Unbiased, systematic surfaceome profiling of Acute Leukemia to identify novel immunotherapy targets

Abstract

Cell surface proteomics provides a direct topological assessment of the outer membrane of cells and enables the capture of low abundance proteins that may be missed by whole cell proteomics. Here we present an unbiased atlas of the whole cell and surface proteomes of 25 commonly used leukemic cell lines, encompassing both lymphoid and myeloid lineages, and a variety of driver mutations. Paired-wise analysis highlights recurrent surface proteins that are not detected by whole cell proteomics. Coupling this dataset to RNA-sequencing, we also discovered genes where protein and RNA abundances are discordant. In KMT2A-rearranged AML, CD70 expression was increased across cell lines and validated in primary patient samples, supporting CD70 as a candidate therapeutic target in this disease. Several proteins are enriched in the surface proteomes but lack surface annotation, adding to the list of non-canonical cell surface proteins, including RNA-binding proteins, an emerging class of candidate immunotherapeutic targets. Statement of Significance This mass spectrometry atlas pairs whole-cell and cell-surface proteomes across 25 leukemia cell lines, creating a resource for understanding these widely used models. Direct surface profiling captures proteins missed by transcriptomic and whole-proteome data, enabling interrogation of cell interactions and nomination of immunotherapy targets, exemplified by CD70 in KMT2A-rearranged AML.