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Kinome-wide decoding of network-attacking mutations rewiring cancer signaling.

Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R - Cell (2015)

Bottom Line: However, global analysis of these events is currently limited.Here, we identify six types of network-attacking mutations (NAMs), including changes in kinase and SH2 modulation, network rewiring, and the genesis and extinction of phosphorylation sites.We identified and experimentally validated several NAMs, including PKCγ M501I and PKD1 D665N, which encode specificity switches analogous to the appearance of kinases de novo within the kinome.

View Article: PubMed Central - PubMed

Affiliation: Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark.

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Constitutive Activation and Inactivation of Kinases by NAMs(A) ReKINect identified ES2 cells as containing the constitutively activating BRAF V600E mutation.(B) An immunoblot and associated quantification, illustrating the phosphorylation of BRAF substrate MEK in the mutant cell line ES2 (in red) compared to the wild-type cell lines (in black), using total MEK and β-tubulin for normalization.(C) ReKINect identified several cancer mutations in catalytically essential residues of kinase domains.(D) A quantification of all mutations from the global repository of cancer somatic mutations predicted to inactivate kinases and the catalytically essential positions they hit. Mutations leading to kinase domain catalytic inactivation are enriched (χ2 test, p = 1.69 × 10−16) in cancer somatic mutations (with particular preference for the aspartate, D, and glycine, G, in the DFG motif).
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fig6: Constitutive Activation and Inactivation of Kinases by NAMs(A) ReKINect identified ES2 cells as containing the constitutively activating BRAF V600E mutation.(B) An immunoblot and associated quantification, illustrating the phosphorylation of BRAF substrate MEK in the mutant cell line ES2 (in red) compared to the wild-type cell lines (in black), using total MEK and β-tubulin for normalization.(C) ReKINect identified several cancer mutations in catalytically essential residues of kinase domains.(D) A quantification of all mutations from the global repository of cancer somatic mutations predicted to inactivate kinases and the catalytically essential positions they hit. Mutations leading to kinase domain catalytic inactivation are enriched (χ2 test, p = 1.69 × 10−16) in cancer somatic mutations (with particular preference for the aspartate, D, and glycine, G, in the DFG motif).

Mentions: Taking the well-characterized case of BRAF V600E, a phospho-mimicking activating mutation, as a positive test case, we confirmed that ReKINect could identify this mutation in one of the ovarian cell lines (ES2) and predict it as kinase activation. We subsequently experimentally confirmed the hyper-phosphorylated state of the BRAF substrate, MEK by immuno-blot in the ES2 line (Figures 6A and 6B).


Kinome-wide decoding of network-attacking mutations rewiring cancer signaling.

Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R - Cell (2015)

Constitutive Activation and Inactivation of Kinases by NAMs(A) ReKINect identified ES2 cells as containing the constitutively activating BRAF V600E mutation.(B) An immunoblot and associated quantification, illustrating the phosphorylation of BRAF substrate MEK in the mutant cell line ES2 (in red) compared to the wild-type cell lines (in black), using total MEK and β-tubulin for normalization.(C) ReKINect identified several cancer mutations in catalytically essential residues of kinase domains.(D) A quantification of all mutations from the global repository of cancer somatic mutations predicted to inactivate kinases and the catalytically essential positions they hit. Mutations leading to kinase domain catalytic inactivation are enriched (χ2 test, p = 1.69 × 10−16) in cancer somatic mutations (with particular preference for the aspartate, D, and glycine, G, in the DFG motif).
© Copyright Policy - CC BY
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4644236&req=5

fig6: Constitutive Activation and Inactivation of Kinases by NAMs(A) ReKINect identified ES2 cells as containing the constitutively activating BRAF V600E mutation.(B) An immunoblot and associated quantification, illustrating the phosphorylation of BRAF substrate MEK in the mutant cell line ES2 (in red) compared to the wild-type cell lines (in black), using total MEK and β-tubulin for normalization.(C) ReKINect identified several cancer mutations in catalytically essential residues of kinase domains.(D) A quantification of all mutations from the global repository of cancer somatic mutations predicted to inactivate kinases and the catalytically essential positions they hit. Mutations leading to kinase domain catalytic inactivation are enriched (χ2 test, p = 1.69 × 10−16) in cancer somatic mutations (with particular preference for the aspartate, D, and glycine, G, in the DFG motif).
Mentions: Taking the well-characterized case of BRAF V600E, a phospho-mimicking activating mutation, as a positive test case, we confirmed that ReKINect could identify this mutation in one of the ovarian cell lines (ES2) and predict it as kinase activation. We subsequently experimentally confirmed the hyper-phosphorylated state of the BRAF substrate, MEK by immuno-blot in the ES2 line (Figures 6A and 6B).

Bottom Line: However, global analysis of these events is currently limited.Here, we identify six types of network-attacking mutations (NAMs), including changes in kinase and SH2 modulation, network rewiring, and the genesis and extinction of phosphorylation sites.We identified and experimentally validated several NAMs, including PKCγ M501I and PKD1 D665N, which encode specificity switches analogous to the appearance of kinases de novo within the kinome.

View Article: PubMed Central - PubMed

Affiliation: Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark.

Show MeSH
Related in: MedlinePlus