Structural and functional aspects of RET receptor tyrosine kinase maturation, signalling and chemical inhibition Emily May Burns University College London and Cancer Research UK London Research Institute PhD Supervisor: Neil McDonald A thesis submitted for the degree of Doctor of Philosophy University College London September 2014 Declaration I Emily Burns 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 The RET receptor tyrosine kinase (RTK) is crucial for embryonic and adult development of multiple organs, tissues and neurons. Gain-of-function mutations in the RET gene are found in human cancer, while loss-of-function mutations are associated with congenital anomalies of the kidney and urinary tract (CAGUT) and Hirschsprung's Disease (HSCR). Previous work has identified that some HSCR RET mutations result in a bottleneck in RET folding and a subsequent loss of RET export. This thesis presents work examining the characteristics of wild type (WT) and HSCR RET maturation, export and signalling in stably transfected mammalian cell lines. High throughput siRNA screening was used to identify components involved in WT and HSCR RET maturation and export; preliminary validation has implicated Endoplasmic Reticulum associated degradation (ERAD), autophagy and the N-glycosylation pathway. RET is also a validated cancer target, as a driver of cancers including multiple endocrine neoplasia (MEN) 2A and B. While there are several FDA-approved RET inhibitors available, their lack of specificity and potency has resulted in high levels of off-target toxicity and low life expectancy extensions. As such, a new generation of more optimal inhibitors is required. This thesis presents the investigation of the molecular basis of RET kinase inhibition, through the elucidation of the RET kinase domain (KD) structure bound to several ATP-competitive chemical inhibitors that are known to inhibit RET in vitro. Preliminary development of an updated RET pharmacophore is described, defining key residue interactions and combining observations with biochemical and thermal stability data. 3 Acknowledgement I am eternally grateful to every member of the McDonald Laboratory, with whom I have thoroughly enjoyed spending the last four years. Thank you Neil, for supporting and challenging me, and for your constant enthusiasm throughout the project. Thank you Phil, for teaching me with ceaseless patience. Thank you Andy, for the long nights at the synchrotron and your positive guidance through every aspect of crystallography. Thank you Svend, for all of your work that has heavily influenced my project. This project would not have been possible without the efforts of Rachael Instrell, Ming Jiang and Becky Saunders from the HTS laboratory - thank you. A special thanks to Mike Howell, for refreshingly frank advice. To my friends at the LRI: you have kept me working and smiling, thank you! My family and friends, thank you for your unwavering support throughout the last four years. Thank you for lending your ear, making me laugh and making life outside of the laboratory so satisfying. Mum and dad, thank you for everything. 4 Table of Contents Abstract ............................................................................................................... 3 Acknowledgement .............................................................................................. 4 Table of Contents ................................................................................................ 5 Table of figures ................................................................................................... 9 List of tables ...................................................................................................... 12 Abbreviations .................................................................................................... 13 Chapter 1. Introduction ................................................................................ 19 1.1 Receptor tyrosine kinase structure, regulation and function............ 19 1.1.1 RTK KD structure and phosphorylation ............................................. 21 1.1.2 Structural elements required for catalytic mechanism ....................... 21 1.1.3 RTK autophosphorylation and regulation .......................................... 23 1.1.4 Regulation of RTK activity ................................................................. 23 1.1.5 The regulatory spine ......................................................................... 24 1.2 Synthesis, trafficking and degradation of RTKs ................................. 25 1.2.1 Protein folding and quality control within the ER ............................... 26 1.2.2 ER to Golgi apparatus transport ........................................................ 30 1.2.3 Functions of the Golgi ....................................................................... 31 1.2.4 RTK endocytosis and receptor recycling ........................................... 31 1.2.5 Mechanisms of RTK degradation ...................................................... 33 1.3 RET structure, ligands-co-receptor partners and biological functions ........................................................................................................ 36 1.3.1 Biological functions of RET ............................................................... 36 1.3.2 RET evolution ................................................................................... 37 1.3.3 RET ligands and co-receptors ........................................................... 38 1.3.4 RET-specific signalling pathways ...................................................... 40 1.3.5 Ligand and co-receptor structures..................................................... 41 1.3.6 RET ectodomain structure ................................................................ 41 1.3.7 RET ternary complex formation ........................................................ 43 1.3.8 RET kinase domain structure and regulation .................................... 45 1.4 The role of RET in human disease ....................................................... 46 1.4.1 Loss-of-function mutations and Hirschsprung’s disease ................... 47 1.4.2 RET gain-of-function mutations and MEN2 ....................................... 49 1.4.3 RET fusion mutations and thyroid cancer, lung cancer and leukaemia .................................................................................................... 50 1.4.4 Over-expression of RET in breast and colorectal cancer .................. 51 1.5 Targeted therapy towards tyrosine kinases in cancer ....................... 51 1.5.1 Chemical inhibition of kinases ........................................................... 52 1.5.2 Clinically approved RET inhibitors..................................................... 53 1.6 Project Aims .......................................................................................... 54 Chapter 2. Materials & Methods .................................................................. 55 2.1 Materials ................................................................................................. 55 2.1.1 Reagents ........................................................................................... 55 2.1.2 Plasticware ........................................................................................ 58 2.2 Methods ................................................................................................. 58 2.2.1 Cell culture ........................................................................................ 58 5 2.2.2 Monitoring RET maturation ............................................................... 60 2.2.3 Detecting RET cell surface expression levels ................................... 62 2.2.4 Mammalian cell transfection.............................................................. 63 2.2.5 Cloning .............................................................................................. 66 2.2.6 Protein expression ............................................................................ 68 2.2.7 Protein purification and analysis ....................................................... 69 2.2.8 X-ray crystallography ........................................................................ 71 Chapter 3. Characterisation of the maturation of a RET S100M missense mutation causal in Hirschsprung’s disease ................................................... 74 3.1 Introduction ........................................................................................... 74 3.2 Structure-based sequence alignments of RET CLD1-2 ..................... 76 3.3 Generating inducible RET and RET mutant Flp-In stable mammalian cell lines responsive to GDNF-GFRα1 ......................................................... 77 3.4 Examining RET maturation and cell surface expression levels ........ 79 3.5 Investigating the role of unpaired cysteine residues in RET maturation ...................................................................................................... 82 3.6 Investigating RET signalling ................................................................ 85 3.7 Efforts to manipulate S100M RET export using chemical chaperones .................................................................................................... 87 3.8 Manipulation of RET cell surface expression by siRNA knockdown of