Mandal et al. used “structural surfaceomics” – a novel approach combining cross-linking mass spectrometry and glycoprotein surface capture – to discover cell surface proteins with cancer-specific conformations. 2390 peptides were identified on Nomo1 AML cells, and manual mapping/mAb analysis identified the activated integrin β2 integrin conformation as widely expressed on AML cells. Recombinant antibodies to the active conformation and corresponding scFV-CD28 CAR T cells were generated. The CAR T cells mediated cytotoxicity of AML cells in vitro, and in mice, had a favorable safety profile and showed efficacy against AML cells and patient-derived xenografts.
Contributed by Paula Hochman
ABSTRACT: Safely expanding indications for cellular therapies has been challenging given a lack of highly cancer-specific surface markers. Here we explore the hypothesis that tumor cells express cancer-specific surface protein conformations that are invisible to standard target discovery pipelines evaluating gene or protein expression, and these conformations can be identified and immunotherapeutically targeted. We term this strategy integrating cross-linking mass spectrometry with glycoprotein surface capture 'structural surfaceomics'. As a proof of principle, we apply this technology to acute myeloid leukemia (AML), a hematologic malignancy with dismal outcomes and no known optimal immunotherapy target. We identify the activated conformation of integrin β2 as a structurally defined, widely expressed AML-specific target. We develop and characterize recombinant antibodies to this protein conformation and show that chimeric antigen receptor T cells eliminate AML cells and patient-derived xenografts without notable toxicity toward normal hematopoietic cells. Our findings validate an AML conformation-specific target antigen and demonstrate a tool kit for applying these strategies more broadly.