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Predictive Biomarkers and Personalized Medicine

Proteomic Markers of DNA Repair and PI3K Pathway Activation Predict Response to the PARP Inhibitor BMN 673 in Small Cell Lung Cancer

Robert J. Cardnell, Ying Feng, Lixia Diao, You-Hong Fan, Fatemah Masrorpour, Jing Wang, Yuqiao Shen, Gordon B. Mills, John D. Minna, John V. Heymach and Lauren A. Byers
Robert J. Cardnell
1Department of Thoracic/Head and Neck Medical Oncology; 2Bioinformatics and Computational Biology; 3Systems Biology, UT MD Anderson Cancer Center, Houston; 4Hamon Center for Therapeutic Oncology Research and the Simmons Comprehensive Cancer Center, UT Southwestern, Dallas, Texas; and 5Biomarin Pharmaceuticals Inc., Novato, California
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Ying Feng
1Department of Thoracic/Head and Neck Medical Oncology; 2Bioinformatics and Computational Biology; 3Systems Biology, UT MD Anderson Cancer Center, Houston; 4Hamon Center for Therapeutic Oncology Research and the Simmons Comprehensive Cancer Center, UT Southwestern, Dallas, Texas; and 5Biomarin Pharmaceuticals Inc., Novato, California
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Lixia Diao
1Department of Thoracic/Head and Neck Medical Oncology; 2Bioinformatics and Computational Biology; 3Systems Biology, UT MD Anderson Cancer Center, Houston; 4Hamon Center for Therapeutic Oncology Research and the Simmons Comprehensive Cancer Center, UT Southwestern, Dallas, Texas; and 5Biomarin Pharmaceuticals Inc., Novato, California
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You-Hong Fan
1Department of Thoracic/Head and Neck Medical Oncology; 2Bioinformatics and Computational Biology; 3Systems Biology, UT MD Anderson Cancer Center, Houston; 4Hamon Center for Therapeutic Oncology Research and the Simmons Comprehensive Cancer Center, UT Southwestern, Dallas, Texas; and 5Biomarin Pharmaceuticals Inc., Novato, California
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Fatemah Masrorpour
1Department of Thoracic/Head and Neck Medical Oncology; 2Bioinformatics and Computational Biology; 3Systems Biology, UT MD Anderson Cancer Center, Houston; 4Hamon Center for Therapeutic Oncology Research and the Simmons Comprehensive Cancer Center, UT Southwestern, Dallas, Texas; and 5Biomarin Pharmaceuticals Inc., Novato, California
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Jing Wang
1Department of Thoracic/Head and Neck Medical Oncology; 2Bioinformatics and Computational Biology; 3Systems Biology, UT MD Anderson Cancer Center, Houston; 4Hamon Center for Therapeutic Oncology Research and the Simmons Comprehensive Cancer Center, UT Southwestern, Dallas, Texas; and 5Biomarin Pharmaceuticals Inc., Novato, California
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Yuqiao Shen
1Department of Thoracic/Head and Neck Medical Oncology; 2Bioinformatics and Computational Biology; 3Systems Biology, UT MD Anderson Cancer Center, Houston; 4Hamon Center for Therapeutic Oncology Research and the Simmons Comprehensive Cancer Center, UT Southwestern, Dallas, Texas; and 5Biomarin Pharmaceuticals Inc., Novato, California
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Gordon B. Mills
1Department of Thoracic/Head and Neck Medical Oncology; 2Bioinformatics and Computational Biology; 3Systems Biology, UT MD Anderson Cancer Center, Houston; 4Hamon Center for Therapeutic Oncology Research and the Simmons Comprehensive Cancer Center, UT Southwestern, Dallas, Texas; and 5Biomarin Pharmaceuticals Inc., Novato, California
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John D. Minna
1Department of Thoracic/Head and Neck Medical Oncology; 2Bioinformatics and Computational Biology; 3Systems Biology, UT MD Anderson Cancer Center, Houston; 4Hamon Center for Therapeutic Oncology Research and the Simmons Comprehensive Cancer Center, UT Southwestern, Dallas, Texas; and 5Biomarin Pharmaceuticals Inc., Novato, California
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John V. Heymach
1Department of Thoracic/Head and Neck Medical Oncology; 2Bioinformatics and Computational Biology; 3Systems Biology, UT MD Anderson Cancer Center, Houston; 4Hamon Center for Therapeutic Oncology Research and the Simmons Comprehensive Cancer Center, UT Southwestern, Dallas, Texas; and 5Biomarin Pharmaceuticals Inc., Novato, California
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Lauren A. Byers
1Department of Thoracic/Head and Neck Medical Oncology; 2Bioinformatics and Computational Biology; 3Systems Biology, UT MD Anderson Cancer Center, Houston; 4Hamon Center for Therapeutic Oncology Research and the Simmons Comprehensive Cancer Center, UT Southwestern, Dallas, Texas; and 5Biomarin Pharmaceuticals Inc., Novato, California
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DOI: 10.1158/1078-0432.CCR-13-1975 Published November 2013
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    Figure 1.

