Discovery of candidate antibodies and antigens for acute myeloid leukemia therapy by combining whole-cell phage display selection and CRISPR-Cas9 library screening

Background Acute myeloid leukemia (AML) remains challenging to treat and often requires intensive chemotherapy. In contrast to other hematologic malignancies, the development of effective antibody-based and cellular immunotherapies for AML has been limited by the scarcity of suitable target antigens. Methods We applied a phage display-based whole-cell panning method in which Fab-phage were biotinylated and captured, followed by next-generation sequencing (NGS), bioinformatic, and statistical analyses. Target deconvolution was performed using a CRISPR-Cas9 knockout library, fluorescence-activated cell sorting of antigen-negative cells, and NGS-based gRNA analysis. Selected candidates were further evaluated using primary AML patient cells and chimeric antigen receptor (CAR)-T cell assays. Results We identified 28 unique monoclonal antibodies that preferentially bound AML cell lines. CRISPR-Cas9-based target deconvolution enabled efficient identification of three cognate antigens. Selected lead candidates were validated by staining primary cells from AML patients and were engineered into CAR constructs. CAR-T cells targeting the identified antigens mediated efficient eradication of AML cell lines and primary AML cells. Conclusions This integrated antibody-based antigen discovery and validation approach may accelerate the development of monoclonal antibody- and CAR-based immunotherapies for AML and other indications.