A Distinct Gene Expression Profile Is Associated with Aggressive Breast Carcinomas (BC) Showing Prominent Retraction Artifact (RA)
Z Rakosy, G Paragh, G Acs. Moffitt Cancer Center, Tampa, FL
Background: RA resulting in clear spaces around tumor cell nests is frequently seen in histologic material of BC and may present difficulty in its differentiation from lymphatic invasion (LVI). We have recently reported that the extent of RA in BC is a strong predictor of LVI and nodal metastasis and suggested that the characteristic clear spaces separating tumor cells from the stroma are not just a random artifactual phenomenon resulting from tissue fixation and processing, but rather, they are likely related to molecular alterations in BC resulting in altered tumor-stromal interactions which might play an important role in lymphatic tumor spread. Using microarray technology we examined whether extensive RA is associated with a specific gene expression signature in invasive human BC.
Design: Fifty and 21 samples of formalin-fixed paraffin-embedded (FFPE) invasive BC showing high (≥ 20%) and low (<20%) levels of RA, respectively, were macrodissected and RNA was isolated after DNase digestion. Sample quality was assessed by RLP13a ribosomal protein mRNA specific TaqMan quantitative real time PCR (q-RT-PCR) after reverse transcription. cDNA from the 71 invasive BC were subjected to whole genome gene expression analysis using Illumina's cDNA-mediated annealing, selection, extension and ligation (DASL) assay based bead arrays, which are specifically designed to allow expression analysis of more than 24,000 human genes from partially degraded RNA of FFPE tissues. Data analysis was carried out using the Significance Analysis of Microarrays (SAM) and Ingenuity Pathway Analysis software tools.
Results: Comparison of whole genome gene expression profiles of tumors with high and low levels of RA resulted in 126 differentially expressed genes at a significance level of p<0.001 and a fold change of >2. Functional analysis revealed that the differentially expressed genes mainly play roles in the control of cellular growth and proliferation, cellular assembly and organization, cellular development and cell death, with emphasis on the Wnt/β-catenin, FGF and TGF-β signaling pathways. Verification of whole genome DASL assay results are being carried out by TaqMan PCR and immunohistochemistry.
Conclusions: Our results suggest that aggressive BC showing extensive RA are assocuiated with a specific gene expression profile compared to tumors without this feature and support the hypothesis that extensive RA is a histologic reflection of important biologic changes resulting in altered tumor-stromal interactions and a propensity for lymphatic tumor spread.
Tuesday, March 23, 2010 11:30 AM
Platform Session: Section C, Tuesday Morning