Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data

Abstract

Endothelins ( EDN ) are peptide hormones that activate a GPCR signalling system and contribute to several diseases, including hypertension and cancer. Current knowledge about EDN signalling is fragmentary, and no systems level understanding is available. We investigated phosphoproteomic changes caused by endothelin B receptor ( ENDRB ) activation in the melanoma cell lines UACC 257 and A2058 and built an integrated model of EDNRB signalling from the phosphoproteomics data. More than 5,000 unique phosphopeptides were quantified. EDN induced quantitative changes in more than 800 phosphopeptides, which were all strictly dependent on EDNRB . Activated kinases were identified based on high confidence EDN target sites and validated by Western blot. The data were combined with prior knowledge to construct the first comprehensive logic model of EDN signalling. Among the kinases predicted by the signalling model, AKT , JNK , PKC and AMP could be functionally linked to EDN ‐induced cell migration. The model contributes to the system‐level understanding of the mechanisms underlying the pleiotropic effects of EDN signalling and supports the rational selection of kinase inhibitors for combination treatments with EDN receptor antagonists.

PHONEMeS: Efficient Modeling of Signaling Networks Derived from Large-Scale Mass Spectrometry Data

“…The multiple-time-points variant of PHONEMeS-ILP (PHONEMeS-mult) was used to infer an endothelin receptor (EDNRB) regulatory signaling network based on prior knowledge and large-scale time-resolved phosphoproteomics for two types of melanoma cell lines . For details, see Text S3.…”

“…8 The models were able to predict the presence of key kinases known to play a central role in cell migration, and major parts of the network proposed by PHONEMeS were experimentally validated. 8 Third, we applied PHONEMeS-ud to study the signaling state of colon cancer. In this case, PHONEMeS-ud was able to provide expected and potentially new mechanistic insights into colon cancer signaling.…”

“…In PHONEMeS, we can set any desired time limit through the time-limit parameter. Second, the application of the new PHONEMeS-mult (time-course form of PHONEMeS-ILP) for the modeling of endothelin signaling pathways was carried out . The models were able to predict the presence of key kinases known to play a central role in cell migration, and major parts of the network proposed by PHONEMeS were experimentally validated .…”

“…The multiple-time-points variant of PHONEMeS-ILP (PHO-NEMeS-mult) was used to infer an endothelin receptor (EDNRB) regulatory signaling network based on prior knowledge and large-scale time-resolved phosphoproteomics for two types of melanoma cell lines. 8 For details, see Text S3. The network models of PHONEMeS-mult for this case study were experimentally validated and contributed to the systemlevel understanding of EDN signaling, which can subsequently be used for the selection of kinase inhibitors in combination with EDN treatments (Text S3).…”

Association of Endothelin-I and A symmetric Dimethylarginine Levels with Insulin Resistance in Type-2 Diabetes Mellitus Patients

“…One paradoxical result has already drawn attention to the stability of serum insulin in diabetic's patient despite increasing serum glucose and HOMA-IR in blood, the only explanation, is due to proinsulin, is a marker of insulin resistance to diagnose T2DM secreted by dysfunctional pancreatic β-cells 26 . It activates the MAP-Kinase pathway via binding to the insulin receptor 27 , initiating inflammations, and secreting ET-I 28 .…”