Supplementary Materials

Supplementary Materials for:

Integrative analysis of kinase networks in TRAIL-induced apoptosis provides a source of potential targets for combination therapy

Jonathan So, Adrian Pasculescu, Anna Y. Dai, Kelly Williton, Andrew James, Vivian Nguyen, Pau Creixell, Erwin M. Schoof, John Sinclair, Miriam Barrios-Rodiles, Jun Gu, Aldis Krizus, Ryan Williams, Marina Olhovsky, James W. Dennis, Jeffrey L. Wrana, Rune Linding,* Claus Jorgensen,* Tony Pawson, Karen Colwill*

*Corresponding author. E-mail: linding{at}lindinglab.org (R.L.); claus.jorgensen{at}cruk.manchester.ac.uk (C.J.); colwill{at}lunenfeld.ca (K.C.)

This PDF file includes:

  • Fig. S1. Diagram of the method for using the EC-RP sensor to detect CASP3 activity.
  • Fig. S2. Selected examples of anisotropy measurements for the siRNA screen.
  • Fig. S3. siRNA screen validation.
  • Fig. S4. Overexpression screen to identify kinases that affect TRAIL-induced apoptosis.
  • Fig. S5. Evolutionary tree of the kinome with the apoptosis-modifying kinases indicated.
  • Fig. S6. Effect of knockdown of apoptosis-modifying kinases in HCT116 and LS174 cells.
  • Fig. S7. Filtering steps for IP-MS.
  • Fig. S8. Coimmunoprecipitation of kinase and interacting partners identified as prey in the IP-MS analysis.
  • Fig. S9. Comparison of interacting partners for kinases identified in previous IP-MS studies.
  • Fig. S10. Box plot of quantified phosphopeptides for β-catenin (CTNNB1) for the t = 60 min/t = 0 min ratio.
  • Fig. S11. Dynamic changes in phosphorylated peptides after TRAIL stimulation.
  • Fig. S12. Validation of a set of modulated phosphorylated sites by quantitative Western blot.
  • Fig. S13. Enrichment of apoptosis-modifying kinases by information flow analysis.
  • Fig. S14. Information flow analysis for t = 60 min.
  • Legends for tables S1 to S9
  • Legends for files S1 to F7
  • Reference (132)

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Results for genes (including GAPDH) screened in siRNA assay.
  • Table S2 (Microsoft Excel format). List of reagents used in this study.
  • Table S3 (Microsoft Excel format). Results for kinases screened in cDNA overexpression assay.
  • Table S4 (Microsoft Excel format). Union of siRNA and cDNA overexpression assays—combined phenotype.
  • Table S5 (Microsoft Excel format). IP-MS filtered results.
  • Table S6 (Microsoft Excel format). Preys for kinases from the TRAIL data set that overlap with the CMGC and Interlab reproducibility data sets.
  • Table S7 (Microsoft Excel format). List of phosphopeptides identified by global phosphorylation analysis.
  • Table S8 (Microsoft Excel format). List of all the protein-protein interactions (edges) used in the information flow analysis.
  • Table S9 (Microsoft Excel format). Matrices of information flow (Ιf) and change in information flow (ΔΙf) from source to sink.
  • File S1 (PDF format). Hierarchical clustering of the polarization anisotropy normalized to t = 0 min for the siRNA screen.
  • File S2 (PDF format). Detailed polarization anisotropy measurements for siRNA targets.
  • File S3 (PDF format). Detailed polarization anisotropy measurements for outliers.
  • File S4 (PDF format). Flow cytometry measurements in response to TRAIL stimulation for the controls ARAF, CSNK2A1, CASP8, and empty vector.
  • File S5 (PDF format). Response of each kinase-expressing stable cell line at 2 and 4 hours of TRAIL stimulation.
  • File S6. Ratios for significantly modulated phosphopeptides after TRAIL stimulation.
  • File S7 (PDF format). Hierarchical clustering of ΔΙf values at different quantiles.

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Citation: J. So, A. Pasculescu, A. Y. Dai, K. Williton, A. James, V. Nguyen, P. Creixell, E. M. Schoof, J. Sinclair, M. Barrios-Rodiles, J. Gu, A. Krizus, R. Williams, M. Olhovsky, J. W. Dennis, J. L. Wrana, R. Linding, C. Jorgensen, T. Pawson, K. Colwill, Integrative analysis of kinase networks in TRAIL-induced apoptosis provides a source of potential targets for combination therapy. Sci. Signal. 8, rs3 (2015).

© 2015 American Association for the Advancement of Science