Abstract
One of the major barriers to widespread adoption of cancer
immunotherapy is a lack of detailed knowledge about the proteins at the cancer
cell surface. Transcriptomic approaches are unreliable and previous proteomic
efforts have failed to enrich sufficiently for plasma membrane proteins and/or
were not quantitative. We adopted a novel viral proteomic technique to quantify
the plasma membrane proteome of primary myeloma cells.
We quantified 2,616 proteins. Validation of several proteins
by flow cytometry and low inter-run variation gave us high confidence in the
data. At least 1,650 (63%) were genuine plasma membrane proteins, representing
an order of magnitude improvement in enrichment over previous datasets. Six
hundred and thirty-three proteins had significant extracellular domains. These
included known immunotherapy targets such as CD38, BCMA, PDL-1, and SLAMF7. Several
highly expressed proteins had not been previously identified in myeloma.
We validated one such protein as a novel antibody-drug
conjugate (ADC) target. Expression was confirmed on primary myeloma cells by
flow cytometry and specificity was demonstrated by tissue microarrays and whole
cell proteomics. Rapid internalization (50% within two hours) was demonstrated
by flow cytometry and confocal microscopy and lysosomal incorporation was shown
by colocalization with LAMP1. We employed a Fab-ZAP assay in expressing and
non-expressing cells to demonstrate specific killing by an intracellular toxin.
Finally, we demonstrated that the target was an essential protein in myeloma
using shRNA, thus preventing resistance via down-regulation. In summary, this protein
has the properties of an ideal target for ADC and other immunotherapies such as
CAR-T cells.
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