Hassan Khonsari College of Health and Life Sciences
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Lentivirus-meditated frataxin gene delivery reverses genome instability in Friedreich ataxia patient and mouse model fibroblasts Thesis submitted for the degree of Doctor of Philosophy by Hassan Khonsari November 2015 College of Health and Life Sciences ABSTRACT Friedreich ataxia (FRDA) is a progressive neurodegenerative disease with primary sites of pathology in the large sensory neurons of the dorsal root ganglia (DRG) and dentate nucleus of the cerebellum. FRDA is also often accompanied by severe cardiomyopathy and diabetes mellitus. FRDA is caused by loss of frataxin (FXN) expression, which is due to GAA repeat expansion in intron 1 of the FXN gene. Frataxin is a mitochondrial protein important in iron-sulphur cluster (ISC) biogenesis and in the electron transport chain (ETC). As a consequence of impaired mitochondrial energy metabolism, FRDA cells show increased levels of and sensitivity to oxidative stress, which is known to be associated with genome instability. In this study, we investigated DNA damage/repair in relation to FXN expression via immunostaining of γ-H2AX, a nuclear protein that is recruited to DNA double strand breaks (DSBs). We found FRDA patient and YG8sR FRDA mouse model fibroblasts to have inherently elevated DNA DSBs (1.8 and 0.9 foci/nucleus) compared to normal fibroblasts (0.6 and 0.2 foci/nucleus, in each case P <0.001). By delivering the FXN gene to these cells with a lentivirus vector (LV) at a copy number of ~1/cell, FXN mRNA levels reached 48 fold (patient cells) and 42 fold (YG8sR cells) and protein levels reached 20 fold (patient cells) and 3.5 fold (YG8sR cells) that of untreated fibroblasts, without observable cytotoxicity. This resulted in a reduction in DNA DSB foci to 0.7 and 0.43 (in each case P <0.001) in human and YG8sR fibroblasts, respectively and an increase in cell survival to that found for normal fibroblasts. We next irradiated the FRDA fibroblasts (2Gy) and measured their DSB repair profiles. Both human and mouse FRDA fibroblasts were unable to repair damaged DNA. However, repair returned to near normal levels following LV FXN gene transfer. Our data suggest frataxin may be important for genome stability and cell survival by ensuring ISC for DNA damage repair enzymes or may be required directly for DNA DSB repair. I ACKNOWLEDGEMENTS First I would like to express the deepest gratitude to my first and second supervisors Dr. Michael Themis and Dr. Mark Pook for their guidance, support and encouragement throughout my PhD. I am highly grateful for this opportunity and I thank them for accepting me as their student. I would like to thank Dr. Sahar Al-Mahdawi and Dr. Matthew Themis for the training, advice and assistances they have always provided in every step of the way. I am grateful to Dr. Christopher Parris for his input in the DNA damage study and also his suggestions with the immunofluorescence assays. I would like to express my sincere thanks to Dr. Yaghoub Gozaly and Dr. Hemad Yasaei for being helpful whenever needed. I would like to thank Dr. Steve Howe (UCL, UK) for providing the vectors used in this project. It is my pleasant honour to thank Ataxia UK, FARA Australia and FARA USA for providing financial support. Finally I would like to thank my parents for been patient and supportive during these years and also I would like to thank my wife for being with me in every step of the way. II DECLARATION I hereby declare that the research presented in this thesis is my own work, except where otherwise specified, and has not been submitted for any other degree. Hassan Khonsari III TABLE OF CONTENTS ABSTRACT ____________________________________________________________________________ I ACKNOWLEDGEMENTS ________________________________________________________________ II DECLARATION _______________________________________________________________________ III TABLE OF CONTENTS _________________________________________________________________ IV LIST OF TABLES _____________________________________________________________________VIII LIST OF FIGURES _____________________________________________________________________ IX ABBREVIATIONS _____________________________________________________________________ XII 1. CHAPTER 1 - FRIEDREICH ATAXIA: LITERATURE REVIEW ______________________________________ 1 1.1 ATAXIA ____________________________________________________________________________ 2 1.2 FRIEDREICH ATAXIA __________________________________________________________________ 4 1.2.1 Clinical Features ________________________________________________________________ 4 1.2.2 Pathophysiology _________________________________________________________________ 6 1.2.3 Prevalence _____________________________________________________________________ 