Microgenomic approaches to identify clinically relevant gene signatures that discriminate histologic types of breast carcinomas.

Background: Breast cancer presents itself in a variety of histologic types, and the two most common types are invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC). Based on comparative genomic hybridization (CGH) analyses, ILC is more closely related to low grade IDC than it is to intermediate and high grade IDC. Results from the BIG 1-98 trial demonstrate that post-menopausal women who are affected with estrogen receptor positive (ER+) ILC or luminal B (high grade) IDC experience a greater magnitude of benefit when they are treated with the aromatase inhibitor (AI) letrozole compared to treatment with the antiestrogen tamoxifen. To contrast, it has been found in the same trial that women affected with luminal A (low grade) IDC experience more benefit when treated with tamoxifen when compared to letrozole. It is therefore imperative to accurately distinguish low grade IDC from ILC considering their varying responses to adjuvant treatment. Despite genetic evidence suggesting a close relationship between ILC and low grade IDC, a clinically relevant gene set underlying a tumor’s biologic responsiveness to letrozole likely exists. The goal of this study is to use microgenomics to identify a clinically relevant candidate gene set that would discriminate between ILC and low grade IDC rather than relying solely on histomorphology and/or immunohistochemistry for the pathologic diagnosis, especially when conventional tests are conflicting. Methods: Using 247 de-identified human breast carcinoma biopsies collected under standardized, stringent conditions, total RNA was extracted from carcinoma cells procured by laser capture microdissection to perform microarray analyses of approximately 22,000 genes to identify expression signatures associated with breast cancer characteristics. Of the 247 LCM-procured samples, 14 were ER+ ILC, 9 were ER+ low grade IDC, and 43 were ER+ high grade IDC. The other 181 samples were either ER- or of another cancer type other than ILC and IDC. Candidate genes were selected by identifying those that were differentially expressed between ILC and low grade IDC (luminal A) and at the same time, had similar expression levels between ILC and high grade IDC (luminal B). qPCR analyses of whole tissue samples were then utilized to validate the selected gene set. Results: Comparison of microarray data from hormone receptor positive tumors yielded 299 probes that were differentially expressed (p0.01) between ILC and high grade IDC (luminal B). 11 of these 99 genes were initially chosen for further investigation by performing qPCR on whole tissue samples from 21 ILC, 19 low grade IDC and 19 high grade IDC tumors. Our initial analysis revealed expression of the gene coding for heparin-binding EGF like growth factor (HBEGF) and collapsin response mediator protein 1 (CRMP1) may be potential markers for differentiating between ILC and low grade (luminal A) IDC