Abstract PD01-06: Activation of the Insulin-Like Growth Factor Pathway Distinguishes African American from European American Patients with Triple-Negative Breast Cancer by Gene Expression Profiling

Background: Triple-negative breast cancer (TNBC) is characterized by high histologic grade, high rates of distant recurrence and a poor overall prognosis. Treatment options are limited due to the lack of specific targets such as hormone receptors or HER2 which drive other breast cancer subtypes. Epidemiological studies show a markedly higher prevalence of TNBC in young women of African ancestry. In this study we sought to identify transcriptional modules that are differentially regulated between African American (AA) and European American (EA) women. Methods: A hospital-based cohort of 130 breast cancer patients diagnosed between 1985 and 2007 was selected by an institutional pathology database (CoPath) search for invasive, triple-negative breast cancer and enriched for patients of African American ethnicity. Racial distribution 47% AA, 33% EA, 8% Hispanic and 12% other or unknown. Clinical data was extracted from the Yale and Bridgeport Hospitals Tumor Registry following IRB approval. Invasive disease was identified on H&E sections and an average of 3 tissue cores from FFPE blocks were subjected to RNA extraction using the RecoverAll Total Nucleic Acid Isolation kit (Applied Biosystems) following the manufacturer's protocol. The extracted material was hybridized to Whole Genome-DASL assays (Illumina). Statistical analysis of gene expression data was carried out using Bioconductor/R software. A set of relevant signatures was selected by enrichment analysis of modules identified by principal component analysis. Signature scores were computed as Pearson correlation between the signature vector of gene contributions and each sample's expression profile for these genes. Results: African American patients show a significantly higher activation score for a 273-gene Insulin-like Growth Factor 1 signature compared with European American patients (stage-adjusted p=0.0006). Similarly, samples from AA patients show higher scores in a BRCA 1 mutant signature defined by van ‘t Veer and colleagues in 2002 (p=0.001) and in a luminal progenitor (CD49f+EpCAM+) signature from Lim et al. (2009) (p=0.01). The Genomic Grade Index (GGI, Sotiriou et al. 2006) in samples from AA patients was also found to be significantly elevated (p=0.0007). Conclusions: Our findings indicate significant activation of the IGF pathway in AA compared to EA patients with TNBC. The 273-gene IGF signature was associated with poor differentiation and high proliferation in an independent cohort, which is in agreement with the high GGI score observed in AA patients. BRCA1 mutant-like and luminal progenitor-like properties in AA tumor samples further support this hypothesis as they both are related to basal-like histology which constitutes an aggressive subgroup of triple-negative tumors. These data suggest that African American patients may benefit from IGF pathway inhibiting drugs.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr PD01-06.

Genome-Wide Profiling of Archived Material from CALGB 9840 and 9342 for Paclitaxel (P) and Trastuzumab (T) Response Biomarkers Using Gene Expression and Copy Number Analysis

