Integration of cancer-related genetic landscape of Eph receptors and ephrins with proteomics identifies a crosstalk between EPHB6 and EGFR

Eph receptors and their ephrin ligands are viewed as promising targets for cancer treatment, however targeting them is hindered by their context-dependent functionalities. To circumvent this, we explored molecular landscapes underlying their pro- and anti-malignant activities. Using unbiased bioinformatics approaches, we constructed a cancer-related network of genetic interactions (GIs) of all Ephs and ephrins to assist their therapeutic manipulation. We also applied genome-wide genetic screening and BioID proteomics, and integrated them with machine learning approaches to select the most relevant GIs of one of Eph receptors, EPHB6. This revealed a crosstalk between EPHB6 and EGFR, and further experiments confirmed EPHB6 ability to modulate EGFR signaling, enhancing both proliferation of cancer cells and tumor development. Taken together, our observations identify a new mechanism of action of EPHB6, suggesting its targeting might be beneficial in EGFR-dependent tumors, and confirm that Eph family genetic interactome presented here can be effectively exploited in developing new treatment approaches. Samples were collected at two different time points after infection with the 90k shRNA libraries and probes were prepared to hybridize to microarray chips to identify SL partners of EphB6 gene.