Differential Copy Number Aberrations in New Candidate Genes Associated with Early Breast Cancer Progression
J Geradts, DP Gaile, L Shepherd, MM Desouki, S Liao. Duke University, Durham, NC; State University of New York, Buffalo, NY; Medical University of South Carolina, Charleston, SC
Background: We recently reported our results of a study identifying a number of DNA copy number changes that differentiated low grade ductal carcinoma in situ (DCIS) lesions with and without associated stromal invasion. We now describe a series of validation experiments that support the role of eight genes in early breast cancer progression, most of which were not previously implicated in mammary neoplasia.
Design: DNA was extracted from microdissected paraffin sections of formalin fixed low grade DCIS lesions with an invasive component (n=25), as well as morphologically similar DCIS lesions without associated invasion within at least 5 years (n=20). The DNA was used for quantitative PCR analysis. Specific primers were designed for nineteen candidate genes. Additional validation studies employed genomic DNA samples from an independent cohort of 35 microdissected DCIS lesions with (n=17) and without (n=18) an associated invasive component.
Results: Our previous profiling study revealed that DNA copy number changes at several chromosomal loci may occur at different rates in low grade DCIS lesions with and without associated stromal invasion. From the differentially amplified or deleted chromosomal sites, we selected nineteen candidate genes for validation by comparative PCR. Eight of these genes were confirmed to have differential copy number changes. GRAP2 (on 22q) was more often amplified in DCIS with associated invasion, whereas TAF1C (on 16q) was more commonly deleted in pure DCIS lesions. NCOR2/SMRT and NR4A1 (both on 12q), DYNLRB2 (on 16q), CELSR1, UPK3A and ST13 (all on 22q) were more frequently amplified in pure DCIS lesions. Moreover, NCOR2/SMRT, NR4A1 and DYNLRB2 showed more frequent copy number losses in DCIS lesions that had progressed to invasive carcinoma. For NCOR2/SMRT, these observations were confirmed in an independent cohort of 35 microdissected low grade DCIS cases. The other eleven candidate genes displayed significant frequencies of copy number changes that were not differentially distributed, however.
Conclusions: Our validation experiments have provided evidence for the role of novel genes in early breast cancer progression. Six of the eight candidate genes may function as invasion suppressors. Loss of NCOR2/SMRT was associated with stromal invasion. This gene was previously implicated in metastasis.
Monday, March 9, 2009 2:15 PM
Platform Session: Section B, Monday Afternoon