Abstract PO5-15-07: Integrative proteomics, phosphoproteomics, and RNA profiling revealed novel timeline-dependent vulnerabilities in HER2-positive breast cancer

Abstract Background: Most personalized breast cancer therapies leverage biomarkers identified in the pre-treatment setting. They do not always reflect the dynamic nature of early indicators of treatment response/resistance. Herein, we have a unique cohort of newly diagnosed HER2-positive breast tumors treated with a single low dose of trastuzumab (50mg), and the corresponding residual tumors that did not achieve pathologic complete response (pCR) to HER2-targeted neoadjuvant therapy. We hypothesize that integrative molecular profiling with proteomics and transcriptomics of these breast tumors could reveal novel time-course dependent contributors of therapy response and resistance. Method: This correlative biomarker study was a secondary objective of a parent study that evaluated 64uc-DOTA-trastuzumab PET imaging to predict response to trastuzumab and pertuzumab-based neoadjuvant therapy in HER2-positive breast cancer patients. Eighteen newly diagnosed breast cancer patients were enrolled, and pCR was achieved in 13 patients (72%). This correlative biomarker study was performed on breast tumors collected within 72 hours following administering a low dose trastuzumab (50mg) to the subjects prior to imaging and neoadjuvant therapy. Deep expression proteomics and phosphoproteomics data acquisition were performed on a Thermo Orbitrap Eclipse mass spectrometer. RNA profiling was performed using Nanostring breast cancer profiler. Results: Our multi-omic approach identified increased abundance or activity in the pCR group on the following (p 0.05): Her2 protein and ERBB2 transcript levels, increased phosphorylation of ERBB2 (T1052), increase in Golgi trafficking activities, posttranslational modification with protein glycosylation, and lipid biosynthesis. Interestingly, compared to the non-pCR group, the pCR group showed lower activity level in ERBB2’s downstream pathways, such as MAPK, SRC, and PI3K. In the non-pCR group, the residual tumor showed decrease in the following (p 0.05): Golgi trafficking, glycosylation, antigen processing, and Her2 protein and phosphorylation (T1166). The pCR group had a negative enrichment for SGK1, a kinase which mediates PI3K pathway independently of AKT. SGK1 abundance was highest in residual tumors following neoadjuvant therapy. Conclusion: Using integrative proteomic and RNA profiling, we identified several in-vivo biological pertubations following administration of low dose trastuzumab. Increased Her2 abundance and ERBB2 transcript levels are associated with pCR, in keeping with previous reports of known pCR predictors. Decreased abundance of ERBB’s downstream signaling proteins in the pCR group suggests that early treatment response to trastuzumab may be a predictor of pCR. Our integrative approach identified other dynamic biomarkers. For example, compared to non-pCR group, Golgi trafficking is more active in pCR group tumors, and lowest in residual tumors following neoadjuvant therapy. This suggests that novel Golgi-targeting agents may be best utilized in neoadjuvant setting. Further, we identified SGK1 may be an important kinase for mediating therapy resistance early in treatment course, since its level is higher in non-pCR group following early exposure to trastuzumab compared to pCR group, with highest level detected in the residual tumors. These findings warrant orthogonal validation using in-vitro functional assays. Citation Format: Christina Wei, Lixin Yang, Krystine Mansfield, Jessica Liu, Ritin Sharma, Russell Rockne, Raju Pillai, Patrick Pirrotte, Joanne Mortimer. Integrative proteomics, phosphoproteomics, and RNA profiling revealed novel timeline-dependent vulnerabilities in HER2-positive breast cancer abstract. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-15-07.