth and cell fate 1-3. The ability to define cancer subtypes, recurrence of disease and response to specific therapies using DNA microarray-based gene expression signatures has been demonstrated in multiple studies4. Various studies have also demonstrated the potential for using gene expression profiles for the analysis of oncogenic pathways5-11. Here we show that gene expression signatures can be identified that reflect the activation status of several oncogenic pathways. When evaluated in several large collections of human cancers, these gene expression signatures identify patterns of pathway deregulation in tumours and clinically relevant associations with disease outcomes. Combining signature-based predictions across several pathways identifies coordinated patterns of pathway deregulation that distinguish between specific cancers and tumour subtypes. Clustering tumours based on pathway signatures further defines prognosis in respective patient subsets, demonstrating that patterns of oncogenic pathway deregulation underlie the development of the oncogenic phenotype and reflect the biology and outcome of specific cancers. Predictions of pathway deregulation in cancer cell lines are also shown to predict the sensitivity to therapeutic agents that target components of the pathway. Linking pathway deregulation with sensitivity to therapeutics that target components of the pathway provides an opportunity to make use of these oncogenic pathway signatures to guide the use of targeted therapeutics.",
author = "Bild, {Andrea H.} and Guang Yao and Chang, {Jeffrey T.} and Quanli Wang and Anil Potti and Dawn Chasse and Joshi, {Mary Beth} and David Harpole and Lancaster, {Johnathan M.} and Andrew Berchuck and Olson, {John A.} and Marks, {Jeffrey R.} and Dressman, {Holly K.} and Mike West and Nevins, {Joseph R.}",
year = "2006",
month = "1",
day = "19",
doi = "10.1038/nature04296",
language = "English (US)",
volume = "439",
pages = "353--357",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7074",

}

TY - JOUR

T1 - Oncogenic pathway signatures in human cancers as a guide to targeted therapies

AU - Bild, Andrea H.

AU - Yao, Guang

AU - Chang, Jeffrey T.

AU - Wang, Quanli

AU - Potti, Anil

AU - Chasse, Dawn

AU - Joshi, Mary Beth

AU - Harpole, David

AU - Lancaster, Johnathan M.

AU - Berchuck, Andrew

AU - Olson, John A.

AU - Marks, Jeffrey R.

AU - Dressman, Holly K.

AU - West, Mike

AU - Nevins, Joseph R.

PY - 2006/1/19

Y1 - 2006/1/19

N2 - The development of an oncogenic state is a complex process involving the accumulation of multiple independent mutations that lead to deregulation of cell signalling pathways central to the control of cell growth and cell fate 1-3. The ability to define cancer subtypes, recurrence of disease and response to specific therapies using DNA microarray-based gene expression signatures has been demonstrated in multiple studies4. Various studies have also demonstrated the potential for using gene expression profiles for the analysis of oncogenic pathways5-11. Here we show that gene expression signatures can be identified that reflect the activation status of several oncogenic pathways. When evaluated in several large collections of human cancers, these gene expression signatures identify patterns of pathway deregulation in tumours and clinically relevant associations with disease outcomes. Combining signature-based predictions across several pathways identifies coordinated patterns of pathway deregulation that distinguish between specific cancers and tumour subtypes. Clustering tumours based on pathway signatures further defines prognosis in respective patient subsets, demonstrating that patterns of oncogenic pathway deregulation underlie the development of the oncogenic phenotype and reflect the biology and outcome of specific cancers. Predictions of pathway deregulation in cancer cell lines are also shown to predict the sensitivity to therapeutic agents that target components of the pathway. Linking pathway deregulation with sensitivity to therapeutics that target components of the pathway provides an opportunity to make use of these oncogenic pathway signatures to guide the use of targeted therapeutics.

AB - The development of an oncogenic state is a complex process involving the accumulation of multiple independent mutations that lead to deregulation of cell signalling pathways central to the control of cell growth and cell fate 1-3. The ability to define cancer subtypes, recurrence of disease and response to specific therapies using DNA microarray-based gene expression signatures has been demonstrated in multiple studies4. Various studies have also demonstrated the potential for using gene expression profiles for the analysis of oncogenic pathways5-11. Here we show that gene expression signatures can be identified that reflect the activation status of several oncogenic pathways. When evaluated in several large collections of human cancers, these gene expression signatures identify patterns of pathway deregulation in tumours and clinically relevant associations with disease outcomes. Combining signature-based predictions across several pathways identifies coordinated patterns of pathway deregulation that distinguish between specific cancers and tumour subtypes. Clustering tumours based on pathway signatures further defines prognosis in respective patient subsets, demonstrating that patterns of oncogenic pathway deregulation underlie the development of the oncogenic phenotype and reflect the biology and outcome of specific cancers. Predictions of pathway deregulation in cancer cell lines are also shown to predict the sensitivity to therapeutic agents that target components of the pathway. Linking pathway deregulation with sensitivity to therapeutics that target components of the pathway provides an opportunity to make use of these oncogenic pathway signatures to guide the use of targeted therapeutics.

UR - http://www.scopus.com/inward/record.url?scp=31144459985&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=31144459985&partnerID=8YFLogxK

U2 - 10.1038/nature04296

DO - 10.1038/nature04296

M3 - Article

C2 - 16273092

AN - SCOPUS:31144459985

VL - 439

SP - 353

EP - 357

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7074

ER -