High-throughput quantification of cell-surface proteins for accelerated cancer therapeutic discovery

Cell-surface proteins on tumor cells serve as both key targets for immunotherapeutic strategies and markers of blast phenotype and differentiation status. Compounds that modulate surface expression of key immunotherapeutic targets offer an attractive strategy for more robust and precise targeting by immunotherapeutics when delivered as a co-therapy. Similarly, identification of compounds that induce differentiation of tumor blasts over indeterminate self-renewal is an area of great therapeutic promise. Both conventional and newer methods for characterizing cell surface protein expression on tumor cells, including flow cytometry and CITE-Seq, are invaluable for characterizing phenotypes but do not readily scale for high-throughput drug screening. Here we present Surface-plex, a new technology which enables a multiplexed, high-throughput sequencing readout of cell-surface proteins on tumor cells following treatment with thousands of compounds. We applied this technology to acute myeloid leukemia and identified PFI90 as an inducer of the therapeutically targetable antigen CD47 and several compounds as inducers of blast differentiation. Surface-plex thus offers a scalable platform enabling the rapid identification of compounds with therapeutic potential, applicable across cancer types, to accelerate targeted cancer therapeutic development. Overall design: A high-throughput assay that measures cell surface expression on acute myeloid leukemia (MOLM-13) cells by sequencing antibody-oligo conjugates. The data here are sequencing of antibody feature barcodes for two assays; Assay 1 = MOLM-13 cells treated with 85 compounds (5xreplicates) and Assay 2 = MOLM-13 cells treated with 1101 compounds (4xreplicates).