Quantitative Proteomic Verification of Membrane Proteins as Potential Therapeutic Targets Located in the 11q13 Amplicon in Cancers

Tumor
types can be defined cytologically by their regions of chromosomal
amplification, which often results in the high expression of both
mRNA and proteins of certain genes contained within the amplicon.
An important strategy for defining therapeutically relevant targets
in these situations is to ascertain which genes are amplified at the
protein level and, concomitantly, are key drivers for tumor growth
or maintenance. Furthermore, so-called passenger genes that are amplified
with driver genes and a manifest on the cell surface can be attractive
targets for an antibody–drug conjugate approach (ADC). We employed
a tandem mass spectrometry proteomics approach using tumor cell lines
to identify the cell surface proteins whose expression correlates
with the 11q13 amplicon. The 11q13 amplicon is one of the most frequently
amplified chromosomal regions in human cancer, being present in 45%
of head and neck and oral squamous cell carcinoma (OSCC) and 13–21%
of breast and liver carcinomas. Using a panel of tumor cell lines
with defined 11q13 genomic amplification, we identified the membrane
proteins that are differentially expressed in an 11q13 amplified cell
line panel using membrane-enriched proteomic profiling. We found that
DSG3, CD109, and CD14 were differentially overexpressed in head and
neck and breast tumor cells with 11q13 amplification. The level of
protein expression of each gene was confirmed by Western blot and
FACS analysis. Because proteins with high cell surface expression
on selected tumor cells could be potential antibody drug conjugate
targets, we tested DSG3 and CD109 in antibody piggyback assays and
validated that DSG3 and CD109 expression was sufficient to induce
antibody internalization and cell killing in 11q13-amplified cell
lines. Our results suggest that proteomic profiling using genetically
stratified tumors can identify candidate antibody drug conjugate targets.
Data are available via ProteomeXchange with the identifier PXD002486.