Integration of cancer-related genetic landscape of Eph receptors and ephrins with proteomics identifies a crosstalk between EPHB6 and EGFR
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PROVIDER: PRJNA853195 | ENA |
REPOSITORIES: ENA
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Project description: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.
2023-05-23 | GSE206981 | GEO
Project description:Aberrant activities of fourteen Eph receptor tyrosine kinases (RTKs) and their eight ephrin ligands are often observed in human malignancies, where they control cancer development, progression, and aggressiveness. While multiple attempts have been made to target Eph receptors in tumors, their effectiveness has been hindered by distinct contexts in which these proteins operate to enhance or suppress the disease. One of the strategies to overcoming this challenge is to define the molecular landscape/genetic interactions (GIs) associated with pro- and anti-malignant activities of Ephs and ephrins, as this should outline context-specific genetic dependencies associated with these molecules. Here, we used a multi-step bioinformatics analysis of the TCGA database and the DepMap gene essentiality data from cancer cell lines to construct a network of GIs of Ephs and ephrins in human malignancies. Validation of the relevance of this network was centered on an unusual Eph receptor EPHB6, which is innately kinase-incompetent, but nevertheless, actively controls aggressiveness and tumor initiation in several cancer types. To select the most relevant GI from the generated network, we performed genome-wide screening and EPHB6 BioID analysis. While, the BioID approach pointed towards EPHB6 interactions with several RTKs, including all kinase-active members of the EGFR/ErbB class, its integration with shRNA screening and computationally predicted GIs, unambiguously pointed towards EGFR as a key EPHB6 partner. Indeed, our further experiments confirmed EPHB6 interactions with all kinase-competent ErbBs, including EGFR, and revealed its ability to modulate EGF-induced EGFR tyrosine phosphorylation and downstream signaling. This ultimately, enhanced proliferation of cancer cells, culminating in efficient tumor development. In agreement, we found high levels of EGFR to positively correlate with higher EPHB6 expression in several tumor types. Taken together, these observations indicate that EPHB6 should serve as an effective target in tumors with high EGFR levels and that co-targeting these receptors might provide therapeutic benefits. More importantly, these experiments provide a strong support for the relevance of our computational strategy and suggest that the generated network describing GIs of Eph receptors and their ligands is a valuable resource that can be used for developing new treatment approaches aiming to hunt these proteins in human malignancies.
2023-05-16 | PXD033912 | Pride
Project description:Ephrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and also functions as a cell entry receptor for several henipaviruses, which are zoonotic viruses with pandemic potential. Two such viruses, Nipah (NiV) and Hendra (HeV), are highly pathogenic in humans yet do not have any widely approved virus-specific therapeutics or vaccines. Soluble Fc-fusions of EFNB2 (sEFNB2-Fc) are known to bind the attachment glycoprotein G of both viruses and inhibit viral infection of cells. However, the potential of sEFNB2-Fc as a neutralizing agent in vivo is hindered by its binding activity to native Eph receptors. Therefore, using deep mutagenesis, variants of EFNB2 at cell surface are identified with increased binding to the soluble head domain of NiV-G over soluble Fc-fusions of the extracellular domains of Eph receptors. Specificity mutations for NiV-G are found primarily at the binding interface, especially around the G-H binding loop. The mutational landscape offers a preliminary blueprint for engineering sEFNB2-Fc variants with high specificity and affinity for potent neutralization of henipaviruses.
2023-06-12 | GSE234213 | GEO
Project description:Ephrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and also functions as a cell entry receptor for several henipaviruses, which are zoonotic viruses with pandemic potential. Two such viruses, Nipah (NiV) and Hendra (HeV), are highly pathogenic in humans yet do not have any widely approved virus-specific therapeutics or vaccines. Soluble Fc-fusions of EFNB2 (sEFNB2-Fc) are known to bind the attachment glycoprotein G of both viruses and inhibit viral infection of cells. However, the potential of sEFNB2-Fc as a neutralizing agent in vivo is hindered by its binding activity to native Eph receptors. Therefore, using deep mutagenesis, variants of EFNB2 at cell surface are identified with increased binding to the soluble head domain of NiV-G over soluble Fc-fusions of the extracellular domains of Eph receptors. Specificity mutations for NiV-G are found primarily at the binding interface, especially around the G-H binding loop. The mutational landscape offers a preliminary blueprint for engineering sEFNB2-Fc variants with high specificity and affinity for potent neutralization of henipaviruses.
2023-06-12 | GSE234214 | GEO
Project description:The hypothesis tested in the present study was that activation of Eph or ephrin signaling in neural progenitors induces a transcriptional response which participate in the control of progenitor self-renewal. Results provide important information on transcriptional changes in response to activation of Eph receptors. They also show that activation of ephrin signaling does not induce a transcriptional response at genome-wide level.
