alexa Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications.
Immunology

Immunology

Immunotherapy: Open Access

Author(s): Therese Srlie, Charles M Perou, Robert Tibshirani, Turid Aas, Stephanie Geisler

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The purpose of this study was to classify breast carcinomas based on variations in gene expression patterns derived from cDNA microarrays and to correlate tumor characteristics to clinical outcome. A total of 85 cDNA microarray experiments representing 78 cancers, three fibroadenomas, and four normal breast tissues were analyzed by hierarchical clustering. As reported previously, the cancers could be classified into a basal epithelial-like group, an ERBB2-overexpressing group and a normal breast-like group based on variations in gene expression. A novel finding was that the previously characterized luminal epithelial/estrogen receptor-positive group could be divided into at least two subgroups, each with a distinctive expression profile. These subtypes proved to be reasonably robust by clustering using two different gene sets: first, a set of 456 cDNA clones previously selected to reflect intrinsic properties of the tumors and, second, a gene set that highly correlated with patient outcome. Survival analyses on a subcohort of patients with locally advanced breast cancer uniformly treated in a prospective study showed significantly different outcomes for the patients belonging to the various groups, including a poor prognosis for the basal-like subtype and a significant difference in outcome for the two estrogen receptor-positive groups. The biology of breast cancer remains poorly understood. Although lymph node metastases (1), histologic grade (2), expression of steroid and growth factor receptors (3, 4), estrogen-inducible genes like cathepsin D (5), protooncogenes like ERBB2 (6), and mutations in the TP53 gene (7, 8) all have been correlated to prognosis, knowledge about individual prognostic factors provides limited information about the biology of the disease. Thus, because of their internal correlations in multivariate analysis, the prognostic value of many of these parameters fades away (9, 10). The cellular and molecular heterogeneity of breast tumors and the large number of genes potentially involved in controlling cell growth, death, and differentiation emphasize the importance of studying multiple genetic alterations in concert. Systematic investigation of expression patterns of thousands of genes in tumors using cDNA microarrays, and their correlation to specific features of phenotypic variation, might provide the basis for an improved taxonomy of cancer (11–14). Recently, we reported that variations in gene expression patterns in 40 grossly dissected human breast tumors analyzed by cDNA microarrays and hierarchical clustering provided a distinctive “molecular portrait” of each tumor, and that the tumors could be classified into subtypes based solely on differences in these patterns (14). The present work refines our previous classifications by analyzing a larger number of tumors and explores the clinical value of the subtypes by searching for correlations between gene expression patterns and clinically relevant parameters. We found that classification of tumors based on gene expression patterns can be used as a prognostic marker with respect to overall and relapse-free survival in a subset of patients that had received uniform therapy. One finding was the separation of estrogen receptor (ER)-positive tumors into at least two distinctive groups with characteristic gene expression profiles and different prognosis. This article was published in Proceedings of the National Academy of Sciences and referenced in Immunotherapy: Open Access

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