Physical and functional interactome atlas of human receptor tyrosine kinases

Abstract

Much cell‐to‐cell communication is facilitated by cell surface receptor tyrosine kinases (RTKs). These proteins phosphorylate their downstream cytoplasmic substrates in response to stimuli such as growth factors. Despite their central roles, the functions of many RTKs are still poorly understood. To resolve the lack of systematic knowledge, we apply three complementary methods to map the molecular context and substrate profiles of RTKs. We use affinity purification coupled to mass spectrometry (AP‐MS) to characterize stable binding partners and RTK–protein complexes, proximity‐dependent biotin identification (BioID) to identify transient and proximal interactions, and an in vitro kinase assay to identify RTK substrates. To identify how kinase interactions depend on kinase activity, we also use kinase‐deficient mutants. Our data represent a comprehensive, systemic mapping of RTK interactions and substrates. This resource adds information regarding well‐studied RTKs, offers insights into the functions of less well‐studied RTKs, and highlights RTK‐RTK interactions and shared signaling pathways.

Integrative analysis of cancer dependency data and comprehensive phosphoproteomics data revealed the EPHA2-PARD3 axis as a cancer vulnerability in KRAS-mutant colorectal cancer

“…63 The EPHA2-EPHA4 interaction has been previously observed using BioID data. 64 Based on these data, PARD3 Y378 is also a potential downstream candidate of EPHA2. Although the phosphorylation site of Y378 on PARD3 has not been functionally annotated previously, aberrant tyrosine phosphorylation of Par3 is thought to be associated with dysfunction of growth factor receptors, leading to pathological tight junction assembly and disassembly in tumour cells.…”

Ubiquitin ligase and signalling hub MYCBP2 is required for efficient EPHB2 tyrosine kinase receptor function

“…One of the most prominent, novel hits was the E3 ubiquitin ligase and signalling hub protein MYCBP2, and its binding partner FBXO45. FBXO45 was previously identified as a putative EPHB2 interacting protein in large-scale, cell-based interactome studies (Huttlin et al, 2021;Salokas et al, 2022).…”

An extracellular receptor tyrosine kinase motif orchestrating intracellular STAT activation

“…To examine the clusterization of JM-a-like RTKs (RTKs with a JM-a sequence motif) and JM-b-like RTKs (RTKs with a JM-b sequence motif) on the basis of RTK protein-protein associations, affinity purification coupled to mass spectrometry (AP-MS) and proximity-dependent biotin identification (BioID) data on RTK interactomes 37 were analyzed. The interactome data were subjected to neighborhood component analysis, where the RTKs where either categorized based on their eJM sequence motifs or by 1000 randomized classes to estimate the statistical significance of the clusterization.…”