Abstract 4546: Functional cell surface proteomics of acute myeloid leukemia enables predictive modeling of antibody-drug conjugate cytotoxicity

Abstract Acute myeloid leukemia (AML) remains a significant unmet medical need. The development of targeted therapies for AML is challenging due to the heterogeneity of immunological and genetic disease subtypes and physiological similarities shared by blasts and normal myeloid progenitor cells. The identification of abundant cell surface markers on AML blasts with limited expression on bone marrow progenitors could drive the development of novel antibody-drug conjugates (ADCs) and other antibody-based therapeutics with improved therapeutic windows. Here we used hydrazide chemistry and mass spectrometry-based proteomics to profile the cell surface landscape of 95 primary blast samples from the Beat AML research consortium and normal bone marrow progenitor cells from healthy donors. We measured the abundance of over 5,000 proteins with high reproducibility (R2 = 0.89) and coverage of known cell surface markers (240/371). We also identified more than 2,500 N-glycosylation sites, many of which are predicted by canonical sequence motifs but have not been demonstrated experimentally. These findings thereby expand our knowledge of both the AML and normal hematological cell surface proteome. Additionally, we used pulsed stable isotope labeling coupled with the aforementioned hydrazide method to assess global surface protein abundance and turnover dynamics in a panel of malignant cell lines. We integrated our cell surface characterization with Beat AML’s mRNA expression, mutation, and AML subtype classification data to prioritize proteins for further exploration as candidate targets for ADC therapeutics. We generated a library of ADCs using monoclonal antibodies conjugated with Auristatin T, a highly potent membrane impermeable microtubule inhibitor, and measured ADC cytotoxic activity on a panel of AML cell lines as well as primary bone marrow progenitor cells. We used these integrated datasets to more precisely refine AML subtypes and identify patient populations that could benefit from novel AML ADCs. We report the preclinical validation of CD317 as a proof-of-concept for the utility of cell surface proteomics to identify novel targets for ADC therapeutics. Citation Format: Robert Lawrence, Robert Thurman, Travis Biechele, Cristina Tognon, Samantha Savage, Anna Reister Schultz, Jeffrey Tyner, William Arthur. Functional cell surface proteomics of acute myeloid leukemia enables predictive modeling of antibody-drug conjugate cytotoxicity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4546.