Gene Expression Alterations in Premalignant and Preinvasive Breast Disease
LA Emery, A de las Morenas, A Tripathi, P Sebastiani, CL Rosenberg. Boston University Medical Center, Boston, MA
Background: Atypical ductal hyperplasia (ADH) and DCIS are candidate, non-obligate, breast cancer precursors based on clinical and histopathological evidence. Their relationship to invasive breast cancer remains poorly understood, as studies involving the genetic abnormalities associated with premalignant and preinvasive breast disease are limited. We aim to characterize the gene expression alteration associated with these early breast lesions.
Design: Epithelial-specific mRNA from normal-appearing breast (CN), ADH, and DCIS from 12 previously untreated surgical patients (36 lesions total) with ER+ sporadic breast cancer, were obtained by LCM of fresh frozen breast tissue. Gene expression profiles were characterized using the Affymetrix U133A array. After initial filters, Bayesian Analysis of Differential Gene Expression was used to make 3 comparisons: ADH-CN, ADH-DCIS, and DCIS-CN, with cut-off fold changes of 1.5. Patient-matched sets (CN-ADH-DCIS) were analyzed using a regression model with log-normal errors and a variance component per subject, taking into account that samples are matched by subjects and applying this across all genes. The data were first validated by qRT-PCR using 6 genes identified as differentially expressed: FN1, GPRC5A, CAPN6, MME, OXTR, and CDKN1C, on unamplified RNA from 8 cases used for microarray. Further validation was done on newly isolated CN, ADH, and DCIS lesions from 12 independent cases with the same 6 genes. DAVID and Ingenuity were used for pathway analysis.
Results: We found 824 differentially expressed genes between DCIS-CN and 438 genes between ADH-CN, with 400/438 (91%) of ADH-CN genes also present in DCIS-CN. Only 61 genes were differentially expressed between ADH-DCIS. qRT-PCR validation showed all 6 genes were differentially expressed in the expected direction with 58/65 (89%) of the technical comparisons and 93/106 (88%) of the prospective comparisons validating. Biologically important pathways including focal adhesion, cell signaling, and cell cycle regulation were implicated, even in ADH-CN.
Conclusions: We conclude that ADH and DCIS epithelium from patients with sporadic breast cancer are highly similar at the gene expression level. Many of the gene expression alterations seen in DCIS have already developed by the time a histological diagnosis of ADH is reached. Pathways crucial in breast carcinogenesis are already dysregulated in the transition from CN to ADH. These data provide strong genetic evidence that ADH is a breast cancer precursor.
Category: Special Category for 2009 - Pan-genomic/Pan-proteomic approaches to Cancer
Monday, March 9, 2009 1:30 PM
Platform Session: Section G, Monday Afternoon