2017-09-21 | GSE104068 | GEO
Project description:In the developing mouse anterior forebrain, the rostral migratory stream (RMS) supports continued proliferation and efficient transportation of large quantities of neuroblasts from the ventricular-subventricular (V-SVZ) stem cell niche to the olfactory bulb (OB). Astrocytes aid this migration by providing a glial network through which chains of fasciculated neuroblasts move. The largest receptor tyrosine kinase family, Eph receptors, and their ephrin ligands have been implicated in controlling neuroblast migration and astrocyte organization within this pathway. However, a clear understanding of the regulatory mechanisms underlying Eph/ephrin signaling remains elusive, in part due to the complexity of heterogeneous expression patterns in both neuroblasts and astrocytes, as well as the cytoarchitectural changes that occur during postnatal development. Our studies provide a framework to deconvolute and characterize Eph and ephrin signaling as the RMS changes from a diffuse stream of migratory neuroblasts to a highly constricted pathway of neuroblast chains within astrocytic networks. Specifically, we identify temporally regulated, cell type-specific receptor-ligand interactions, revealing the prevalence and dynamic shifts of neuroblast-neuroblast, neuroblast-astrocyte, astrocyte-astrocyte interactions.
2025-09-04 | GSE306762 | GEO
Project description:Eph kinases constitute the largest receptor tyrosine kinase family, and their ligands, ephrins (Efns), are also cell surface molecules. Our purpose is to compare the expression levels of genes in adrenal gland chromaffin cells in EphB6 KO and WT male/female/castrated mice.
2018-09-26 | GSE120400 | GEO
Project description:Despite advances, treatment of unresectable colorectal cancer remains a clinical challenge and the incidence of this malignancy is increasing in individuals below the age of fifty. Integrated genomic, transcriptomic, proteomic, and mechanistic studies identified the tyrosine kinase receptors EphB2 and EphB4 as colorectal cancer drivers, and EphA2 activity as a cancer resistance mechanism to epidermal growth factor receptor and BRAF inhibitors. Reduction of EphB2 and EphB4 activity suppresses colorectal cancer cell growth and survival and is a potential target for colorectal cancer therapy. Here, we report the design and synthesis of two novel inhibitors, 1 and 3, that selectively bind with high affinity to A and B-type Eph receptor tyrosine kinases, inhibit A and B-type Eph tyrosine kinase activity, induce cell cycle arrest and confer a protracted state of growth reduction to colorectal cancer cells. 1 and 3 bind to EphA2 arresting the activation loop containing the conserved Asp-Phe-Gly (“DFG”)-motif in an inactive conformation and show a conserved hydrogen bond interaction with the so-called gatekeeper residue, the activation loop, alphaC helix, and hinge region of the kinase, typical of kinase inhibitors. These results demonstrate that pharmacological inhibition of Eph tyrosine kinase receptors is a valid therapeutic approach for the treatment of colorectal cancer.
2024-05-23 | PXD031880 | Pride
Project description:This submission contains the mass spectrometry files for the manuscript by Sara L. Banerjee et al. that describes identification of new downstream effector proteins for EPH receptors (EPHRs). To unravel EPHR-associated signaling complexes under native conditions, we applied a mass spectrometry (MS)-based proximity labeling approach, namely BioID. We obtained a composite signaling network from EPHA4, -B2, -B3 and -B4 receptors. This network comprises 395 proteins, most of which not previously linked to EPH signaling. We examined the requirement of some of BioID-identified candidates for EPHR-regulated functions and showed that depletion of the signaling scaffold PARD3, blocks EPH-dependent cell sorting. Using affinity purification combined to MS, we further delineated a signaling complex involving C-SRC kinase (CSK), whose recruitment to PARD3 complexes is dependent on EPHR signals. The BioID and AP-MS experiments were performed from HEK293 and HEK293T cells, respectively and 30 MS files were acquired on an Orbitrap Fusion mass spectrometer in data dependent acquisition mode. All the DDA files are associated with this deposition. Please refer to the Table 1 for additional details of submitted files. For questions, please contact Jean-Philippe Lambert (Jean-Philippe.Lambert@crchudequebec.ulaval.ca) or Nicolas Bisson (nick.bisson@crchudequebec.ulaval.ca).
| MSV000086054 | MassIVE
Project description:This submission contains the mass spectrometry files for the manuscript by Sara L. Banerjee et al. that describes identification of new downstream effector proteins for EPH receptors (EPHRs). To unravel EPHR-associated signaling complexes under native conditions, we applied a mass spectrometry (MS)-based proximity labeling approach, namely BioID. We obtained a composite signaling network from EPHA4, -B2, -B3 and -B4 receptors. This network comprises 395 proteins, most of which not previously linked to EPH signaling. We examined the requirement of some of BioID-identified candidates for EPHR-regulated functions and showed that depletion of the signaling scaffold PARD3, blocks EPH-dependent cell sorting. Using affinity purification combined to MS, we further delineated a signaling complex involving C-SRC kinase (CSK), whose recruitment to PARD3 complexes is dependent on EPHR signals. The BioID and AP-MS experiments were performed from HEK293 and HEK293T cells, respectively and 30 MS files were acquired on an Orbitrap Fusion mass spectrometer in data dependent acquisition mode. All the DDA files are associated with this deposition. Please refer to the Table 1 for additional details of submitted files. For questions, please contact Jean-Philippe Lambert (Jean-Philippe.Lambert@crchudequebec.ulaval.ca) or Nicolas Bisson (nick.bisson@crchudequebec.ulaval.ca).
2022-03-31 | MSV000089185 | MassIVE