8 1.2.4 Friedreich ataxia gene structure ____________________________________________________ 10 1.2.5 Friedreich ataxia gene expression __________________________________________________ 12 1.2.6 Frataxin protein structure _________________________________________________________ 13 1.2.7 Cellular function of frataxin _______________________________________________________ 14 1.3 GAA REPEAT MUTATION ______________________________________________________________ 16 1.3.1 Instability of the GAA repeat: ______________________________________________________ 17 1.3.2 Somatic instability is tissue and age dependent ________________________________________ 18 1.3.3 Meiotic (intergenerational) instability of GAA repeats __________________________________ 20 1.4 MECHANISMS REDUCING FXN TRANSCRIPTION _____________________________________________ 20 1.4.1 Triplex formation _______________________________________________________________ 21 1.4.2 Sticky DNA ____________________________________________________________________ 23 1.4.3 Histone modifications ____________________________________________________________ 26 1.4.4 DNA methylation changes _________________________________________________________ 28 1.5 FRIEDREICH ATAXIA MOUSE MODELS ____________________________________________________ 29 1.5.1 Knockout mouse models __________________________________________________________ 29 1.5.2 Knockin mouse models ___________________________________________________________ 29 1.5.3 FXN YAC transgenic mouse model __________________________________________________ 30 1.5.4 Human frataxin is functional and rescues FXN knockout mouse ___________________________ 30 1.5.5 Human FXN YAC transgenic mouse containing a GAA repeat ____________________________ 32 1.6 THERAPEUTICS _____________________________________________________________________ 35 1.6.1 Antioxidants and oxidative stress ___________________________________________________ 35 1.6.2 Removal of mitochondrial iron _____________________________________________________ 35 1.6.3 Increasing frataxin levels _________________________________________________________ 36 1.6.3.1 Inhibition of triplex formation ____________________________________________________ 36 1.6.3.2 Inhibition of heterochromatin mediated silencing _____________________________________ 37 1.6.3.3 HDAC inhibitors as a therapy for FRDA ____________________________________________ 38 1.7 DEVELOPING GENE THERAPIES FOR FRDA ________________________________________________ 39 1.7.1 Retroviral and lentiviral vectors. ___________________________________________________ 41 1.7.2 Adeno-associated virus ___________________________________________________________ 42 1.7.3 Herpes simplex virus type 1 _______________________________________________________ 44 1.7.4 Nonviral-based delivery __________________________________________________________ 45 1.7.4 The challenges faced in gene therapies for FRDA ______________________________________ 46 1.8 GENE THERAPY STRATEGIES FOR MONOGENIC DISEASES ______________________________________ 47 1.9 VIRAL VECTORS FOR GENE THERAPY _____________________________________________________ 50 1.10 RETROVIRUSES ____________________________________________________________________ 52 1.10.1 Retrovirus biology ______________________________________________________________ 54 1.10.1.1 Coding sequences _____________________________________________________________ 55 IV 1.10.1.2 Non‐coding sequences _________________________________________________________ 56 1.10.2 Retrovirus Structure ____________________________________________________________ 57 1.11 LENTIVIRAL LIFE CYCLE _____________________________________________________________ 59 1.11.1 Entry and uncoating ____________________________________________________________ 61 1.11.2 Reverse transcription ___________________________________________________________ 61 1.11.3 Integration ___________________________________________________________________ 63 1.11.4 Transcription _________________________________________________________________ 64 1.11.5 Translation ___________________________________________________________________ 64 1.11.6 Virion assembly and budding _____________________________________________________ 65 1.12 LENTIVIRAL VECTORS _______________________________________________________________ 66 1.12.1 Early HIV-1 vectors ____________________________________________________________ 67 1.12.2 Expanded tropism through pseudotyping with vesicular stomatitis virus envelope-glycoprotein G (VSV-G). ___________________________________________________________________________ 68 1.12.3 First-generation HIV-1-based lentiviral vectors _______________________________________ 68 1.12.4 Second generation lentiviral vectors ________________________________________________ 70