Dataset Information

Lambert_AP_SWATH_P93_VS6_CDK4_original

ABSTRACT: This submission is part of the mass spectrometry datasets for the manuscript by Lambert et al. that describes the use of SWATH to rapidly monitor differential interactomes. This submission contains 9 SWATH files and 3 IDA files for the following baits: CDK4 WT, CDK4 R24C and CDK4 R24H. Three biological replicates for each bait were analyzed by SWATH, and one of the biological replicates was used for IDA. See the README file within "Methods and Protocols" and the accompanying File description. Additional details and files are found on prohits-web.lunenfeld.ca. Please note that one of the biological replicates for each of the two mutants is of significantly poorer quality than the other two.

PROVIDER: MSV000078453 | MassIVE | Thu Jul 04 00:00:00 BST 2013

REPOSITORIES: MassIVE

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Publications

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition.

Lambert Jean-Philippe JP Ivosev Gordana G Couzens Amber L AL Larsen Brett B Taipale Mikko M Lin Zhen-Yuan ZY Zhong Quan Q Lindquist Susan S Vidal Marc M Aebersold Ruedi R Pawson Tony T Bonner Ron R Tate Stephen S Gingras Anne-Claude AC

Nature methods 20131027 12

Characterizing changes in protein-protein interactions associated with sequence variants (e.g., disease-associated mutations or splice forms) or following exposure to drugs, growth factors or hormones is critical to understanding how protein complexes are built, localized and regulated. Affinity purification (AP) coupled with mass spectrometry permits the analysis of protein interactions under near-physiological conditions, yet monitoring interaction changes requires the development of a robust ...[more]

PMID: 24162924

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Project description:Cdk4 and Cdk6 are two related kinases that bind D-type cyclins and regulate cell cycle progression. Due to their relevance in cancer, Cdk4/6 inhibitors are currently in advanced clinical trials in multiple tumor types. Cdk4/6 are inhibited by INK4 proteins that exert tumor suppressing functions. To test the significance of this inhibitory mechanism we have generated knock-in mice that express a Cdk6 mutant (Cdk6 R31C) insensitive to INK4-mediated inhibition. Cdk6R/R mice display altered development of the hematopoietic system without resulting in enhanced tumor susceptibility, either in the presence or absence of p53. The presence of the Cdk6 R31C allele results in defective potential of hematopoietic progenitors in adoptive transfer assays or after induced damage. These defects are rescued after complete insensitivity to INK4 inhibitors in Cdk4R/R; Cdk6R/R double mutant mice, and INK4-resistant mice display increased susceptibility to hematopoietic and endocrine tumors. In BCR-ABL-transformed hematopoietic cells, the presence of the Cdk6 R31C allele results in increased binding of p16INK4a to wild-type Cdk4, whereas the double mutant is fully insensitive to INK4 inhibitors resulting in accelerated disease onset. Our observations reveal that Cdk4 and Cdk6 cooperate in tumor development and suggest a role for Cdk6 in buffering INK4 protein levels thus contributing to the development of hematopoietic tumors. The presence of the Cdk4 R24C and Cdk6 R31C alleles results in relevant changes in the expression profiles of cancer cells including deregulation of apoptosis and other processes. p185BCR-ABL1 was used to transform wild-type or double knock-in Cdk4 R24C; Cdk6 R31C fetal livers. Cell lines were isolated as spontaneous immortal and transformed clones after transduction of fetal liver with a p185 BCR-ABL1-transgene. RNA was isolated from asynchronous cultures. Two-condition experiment, Cdk4R-Cdk6R cells versus wild-type cells. Biological replicates: 3 control replicates, 3 transfected replicates.

Dataset Information

Lambert_AP_SWATH_P93_VS6_CDK4_original

Publications

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition.

Similar Datasets

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