Unraveling the role of receptor-like protein tyrosine phosphatase PTPRH in cell signaling regulation and biological processes of non-small cell lung cancer

The balance of protein phosphorylation is often disrupted in cancer, with hyperactivity of kinases and inactivation of phosphatases driving cell proliferation and survival pathways. PTPRH, a protein tyrosine phosphatase, is mutated in ∼5% of non-small cell lung cancers (NSCLC). However, how PTPRH contributes to biological processes and tumorigenesis was unknown. We uncovered PTPRH’s candidate interactors and associated pathways by applying a proximity-dependent biotinylation assay (BioID) and generating a signature transcriptome in two NSCLC cell lines derived from the primary tumor (NCI-H23) or a metastatic site (NCI-H2023), followed by functional validation. Candidate interactors included signaling molecules and structural proteins linked to integrins and focal adhesions, adherens junctions, migration, and the cytoskeleton, in addition to interactions with the receptor tyrosine kinases EGFR, EPHA2, and ROR2, and the phosphatases PTPN3 and PTPRJ. Considering the importance of EGFR in lung cancers and the role of EPHA2 in regulating cell adhesion, we examined how PTPRH regulates their signaling. Overexpression of PTPRH decreased EGFR phosphorylation at tyrosine 1173. It also reduced phospho-EPHA2, with one of the target tyrosine residues identified as the ligand-dependent Y588. At the cellular level, PTPRH and EPHA2 colocalize, with PTPRH gain inducing morphological alterations, such as increased eccentricity, smaller size and changes in the cytoskeleton organization in NCI-H23 cells. These changes are accompanied by increased FAK Y397 phosphorylation, but reduced cell adhesion to the ECM. Additionally, pathway enrichment analysis revealed downregulation of multiple oncogenic, metabolic, and cell adhesion signaling pathways, with increased levels of PTPRH leading to reduced migration in vitro, suppressed tumor growth and lung colonization and tumor differentiation in vivo. Interestingly, some alterations may be independent of PTPRH catalytic activity and tailored to a cell line’s site of origin and genetic background. These results indicate that PTPRH regulates key signaling, structural networks, and tumor behavior with loss facilitating NSCLC progression.