Genes Are Differentially Expressed in Normal-Appearing Breast Epithelium between Cohorts of Breast Cancer Cases When Compared to Reduction Mammoplasty Controls
K Graham, A Tripathi, A de las Morenas, P Sebastiani, C Rosenberg. Boston University Medical Center (BUMC), Boston, MA
Background: Genetic abnormalities have been identified in preinvasive breast lesions. The normal-appearing epithelium (NlEpi) from breast cancer patients (cancer normal, CN) is not well-characterized, but may also contain genetic abnormalities. We have shown that gene expression of NlEpi from reduction mammoplasty controls (RM) differs from NlEpi from ER+ breast cancer cases (CNER+). Here we compare the NlEpi from RM controls to NlEpi from a population of immunophenotypically heterogeneous untreated breast cancer patients. We expanded the RM-CNER+ comparison by adding new cases and extended our study by comparing RM controls to NlEpi from ER- breast cancer cases (CNER-). We also conducted a more robust statistical analysis and performed tight age matching between cases and controls.
Design: 63 fresh frozen breast tissues were collected from BUMC's Pathology Department; 10um sections were prepared and NlEpi was microdissected. RNA was extracted, amplified and hybridized to an Affy U133A chip. Data were preprocessed with Affy GCOS 1.4 software. Data analysis was performed with Bayesian Analysis of Differential Gene Expression with subsequent 80% extrinsic cross-validation of gene lists. Microarray results were technically validated with qPCR using unamplified RNA from the original cases. 7 test (ATF3, BTG2, CLU, EGR1, FOS, IER2, NR4A2) and one control primer (CPSF6) were used. Gene lists were analyzed with DAVID and Ingenuity Pathways Analysis (IPA).
|# samples||18 RM, 18 CN (9 CNER+, 9 CNER-)||17 RM, 17 CNER+||10 RM, 10 CNER-|
|# probes (genes)||90 (88)||84 (80)||194 (186)|
|Technical Validation % (# validated/total)||88 (35/40)||93 (28/30)||90 (28/31)|
|Pathway Analysis (top 3 canonical pathways from IPA)||-ERK/MAPK Signaling -IL-10 Signaling -Neurotrophin/TRK Signaling||-RAR Activation -Oxidative Stress -Gene Reg. by Peroxisome Proliferators via PPAR||-Hypoxia-Inducible Factor Signaling -FXR/RXR Activation -LXR/RXR Activation|
Prospective qPCR validation of NlEpi RNA from a set of 36 independent age-matched RMs and CNs is ongoing.
Conclusions: Gene expression differs among the NlEpi of women without breast cancer and age-matched women with ER+ or with ER- breast cancer. Pathways that may participate in early breast cancer progression are deregulated even before the cells are phenotypically abnormal.
Category: Special Category for 2009 - Pan-genomic/Pan-proteomic approaches to Cancer
Tuesday, March 10, 2009 9:30 AM
Poster Session III # 220, Tuesday Morning