Abstract P2-08-18: Evaluation of the activity of key actionable oncogenic driving pathways in triple negative breast cancer using OncoSignal™; a novel molecular assay based on transcriptional profile analysis
Authors: Magliocco Genevra , den Biezen Eveline , Keizer Diederick , Akse Martijn , van Zelst Martijn , van Strijp Dianne , Vermeer Saskia , van de Stolpe Anja , Magliocco Anthony 
Published: March 2022

Abstract
Introduction: Triple negative breast cancer (TNBC), defined by the absence of expression of estrogen receptor (ER), progesterone receptor, and HER2, is a heterogenous subgroup of breast cancer which currently accounts for a significant proportion of the mortality from the disease. Consequently, there is an urgent need to identify more effective therapy for women with this type of breast cancer. We have recently developed a novel assay, OncoSignal™ which is capable of precisely measuring the activity of seven key signaling pathways through utilizing measurements of mRNA. The assay quantitatively determines the specific activity of ER, androgen receptor, PI3K, MAPK, HedgeHog, Notch, and TGFβ signal pathways via measurement and analysis of mRNA expression from transcriptional targets of these pathways. This approach overcomes some of the limitations of NGS and other methods which analyze only partial components of a complex signaling pathway, producing significant risk of false positive and negative results, and resulting in potentially inaccurate diagnosis and treatment selection. In this study we evaluated oncogenic pathway activation in 88 cases of TNBC using the OncoSignal™ assay. Materials and methods: Samples and pathway scores for TNBC tumors were calculated using a publicly available Affymetrix dataset GSE76275. This study included 88 cases of TNBC obtained at Baylor College of Medicine. OncoSignal™ pathway activity scores (PAS) were calculated from the transcriptional profile for each case. In addition, 10 samples of benign breast tissue were available for analysis of PAS and used as controls for this evaluation. The mean pathway activity scores and ranges were calculated from the benign tissues. The PAS results for each of the 7 oncogenic pathways from the TNBC cases were compared with PAS results from benign tissues. Results: The OncoSignal™ PAS were significantly higher in TNBC compared to benign tissues for MAPK, PI3K, and HH pathways. The PAS of ER and TGFβ pathways were significantly lower in TNBC compared to the benign tissue. MAPK, AR, ER, PI3K, and HH were elevated in 86%, 17%, 8%, 95%, and 94% of TNBC cases respectively. TGFβ pathway, for which oncogenic versus tumor suppressive functionality is contextually determined, showed reduced PAS in 85% of TNBC cases compared to benign tissue controls. Conclusion: OncoSignal™ analysis identifies enhanced targetable oncogenic pathway activity in a majority of TNBC breast cancers. Of interest, 7 of 88 cases (8%) classified as TNBC using IHC methods showed evidence of estrogen receptor signal pathway activation, and 15 (17%) showed elevated AR PAS. PI3K and MAPK had high PAS in over 85% of TNBC cases. Results suggest loss of tumor suppressive function of the TGFβ pathway. We conclude that OncoSignal™ analysis may help identify TNBC tumors with targetable signal transformation pathways.
Citation Format: Genevra Magliocco, Eveline den Biezen, Diederick Keizer, Martijn Akse, Martijn van Zelst, Dianne van Strijp, Saskia Vermeer, Anja van de Stolpe, Anthony Magliocco. Evaluation of the activity of key actionable oncogenic driving pathways in triple negative breast cancer using OncoSignal™; a novel molecular assay based on transcriptional profile analysis [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-08-18.