Global phosphoproteome profiling reveals unanticipated networks responsive to cisplatin treatment of embryonic stem cells

TY - JOUR

T1 - Global phosphoproteome profiling reveals unanticipated networks responsive to cisplatin treatment of embryonic stem cells

AU - Pines, Alex

AU - Kelstrup, Christian D

AU - Vrouwe, Mischa G

AU - Puigvert, Jordi C

AU - Typas, Dimitris

AU - Misovic, Branislav

AU - de Groot, Anton

AU - von Stechow, Louise

AU - van de Water, Bob

AU - Danen, Erik H J

AU - Vrieling, Harry

AU - Mullenders, Leon H F

AU - Olsen, Jesper V

PY - 2011/12

Y1 - 2011/12

N2 - Cellular responses to DNA-damaging agents involve the activation of various DNA damage signaling and transduction pathways. Using quantitative and high-resolution tandem mass spectrometry, we determined global changes in protein level and phosphorylation site profiles following treatment of SILAC (stable isotope labeling by amino acids in cell culture)-labeled murine embryonic stem cells with the anticancer drug cisplatin. Network and pathway analyses indicated that processes related to the DNA damage response and cytoskeleton organization were significantly affected. Although the ATM (ataxia telangiectasia mutated) and ATR (ATM and Rad3-related) consensus sequence (S/T-Q motif) was significantly overrepresented among hyperphosphorylated peptides, about half of the >2-fold-upregulated phosphorylation sites based on the consensus sequence were not direct substrates of ATM and ATR. Eleven protein kinases mainly belonging to the mitogen-activated protein kinase (MAPK) family were identified as being regulated in their kinase domain activation loop. The biological importance of three of these kinases (cyclin-dependent kinase 7 [CDK7], Plk1, and KPCD1) in the protection against cisplatin-induced cytotoxicity was demonstrated by small interfering RNA (siRNA)-mediated knockdown. Our results indicate that the cellular response to cisplatin involves a variety of kinases and phosphatases not only acting in the nucleus but also regulating cytoplasmic targets, resulting in extensive cytoskeletal rearrangements. Integration of transcriptomic and proteomic data revealed a poor correlation between changes in the relative levels of transcripts and their corresponding proteins, but a large overlap in affected pathways at the levels of mRNA, protein, and phosphoprotein. This study provides an integrated view of pathways activated by genotoxic stress and deciphers kinases that play a pivotal role in regulating cellular processes other than the DNA damage response.

AB - Cellular responses to DNA-damaging agents involve the activation of various DNA damage signaling and transduction pathways. Using quantitative and high-resolution tandem mass spectrometry, we determined global changes in protein level and phosphorylation site profiles following treatment of SILAC (stable isotope labeling by amino acids in cell culture)-labeled murine embryonic stem cells with the anticancer drug cisplatin. Network and pathway analyses indicated that processes related to the DNA damage response and cytoskeleton organization were significantly affected. Although the ATM (ataxia telangiectasia mutated) and ATR (ATM and Rad3-related) consensus sequence (S/T-Q motif) was significantly overrepresented among hyperphosphorylated peptides, about half of the >2-fold-upregulated phosphorylation sites based on the consensus sequence were not direct substrates of ATM and ATR. Eleven protein kinases mainly belonging to the mitogen-activated protein kinase (MAPK) family were identified as being regulated in their kinase domain activation loop. The biological importance of three of these kinases (cyclin-dependent kinase 7 [CDK7], Plk1, and KPCD1) in the protection against cisplatin-induced cytotoxicity was demonstrated by small interfering RNA (siRNA)-mediated knockdown. Our results indicate that the cellular response to cisplatin involves a variety of kinases and phosphatases not only acting in the nucleus but also regulating cytoplasmic targets, resulting in extensive cytoskeletal rearrangements. Integration of transcriptomic and proteomic data revealed a poor correlation between changes in the relative levels of transcripts and their corresponding proteins, but a large overlap in affected pathways at the levels of mRNA, protein, and phosphoprotein. This study provides an integrated view of pathways activated by genotoxic stress and deciphers kinases that play a pivotal role in regulating cellular processes other than the DNA damage response.

KW - Animals

KW - Antineoplastic Agents

KW - Ataxia Telangiectasia

KW - Cisplatin

KW - DNA Damage

KW - Embryonic Stem Cells

KW - Gene Expression Profiling

KW - Mice

KW - Mice, Inbred C57BL

KW - Mitogen-Activated Protein Kinases

KW - Phosphoproteins

KW - Phosphorylation

KW - Proteomics

KW - Signal Transduction

U2 - 10.1128/MCB.05258-11

DO - 10.1128/MCB.05258-11

M3 - Journal article

C2 - 22006019

SN - 0270-7306

VL - 31

SP - 4964

EP - 4977

JO - Molecular and Cellular Biology

JF - Molecular and Cellular Biology

IS - 24

ER -