Limits...
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.

Show MeSH

Related in: MedlinePlus

Genesis of Phosphorylation Sites by Cancer Mutations Experimentally Confirmed by Mass Spectrometry, Related to Figure 3(A) Samples are processed following Spike-In SILAC standard procedures, where a mix of all the samples, in our case the five ovarian cancer cell lines, is used as an internal reference, so that peptides from different samples can be compared (Geiger et al., 2011; Monetti et al., 2011).(B) Additional examples of NGS and MS-annotated NAMs generating phosphorylation sites, including KIAA1279 G66S, ZBED4 N105S, AHNAK P4206S and MDN1 T4534S, showing the mapping of NGS and MS data, where the mutation toward phosphorylatable residues are confirmed as phosphorylation sites by the MS data using genome-specific searches.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4644236&req=5

figs2: Genesis of Phosphorylation Sites by Cancer Mutations Experimentally Confirmed by Mass Spectrometry, Related to Figure 3(A) Samples are processed following Spike-In SILAC standard procedures, where a mix of all the samples, in our case the five ovarian cancer cell lines, is used as an internal reference, so that peptides from different samples can be compared (Geiger et al., 2011; Monetti et al., 2011).(B) Additional examples of NGS and MS-annotated NAMs generating phosphorylation sites, including KIAA1279 G66S, ZBED4 N105S, AHNAK P4206S and MDN1 T4534S, showing the mapping of NGS and MS data, where the mutation toward phosphorylatable residues are confirmed as phosphorylation sites by the MS data using genome-specific searches.

Mentions: In order to experimentally investigate NAMs, we performed a global integrative analysis by combining exome next-generation sequencing (NGS) and quantitative mass spectrometry (MS)-based (phospho-)proteomics on a set of five ovarian cancer cell lines (ES2, OVAS, OVISE, TOV-21, and KOC-7C; Figures S1 and S2) and conducted genome-specific proteomics analyses (Experimental Procedures). By following a Spike-in SILAC-based labeling strategy (Geiger et al., 2011) (Figures S1 and S2; Experimental Procedures), we could identify and accurately quantify on average more than 6,000 unique phosphorylation sites across over 2,000 proteins in each of the five cell lines. Furthermore, NGS identified close to 9,000 unique missense variants per cell line (including SNPs and germline mutations as well as somatic mutations) that were subsequently interpreted by ReKINect (Figure 2).


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)

Genesis of Phosphorylation Sites by Cancer Mutations Experimentally Confirmed by Mass Spectrometry, Related to Figure 3(A) Samples are processed following Spike-In SILAC standard procedures, where a mix of all the samples, in our case the five ovarian cancer cell lines, is used as an internal reference, so that peptides from different samples can be compared (Geiger et al., 2011; Monetti et al., 2011).(B) Additional examples of NGS and MS-annotated NAMs generating phosphorylation sites, including KIAA1279 G66S, ZBED4 N105S, AHNAK P4206S and MDN1 T4534S, showing the mapping of NGS and MS data, where the mutation toward phosphorylatable residues are confirmed as phosphorylation sites by the MS data using genome-specific searches.
© Copyright Policy - CC BY
Related In: Results  -  Collection

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

figs2: Genesis of Phosphorylation Sites by Cancer Mutations Experimentally Confirmed by Mass Spectrometry, Related to Figure 3(A) Samples are processed following Spike-In SILAC standard procedures, where a mix of all the samples, in our case the five ovarian cancer cell lines, is used as an internal reference, so that peptides from different samples can be compared (Geiger et al., 2011; Monetti et al., 2011).(B) Additional examples of NGS and MS-annotated NAMs generating phosphorylation sites, including KIAA1279 G66S, ZBED4 N105S, AHNAK P4206S and MDN1 T4534S, showing the mapping of NGS and MS data, where the mutation toward phosphorylatable residues are confirmed as phosphorylation sites by the MS data using genome-specific searches.
Mentions: In order to experimentally investigate NAMs, we performed a global integrative analysis by combining exome next-generation sequencing (NGS) and quantitative mass spectrometry (MS)-based (phospho-)proteomics on a set of five ovarian cancer cell lines (ES2, OVAS, OVISE, TOV-21, and KOC-7C; Figures S1 and S2) and conducted genome-specific proteomics analyses (Experimental Procedures). By following a Spike-in SILAC-based labeling strategy (Geiger et al., 2011) (Figures S1 and S2; Experimental Procedures), we could identify and accurately quantify on average more than 6,000 unique phosphorylation sites across over 2,000 proteins in each of the five cell lines. Furthermore, NGS identified close to 9,000 unique missense variants per cell line (including SNPs and germline mutations as well as somatic mutations) that were subsequently interpreted by ReKINect (Figure 2).

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