Differentiation of Lobular versus Ductal Breast Carcinomas by Expression Microarray Analysis

James Korkola, Sandy DeVries, Jane Fridlyand, E. Shelley Hwang, Anne L H Estep, Yunn Yi Chen, Karen L. Chew, Shanaz H. Dairkee, Ronald M. Jensen, Frederic M. Waldman

Research output: Contribution to journalArticle

169 Citations (Scopus)

Abstract

Invasive lobular and ductal breast tumors have distinct histologies and clinical presentation. Other than altered expression of E-cadherin, little is known about the underlying biology that distinguishes the tumor subtypes. We used cDNA microarrays to identify genes differentially expressed between lobular and ductal tumors. Unsupervised clustering of tumors failed to distinguish between the two subtypes. Prediction analysis for microarrays (PAM) was able to predict tumor type with an accuracy of 93.7%. Genes that were significantly differentially expressed between the two groups were identified by MaxT permutation analysis using t tests (20 cDNA clones and 10 unique genes), significance analysis for microarrays (33 cDNA clones and 15 genes, at an estimated false discovery rate of 2%), and PAM (31 cDNAs and 15 genes). There were 8 genes identified by all three of these related methods (E-cadherin, survivin, cathepsin B, TPI1, SPRY1, SCYA14, TFAP2B, and thrombospondin 4), and an additional 3 that were identified by significance analysis for microarrays and PAM (osteopontin, HLA-G, and CHC1). To validate the differential expression of these genes, 7 of them were tested by real-time quantitative PCR, which verified that they were differentially expressed in lobular versus ductal tumors. In conclusion, specific changes in gene expression distinguish lobular from ductal breast carcinomas. These genes may be important in understanding the basis of phenotypic differences among breast cancers.

Original languageEnglish (US)
Pages (from-to)7167-7175
Number of pages9
JournalCancer Research
Volume63
Issue number21
StatePublished - Nov 1 2003
Externally publishedYes

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Carcinoma, Ductal, Breast
Microarray Analysis
Genes
Oligonucleotide Array Sequence Analysis
Cadherins
Neoplasms
Clone Cells
HLA-G Antigens
Breast Neoplasms
Gene Expression
Cathepsin B
Osteopontin
Cluster Analysis
Real-Time Polymerase Chain Reaction
Histology
Complementary DNA

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Korkola, J., DeVries, S., Fridlyand, J., Hwang, E. S., Estep, A. L. H., Chen, Y. Y., ... Waldman, F. M. (2003). Differentiation of Lobular versus Ductal Breast Carcinomas by Expression Microarray Analysis. Cancer Research, 63(21), 7167-7175.

Differentiation of Lobular versus Ductal Breast Carcinomas by Expression Microarray Analysis. / Korkola, James; DeVries, Sandy; Fridlyand, Jane; Hwang, E. Shelley; Estep, Anne L H; Chen, Yunn Yi; Chew, Karen L.; Dairkee, Shanaz H.; Jensen, Ronald M.; Waldman, Frederic M.

In: Cancer Research, Vol. 63, No. 21, 01.11.2003, p. 7167-7175.

Research output: Contribution to journalArticle

Korkola, J, DeVries, S, Fridlyand, J, Hwang, ES, Estep, ALH, Chen, YY, Chew, KL, Dairkee, SH, Jensen, RM & Waldman, FM 2003, 'Differentiation of Lobular versus Ductal Breast Carcinomas by Expression Microarray Analysis', Cancer Research, vol. 63, no. 21, pp. 7167-7175.
Korkola J, DeVries S, Fridlyand J, Hwang ES, Estep ALH, Chen YY et al. Differentiation of Lobular versus Ductal Breast Carcinomas by Expression Microarray Analysis. Cancer Research. 2003 Nov 1;63(21):7167-7175.
Korkola, James ; DeVries, Sandy ; Fridlyand, Jane ; Hwang, E. Shelley ; Estep, Anne L H ; Chen, Yunn Yi ; Chew, Karen L. ; Dairkee, Shanaz H. ; Jensen, Ronald M. ; Waldman, Frederic M. / Differentiation of Lobular versus Ductal Breast Carcinomas by Expression Microarray Analysis. In: Cancer Research. 2003 ; Vol. 63, No. 21. pp. 7167-7175.
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