Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer

Evan O. Paull, Nicholas A. Graham, John K. Lee, Bryan A. Smith, Bjoern Titz, Tanya Stoyanova, Claire M. Faltermeier, Vladislav Uzunangelov, Daniel E. Carlin, Daniel Teo Fleming, Christopher K. Wong, Yulia Newton, Sud Sudha, Ajay A. Vashisht, Jiaoti Huang, James A. Wohlschlegel, Thomas G. Graeber, Owen N. Witte, Joshua M. Stuart

    Research output: Contribution to journalArticle

    60 Citations (Scopus)

    Abstract

    We used clinical tissue from lethal metastatic castration-resistant prostate cancer (CRPC) patients obtained at rapid autopsy to evaluate diverse genomic, transcriptomic, and phosphoproteomic datasets for pathway analysis. Using Tied Diffusion through Interacting Events (TieDIE), we integrated differentially expressed master transcriptional regulators, functionally mutated genes, and differentially activated kinases in CRPC tissues to synthesize a robust signaling network consisting of druggable kinase pathways. Using MSigDB hallmark gene sets, six major signaling pathways with phosphorylation of several key residues were significantly enriched in CRPC tumors after incorporation of phosphoproteomic data. Individual autopsy profiles developed using these hallmarks revealed clinically relevant pathway information potentially suitable for patient stratification and targeted therapies in late stage prostate cancer. Here, we describe phosphorylation-based cancer hallmarks using integrated personalized signatures (pCHIPS) that shed light on the diversity of activated signaling pathways in metastatic CRPC while providing an integrative, pathway-based reference for drug prioritization in individual patients.

    Original languageEnglish (US)
    Pages (from-to)1041-1054
    Number of pages14
    JournalCell
    Volume166
    Issue number4
    DOIs
    StatePublished - Aug 11 2016

    Fingerprint

    Castration
    Prostatic Neoplasms
    Phosphorylation
    Phosphotransferases
    Genes
    Tissue
    Autopsy
    Tumors
    Neoplasms
    Pharmaceutical Preparations
    Therapeutics

    All Science Journal Classification (ASJC) codes

    • Biochemistry, Genetics and Molecular Biology(all)

    Cite this

    Paull, E. O., Graham, N. A., Lee, J. K., Smith, B. A., Titz, B., Stoyanova, T., ... Stuart, J. M. (2016). Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer. Cell, 166(4), 1041-1054. https://doi.org/10.1016/j.cell.2016.07.007
    Paull, Evan O. ; Graham, Nicholas A. ; Lee, John K. ; Smith, Bryan A. ; Titz, Bjoern ; Stoyanova, Tanya ; Faltermeier, Claire M. ; Uzunangelov, Vladislav ; Carlin, Daniel E. ; Fleming, Daniel Teo ; Wong, Christopher K. ; Newton, Yulia ; Sudha, Sud ; Vashisht, Ajay A. ; Huang, Jiaoti ; Wohlschlegel, James A. ; Graeber, Thomas G. ; Witte, Owen N. ; Stuart, Joshua M. / Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer. In: Cell. 2016 ; Vol. 166, No. 4. pp. 1041-1054.
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    title = "Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer",
    abstract = "We used clinical tissue from lethal metastatic castration-resistant prostate cancer (CRPC) patients obtained at rapid autopsy to evaluate diverse genomic, transcriptomic, and phosphoproteomic datasets for pathway analysis. Using Tied Diffusion through Interacting Events (TieDIE), we integrated differentially expressed master transcriptional regulators, functionally mutated genes, and differentially activated kinases in CRPC tissues to synthesize a robust signaling network consisting of druggable kinase pathways. Using MSigDB hallmark gene sets, six major signaling pathways with phosphorylation of several key residues were significantly enriched in CRPC tumors after incorporation of phosphoproteomic data. Individual autopsy profiles developed using these hallmarks revealed clinically relevant pathway information potentially suitable for patient stratification and targeted therapies in late stage prostate cancer. Here, we describe phosphorylation-based cancer hallmarks using integrated personalized signatures (pCHIPS) that shed light on the diversity of activated signaling pathways in metastatic CRPC while providing an integrative, pathway-based reference for drug prioritization in individual patients.",
    author = "Paull, {Evan O.} and Graham, {Nicholas A.} and Lee, {John K.} and Smith, {Bryan A.} and Bjoern Titz and Tanya Stoyanova and Faltermeier, {Claire M.} and Vladislav Uzunangelov and Carlin, {Daniel E.} and Fleming, {Daniel Teo} and Wong, {Christopher K.} and Yulia Newton and Sud Sudha and Vashisht, {Ajay A.} and Jiaoti Huang and Wohlschlegel, {James A.} and Graeber, {Thomas G.} and Witte, {Owen N.} and Stuart, {Joshua M.}",
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    Paull, EO, Graham, NA, Lee, JK, Smith, BA, Titz, B, Stoyanova, T, Faltermeier, CM, Uzunangelov, V, Carlin, DE, Fleming, DT, Wong, CK, Newton, Y, Sudha, S, Vashisht, AA, Huang, J, Wohlschlegel, JA, Graeber, TG, Witte, ON & Stuart, JM 2016, 'Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer', Cell, vol. 166, no. 4, pp. 1041-1054. https://doi.org/10.1016/j.cell.2016.07.007

    Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer. / Paull, Evan O.; Graham, Nicholas A.; Lee, John K.; Smith, Bryan A.; Titz, Bjoern; Stoyanova, Tanya; Faltermeier, Claire M.; Uzunangelov, Vladislav; Carlin, Daniel E.; Fleming, Daniel Teo; Wong, Christopher K.; Newton, Yulia; Sudha, Sud; Vashisht, Ajay A.; Huang, Jiaoti; Wohlschlegel, James A.; Graeber, Thomas G.; Witte, Owen N.; Stuart, Joshua M.

    In: Cell, Vol. 166, No. 4, 11.08.2016, p. 1041-1054.

    Research output: Contribution to journalArticle

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    AU - Paull, Evan O.

    AU - Graham, Nicholas A.

    AU - Lee, John K.

    AU - Smith, Bryan A.

    AU - Titz, Bjoern

    AU - Stoyanova, Tanya

    AU - Faltermeier, Claire M.

    AU - Uzunangelov, Vladislav

    AU - Carlin, Daniel E.

    AU - Fleming, Daniel Teo

    AU - Wong, Christopher K.

    AU - Newton, Yulia

    AU - Sudha, Sud

    AU - Vashisht, Ajay A.

    AU - Huang, Jiaoti

    AU - Wohlschlegel, James A.

    AU - Graeber, Thomas G.

    AU - Witte, Owen N.

    AU - Stuart, Joshua M.

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    N2 - We used clinical tissue from lethal metastatic castration-resistant prostate cancer (CRPC) patients obtained at rapid autopsy to evaluate diverse genomic, transcriptomic, and phosphoproteomic datasets for pathway analysis. Using Tied Diffusion through Interacting Events (TieDIE), we integrated differentially expressed master transcriptional regulators, functionally mutated genes, and differentially activated kinases in CRPC tissues to synthesize a robust signaling network consisting of druggable kinase pathways. Using MSigDB hallmark gene sets, six major signaling pathways with phosphorylation of several key residues were significantly enriched in CRPC tumors after incorporation of phosphoproteomic data. Individual autopsy profiles developed using these hallmarks revealed clinically relevant pathway information potentially suitable for patient stratification and targeted therapies in late stage prostate cancer. Here, we describe phosphorylation-based cancer hallmarks using integrated personalized signatures (pCHIPS) that shed light on the diversity of activated signaling pathways in metastatic CRPC while providing an integrative, pathway-based reference for drug prioritization in individual patients.

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    Paull EO, Graham NA, Lee JK, Smith BA, Titz B, Stoyanova T et al. Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer. Cell. 2016 Aug 11;166(4):1041-1054. https://doi.org/10.1016/j.cell.2016.07.007