Use of gene expression and pathway signatures to characterize the complexity of human melanoma

Jennifer A. Freedman, Douglas Tyler, Joseph R. Nevins, Christina K. Augustine

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

A defining characteristic of most human cancers is heterogeneity, resulting from the somatic acquisition of a complex array of genetic and genomic alterations. Dissecting this heterogeneity is critical to developing an understanding of the underlying mechanisms of disease and to paving the way toward personalized treatments of the disease. We used gene expression data sets from the analysis of primary and metastatic melanomas to develop a molecular description of the heterogeneity that characterizes this disease. Unsupervised hierarchical clustering, gene set enrichment analyses, and pathway activity analyses were used to describe the genetic heterogeneity of melanomas. Patterns of gene expression that revealed two distinct classes of primary melanoma, two distinct classes of in-transit melanoma, and at least three subgroups of metastatic melanoma were identified. Expression signatures developed to predict the status of oncogenic signaling pathways were used to explore the biological basis underlying these differential patterns of expression. This analysis of activities revealed unique pathways that distinguished the primary and metastatic subgroups of melanoma. Distinct patterns of gene expression across primary, in-transit, and metastatic melanomas underline the genetic heterogeneity of this disease. This heterogeneity can be described in terms of deregulation of signaling pathways, thus increasing the knowledge of the biological features underlying individual melanomas and potentially directing therapeutic opportunities to individual patients with melanoma.

Original languageEnglish (US)
Pages (from-to)2513-2522
Number of pages10
JournalAmerican Journal of Pathology
Volume178
Issue number6
DOIs
StatePublished - Jun 2011
Externally publishedYes

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Transcriptome
Melanoma
Genetic Heterogeneity
Gene Expression
Inborn Genetic Diseases
Cluster Analysis
Therapeutics
Genes

ASJC Scopus subject areas

  • Pathology and Forensic Medicine

Cite this

Use of gene expression and pathway signatures to characterize the complexity of human melanoma. / Freedman, Jennifer A.; Tyler, Douglas; Nevins, Joseph R.; Augustine, Christina K.

In: American Journal of Pathology, Vol. 178, No. 6, 06.2011, p. 2513-2522.

Research output: Contribution to journalArticle

Freedman, Jennifer A. ; Tyler, Douglas ; Nevins, Joseph R. ; Augustine, Christina K. / Use of gene expression and pathway signatures to characterize the complexity of human melanoma. In: American Journal of Pathology. 2011 ; Vol. 178, No. 6. pp. 2513-2522.
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