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Phosphotyrosine-based Phosphoproteomics for Target Identification and Drug Response Prediction in AML Cell Lines

Abstract

Full text links full-text provider logo Actions Favorites Share Page navigation Title & authors Abstract Conflict of interest statement Similar articles LinkOut - more resources Mol Cell Proteomics . 2020 May;19(5):884-899. doi: 10.1074/mcp.RA119.001504. Epub 2020 Feb 26. Phosphotyrosine-based Phosphoproteomics for Target Identification and Drug Response Prediction in AML Cell Lines Carolien van Alphen 1 2 3 , Jacqueline Cloos 3 4 , Robin Beekhof 1 2 , David G J Cucchi 3 4 , Sander R Piersma 1 2 , Jaco C Knol 1 2 , Alex A Henneman 1 2 , Thang V Pham 1 2 , Johan van Meerloo 3 , Gert J Ossenkoppele 3 , Henk M W Verheul 1 , Jeroen J W M Janssen 3 , Connie R Jimenez 5 2 Affiliations PMID: 32102969 PMCID: PMC7196578 (available on 2021-05-01) DOI: 10.1074/mcp.RA119.001504 Free PMC article Abstract Acute myeloid leukemia (AML) is a clonal disorder arising from hematopoietic myeloid progenitors. Aberrantly activated tyrosine kinases (TK) are involved in leukemogenesis and are associated with poor treatment outcome. Kinase inhibitor (KI) treatment has shown promise in improving patient outcome in AML. However, inhibitor selection for patients is suboptimal.In a preclinical effort to address KI selection, we analyzed a panel of 16 AML cell lines using phosphotyrosine (pY) enrichment-based, label-free phosphoproteomics. The Integrative Inferred Kinase Activity (INKA) algorithm was used to identify hyperphosphorylated, active kinases as candidates for KI treatment, and efficacy of selected KIs was tested.Heterogeneous signaling was observed with between 241 and 2764 phosphopeptides detected per cell line. Of 4853 identified phosphopeptides with 4229 phosphosites, 4459 phosphopeptides (4430 pY) were linked to 3605 class I sites (3525 pY). INKA analysis in single cell lines successfully pinpointed driver kinases (PDGFRA, JAK2, KIT and FLT3) corresponding with activating mutations present in these cell lines. Furthermore, potential receptor tyrosine kinase (RTK) drivers, undetected by standard molecular analyses, were identified in four cell lines (FGFR1 in KG-1 and KG-1a, PDGFRA in Kasumi-3, and FLT3 in MM6). These cell lines proved highly sensitive to specific KIs. Six AML cell lines without a clear RTK driver showed evidence of MAPK1/3 activation, indicative of the presence of activating upstream RAS mutations. Importantly, FLT3 phosphorylation was demonstrated in two clinical AML samples with a FLT3 internal tandem duplication (ITD) mutation.Our data show the potential of pY-phosphoproteomics and INKA analysis to provide insight in AML TK signaling and identify hyperactive kinases as potential targets for treatment in AML cell lines. These results warrant future investigation of clinical samples to further our understanding of TK phosphorylation in relation to clinical response in the individual patient.