Background: To elucidate candidate genes and pathways associated with poor response, we retrospectively analyzed gene expression profiles in serial biopsies from women with locally advanced breast cancer who failed to respond to anthracycline-based chemo followed by taxane in the I-SPY TRIAL (CALGB150007/150012/ACRIN 6657).

Methods: Of the 221 patients who completed neoadjuvant chemotherapy, 215 patients had surgery with 73% not achieving a pathologic complete response (pathCR). In these patients, cDNA microarray expression profiles from pretreatment biopsy (T1) were compared to those biopsy specimens obtained 24-72 hours after initiation of treatment (T2) or in tumors surgically removed after chemotherapy (TS). Paired expression data for T1vsT2 and T1vsTS were available for 29 and 39 patients with no pathCR, respectively. Paired differential expression analyses were performed via significance analysis of microarrays (SAM) and differentially expressed genes were subjected to ingenuity pathway analysis.

Results: Comparison of paired T1vsT2 and T1vsTS profiles detected altered expression of 245 and 272 transcripts, respectively. Compared to baseline levels, MMP9 and FRZB were among the genes that were down regulated after the first dose of chemotherapy in non-responding tumors while CYR61, JUN, and JUNBwere up regulated in remaining tumors after chemotherapy. Further analysis revealed numerous signaling and metabolic pathways that were significantly modulated at T2, including CD40 (p = 0.0002) and Toll-like receptor signaling (p = 0.0006) and at TS, including SAPK/JNK (p = 0.005) and IGF1 (p = 0.03) signaling.

Conclusions: Serial gene expression analysis in non-responders revealed genes and pathways that may serve as biomarkers for poor response. Candidate pathways identified will be further explored in the I-SPY 2 TRIAL where targeted therapies will be tested in combination with standard neoadjuvant chemotherapy.