Phosphoproteomic Analysis Identifies TYRO3 as a Mediator of Sunitinib Resistance in Metastatic Thymomas

Abstract

Background: After initially responding to empiric radio-chemotherapy, most advanced thymomas (TH) and thymic carcinomas (TC) become refractory and require second-line therapy. The multi-target receptor tyrosine kinase (RTK) inhibitor, sunitinib, is one of the few options, especially in patients with thymic carcinomas, and has resulted in partial remissions and prolonged overall survival. However, sunitinib shows variable activity in thymomas, and not all patients benefit equally. A better understanding of its mode of action and the definition of predictive biomarkers would help select patients who profit most. Methods: Six cell lines were treated with sunitinib in vitro. Cell viability was measured by MTS assay and used to define in vitro responders and non-responders. A quantitative real-time assay simultaneously measuring the phosphorylation of 144 tyrosine kinase substrates was used to correlate cell viability with alterations of the phospho-kinome, calculate a sunitinib response index (SRI), and impute upstream tyrosine kinases. Sunitinib was added to protein lysates of 29 malignant TH and TC. Lysates were analyzed with the same phosphorylation assay. The SRI tentatively classified cases into potential clinical responders and non-responders. In addition, the activation patterns of 44 RTKs were studied by phospho-RTK arrays in 37 TH and TC. Results: SRI application separated thymic epithelial tumors (TET) in potential sunitinib responders and resistant cases. Upstream kinase prediction identified multiple RTKs potentially involved in sunitinib response, many of which were subsequently shown to be differentially overexpressed in TH and TC. Among these, TYRO3/Dtk stood out since it was exclusively present in metastatic TH. The function of TYRO3 as a mediator of sunitinib resistance was experimentally validated in vitro. Conclusions: Using indirect and direct phosphoproteomic analyses to predict sunitinib response in malignant TET, we have shown that TH and TC express multiple important sunitinib target RTKs. Among these, TYRO3 was identified as a potent mediator of sunitinib resistance activity, specifically in metastatic TH. TYRO3 may thus be both a novel biomarker of sunitinib resistance and a potential therapeutic target in advanced thymomas and thymic carcinomas.

Phosphoproteomics Profile of Chicken Cecum in the Response to Salmonella enterica Serovar Enteritidis Inoculation

“…Additionally, there has been little research to reveal the regulation mechanism of chicken cecum infected with S. Enteritidis in the phosphorylation levels of proteins. There has been a large amount of research on phosphorylated proteomics in human disease [21][22][23][24], bacteria [25], geese [26], goats [27,28], cattle [29], rats, and mice [30][31][32][33]. There were 62 phosphosites on 43 phosphoproteins which were determined to be up-regulated while 113 on 80 phosphoproteins were down-regulated in the research by Huang et al [34]; the up-regulated phosphoproteins were fewer than the down-regulated phosphoproteins.…”

Non-Mutational Key Features in the Biology of Thymomas

“…However, the overexpression of a protein does not necessarily prove its functional relevance (e.g., as a predictive biomarker for therapeutic response). Using phospho-RTK arrays, Küffer et al, studied the activation of 44 RTKs in 37 type B2 and B3 thymomas [ 138 ]. EGFR was by far the most prevalent active RTK (74% of cases).…”