Novel Mechanisms of Resistance to EGFR Inhibitory Drugs in Non-Small

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Novel Mechanisms of Resistance to EGFR Inhibitory Drugs in Non-Small Novel mechanisms of resistance to EGFR inhibitory drugs in non-small cell lung cancer Catherine Cowell University College London and Cancer Research UK London Research Institute PhD Supervisor: Professor Julian Downward A thesis submitted for the degree of Doctor of Philosophy University College London September 2012 Declaration I Catherine Frances Cowell confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. 2 Abstract EGFR activating mutations are present in 10-40% of non-small cell lung cancer. Such mutations render tumour cells sensitive to EGFR tyrosine kinase inhibitors (EGFR TKIs), with responses of up to 80% in populations selected for the presence of an activating mutation. Unfortunately, almost all patients develop resistance after about a year. Clinically described mechanisms of resistance include the presence of a secondary mutation (T790M) in EGFR which prevents EGFR TKIs binding to the EGF receptor, and amplification MET which permits survival signalling via the ERBB3 receptor. However in 30% of cases, the mechanism of acquired resistance to EGFR TKIs is still unknown. My aim was to carry out a genome-wide siRNA screen to identify novel mechanisms of resistance to EGFR TKIs. I identified two genes that have not been implicated in EGFR TKI resistance previously, NF1 and DEPTOR, which are negative regulators of RAS and mTOR respectively. Depletion of NF1 or DEPTOR leads to increased resistance to EGFR TKIs via upregulation of MAPK signalling by direct and indirect mechanisms. 3 Acknowledgements The work presented here would have not been possible without the help of many people. Firstly, I would like to thank my supervisor, Julian Downward, for giving me the opportunity to work in his lab, and for his support and direction. I would like to thank all the members of the Signal Transduction Laboratory – Clare, Elza, Esther, Elena, Ralph, Nadia, Miriam, Miguel, Georgios, Pat, Dave, Britta, and Madhu, for all their helpful advice and for making the lab an enjoyable place to work. I would particularly like to thank Elza, for her guidance and contribution to the project. Further I would like to thank my thesis committee Almut Schulze and Peter Parker for their advice and assistance. Also, thanks to the staff of the excellent research services including the Equipment Park and FACS Laboratory, and especially Mike, Ming, Becky and Rachael in the High-throughput Laboratory. Outside the lab, many people made the last four years an amazing period of my life full of friendship. Special thanks go to Amy, Sara, Lisa, Nicola, and Victoria, as well as the amazing Whitby Road girls and my friends from Billericay who have made many special dispensations for me whilst studying for my PhD. Above all, I have to thank my incredible parents and my wonderful sister Laura. I really could not have done this without their love and encouragement. 4 Table of Contents Abstract ................................................................................................................ 3 Acknowledgements ............................................................................................. 4 Table of Contents ................................................................................................ 5 Table of figures .................................................................................................... 8 List of tables ...................................................................................................... 12 Abbreviations .................................................................................................... 13 Chapter 1. Introduction .................................................................................. 15 1.1 Cancer .................................................................................................................. 15 1.2 Non-small Cell Lung Cancer ............................................................................. 16 1.3 EGFR signalling .................................................................................................. 18 1.4 EGFR signalling in NSCLC ............................................................................... 20 1.5 RAS signalling ..................................................................................................... 22 1.5.1 RAS family proteins ...................................................................................... 22 1.5.2 RAS function ................................................................................................. 23 1.5.3 RAS activation in response to EGFR stimulation ......................................... 24 1.6 RAF/MEK/ERK ................................................................................................. 25 1.6.1 RAF/MEK/ERK activation in cancer ............................................................ 26 1.7 PI3K signalling .................................................................................................... 27 1.7.1 PI3K/AKT signalling in cancer ..................................................................... 28 1.7.2 mTOR signalling ........................................................................................... 29 1.7.3 mTOR signalling in cancer ............................................................................ 34 1.8 Mechanisms of resistance to EGFR TKIs in EGFR-mutant NSCLC ............ 34 1.8.1 Primary resistance to EGFR TKIs ................................................................. 34 1.8.2 The T790M mutation ..................................................................................... 35 1.8.3 Other secondary EGFR mutations that confer resistance to EGFR TKIs ..... 37 1.8.4 Amplification of MET ................................................................................... 37 1.8.5 Histological transformation to SCLC ............................................................ 38 1.8.6 Activation of PI3K/AKT signalling by somatic mutations in PIK3CA and PTEN 39 1.8.7 Epithelial-Mesenchymal Transition .............................................................. 40 1.8.8 Alterations in IGFR signalling ...................................................................... 40 1.8.9 NF Kappa B signalling .................................................................................. 41 1.8.10 CRKL amplification ....................................................................................... 42 1.8.11 Activation of AXL kinase ............................................................................. 42 1.8.12 Alternative mechanisms of resistance ........................................................... 42 1.8.13 Outline of subsequent chapters ...................................................................... 43 Chapter 2. Materials & Methods .................................................................... 44 2.1 Materials .............................................................................................................. 44 2.1.1 Drugs ............................................................................................................. 44 2.1.2 Antibodies ..................................................................................................... 44 2.1.3 Buffers and solutions ..................................................................................... 46 2.1.4 siRNA oligonucleotides ................................................................................ 47 2.1.5 ShRNA constructs ......................................................................................... 51 2.2 Methods ............................................................................................................... 52 2.2.1 Mammalian cell culture ................................................................................. 52 5 2.2.2 Screening ....................................................................................................... 53 2.2.3 RNAi follow up experiments ....................................................................... 56 2.2.4 Quantitative Real Time PCR ......................................................................... 58 2.2.5 Protein analysis .............................................................................................. 59 2.2.6 Statistical analysis ......................................................................................... 62 Chapter 3. Identifying determinants of resistance to erlotinib treatment – a genome-wide screen ...................................................................................... 63 3.1 Introduction ........................................................................................................ 63 3.2 RNAi technology ................................................................................................. 63 3.3 Genome-wide screen set up ................................................................................ 64 3.3.1 siRNA library ................................................................................................ 64 3.3.2 Choice of cell line .......................................................................................... 64 3.3.3 Screen read-out .............................................................................................. 64 3.3.4 Erlotinib treatment ......................................................................................... 66 3.3.5 Transfection
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