    BMN 673 potently inhibits growth of SCLC in vitro. Proliferation assays using BMN 673 showed SCLC to be exquisitely sensitive to BMN 673 (A). Interestingly the IC50 values of SCLC to BMN 673 and cisplatin indicated a moderate correlation (B).

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    Figure 2.

    BMN 673 inhibits SCLC growth in vivo. Animals bearing NCI-H209 and NCI-H1048 flank xenografts treated with BMN 673 showed delayed tumor growth without significant toxicity (A). Lysates prepared from xenografts harvested 2 hours after treatment on day 3 showed decreased poly-ADP ribose (PAR) levels (B) indicating strong inhibition of PARP activity in vivo by BMN 673. (Data presented as mean ± SEM, *P < 0.05, ***P < 0.01).

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    Figure 3.

    SCLC IC50 to BMN 673 is inversely correlated to DNA repair protein expression. IC50 to BMN correlated to expression of DNA repair proteins (A) demonstrates a strong inverse correlation, as cell lines with higher expression of DNA repair proteins by RPPA are more sensitive to PARP inhibition. DNA repair cluster within the correlation matrix, made up of a group of DNA repair proteins whose expression is highly correlated (B). The correlation to DNA repair is also observed when the “DNA repair score” is applied to the RPPA dataset (C). Proposed model of PARP inhibitor activity in SCLC (D).

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    Figure 4.

    PI3K pathway activity correlates to PARP inhibitor resistance. SCLC cell lines with more active PI3K signaling are less sensitive to BMN 673 (A). Similarly, higher pAkt correlates to decreased sensitivity to cisplatin (B).

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  • Table 1.

    SCLC cell lines: mutational status and IC50 values

    Cell lineTP53RB1MYC amp.BMN 673 IC50 (nmol/L)Cisplatin IC50 (nmol/L)
    H209amtmtNone1.745.5
    H1048mtmtNone2.21,087
    H524amtmtMYC3.1976
    H1930amtwtNone4.1153
    H69amtmtMYCN5.22,723
    H2081wtmtNone6.32,669
    H2107amtmtMYCL17.3811
    H1092amtwtMYCL18.91,611
    DMS-79amtmtNone9.31,189
    H446amtmtMYC132,074
    COR-L279mtmtUnk15620

    NOTE: BMN 673 and cisplatin IC50 values calculated from proliferation assays. Mutational status of SCLC cell lines tested for TP53, RB1, and MYC amplification (mt, mutant; wt, wild type; Unk, unknown) are shown.

    • ↵aProtein profile included in proteomic analysis.

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    • Supplementary Figure 1 - PDF file - 233K, Plots correlating protein expression for components of the DNA Repair Score not shown in Figure 3.
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Clinical Cancer Research: 19 (22)
November 2013
Volume 19, Issue 22
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Proteomic Markers of DNA Repair and PI3K Pathway Activation Predict Response to the PARP Inhibitor BMN 673 in Small Cell Lung Cancer
Robert J. Cardnell, Ying Feng, Lixia Diao, You-Hong Fan, Fatemah Masrorpour, Jing Wang, Yuqiao Shen, Gordon B. Mills, John D. Minna, John V. Heymach and Lauren A. Byers
Clin Cancer Res November 15 2013 (19) (22) 6322-6328; DOI: 10.1158/1078-0432.CCR-13-1975

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Proteomic Markers of DNA Repair and PI3K Pathway Activation Predict Response to the PARP Inhibitor BMN 673 in Small Cell Lung Cancer
Robert J. Cardnell, Ying Feng, Lixia Diao, You-Hong Fan, Fatemah Masrorpour, Jing Wang, Yuqiao Shen, Gordon B. Mills, John D. Minna, John V. Heymach and Lauren A. Byers
Clin Cancer Res November 15 2013 (19) (22) 6322-6328; DOI: 10.1158/1078-0432.CCR-13-1975
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Clinical Cancer Research
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