Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms.
The RAS-RAF-MEK-ERK (MAPK) pathway is prevalently perturbed in cancer. Recent large-scale sequencing initiatives profiled thousands of tumors providing insight into alterations at the DNA and RNA levels. These efforts confirmed that key nodes of the MAPK pathway, in particular KRAS and BRAF, are among the most frequently altered proteins in cancer. The establishment of targeted therapies, however, has proven difficult. To decipher the underlying challenges, it is essential to decrypt the phosphorylation network spanned by the MAPK core axis. Using mass spectrometry we identified 2241 phosphorylation sites on 1020 proteins, and measured their responses to inhibition of MEK or ERK. Multiple phosphorylation patterns revealed previously undetected feedback, as upstream signaling nodes, including receptor kinases, showed changes at the phosphorylation level. We provide a dataset rich in potential therapeutic targets downstream of the MAPK cascade. By integrating TCGA (The Cancer Genome Atlas) data, we highlight some downstream phosphoproteins that are frequently altered in cancer. All MS data have been deposited in the ProteomeXchange with identifier PXD003908 (http://proteomecentral.proteomexchange.org/dataset/PXD003908).
Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, CA, USA.
Florian
F
Gnad
Department of Protein Chemistry, Genentech Inc, South San Francisco, CA, USA.
Sophia
S
Doll
Department of Translational Oncology, Genentech Inc, South San Francisco, CA, USA.
Kyung
K
Song
Cell Signaling Technology Inc, Danvers, MA, USA.
Matthew P
MP
Stokes
Department of Biochemical Pharmacology, Genentech Inc, South San Francisco, CA, USA.
John
J
Moffat
Department of Translational Oncology, Genentech Inc, South San Francisco, CA, USA.
Bonnie
B
Liu
Department of Protein Chemistry, Genentech Inc, South San Francisco, CA, USA.
David
D
Arnott
Department of Translational Oncology, Genentech Inc, South San Francisco, CA, USA.
Jeffrey
J
Wallin
Department of Translational Oncology, Genentech Inc, South San Francisco, CA, USA.
Lori S
LS
Friedman
Department of Translational Oncology, Genentech Inc, South San Francisco, CA, USA.
Georgia
G
Hatzivassiliou
Department of Translational Oncology, Genentech Inc, South San Francisco, CA, USA.
Marcia
M
Belvin
D000595:Amino Acid Sequence; D000970:Antineoplastic Agents / Q000494:pharmacology; D001271:Atlases as Topic; D003110:Colonic Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D025461:Feedback, Physiological; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D045325:HCT116 Cells; D006801:Humans; D020407:Internet; D020935:MAP Kinase Signaling System / Q000187:drug effects*; D020929:Mitogen-Activated Protein Kinase Kinases / Q000037:antagonists & inhibitors / Q000235:genetics* / Q000378:metabolism; D009363:Neoplasm Proteins / Q000037:antagonists & inhibitors / Q000235:genetics* / Q000378:metabolism; D010750:Phosphoproteins / Q000037:antagonists & inhibitors / Q000235:genetics* / Q000378:metabolism; D010766:Phosphorylation; D047428:Protein Kinase Inhibitors / Q000494:pharmacology; D040901:Proteomics / Q000379:methods; D012984:Software
D000970:Antineoplastic Agents; D009363:Neoplasm Proteins; D010750:Phosphoproteins; D047428:Protein Kinase Inhibitors; D020929:Mitogen-Activated Protein Kinase Kinases
Cell Biology; ERK; MAPK; MEK; Mass spectrometry; Phosphoproteomics; Signaling