Abstract Despite the proven clinical benefits of HER2-targeted therapy, resistance to trastuzumab and lapatinib exists. Understanding the molecular mechanisms responsible for resistance is critical to improving the survival rates of patients with this aggressive subtype of breast cancer. Currently, there are no clinically validated biomarkers of resistance to therapy. To address this issue, we measured the responses of a panel of 18 HER2-amplified breast cancer cell lines to both trastuzumab and lapatinib and evaluated the activity of PI3K/AKT/mTOR and RAS/MAPK/ERK signaling in resistance. Eight of the cell lines were identified as resistant to trastuzumab and seven as resistant to lapatinib by both two and three dimensional response assays. Five of the trastuzumab resistant cell lines remained sensitive to lapatinib (IC50 < 1 μM), indicating that these two agents have at least partially non-overlapping mechanisms of resistance. The combination of low PTEN or the presence of activating mutations of PI3K, and thus increased activity of PI3K/AKT signaling, is a strong predictor of resistance to trastuzumab. However, this is not the case with lapatinib, two of the cell lines with activating mutations of PI3K (MDA-361 and HCC-202) were resistant to lapatinib whereas two other PI3K mutant cells lines (SUM-190 and HCC-1954) were lapatinib sensitive, indicating that lapatinib resistance can occurindependently of increased PI3K/AKT signaling. To further investigate these mechanisms, we measured the effects of trastuzumab and lapatinib treatment on AKT/mTOR and ERK activation. Cell lines sensitive to trastuzumab or lapatinib showed a marked reduction in pAKT, pS6K and pERK in response to either agent, whereas the resistant cells maintained high pAKT, pS6K and pERK levels in the presence of trastuzumab and lapatinib. In cell lines resistant to trastuzumab yet sensitive to lapatinib, treatment with lapatinib significantly reduced the phosphorylation of AKT, S6K and ERK. Thus in a subpopulation of cell lines lapatinib can overcome trastuzumab resistance via continued deactivation of PI3K/AKT/mTOR and MAPK/ERK signaling. However, there still remains a subgroup of HER2-positive cells that are resistant to both trastuzumab and lapatinib. We used global expression analysis by both mRNA microarray and proteomic screening to identify a set of genes and proteins that are consistently altered in these innately resistant cells relative to the sensitive cell lines. In vitro validation of these targets will reveal which are playing a functional role in resistance and are thus potentially druggable targets to be used in improving the survival of patients with HER2-positive disease. Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-01-06.