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SYSTEMS BIOLOGY REGULATION OF MAPK PATHWAYS: APPLICATIONS TO CANCER THERAPY
[Thesis]. Manchester, UK: The University of Manchester; 2019.
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Abstract
Breast cancer remains the most lethal type of cancer for women. A quarter of breast cancer cases display overexpression of the HER2 protein, which is associated with poor prognosis. A major drug for treating HER2 (human epidermal growth factor receptor 2)-positive breast cancer is Herceptin, which reduces HER2 dimerization, thereby inhibiting the major cell proliferation pathways. Despite its effectiveness, resistance to Herceptin is a very significant clinical problem: only a third of patients respond to Herceptin, and two thirds of these relapse within one year due to resistance to the drug. Specific members of the Dual-specificity phosphatases (DUSPs) family act downstream of the HER2 protein in breast cancer and contribute to development of Herceptin resistance. I aimed to model the role of dual specificity phosphatases (DUSPs) and the effect of their inhibition in signalling pathways in HER2-positive breast cancer and resistance to Herceptin. This thesis focuses on the implementation of a multi-disciplinary approach to identify a specific profile of DUSPs, whose inhibition could reduce Herceptin resistance in breast cancer cells or resensitize resistant cells. A further aim was to assess druggability among these DUSPs to guide future drug discovery efforts. First, using Boolean modelling and experimental measurements of DUSP expression during initial treatment of HER2-positive breast cancer cells with Herceptin, I was able to predict regulatory mechanisms of DUSPs, where these mechanisms were partially known. Next, I used a systems biology approach together with experimental data to investigate how DUSP overexpression could favour cell proliferation in resistant HER2-positive breast cancer and to predict how this mechanism could be reversed by targeted inhibition of selected DUSPs. After showing that our Boolean models correctly accounted for resistance when overexpressed DUSPs were kept activated, I then simulated inhibition of both individual and combinations of DUSPs, and determined conditions under which the resistance could be reversed. Further on, I investigated whether inhibiting certain DUSPs resensitized Herceptin-resistant breast cancer cells to the drug. I built a series of kinetic models incorporating the key players of HER2 signalling pathways and simulating a range of inhibition intensities. I observed that when silencing certain DUSPs, resistant HER2-positive breast cancer cells became more responsive to the drug, showing a decrease in resistance, in agreement with the model predictions. Finally, by applying molecular docking and virtual screening of compound libraries together with predictions of pockets and protein-protein interactions, I could assess the druggability among DUSPs in order to guide future drug discovery efforts. Overall, this thesis highlights the value of combining a systems biology approach with wet lab experimentation and computational screening of chemical compounds, with regards to the identification of specific DUSPs playing a role in resistance to Herceptin of HER2-positive breast cancer cells.
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The models presented in the thesis are available from: https://github.com/elabuiga/Sysbio_DUSPs.
Keyword(s)
Boolean model; Drug resistance; Druggability; Dual specificity phosphatases; HER2-positive breast cancer; Herceptin; Kinetic model