Cisplatin-based chemotherapy promotes DNA inter- and intra-strand cross-links and is effective treatment in multiple cancer types, yet it is rarely used for first-line therapy of breast cancer. Cisplatin is an effective cytotoxic in BRCA1 mutant cancer cell lines and in breast and ovarian cancers with BRCA1 mutations, prompting speculation that defective DNA double-strand break repair is associated with cisplatin sensitivity. Furthermore, tumors with BRCA1 mutation are presumed to be defective in various aspects of DNA repair and also display increased levels of chromosomal instability. Thus, we hypothesized that the total number of chromosomal breakpoints in a specific tumor may reflect defective DNA repair and/or chromosomal instability, and may therefore be used as a predictor of cisplatin sensitivity. Supporting this relationship, we identified a correlation (r = 0.8, P = 0.08) between the total number of chromosomal breakpoints, estimated by the number of genomic regions showing allelic imbalance, and cisplatin sensitivity in five triple negative breast cancer cell lines. To validate this relationship in a clinical setting we compared the total number of chromosomal breakpoints to therapy response in a cisplatin treated breast cancer cohort. A total of 28 women with stage II or III ER-/PR-/HER2- breast cancer were treated with cisplatin in the neo-adjuvant setting followed by surgery and standard adjuvant chemotherapy. A core biopsy was obtained before treatment commenced, tumor cells were enriched by needle microdissection, and DNA was extracted for genotyping. As only limited amounts of DNA were available, we used a Molecular Inversion Probe assay (in collaboration with Affymetrix), which allowed us to genotype 42,000 SNPs with only 40 ng of starting DNA. We then estimated the total number of putative genomic breakpoints in 21 samples containing at least 75% tumor cells. We compared this summary genomic measure to the response rate as quantitated by the Miller-Payne score determined on the pathological specimen obtained at surgery. This genomic measure showed a remarkably accurate separation of patients by degree of response, correctly classifying 20 out of 21 patients (P < 0.001).These results suggest that the total number of DNA breakpoints may be an accurate biomarker of breast cancers which may be sensitive to cisplatin treatment. The molecular explanations for these findings await further work. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 111.

15529 Background: The past 20 years have seen a shift in the paradigm that the stromal compartment in tissues is merely a passive, supporting tissue for epithelial cells. Recent evidence shows that it plays a critical role not only in normal tissue development and homeostasis, but also in the progression of cancer. Further, as the stromal compartment is more readily accessible to vascular-delivered agents, this region might be particularly amenable to clinical intervention. As such, a broad-based study of the carcinoma-associated changes in stromal cells from patient samples could yield a wealth of information on the molecular mechansisms of tumorigenesis, and identify clinically important molecular targets. Methods: Five whole-mount frozen prostatectomy specimens were microdissected in four regions: normal epithelium, tumor epithelium, normal stroma, and tumor-associated stroma. Extracted and amplified mRNA was hybridized to the Human Genome U133 Plus 2.0 GeneChip (Affymetrix). Using the intersection of two statistical analysis packages (GCOS and RMA), we identified differentially expressed genes between the dissection groups. Quantitative RT-PCR was used to validate selected transcripts and immunohistochemistry to evaluate potential stromal molecular targets. Results: Tumor-associated stroma showed a distinctly different expression pattern compared to normal stroma with 675 differentially expressed transcripts, the majority of which were up-regulated. In contrast, tumor epithelium showed more down-regulation in the 829 transcripts that were differentially expressed relative to normal epithelium. Classes of up-regulated genes in the tumor-associated stroma showed a strong linkage to cell adhesion and migration as well as the calcium, MAPK, and TGF-beta signaling pathways. Quantitative RT-PCR was conducted to verify GeneChip findings and revealed over 80% concordance with the original data. Immunohistochemical staining further supported the expression differences. Conclusions: Global mRNA expression analysis of stromal cells within tumors provides insight into prostate cancer progression, and yields novel targets for future diagnostic and therapeutic intervention. No significant financial relationships to disclose.