Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling.
Comprehensive characterization of signaling in pancreatic ductal adenocarcinoma (PDAC) promises to enhance our understanding of the molecular aberrations driving this devastating disease, and may identify novel therapeutic targets as well as biomarkers that enable stratification of patients for optimal therapy. Here, we use immunoaffinity-coupled high-resolution mass spectrometry to characterize global tyrosine phosphorylation patterns across two large panels of human PDAC cell lines: the ATCC series (19 cell lines) and TKCC series (17 cell lines). This resulted in the identification and quantification of over 1800 class 1 tyrosine phosphorylation sites and the consistent segregation of both PDAC cell line series into three subtypes with distinct tyrosine phosphorylation profiles. Subtype-selective signaling networks were characterized by identification of subtype-enriched phosphosites together with pathway and network analyses. This revealed that the three subtypes characteristic of the ATCC series were associated with perturbations in signaling networks associated with cell-cell adhesion and epithelial-mesenchyme transition, mRNA metabolism, and receptor tyrosine kinase (RTK) signaling, respectively. Specifically, the third subtype exhibited enhanced tyrosine phosphorylation of multiple RTKs including the EGFR, ERBB3 and MET. Interestingly, a similar RTK-enriched subtype was identified in the TKCC series, and 'classifier' sites for each series identified using Random Forest models were able to predict the subtypes of the alternate series with high accuracy, highlighting the conservation of the three subtypes across the two series. Finally, RTK-enriched cell lines from both series exhibited enhanced sensitivity to the small molecule EGFR inhibitor erlotinib, indicating that their phosphosignature may provide a predictive biomarker for response to this targeted therapy. These studies highlight how resolution of subtype-selective signaling networks can provide a novel taxonomy for particular cancers, and provide insights into PDAC biology that can be exploited for improved patient management.
From the ‡Cancer Division and Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; §St Vincent's Hospital Clinical School, Faculty of Medicine, University of New South Wales, NSW 2052, Australia;
Emily S
ES
Humphrey
¶Cancer Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Level 1, Building 77, Monash University, VIC 3800, Australia;
Shih-Ping
SP
Su
From the ‡Cancer Division and Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; §St Vincent's Hospital Clinical School, Faculty of Medicine, University of New South Wales, NSW 2052, Australia;
Adnan M
AM
Nagrial
‖Competence Center Functional Genomics, University of Greifswald, F.-L-Jahnstr. 15, 17489 Greifswald, Germany;
Falko
F
Hochgräfe
From the ‡Cancer Division and Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; §St Vincent's Hospital Clinical School, Faculty of Medicine, University of New South Wales, NSW 2052, Australia;
Marina
M
Pajic
From the ‡Cancer Division and Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia;
Gillian M
GM
Lehrbach
**Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane QLD 4072, Australia;
Robert G
RG
Parton
**Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane QLD 4072, Australia;
Alpha S
AS
Yap
From the ‡Cancer Division and Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; ‡‡Chris O'Brien Lifehouse, Missenden Road, Camperdown, NSW 2050, Australia;
Lisa G
LG
Horvath
§§Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK;
David K
DK
Chang
§§Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK; andrew.biankin@glasgow.ac.uk.
Andrew V
AV
Biankin
¶¶Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, 52 Fu-Cheng Road, Hai-Dian District, Beijing 100142, China From the ‡Cancer Division and Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; §St Vincent's Hospital Clinical School, Faculty of Medicine, University of New South Wales, NSW 2052, Australia; roger.daly@monash.edu wujm@bjmu.edu.cn.
Jianmin
J
Wu
¶Cancer Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Level 1, Building 77, Monash University, VIC 3800, Australia; roger.daly@monash.edu wujm@bjmu.edu.cn.
Roger J
RJ
Daly
D021441:Carcinoma, Pancreatic Ductal / Q000378:metabolism*; D045744:Cell Line, Tumor; D002470:Cell Survival; D002853:Chromatography, Liquid; D006801:Humans; D013058:Mass Spectrometry; D010190:Pancreatic Neoplasms / Q000378:metabolism*; D019000:Phosphotyrosine / Q000378:metabolism*; D060066:Protein Interaction Maps; D040901:Proteomics / Q000379:methods*; D015398:Signal Transduction; D053719:Tandem Mass Spectrometry
D019000:Phosphotyrosine