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

Abstract

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.

Dissecting the Role of the FGF19-FGFR4 Signaling Pathway in Cancer Development and Progression

“…The FGF19 genomic locus is on the chromosome 11q13.3, and is frequently amplified in human cancers. For example, amplification of the FGF19 genomic locus including the wellestablished proto-oncogene CCND1, was found in liver cancer, breast cancer, lung cancer, bladder cancer and esophageal cancer (Sawey et al, 2011;Hoover et al, 2015;Tiong et al, 2016;Zhang et al, 2017). Hyperactivation of FGFR4 by FGF19 was reported in colon cancer cells and hepatocellar carcinoma.…”

Targeting FGF19/FGFR4 Pathway: A Novel Therapeutic Strategy for Hepatocellular Carcinoma

“…Amplification of the 11q13 amplicon is one of the most common events in cancer and has a well-recognized role in carcinogenesis of several tumours including head and neck and breast cancers [ 43 ]. The 11q13 amplicon contains Cyclin D1 which is a known oncogene but also FGF19, FGF23 and ANO1 which are tumour promoting genes.…”

CD109: a multifunctional GPI‐anchored protein with key roles in tumor progression and physiological homeostasis

“…CD109 is potentially advantageous for drug development not only based on its expression on the cell surface and ability to bind the anti‐CD109 antibody in vivo but also because CD109‐deficient mice exhibit no lethal phenotype, with no significant difference in life span between WT and CD109‐deficient mice . Although there are no reports that the anti‐CD109 antibody acts as a therapeutic agent in vivo, one study showed that CD109 expression was sufficient to induce antibody internalization and cell killing in 11q13‐amplified cell lines via an antibody/drug‐conjugate approach . Further research is needed to develop tumor treatments involving antibody based drugs targeting CD109.…”

“…8 Although there are no reports that the anti-CD109 antibody acts as a therapeutic agent in vivo, one study showed that CD109 expression was sufficient to induce antibody internalization and cell killing in 11q13amplified cell lines via an antibody/drug-conjugate approach. 61 Further research is needed to develop tumor treatments involving antibody based drugs targeting CD109.…”