Background:Emerging data suggest that RNA obtained from formalin-fixed, paraffin-embedded (FFPE) tissue can produce reliable gene expression profiles. Archived material from two taxane monotherapy studies, CALGB 9342 (comparison of 3 doses of P) and 9840 (weekly vs. q3 week P)were profiled for gene expression and DNA copy number.Methods: A total of 238 patients had primary tumor blocks available from a combined sample size of 680. DNA and RNA was extracted from 1.5mm punch cores and the Ambion Recover-All kit™. quality was measured by spectrophotometric analysis, Bioanalyzer RNA Integrity Number (RIN), and housekeeping genes (RPL13A and Actin). A custom DASL™ array containing 779 genes in two-fold redundancy was designed with genes selected to represent the PAM50 intrinsic subtypes, the Oncotype Dx Score, the Netherlands prognostic signature and the genes most frequently found on recurrent breast cancer amplicons. Several methods for identifying outliers were evaluated, including principal components analysis, pairwise correlations as well as the reproducibility of the platform based on replicate samples.Results: Adequate RNA was obtained from 237/238 of these cases which ranged in age from 12-18 years. Of these, 215/237DASL arrays passed further quality control measures. Adequate DNA for CGH was obtained from 227/238 samples. Analysis of PAM50 intrinsic subtypes showed an excess of basal-like tumors (30%) in the primary tumors of this metastatic cohort compared with expected frequency in an early stage population. Luminal A tumors were less frequent than expected (20%). Patients with basal-like tumors did far worse than other tumor types for both PFS on P (p=0.015) and OS (p=2.7X10-6), which persisted in multivariable analysis (p=0.0047), however the interaction term was not significant (Wald p=0.26). While basal-like tumors had similar PFS and OS on both weekly and q3 week P, luminal A tumors appear to achieve more benefit from weekly P (p= 0.0041).The HER2-enriched expression subtype had a similar prognosis to Luminal A and B tumors. This appeared to be due to the presence of T, as the addition of this agent improved PFS (p=0.026) and OS (p=2.0X10-4). Of note, some centrally confirmed HER2 FISH amplified tumors were classified into luminal A, B, and basal-like subtypes. These tumors have similar prognoses to the overall group, for example the basal-like and HER2 tumors had a poor prognosis despite T (p=0.00086). This suggests that HER2 FISH positive tumors may behave based on the underlying tumor subtype. Sawtooth genomes (45% vs 15%) were more frequent than predicted by an early stage tumor dataset as were simplex genomes (3% vs 24%). HER2 by FISH and CGH were highly concordant suggesting data on gene amplification from this platform is robust.Conclusions: Gene expression and copy number profiling of FFPE material from archived tumor blocks (>10 years) produces quality data for biomarker discovery in CALGB clinical trial datasets. These tools allow discovery of novel patterns of gene expression and genomic aberrations that are associated with differential response to P and T. Further studies using these platforms should be performed.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4032.

Molecular Classification of Normal and Cancer Mammospheres

Introduction: For decades, scientists have attempted to develop models for growing and studying primary tumors outside of the human body. These techniques have ranged from growth assays in immuno-compromised mice to simple monolayer cultures. Unfortunately, these techniques are either too complex and expensive (animal models), or too simple (monolayer cultures) to effectively recapitulate the growth characteristics of human tumors. The recent discovery of cancer stem cells (CSCs) has provided new insight into the reasons that ex-vivo cultures have been unable to provide an accurate model for in-vivo tumors.Hypothesis: Our hypothesis is that three-dimensional mammosphere culture represents a practical means of enriching cancer stem cells and assessing, ex-vivo, the growth characteristics of human breast cancer. We believe this technique will provide a more accurate model system for testing novel drug targets specific for cancer stem cells and tailor specific therapies for patients.Method: By combining ideas from a number of previously described methods, we have recently developed a protocol to grow and maintain breast cancer specimens in a simple three-dimensional culture system using serum-free media, MEGM supplemented with BT-20, insulin, EGF and bFGF. We have successfully cultured both normal and tumor cells from clinical samples as small as a fine needle aspiration. In each case, small subset of epithelial cells from each sample grow into mammospheres.Results: Our preliminary data in characterization of the mammospheres shows that different morphologies and histotypes can be achieved in culture. We are currently using protein expression and transcriptional profiling methods to characterize the cell types within mammospheres and the histotypes of cancer that can generate mammospheres. Using immunofluorescence of a few key protein markers we have found that mammospheres, derived both from normal breast tissue and from tumor tissue samples, express putative stem cells markers as determined by expression of CD44 in the absence of CD24. Only a subset (30-50%) of CD44 positive cells in mammospheres are also positive for ALDH1 in both normal and cancer derived cultures suggesting an undifferentiating population of cells, potentially indicative of the presence of stem cells. Cells in the mammospheres are also positive for both epithelial and myoepithelial markers (e.g. broad-range cytokeratin, CK8, CK5, CK17, vimentin, P63) suggesting variable differentiation potential of progenitor cells. Preliminary transcriptional profiling data suggests that gene sets useful in molecular subtyping of primary tumors may also be informative in mammospheres, and that segregation of profiles of stromal and tumor cells can be elucidated through studies of mammospheres vs. core biopsies.Conclusion: This model system has the potential to be an inexpensive, accurate and robust model for breast cancer. It could help in the understanding of mechanisms of drug resistance, recurrence and metastasis, as well as in predicting treatment success or failure as we move towards personalized medicine.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 501.