Abstract PO4-03-01: Enhancing Breast Cancer Subtyping: APIS Breast Cancer Subtyping Kit Proliferative Signature's Potential for Improved Proliferation Assessment and Recurrence Prediction

Abstract Background: Ki67, a widely recognized biomarker for measuring tumor cell proliferation in breast cancer (BC), plays a crucial role in classifying BC into luminal A and luminal B subtypes, subsequently aiding treatment decisions. However, the inconsistency in Ki67 assessment and the lack of standardization in methods and interpretation of immunohistochemistry (IHC) staining has hindered its recommendation for routine diagnostic use. The standardization of measurement techniques, especially for Ki67, holds immense potential for improving patient treatment outcomes. The APIS Breast Cancer Subtyping Kit (APIS BCS Kit) addresses these challenges by utilizing RT-qPCR to accurately determine the mRNA expression of BC markers, including Ki67, along with a novel four-gene proliferative signature, comprising four markers (MKI67, CCNA2, KIF23, and PCNA) associated with proliferation and expressed throughout all cell cycle stages, thereby providing a more accurate measure of tumor proliferation. In this study, we present the preliminary findings of our ongoing evaluation of the APIS BCS Kit proliferative signature's ability to distinguish between Luminal A and Luminal B subtypes and to determine the risk of recurrence in hormone receptor-positive (HR+) patients. Method: A total of N=153 retrospectively collected HR+/HER2 negative samples were provided by University of Basel. For each sample the following clinical annotations were included: relapse free survival, treatment regimen (Chemotherapy (ChT) or Hormone Therapy (HT)) as well as OncotypeDx (ODx) risk score (RS). N=40 samples underwent additional testing using PAM50 (Prosigna®) test. Only samples collected since 2018 were included, resulting in 10 observed relapse events (N=7 in HT cohort and N=3 in ChT cohort). RNA isolation from tissue sections and gene expression analysis were performed as per APIS BCS Kit instructions for use. The agreement of subtype calls between IHC, APIS BCS Kit, and PAM50 was assessed. The correlation between RS obtained from ODx, PAM50 and the APIS BCS Kit proliferation signature was also explored. Results: The agreement between IHC and the APIS BCS Kit subtype call, utilizing Ki67 alone as a measure of proliferation, was 67.3% (103/153). Replacing Ki67 with the APIS BCS Kit proliferation signature increased the concordance to 69.9% (107/153). The concordance between IHC and PAM50 subtype calls was comparable at 62.5% (25/40). The agreement between the APIS BCS Kit and PAM50 subtype call was notably higher (80%; 32/40). Significant association was observed between the APIS BCS Kit proliferation signature and ODx RS (P=.0001), and PAM50 RS (P=.002). In the HT cohort, both ODx and the APIS BCS Kit proliferation signature accurately predicted recurrence (by assigning high RS) in n=2 cases. In some cases both the APIS BCS Kit and ODx erroneously assigned low risk and subsequently missed n=4 recurrence events. Notably, APIS BCS Kit proliferation signature correctly identified one recurrence event (high RS), which was missed by ODx (low RS). Conclusion: The APIS Breast Cancer Subtyping Kit exhibits improved agreement with the PAM50 molecular subtype in contrast to the IHC-derived subtype, indicating that molecular testing may be a more suitable method for determining proliferation and distinguishing between luminal A and B subtypes. Furthermore, there is a significant correlation between the RS generated by APIS Breast Cancer Subtyping Kit proliferation signature and both PAM50 and Oncotype RS. These initial findings indicate that the APIS Breast Cancer Subtyping Kit proliferation signature has the potential to accurately identify patients at risk of recurrence, although additional studies including a larger proportion of events are needed to validate these results. Citation Format: Marcus Vetter, Anna Gasior, Elena-Diana Chiru, Joanna Gorniak, Leanne Gough, Mathew Harrison, Sara Rollinson, Simone Muenst, Christian Kurzeder. Enhancing Breast Cancer Subtyping: APIS Breast Cancer Subtyping Kit Proliferative Signature's Potential for Improved Proliferation Assessment and Recurrence Prediction 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 PO4-03-01.